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Sylvester, Dianne. "Genes underpinning predisposition to childhood cancer." Thesis, The University of Sydney, 2020. https://hdl.handle.net/2123/22458.
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The genetic changes underpinning cancer predisposition in children are not clearly defined and warrant further research, as identification of a genetic contribution to a patient’s disease can be beneficial for patients and their families. With technological advances, it is now possible to discover a broad spectrum of genetic changes implicated in cancer predisposition by sequencing the genome. An analytical review of six publications utilising germline genome sequencing in paediatric oncology found that these studies differed in the selected childhood cancer diagnoses and the genes considered for interpretation, resulting in differences in the proportions of childhood cancer patients that were reported to carry clinically relevant pathogenic germline variants. In this study, childhood cancer patients that presented with phenotypes indicative of a genetic susceptibility to cancer, such as multiple cancer diagnoses, a family history of cancer and/or a genetic diagnosis, underwent germline exome sequencing. Sequencing data were analysed for rare germline variants in over 1000 cancer predisposition, cancer associated and DNA repair genes, that were predicted to cause a loss of function or to be deleterious. Almost one quarter of childhood cancer patients with features suggestive of a genetic predisposition to cancer were found to carry pathogenic or likely pathogenic germline variant/s in 12 known cancer predisposition genes. A rare variant burden analysis of 31 autosomal dominant cancer predisposition genes found that deleterious germline variants were significantly enriched in a cohort of 63 childhood cancer patients compared to a cohort of 1107 genetically matched healthy aged controls. Novel germline variants not previously associated with cancer predisposition were also detected in 10 genes in 16 childhood cancer patients. This study has expanded our understanding of cancer predisposition in children, by discovering the diagnostic potential of sequencing patients with defined phenotypic features, and by linking pathogenic or likely pathogenic germline variants in known predisposition genes with new cancer diagnoses. Ultimately, by combining the analysis of family pedigrees with functional gene studies and data-sharing, the significance of novel germline variants associated with the onset of cancer in childhood will be established. As more childhood cancer predisposition genes are identified and characterised, screening processes may be more routinely incorporated into paediatric clinical care.
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Rapakko, K. (Katrin). "Hereditary predisposition to breast cancer—evaluation of candidate genes." Doctoral thesis, University of Oulu, 2007. http://urn.fi/urn:isbn:9789514284502.
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Abstract
In Western countries, breast and ovarian cancer are among the most frequent malignancies affecting women. Approximately 5–10% of the cases in the general population have been suggested to be attributed to inherited disease susceptibility. BRCA1 and BRCA2 are the main genes associated with predisposition to breast and ovarian cancer. Mutations in these two genes explain a major part of the families displaying a large number of early-onset breast and/or ovarian cancers, but at least one third of the cases appear to be influenced by other, as yet unidentified genes. Therefore, it is likely that defects in other cancer predisposing genes, perhaps associated with lower disease penetrance and action in a polygenic context, will also be discovered.
In the present study, the contribution of germline mutations in putative breast and/or ovarian cancer susceptibility genes, based on their biological function, has been investigated in Finnish breast cancer families. The role of large genomic deletions or other rearrangements in the BRCA1 and BRCA2 genes was evaluated by Southern blot analysis, and mutation analysis of TP53, RAD51, the BRC repeats of BRCA2, and 53BP1 was performed by conformation sensitive gel electrophoresis and DNA sequencing.
Germline TP53 mutations were searched for in 108 Finnish breast cancer families without BRCA1 or BRCA2 alterations. In this study, the pathogenic TP53 germline mutation, Arg248Gln, was identified in only one family. This family showed a strong family history of breast cancer and other cancers also fulfilling the criteria for Li-Fraumeni-like syndrome. Germline TP53 mutations are expected to be found in cancer families with clinical features seen in Li-Fraumeni or Li-Fraumeni-like syndromes.
In this study, large deletions in BRCA1 and BRCA2 were not observed in 82 breast and/or ovarian cancer families. Likewise, no disease-related aberrations were detected in RAD51, the BRC repeats of BRCA2 or 53BP1 in the 126 breast and/or ovarian cancer families studied. The obtained results were validated by comparing to the occurrence in 288–300 female cancer-free control individuals. These results do not support the hypothesis that alterations in these particular genomic regions play a significant role in breast cancer predisposition in Finland. Thus, there are still genes to be discovered to explain the molecular background of breast cancer.
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Jegundo, Patrícia Alexandra Sousa. "Antioxidant and detoxify genes polymorphisms in colorectal cancer predisposition." Master's thesis, Universidade de Aveiro, 2016. http://hdl.handle.net/10773/15947.
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Mestrado em Biologia Molecular e CelularColorectal cancer (CRC) results from histologic and gene alterations can lead to a massive cellular proliferation. Most of the authors assume multifactorial causes to CRC genesis. Low physical activity, a fat diet poor in fibers and smoking habits seems to have an important role in CRC. However, there are also genetic causes associated with CRC risk. It has been described that oxidative stress levels could influence CRC development. Thus, cellular balance reactive species and defense enzymes involved in oxidative stress are crucial to maintain a good tissue function and avoid neoplasic process. Therefore, genome variations on these defense enzymes, such as MNSOD, SOD3, GSTP1, GSTT1 and GSTM1, could be important biomarkers to colorectal adenocarcinomas. We intend to determine frequencies distribution of most common polymorphisms involved on oxidative stress regulation (MNSOD, SOD3, GSTP1, GSTT1 and GSTM1) in patients with sporadic colorectal adenocarcinoma (SCA) and in healthy controls, evaluation their possible correlation with SCA risk. Samples common polymorphisms of antioxidant and detoxify genes (MNSOD T175C, SOD3 R213G, GSTP1 A105G, GSTP1 C114T, GSTT1del and GSTM1del) analysis was done by PCR-SSP techniques. In this study we found a higher prevalence of MNSOD 175CC (55% vs 2%; p<0.0001; OR: 58.5; CI 13.3 to 256.7), SOD3 213GG (31% vs 2%; p<0.0001; OR: 21.89; CI 4.93 to 97.29), GSTP1 105GG (46% vs 12%; p<0.0001; OR: 6.14; CI 2.85 to 13.26), GSTP1 114TT (38% vs 0%; p<0.0001; OR: Infinity) and GSTT1 null (75% vs 28%; p<0.0001; OR: 7.71; CI 3.83 to 15.56) mutated genotypes among SCA patients, while the normal genotypes were associated with SCA absence. Furthermore, we found GSTP1 114TT mutated genotype (52% vs 27%; p=0.003; OR: 2.88; CI: 1.41 to 5.89) and GSTT1 null genotype (87% vs 65%; p=0.003; OR: 3.66; CI 1.51 to 8.84) associated with colon samples. These findings suggest a positive association between most of common polymorphisms involved on oxidative stress regulation and SCA prevalence. Dysregulation of MNSOD, SOD3, GSTP1, GSTT1 and GSTM1 genes could be associated with an increase of ROS in colon and rectum tissue and p53 pathway deregulation, induced by oxidative stress on colonic and rectal cells. The present study also provides preliminary evidence that MNSOD 175C, SOD3 213G, GSTP1 105G, GSTP1 114T and GSTT1 null polymorphisms, may be involved in SCA risk and could be useful to clarify this multifactorial disorder.
O cancro colo-retal (CCR) resulta de um conjunto gradual de alterações histológicas e genéticas, que se traduz numa proliferação celular descontrolada. Embora existam causas genéticas para a origem deste carcinoma, a maioria dos autores assume causas multifactoriais para a génese do CCR. Das causas não genéticas, a baixa atividade física, uma dieta rica em gorduras e pobre em fibras, bem como, os hábitos tabágicos parecem ter um papel preponderante no desenvolvimento desta patologia. Do mesmo modo, tem vindo a ser descrito que diferentes níveis de stresse oxidativo podem influenciar o desenvolvimento deste tipo de cancro. Desta forma, a manutenção celular do estado oxidação-redução parece ser crucial para a conservação da função dos tecidos e prevenção da carcinogénese. Variações genotípicas nos genes envolvidos neste processo, tais como, MNSOD, SOD3, GSTP1, GSTT1 e GSTM1, podem ser importantes biomarcadores para o CCR. Neste trabalho pretendeu-se determinar a distribuição da frequência dos polimorfismos mais comuns dos genes envolvidos na regulação do stresse oxidativo (MNSOD, SOD3, GSTP1, GSTT1 e GSTM1) em indivíduos com adenocarcinoma colo-retal esporádico (ACE) e em controlos saudáveis, avaliando assim a sua possível correlação com o risco para o desenvolvimento do ACE. A análise dos polimorfismos dos genes com atividade desintoxicante e desintoxicante (MNSOD T175C, SOD3 R213G, GSTP1 A105G, GSTP1 C114T, GSTT1del e GSTM1del) foi feita através da técnica de PCR-SSP. Neste estudo encontrámos uma prevalência dos genes mutados nos pacientes com ACE, comparativamente com o grupo controlo: MNSOD 175CC (55% vs 2%; p<0,0001; OR: 58,5; CI 13,3 a 256,7), SOD3 213GG (31% vs 2%; p<0,0001; OR: 21,89; CI 4,93 a 97,29), GSTP1 105GG (46% vs 12%; p<0,0001; OR: 6,14; CI 2,85 a 13,26), GSTP1 114TT 38% vs 0%; p<0,0001; OR: Infinito) e GSTT1 del (75% vs 28%; p<0,0001; OR: 7,71; CI 3,83 a 15,56). Além disto, observámos também que os genótipos mutados GSTP1 114TT (52% vs 27%; p=0,003; OR: 2,88; CI: 1,41 a 5,89) e GSTT1 del (87% vs 65%; p=0.003; OR: 3.66; CI 1.51 a 8.84) estavam associados com o colon. Deste modo, os nossos resultados sugerem uma associação positiva entre os polimorfismos dos genes estudados e a prevalência do ACE. Assim sendo, a desregulação dos genes MNSOD, SOD3, GSTP1, GSTT1 e GSTM1 pode ser associada com um aumento de ROS no tecido do colon-retal. Além disto, o stresse oxidativo nas células do tecido colon-retal pode também induzir uma desregulação da via da p53. Este estudo evidência assim que os polimorfismos MNSOD 175C, SOD3 213G, GSTP1 105G, GSTP1 114T e GSTT1 del poderão estar envolvidos no risco para o ACE, permitindo clarificar esta patologia multifactorial.
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Solyom, S. (Szilvia). "BRCA/Fanconi anemia pathway genes in hereditary predisposition to breast cancer." Doctoral thesis, Oulun yliopisto, 2011. http://urn.fi/urn:isbn:9789514294099.
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Abstract Two major genes are involved in hereditary predisposition to breast and ovarian cancer – BRCA1 and BRCA2. However, germline mutations in these tumor suppressors account for a maximum 20% of the familial breast cancer cases. A significant portion of the genes predisposing to this disease is unknown and therefore needs to be discovered. The aim of this study was to identify novel breast cancer susceptibility genes from the interweaving BRCA/Fanconi anemia (FA) pathway. Five candidate genes – MERIT40, ABRAXAS, BRIP1, CHK1, and FANCA – were screened for mutations by utilizing conformation-sensitive gel electrophoresis and sequencing, or with multiplex ligation-dependent probe amplification in blood DNA samples of Finnish familial breast cancer patients. Investigation of the MERIT40 gene revealed novel nucleotide changes, being the first report on mutation screening of this gene. None of the observed alterations, however, appeared to be disease related, suggesting that germline mutations in MERIT40 are rare or absent in breast cancer patients. A missense alteration (c.1082G>A, leading to Arg361Gln) was identified in ABRAXAS in 3 out of 125 Northern Finnish breast cancer families (2.4%), but not in any of the 867 healthy controls. The prevalence of the mutation between familial and control cases was statistically significantly different (p=0.002). ABRAXAS c.1082G>A appears to have pathological significance based on its exclusive occurrence in cancer cases, evolutionary conservation, disruption of a putative nuclear localization signal, reduced nuclear localization of the protein, and defective accumulation at DNA damage sites. The BRIP1 (FANCJ) and CHK1 genes were screened for large genomic rearrangements, but no abnormalities were detected, ruling out a significant contribution to breast cancer susceptibility in the Northern Finnish population. A novel large heterozygous deletion was identified in the FANCA gene in one out of 100 breast cancer families, removing the promoter and the first 12 exons. The deletion allele was not present in the tested controls, suggesting that it might contribute to breast cancer susceptibility. This is the first report on the association of a large-size germline deletion in a gene acting in the upstream part of the FA signaling pathway with familial breast cancerTiivistelmä BRCA1 ja BRCA2 ovat kaksi tärkeintä perinnöllisen rinta- ja munasarjasyövän alttiusgeeniä. Niissä esiintyvät ituradan muutokset selittävät kuitenkin vain noin 20 % familiaalisista rintasyöpätapauksista. Suurin osa alttiusgeeneistä on edelleen tunnistamatta ja näitä tekijöitä etsitään aktiivisesti. Tämän tutkimuksen tarkoituksena on ollut tunnistaa uusia alttiustekijöitä toisiinsa läheisesti liittyviltä BRCA/Fanconin anemia (FA) signaalinsiirtoreiteiltä. Viisi kandidaattigeeniä - MERIT40, ABRAXAS, BRIP1, CHK1 ja FANCA – kartoitettiin mutaatioiden suhteen suomalaisissa rintasyöpäperheissä käyttämällä konformaatiosensitiivistä geelielektroforeesia ja sekvensointia, tai multiplex ligation-dependent probe amplification- menetelmää. MERIT40-geenissä havaittiin useita aikaisemmin raportoimattomia nukleotidimuutoksia, mutta yhdenkään niistä ei havaittu liittyvän rintasyöpäalttiuteen. MERIT40-geenimuutosten mahdollista yhteyttä rintasyöpäalttiuteen ei ole tutkittu aikaisemmin. ABRAXAS-geenissä havaittiin missense-mutaatio (c.1082G>A, joka johtaa Arg361Gln aminohappokorvautumiseen) kolmessa pohjoissuomalaisessa rintasyöpäperheessä (3/125, 2.4 %). Muutosta ei havaittu terveissä kontrolleissa (N=867), ja ero mutaation esiintyvyydessä familiaalisten rintasyöpätapausten ja terveiden kontrollien välillä oli tilastollisesti merkitsevä (p=0.002). ABRAXAS c.1082G>A-muutos on todennäköisesti patogeeninen, sillä kyseinen aminohappopaikka on evolutiivisesti konservoitunut ja sijaitsee todennäköisellä tumaanohjaussignaalialueella. Funktionaaliset kokeet osoittivat, että mutatoitunut proteiinituote lokalisoitui villityypin proteiinia heikommin tumaan ja sen ohjautuminen DNA-vaurioalueille oli puutteellista. BRIP1- (FANCJ) ja CHK1-geeneistä etsittiin laajoja genomisia uudelleenjärjestelyjä, mutta niitä ei havaittu. Näin ollen kyseisillä muutoksilla ei ole merkittävää roolia perinnöllisessä rintasyöpäalttiudessa suomalaisessa väestössä. FANCA-geenissä havaittiin laaja heterotsygoottinen deleetio yhdessä tutkitusta 100 rintasyöpäperheestä. Deleetio poistaa geenin promoottorialueen lisäksi sen 12 ensimmäistä eksonia. Deleetioalleelia ei havaittu terveissä kontrolleissa, joten se mahdollisesti liittyy perinnölliseen rintasyöpäalttiuteen. Tutkimus on ensimmäinen, jossa raportoidaan laaja genominen deleetio FA-signaalinsiirtoreitin ylävirran geenissä familiaalisessa rintasyövässä
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Nikkilä, J. (Jenni). "PALB2 and RAP80 genes in hereditary breast cancer predisposition." Doctoral thesis, Oulun yliopisto, 2013. http://urn.fi/urn:isbn:9789526200446.
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Abstract Around 5–10% of all breast cancers stem from a strong hereditary predisposition to the disease. Mutations in currently known breast cancer predisposing genes, however, account for only 25–30% of all hereditary breast cancer cases, BRCA1 and BRCA2 being the two major ones. Since BRCA1 and BRCA2 participate in the DNA damage response, mutations in other genes, such as PALB2 and RAP80, which are involved in these pathways, may also predispose to breast tumours. Therefore, the aim of this study was to evaluate variations of the human PALB2 and RAP80 genes as novel potential candidates for breast cancer susceptibility and to further characterize the role of PALB2-deficiency in cancer development. A mutation, c.1592delT, was identified in PALB2 at an elevated frequency among breast cancer patients (0.9%) compared to controls (0.2%) (P = 0.003, OR 3.94, 95% CI 1.5–12.1). Among familial cases the frequency was even higher (2.7%). This mutation represents a genuine loss-of-function mutation since its protein product showed significantly decreased BRCA2-binding affinity and could neither support homologous recombination nor restore crosslink repair in PALB2-deficient cells. Heterozygous PALB2 c.1592delT carriers displayed haploinsufficiency of PALB2 marked by aberrant DNA replication and DNA damage response that led to a significant increase in genomic instability. As the tumours were negative for loss of heterozygosity at this chromosomal locus, these findings provide a mechanism for the early stages of breast cancer development in PALB2 c.1592delT carriers. Palb2 was also found to play a critical role in early mouse development. As in Brca1/2-deficient embryos, homozygous inactivation of Palb2 resulted in embryonic lethality due to mesoderm differentiation and cell proliferation defects. The phenotypic similarity of Palb2 and Brca1/2-deficient mice further supports the close functional relationship shown in vitro for these proteins. A novel mutation, delE81, was identified in RAP80 in one out of 112 breast cancer families, and in one patient diagnosed with bilateral breast cancer out of 503 unselected breast cancers. The resultant delE81 protein displayed significantly reduced ubiquitin binding and double-strand break (DSB) localization. Furthermore, it impaired the recruitment of the whole BRCA1-A complex to the site of DSBs, thus compromising BRCA1-mediated DNA damage response signalling. Although the mutation is quite rare, the current results indicate that the RAP80 delE81 defect is biologically relevant and is likely associated with a hereditary predisposition to breast cancerTiivistelmä Arviolta 5–10 % rintasyöpätapauksista aiheutuuu merkittävästä perinnöllisestä alttiudesta sairauteen. Mutaatiot tähän mennessä tunnistetuissa rintasyövän alttiusgeeneissä, joista BRCA1 ja BRCA2 ovat tärkeimmät, selittävät kuitenkin vain 25–30 % kaikista perinnöllisistä rintasyöpätapauksista. Tämän tutkimuksen tarkoituksena on arvioida PALB2- ja RAP80-geenien mahdolliset vaikutukset rintasyöpäalttiuteen, sekä määrittää tarkemmin PALB2:n vaikutus syövän kehitykseen. PALB2:sta löydettiin mutaatio, c.1592delT, jota esiintyi merkittävästi enemmän rintasyöpäpotilailla (0,9 %) kuin kontrollihenkilöillä (0,2 %) [P = 0.003, OR 3.94, 95 % CI 1.5–12.1]. Kaikista yleisimmin geenimuutos esiintyi perinnöllisten ritasyöpätapausten joukossa (2,7 %). Mutaatio aiheuttaa toiminnallisesti viallisen proteiinin, joka sitoutuu BRCA2:n kanssa normaalia heikommin, eikä se pysty kunnolla toimimaan homologisessa rekombinaatiossa tai ristikkäiden DNA-virheiden korjauksessa. Heterotsygoottisen PALB2 c.1592delT-mutaation aiheuttaa PALB2-geenin haploinsuffisienssi joka ilmentyy kantajien soluissa epänormaalina DNA:n kahdentumisena ja DNA-vauriovasteena, jotka johtavat merkittävästi kohonneeseen genomin epävakaisuuteen. Jo kyseiset toiminnalliset puutteet näyttävät tarjoavan pätevän selityksen PALB2 c.1592delT kantajien merkittävästi suurentuneelle rintasyöpäriskille ja lienee myös syy siihen, ettei potilaiden kasvaimissa havaittu normaalin vastinaleelin menetystä. Palb2:lla on keskeinen rooli hiiren alkiokehityksessä. Kuten Brca1/2-puutteellisissa alkioissa, myös homotsygoottinen Palb2-inaktivaatio aiheuttaa alkioiden enneaikaisen kuoleman, joka aiheutuu puutteista mesodermin erilaistumisessa ja hidastuneesta solujen kasvussa. Palb2- ja Brca1/2-puuttellisten hiirien samankaltaisuus vahvistaa ennestään näiden proteiinien toiminnallista yhteyttä, joka on osoitettu jo aikaisemmin laboratorio-oloissa. RAP80-geenistä löydettiin uusi mutaatio, delE81, yhdestä 112 tutkitusta rintasyöpäperheestä. Kyseinen muutos nähtiin myös yhdessä molemminpuoliseen rintasyöpään sairastaneessa potilaassa valikoimattomassa 503 tapauksen kattavasta aineistosta. Mutatoitunut proteiinituote vähensi huomattavasti DNA-vauriovastekompleksin kykyä sitoutua ubikitiiniin ja paikallistua DNA-kaksoisjuostekatkoksille. Ennen kaikkea mutaatio heikensi BRCA1-A kompleksin kuljetuksen DNA-vauriopaikalle, vaarantaen BRCA1-välitteisen DNA-vauriovasteen. Harvinaisuudesta huolimatta nämä tutkimustulokset osoittavat RAP80 delE81 vaikutuksen olevan biologisesti merkittävä. Kyseinen synnynnäinen RAP80-geenimuutos altistaa mitä todennäköisimmin kantajansa rintasyövälle
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Luo, Liping. "A genetic study on familial breast cancer predisposing genes /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-628-5184-5.
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Margolin, Sara. "Family history and breast cancer susceptibility : clinical and molecular studies /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-868-1/.
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Maguire, Paula. "Investigation of the genetic basis of familial non-BRCA1/2 breast cancer /." Stockholm, 2005. http://diss.kib.ki.se/2006/91-7140-602-6/.
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Bose, M. (Muthiah). "Molecular and functional characterization of ABRAXAS and PALB2 genes in hereditary breast cancer predisposition." Doctoral thesis, Oulun yliopisto, 2019. http://urn.fi/urn:isbn:9789526218656.
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Abstract Hereditary mutations in DNA damage response (DDR) genes often lead to genomic instability and ultimately tumor development. However, the molecular mechanism of how these DDR deficiencies promote genomic instability and malignancy is not well understood. Thus, the specific aim of this thesis is to identify the functional and molecular framework behind the elevated breast cancer risk observed in heterozygous PALB2 and ABRAXAS mutation carriers. The heterozygous germline alteration in PALB2 (c.1592delT) causes a haploinsufficiency phenotype in the mutation carrier cells. Due to PALB2 haploinsufficiency, elevated Cdk activity and consequently aberrant DNA replication/damage response was observed in the PALB2 mutation carrier cells. Excessive origin firing that is indicative of replication stress was also seen in the PALB2 mutation carrier cells. In addition to replication stress, PALB2 mutation carrier cells also experience G2/M checkpoint maintenance defects. The increased malignancy risk in females associated with heterozygosity for the Finnish PALB2 founder mutation is likely to be due to aberrant DNA replication, elevated genomic instability and multiple different cell cycle checkpoint defects. The heterozygous germline alteration in ABRAXAS (c.1082G>A) causes a dominant-negative phenotype in the mutation carrier cells. Decreased BRCA1 protein levels as well as reduced nuclear localization and foci formation of BRCA1 and CtIP was observed in the ABRAXAS mutation carrier cells. This causes disturbances in basal BRCA1-A complex localization, which is reflected by a restraint in error-prone DNA double-strand break (DSB) repair pathway usage, attenuated DNA damage response, deregulated G2/M checkpoint control and apoptosis. Most importantly, mutation carrier cells display a change in their transcriptional profile, which we attribute to the reduced nuclear levels of BRCA1. Thus, the Finnish ABRAXAS founder mutation acts in a dominant-negative manner on BRCA1 to promote genome destabilization in the heterozygous carrier cellsTiivistelmä Perinnölliset muutokset DNA-vauriovasteen geeneissä johtavat usein genomin epävakauteen ja lopulta syövän kehittymiseen. Molekyylitason mekanismeja, joilla vauriovasteen vajaatoiminta ajaa genomin epävakautta ja syöpää, ei kuitenkaan ymmärretä kunnolla. Tämän väitöskirjan tavoitteena on tunnistaa solutoiminnan ja molekyylitason vaikuttajat heterotsygoottisten PALB2- ja ABRAXAS-geenimuutosten kantajien kohonneen rintasyöpäriskin taustalla. Heterotsygoottinen ituradan suomalainen perustajamuutos PALB2-geenissä (c.1592delT) aiheuttaa haploinsuffisienssin kantajahenkilöiden soluissa. PALB2:n haploinsuffisienssin seurauksena kantajasoluissa havaittiin kohonnutta Cdk-proteiinin aktiivisuutta ja siitä johtuvaa kiihtynyttä DNA:n kahdentumista. PALB2-mutaatiota kantavissa soluissa nähtiin myös liiallista replikaation aloituskohtien käyttöä, mikä viittaa replikaatiostressiin. Replikaatiostressin lisäksi PALB2-mutaation kantajasoluilla havaittiin vaikeuksia ylläpitää solusyklin G2/M-tarkastuspisteen toimintaa. Näiden solutoiminnan poikkeavuuksien takia heterotsygoottisen PALB2 c.1592delT -mutaation kantajilla todettiin genomin epävakautta ja kohonnut syöpäriski. Heterotsygoottinen ituradan mutaatio ABRAXAS-geenissä (c.1082G>A) aiheuttaa dominantti-negatiivisen fenotyypin mutaation kantajasoluissa. ABRAXAS-mutaatiota kantavissa soluissa havaittiin BRCA1-proteiinitasojen laskua sekä BRCA1- ja CtIP-proteiinien vähentynyttä lokalisaatiota tumaan ja DNA-vauriopaikoille. Tämä aiheuttaa häiriöitä BRCA1-A-kompleksin paikallistumisessa, mikä johtaa häiriöihin virhealttiiden DNA-kaksoisjuoste¬katkoksien korjausmekanismien käytössä, DNA-vauriovasteessa, G2/M-tarkastus-pisteen säätelyssä ja ohjelmoidussa solukuolemassa. Tärkeimpänä löydöksenä havaittiin mutaation kantajasoluissa muuttunut transkriptioprofiili, joka johtunee BRCA1-proteiinitasojen laskusta tumassa. Näin ollen suomalainen ABRAXAS-perustajamutaatio toimii dominantti-negatiivisena BRCA1:n suhteen, aiheuttaen genomin epävakautta heterotsygoottisissa kantajasoluissa
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Fewings, Eleanor Rose. "The use of whole exome sequencing data to identify candidate genes involved in cancer and benign tumour predisposition." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/285963.
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The development of whole exome sequencing has transformed the study of disease predisposition. The sequencing of both large disease sets and smaller rare disease families enables the identification of new predisposition variants and potentially provide clinical insight into disease management. There is no standard protocol for analysing exome sequencing data. Outside of extremely large sequencing studies including thousands of individuals, statistical approaches are often underpowered to detect rare disease associated variants. Aggregation of variants into functionally related regions, including genes, gene clusters, and pathways, allows for the detection of biological processes that, when interrupted, may impact disease risk. In silico functional studies can also be utilised to further understand how variants disrupt biological processes and identify genotype-phenotype relationships. This study describes the exploration of sequencing datasets from cancers and benign tumour diseases including: i) hereditary diffuse gastric cancer, ii) sweat duct proliferation tumours, iii) adrenocortical carcinoma, and iv) breast cancer. Each set underwent germline whole exome sequencing followed by additional tumour or targeted sequencing to identify associated predisposition genes. Variants within a cluster of risk genes that are involved in double strand break repair were identified as associated with hereditary diffuse gastric cancer risk via gene ontology enrichment analysis. This cluster included PALB2 within which, using externally collated data, loss of function variants were identified as significantly associated with hereditary diffuse gastric cancer risk. Germline protein-affecting variants in the myosin gene MYH9 were identified in all individuals with a rare sweat duct proliferative syndrome, suggesting a role for MYH9 in skin development, regulation and tumorigenesis. These MYH9 variants were analysed in silico to identify a genotype-phenotype relationship between the clinical presentation and variants in the ATP binding pocket of the protein. Tumour matched normal sequence data from adrenocortical carcinoma cases was used to elucidate the role of Lynch syndrome genes in disease pathogenesis. Within the breast cancer set, candidate genes were selected to undergo targeted sequencing in a larger set of cases to further explore their role in breast cancer risk. Risk associated genes identified within this study may ultimately aid in diagnosis and management of disease. This thesis has also generated multiple novel tools and sequencing analysis techniques that may be of use for further studies by aiding in the prioritisation of candidate variants. The described techniques will provide support to researchers working on rare, statistically underpowered datasets and to provide standard analysis pipelines for a range of dataset sizes and types, including familial data and unrelated individuals.
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Qianren, Jin. "Search for susceptibility loci and candidate genes for breast cancer /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-030-3/.
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Zhou, ZiaoLei. "Molecular genetic studies of colorectal cancer /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-489-9/.
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Díaz, Gay Marcos. "Identification of new candidate genes for germline predisposition to familial colorectal cancer using somatic mutational profiling." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/668900.
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Colorectal cancer (CRC) is one of the malignant neoplasms with higher incidence and mortality in Spain, Europe and worldwide. As a complex disease, both environmental and genetic factors influence CRC predisposition. Up to 35% of CRC patients present familial aggregation for the disease, whereas only around 2-8% of cases are linked to a well-known hereditary syndrome associated to pathogenic germline alterations in specific genes, namely APC, MUTYH, POLE, POLD1 or the DNA mismatch repair genes. During last years, next generation sequencing (NGS) techniques such as whole exome sequencing (WES) have been used to address this gap of missing heritability. Characterization of somatic mutational profiles, performed by the application of NGS to both germline and tumor DNA, has also been recently established as a powerful tool to identify novel genes linked to CRC predisposition. However, although some bioinformatic packages have been developed to address this analysis, it remains inaccessible for a substantial proportion of the scientific community. Accordingly, the main purpose of this doctoral thesis was to identify new genes involved in germline predisposition to familial CRC, by using an integrated germline-tumor WES analysis and somatic mutational profiling, as well as facilitating the application of these genomic analyses to the scientific community.
As a first step, a bioinformatic tool to deal with somatic mutational profiling was developed. Shiny framework was used to build MuSiCa, a user-friendly web application freely accessible and potentially useful for non-specialized researchers. Tumor mutational burden calculation and mutational signature refitting analysis according to the information present in COSMIC database is available, as well as different options for sample classification through clustering and principal component analysis.
Subsequently, an integrated germline-tumor analysis was implemented in a cohort of 18 familial CRC unrelated patients. WES data of both germline and tumor DNA was available, allowing the identification of new potential tumor suppressor genes according to Knudson’s two-hit hypothesis. Benefitting from the development of MuSiCa application, somatic mutational profiling was also analyzed, uncovering five hypermutated samples. An enrichment of DNA repair-associated genes was found, as well as some genes previously linked to predisposition syndromes to other cancer types. BRCA2, BLM, ERCC2, RECQL, REV3L and RIF1 were found as the most promising candidate genes for germline CRC predisposition. Interestingly, a germline mutation was found in the DNA repair gene RECQL in a patient with one of the hypermutated tumors, reinforcing the putative role of this gene in hereditary CRC. These findings could be helpful in clinical practice improving genetic counseling in the affected families.El cáncer colorrectal (CCR) es una de las neoplasias con mayor incidencia y mortalidad en España y el mundo. Aunque un 35% de los pacientes presentan agregación familiar, sólo un 2-8% se asocia con un síndrome hereditario conocido, causado por mutaciones germinales en genes como APC, MUTYH, POLE, POLD1 o los genes del sistema de reparación del ADN por mal apareamiento de bases. En los últimos años, las técnicas de secuenciación de nueva generación (SNG), como la secuenciación del exoma completo (SEC), han sido utilizadas para el descubrimiento de nuevos genes implicados en la predisposición al CCR. La caracterización de los perfiles mutacionales somáticos, aplicando SNG al ADN germinal y tumoral, también se ha utilizado recientemente en este proceso. Sin embargo, aunque se han desarrollado algunos paquetes bioinformáticos para su análisis, todavía permanece inaccesible para una gran parte de la comunidad científica. En consecuencia, el objetivo principal de esta tesis doctoral ha sido el de identificar nuevos genes implicados en la predisposición germinal al CCR familiar, utilizando un análisis de SEC germinal-tumoral y caracterización mutacional somática, así como facilitar la aplicación de estos análisis genómicos a la comunidad científica. En primer lugar, se llevó a cabo el desarrollo de una herramienta bioinformática denominada Mutational Signatures in Cancer (MuSiCa), una aplicación web de manejo sencillo y acceso libre desarrollada a través de la plataforma Shiny, que permite el cálculo de la carga mutacional tumoral y la caracterización de las firmas mutacionales según la información disponible en la base de datos COSMIC. Posteriormente, se implementó un análisis integrado de SEC germinal-tumoral en una cohorte de 18 pacientes de CCR familiar, complementado con una caracterización mutacional somática, gracias al desarrollo de MuSiCa. Se detectaron cinco tumores hipermutados, así como un enriquecimiento de mutaciones germinales en genes involucrados previamente en síndromes de predisposición a otros tipos de cáncer y a la reparación del ADN. Los genes BRCA2, BLM, ERCC2, RECQL, REV3L y RIF1 fueron priorizados como los más prometedores de cara a la predisposición al CCR. Estos descubrimientos podrían ser de utilidad en la práctica clínica, mejorando el consejo genético en las familias afectadas.
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CATTEAU, AURELIE. "Predisposition genetique au cancer du poumon : polymorphisme genetique des cytochromes p4501as et etude de genes candidats." Paris 11, 1994. http://www.theses.fr/1994PA112273.
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Le cancer du poumon represente encore la premiere cause de mortalite par cancer en france. Le tabagisme est un facteur de risque majeur, mais seule une fraction de fumeurs developpe ce cancer. L'objectif de ce travail etait d'etudier des facteurs de susceptibilite genetiques, par l'approche gene-candidat en utilisant des outils genetiques et moleculaires. Les cytochromes p450 de la famille 1 (cyp1a1 et cyp1a2) sont des enzymes qui participent au metabolisme des hpa, carcinogenes contenus dans le tabac. Leur activite est induite par les hpa par l'intermediaire d'un recepteur cytosolique ah. Nous avons etudie le determinisme genetique de l'induction de ces cytochromes, (evaluee in vitro pour le cyp1a1 et in vivo pour le cyp1a2), en combinant des etudes de population et de familles (analyses de segregation). Les resultats n'indiquent pas de polymorphisme genetique pour l'induction du cyp1a2. En revanche, l'existence de deux classes d'individus (faiblement et fortement inductibles) est compatible avec l'effet d'un gene majeur (et d'une composante polygenique) dans le cas du cyp1a1. Il pourrait s'agir du gene de structure cyp1a1 ou du gene de regulation ahr codant pour le recepteur ah. Nous avons etudie l'implication du cyp1a1 dans le polymorphisme observe et la localisation chromosomique du gene ahr par des analyses de liaison genetique. Cependant, nous avons montre qu'une determination ambigue du genotype (sur la base du phenotype) demeure un obstacle majeur dans ces analyses. Nous avons par ailleurs realise des etudes de type cas-temoins en nous interessant a deux genes candidats a la carcinogenese pulmonaire, cyp1a1 et cyp2e1. Les etudes revelent que les risques associes aux polymorphismes de ces genes different selon le type histologique du cancer et selon la consommation de cigarettes. L'etude combinee de ces genes avec d'autres facteurs (incluant le gene ahr) permettra a terme d'evaluer la predisposition genetique individuelle au cancer du poumon, ouvrant des perspectives sur le plan de la prevention
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DAL, MOLIN MATTEO. "Identification and validation of DNA sequence variants in cancer predisposition genes by next generation sequencing approaches." Doctoral thesis, Università degli studi di Pavia, 2022. https://hdl.handle.net/11571/1468217.
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DAL, MOLIN MATTEO. "Identification and validation of DNA sequence variants in cancer predisposition genes by next generation sequencing approaches." Doctoral thesis, Università degli studi di Pavia, 2022. https://hdl.handle.net/11571/1468215.
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Erkko, H. (Hannele). "TOPBP1, CLSPN and PALB2 genes in familial breast cancer susceptibility." Doctoral thesis, University of Oulu, 2008. http://urn.fi/urn:isbn:9789514289682.
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Abstract
The currently known susceptibility genes account for approximately 25% of familial breast cancer predisposition. Additional factors contributing to the pathogenesis of breast cancer are, therefore, likely to be discovered. Most of the known genes affecting breast cancer predisposition function in the DNA damage response pathway. In this study three genes, TOPBP1, CLSPN and PALB2, involved in this complex process were investigated to reveal potentially pathogenic mutations associated with breast cancer susceptibility.
In the analysis of the TOPBP1 gene, one novel putative pathogenic alteration was observed. The Arg309Cys variant was found at an elevated frequency among familial cases (19/125) vs. controls (49/697) (p = 0.002; OR 2.4; 95% CI 1.3–4.2). In addition, altogether 18 other germline alterations were observed in this gene, but they all appeared to be harmless polymorphisms.
Investigation of CLSPN alterations among familial breast cancer families revealed altogether seven different changes. No clearly pathogenic alterations were observed. However, a potential modifier effect was discovered for the 1195delGlu change. The obtained results suggest that CLSPN alterations are unlikely to be significant breast cancer susceptibility alleles.
In the PALB2 gene, a pathogenic mutation c.1592delT was identified at an elevated frequency among breast cancer patients (0.9%) compared to controls (0.2%) (p = 0.003, OR 3.94, 95% CI 1.5–12.1). Among familial cases the frequency of c.1592delT was even higher (2.7%). This mutation was also functionally deficient. It had a markedly decreased BRCA2-binding affinity and was unable to support homologous recombination or to restore cross link repair in PALB2 knock-down cells. Additionally, this mutation was discovered in a familial prostate cancer family and was found to segregate with the disease, suggesting some association also with prostate cancer.
The penetrance and hazard ratio associated with PALB2 c.1592delT were determined in unselected breast cancer families. A substantially increased risk of breast cancer (HR 6.1; 95% CI 2.2–17.2; p = 0.01) was discovered resulting in an estimated 40% (95% CI 17–77) breast cancer risk by age 70 years, comparable to that for carriers of BRCA2 mutations. This markedly increased cancer risk suggests that genetic counselling for carriers is needed and screening for this mutation should be considered.
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Elander, Nils. "Inflammation-associated genes and genetic variations in colorectal cancer." Doctoral thesis, Linköping : Department of Clinical and Experimental Medicine, Linköping University, 2009. http://www.bibl.liu.se/liupubl/disp/disp2009/med1146s.pdf.
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Lindforss, Ulrik. "On the clinical value of genetic analysis in colorectal cancer patients /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-742-8.
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Vanderwal, April. "Factors that Influence the Management Recommendations Breast Surgeons Provide to Women with Pathogenic Variants in Moderate Penetrance Breast Cancer Susceptibility Genes." University of Cincinnati / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1592133660069865.
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Rahman, Aneela Atta Ur. "Risk factors for prostate cancer : a case-control study investigating selected key exposures and their interactions with predisposition genes." Thesis, University of Nottingham, 2010. http://eprints.nottingham.ac.uk/12579/.
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Prostate cancer is the UK number one male cancer. Evidence from epidemiological studies suggests only age, race and family history as established risk factors. Other factors such as low dose diagnostic radiations and surrogate hormone markers such as baldness, finger length pattern and acne are hypothesized to have a potential role in the aetiology of prostate cancer. It is evident that genetics plays an important role in prostate cancer aetiology. This thesis focuses both environmental and genetic factors. The environmental factors include selected surrogate hormone markers, medical diagnostic radiation procedures and family history of prostate cancer. The genetic part explores genetic polymorphisms that could have implications for interactions with exposures studied. Single nucleotide polymorphisms (SNPs) involved in mechanistic pathways related to DNA repair genes and potential hormone marker genes were the main targets.
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Olsson, Louise. "Early detection of colorectal cancer /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-841-6/.
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Padilla, Sirera Natàlia. "Novel approaches for in silico identification of pathogenic variants in BRCA1 and BRCA2 hereditary breast and ovarian cancer predisposition genes." Doctoral thesis, Universitat Autònoma de Barcelona, 2020. http://hdl.handle.net/10803/670705.
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Variants germinals a les proteïnes BRCA1 i BRCA2 poden alterar la funció protectora d’aquestes a l’ADN, incrementant el risc de desenvolupar càncer de mama i ovari hereditari (HBOC). Identificació d’aquells individus portadors de variants patogèniques permet canalitzar-los en programes específics de prevenció i vigilància, augmentant les seves taxes de supervivència. Per això, en primer lloc, cal identificar quines de les variants són patogèniques. Malauradament, no sempre hi ha prou informació per arribar a una conclusió. En aquesta situació, els predictors de patogenicitat dissenyats per estimar computacionalment el dany causat per les variants poden proporcionar una valuosa informació.
En aquest treball presentem una nova família de predictors de patogenicitat per BRCA1 i BRCA2. Aquests predictors difereixen en el seu objectiu: un està entrenat per estimar l’impacte molecular de les variants sobre la funció HDR de BRCA1 i BRCA2, i l’altre està entrenat per estimar la significació clínica d’una variant, és a dir, si la seva classificació és patogènica o neutra. Els seus rendiments han estat provats i són comparables als d’altres mètodes àmpliament utilitzats en el camp. Addicionalment, vam presentar els predictors al repte ENIGMA de la 5a Avaluació Crítica de la Interpretació del Genoma (CAGI), trobant que els nostres mètodes, especialment aquells que estimen l’impacte funcional de les variants, es classifiquen en les primeres posicions en comparació amb les altres eines.
Per tal de difondre aquesta família de predictors a la comunitat científica, hem construït el lloc web BRASS (https://www.biotoclin.org/BRASS), on els usuaris poden analitzar les seves variants de BRCA1 i BRCA2 amb canvi de sentit. Els usuaris més avançats també poden interpretar les prediccions mitjançant una mètrica de fiabilitat i diversos gràfics contextualitzant la seva puntuació amb la d’un conjunt de variants curades manualment.
Independentment, hem aplicat els nostres coneixements sobre predictors de patogenicitat en un gran projecte internacional per caracteritzar un nou trastorn neurològic pediàtric causat per variants patogèniques a la histona H3.3. Vam combinar l’ús de predictors de patogenicitat estàndard amb evidències d’anàlisis estructurals i càlculs biofísics per proporcionar una visió mecanicista de l’impacte de les variants causals.Variantes germinales en las proteínas BRCA1 y BRCA2 pueden alterar la función protectora de estas en el ADN, incrementando el riesgo de desarrollar cáncer de mama y ovario hereditario (HBOC). Identificación de aquellos individuos portadores de variantes patogénicas permite canalizarlos hacia programas específicos de prevención y vigilancia, aumentando sus tasas de supervivencia. Para ello, en primer lugar, es necesario identificar cuáles de las variantes son patogénicas. Desafortunadamente, no siempre hay suficiente información para llegar a una conclusión. En esta situación, los predictores de patogenicidad diseñados para estimar computacionalmente el daño causado por las variantes pueden proporcionar una valiosa información. En este trabajo presentamos una nueva familia de predictores de patogenicidad para BRCA1 y BRCA2. Estos predictores difieren en su objetivo: uno está entrenado para estimar el impacto molecular de las variantes en la función HDR de BRCA1 y BRCA2, y el otro está entrenado para estimar la significancia clínica de una variante, es decir, si su clasificación es patogénica o neutra. Sus rendimientos han sido probados y son comparables a los de los métodos ampliamente utilizados en el campo. Además, presentamos los predictores al desafío ENIGMA de la 5ª Evaluación Crítica de la Interpretación del Genoma (CAGI), encontrando que nuestros métodos, especialmente aquellos que estiman el impacto funcional de las variantes, se clasifican en las primeras posiciones en comparación con las otras herramientas. Para difundir esta familia de predictores a la comunidad científica, hemos construido el sitio web BRASS (https://www.biotoclin.org/BRASS), donde los usuarios pueden analizar sus variantes de BRCA1 y BRCA2 con cambio de sentido. Los usuarios más avanzados también pueden interpretar las predicciones utilizando una métrica de confiabilidad y varios gráficos que contextualizan su puntuación a la de un conjunto de variantes seleccionadas manualmente. De forma independiente, aplicamos nuestro conocimiento sobre los predictores de patogenicidad en un gran proyecto internacional para caracterizar un nuevo trastorno neurológico pediátrico causado por variantes patogénicas en la histona H3.3. Combinamos el uso de predictores patogénicos estándar con evidencia de análisis estructurales y cálculos biofísicos para proporcionar una visión mecanicista del impacto de las variantes causales.
Germline variants in BRCA1 and BRCA2 can disrupt the DNA protective role of these proteins resulting in an increased risk of developing hereditary breast and ovarian cancer (HBOC). Identification of those individuals carrying pathogenic variants will allow channeling them into specific programs of prevention and surveillance, incrementing their survival rates. For this purpose, first, it is necessary to identify which of the variants are pathogenic. Unfortunately, there is not always enough information to reach a conclusion. In this situation, pathogenicity predictors designed to computationally estimate the damage caused by variants, can provide valuable information. Here, we present a novel family of pathogenicity predictors for BRCA1 and BRCA2. These predictors differ in their objective: one is trained to estimate the molecular impact of variants on the HDR function of BRCA1 and BRCA2, and the other is trained to estimate the clinical significance of a variant, that is, whether it should be classified as pathogenic or neutral. Their performances have been tested and are comparable to those of widely used predictors in the field. Additionally, we presented them to the ENIGMA challenge from the 5th Critical Assessment of Genome Interpretation (CAGI), finding that our predictors, especially those estimating the functional impact of variants, ranked in the top positions compared to other tools. In order to disseminate this family of predictors to the scientific community, we have built the BRASS website (https://www.biotoclin.org/BRASS), where users can analyze their missense BRCA1 and BRCA2 variants. More advanced users can also interpret the predictions using a reliability metric and several plots contextualizing the score to that of a set of manually curated variants. Independently, we applied our knowledge about pathogenicity predictors in a large international effort to characterize a novel pediatric neurologic disorder caused by pathogenic variants in histone H3.3. We combined the use of standard pathogenic predictors with evidence from structural analyses and biophysical computations to provide a mechanistic view of the impact of the causative variants.
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Pylkäs, K. (Katri). "ATM, ATR and Mre11 complex genes in hereditary susceptibility to breast cancer." Doctoral thesis, University of Oulu, 2007. http://urn.fi/urn:isbn:9789514283833.
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Abstract
Mutations in BRCA1 and BRCA2 explain only about 20% of familial aggregation of breast cancer, suggesting involvement of additional susceptibility genes. In this study five DNA damage response genes, ATM, ATR, MRE11, NBS1 and RAD50, were considered as putative candidates to explain some of the remaining familial breast cancer risk, and were screened for germline mutations in families displaying genetic predisposition.
Analysis of ATM indicated that clearly pathogenic mutations seem to be restricted to those reported in ataxia-telangiectasia (A-T). However, a cancer risk modifying effect was suggested for a combination of two ATM polymorphisms, 5557G>A and IVS38-8T>C, as this allele seemed to associate with bilateral breast cancer (OR 10.2, 95% CI 3.1–33.8, p = 0.001).
The relevance of ATM mutations, originally identified in Finnish A-T patients, in breast cancer susceptibility was evaluated by a large case-control study. Two such alleles, 6903insA and 7570G>C, in addition to 8734A>G previously associated with breast cancer susceptibility, were observed. The overall mutation frequency in unselected cases (7/1124) was higher than in controls (1/1107), but a significantly elevated frequency was observed only in familial cases (6/541, p = 0.006, OR 12.4, 95% CI 1.5–103.3). These three mutations showed founder effects in their geographical occurrence, and had different functional consequences at protein level.
In ATR no disease-related mutations were observed, suggesting that it is not a breast cancer susceptibility gene.
The mutation screening of the Mre11 complex genes, MRE11, NBS1 and RAD50, revealed two novel potentially breast cancer associated alleles: NBS1 Leu150Phe and RAD50 687delT were observed in 2.0% (3/151) of the studied families. The subsequent study of newly diagnosed, unselected breast cancer cases indicated that RAD50 687delT is a relatively common low-penetrance susceptibility allele in Northern Finland (cases 8/317 vs. controls 6/1000, OR 4.3, 95% CI 1.5–12.5, p = 0.008). NBS1 Leu150Phe (2/317) together with a novel RAD50 IVS3-1G>A mutation (1/317) was also observed, both being absent from controls. Loss of the wild-type allele was not observed in the tumors of the studied mutation carriers, but they all showed an increase in chromosomal instability of peripheral T-lymphocytes. This suggests an effect for RAD50 and NBS1 haploinsufficiency on genomic integrity and susceptibility to cancer.
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Dong, Linda M. "Genetic variations in calcium and vitamin D related genes and colon cancer risk /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/10926.
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Vaurs-Barrière, Catherine. "Approches de l'oncogenese mammaire liee a brca1 : identification de genes exprimes differentiellement dans un contexte de predisposition hereditaire liee a brca1 et recherche d'une implication potentielle de brca1 dans le phenomene d'instabilite microsatellitaire." Clermont-Ferrand 1, 1998. http://www.theses.fr/1998CLF1MM07.
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Haanpää, M. (Maria). "Hereditary predisposition to breast cancer – with a focus on AATF, MRG15, PALB2, and three Fanconi anaemia genes." Doctoral thesis, Oulun yliopisto, 2014. http://urn.fi/urn:isbn:9789526204581.
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Abstract Around 5−10% of all breast cancer cases are estimated to result from a strong hereditary predisposition to the disease. However, mutations in the currently known breast cancer susceptibility genes account for only 20−30% of all familial cases. Additional factors contributing to the pathogenesis of breast cancer, therefore, await discovery. Aims of this study were to evaluate variations of the AATF and MRG15 genes as novel potential candidates for breast cancer susceptibility, to further examine the prevalence of the cancer-related PALB2 c.1592delT mutation among BRCA-negative high-risk breast cancer families counselled at the Department of Clinical Genetics, Oulu University Hospital, to identify Finnish Fanconi anaemia patients complementation groups as well as causative mutations, and to evaluate the potential role of these mutations in breast cancer susceptibility. The analysis of 121 familial breast cancer cases revealed altogether seven different sequence changes in the AATF gene. However, none of them were considered pathogenic, suggesting that germline mutations in AATF are rare or absent in breast cancer patients. Investigation of the MRG15 gene among familial breast cancer cases revealed seven previously unreported variants, but in silico analyses revealed that none of these variants appeared to modify the function of MRG15. The results suggest that MRG15 alterations are unlikely to be significant breast cancer susceptibility alleles. A previously identified pathogenic PALB2 mutation, c.1592delT, was identified in three patients from a cohort of 62 high-risk BRCA1/2-negative breast cancer patients from the Department of Clinical Genetics. PALB2 c.1592delT mutation testing should thus be a routine part of the genetic counselling protocol, particularly for BRCA1/2-negative high-risk breast cancer patients. Investigation of the complementation groups of Finnish Fanconi anaemia patients revealed a total of six different causative mutations. These mutations were examined further by analysing their prevalence in large cohorts of breast (n=1840) and prostate (n=565) cancers. However, no significant association emerged between cancer predisposition and these FA mutationsTiivistelmä Arviolta 5−10 prosenttia kaikista rintasyöpätapauksista aiheutuu merkittävästä perinnöllisestä alttiudesta sairauteen. Tällä hetkellä tiedossa olevien rintasyövälle altistavien geenivirheiden ajatellaan kuitenkin selittävän vain noin 20−30 prosenttia kaikista perinnöllisistä tapauksista. On todennäköistä, että uusia tekijöitä, jotka osallistuvat rintasyövän patomekanismiin, on vielä löytymättä. Tämän tutkimuksen tarkoituksena oli arvioida AATF- ja MRG15-geeneissä esiintyvien muutosten mahdollista vaikutusta rintasyöpäalttiuteen, tutkia tarkemmin PALB2 c.1592delT -mutaation esiintymistä BRCA-mutaationegatiivisten korkean rintasyöpäriskin potilaiden joukossa (perinnöllisyyspoliklinikka, Oulun yliopistollinen sairaala) ja määrittää suomalaisten Fanconi-anemiapotilaiden komplementaatioryhmät, sairauden taustalla olevat mutaatiot sekä tutkia näihin mutaatioihin mahdollisesti liittyvää rintasyöpäriskiä. 121 familiaalisen rintasyöpätapauksen analyysissä löytyi yhteensä seitsemän erilaista sekvenssimuutosta AATF-geenissä. Näistä yksikään ei kuitenkaan ollut selvästi patogeeninen. Tuloksen perusteella perinnölliset rintasyövälle altistavat muutokset AATF-geenissä ovat joko erittäin harvinaisia tai niitä ei esiinny lainkaan. MRG15-geenin mutaatioanalyysissä havaittiin seitsemän aikaisemmin raportoimatonta muutosta, mutta in silico -analyysien perusteella millään muutoksista ei ole vaikutusta MRG15-proteiinin toimintaan. Tulosten perusteella on epätodennäköistä, että MRG15-geenin muutokset olisivat merkittäviä rintasyövälle altistavia muutoksia. Jo aiemmin patogeeniseksi todettu PALB2 c.1592delT -mutaatio löydettiin kolmelta niistä perinnöllisyyspoliklinikan korkean syöpäriskin 62 potilaasta, jotka olivat BRCA1/2-geenitestauksessa saaneet normaalin tuloksen. Tulostemme perusteella PALB2 c.1592delT -mutaatiotestaus tulisi Suomessa ottaa osaksi perinnöllisyyspoliklinikoiden tarjomaa tutkimusprotokollaa. Suomalaisten Fanconi-anemiapotilaiden komplementaatioryhmiä selvittävässä tutkimuksessa identifioitiin yhteensä kuusi erilaista tautia aiheuttavaa mutaatiota. Näiden muutosten esiintymistä tutkittiin myös laajoissa rinta- (n=1840) ja eturauhassyöpäaineistoissa (n=565). Tilastollisesti merkittävää assosiaatiota ei kuitenkaan todettu suomalaisten FA-mutaatioiden ja syöpäalttiuden välillä
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Karppinen, S. M. (Sanna-Maria). "The role of BACH1, BARD1 and TOPBP1 genes in familial breast cancer." Doctoral thesis, University of Oulu, 2009. http://urn.fi/urn:isbn:9789514291593.
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Abstract
Approximately 5–10% of all breast cancer cases are estimated to result from a hereditary predisposition to the disease. Currently no more than 25–30% of these familial cases can be explained by mutations in the known susceptibility genes, BRCA1 and BRCA2 being the major ones. Additional predisposing genes are therefore likely to be discovered. This study evaluates whether germline alterations in three BRCA1-associated genes, BACH1 (i.e. BRIP1/FANCJ), BARD1 and TOPBP1, contribute to familial breast cancer.
Altogether 214 Finnish patients having breast and/or ovarian cancer were analysed for germline mutations in the BACH1 gene. Nine alterations were observed, four of which located in the protein-encoding region. The previously unidentified Pro1034Leu was considered a possible cancer-associated alteration as it appeared with two-fold higher frequency among cancer cases compared to controls. All the other observed alterations were classified as harmless polymorphisms.
Mutation analysis of the BARD1 gene among 126 Finnish patients having family history of breast and/or ovarian cancer revealed seven alterations in the protein-encoding region. The Cys557Ser alteration was seen at an elevated frequency among familial cancer cases compared to controls (p = 0.005, odds ratio [OR] 4.2, 95% confidence interval [CI] 1.7–10.7). The other alterations appeared to be harmless polymorphisms. To evaluate further the possible effect of Cys557Ser on cancer risk, a large case-control study was performed, consisting of 3,956 cancer patients from the Nordic countries. The highest prevalence of Cys557Ser was found among breast and ovarian cancer patients from BRCA1/BRCA2 mutation-negative families (p < 0.001, OR 2.6, 95% CI 1.7–4.0). In contrast, no significant association with male breast cancer, ovarian, colorectal or prostate cancer was observed.
The current study is the first evaluating the role of TOPBP1 mutations in familial cancer predisposition. The analysis of 125 Finnish patients having breast and/or ovarian cancer revealed one putative pathogenic alteration. The commonly occurring Arg309Cys allele was observed at a significantly higher frequency among familial cancer cases compared to controls (p = 0.002, OR 2.4, 95% CI 1.3–4.2). The other 18 alterations observed were classified as harmless polymorphisms.
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Santana, dos santos Elizabeth. "Contribution of the Missense and Non-Coding BRCA1/2 Variants for the Hereditary Predisposition and Response to Treatment of Breast and Ovarian Cancers Assessment of the Functional Impact of Germline BRCA1/2 Variants Located in Non- Coding Regions in Families with Breast and/or Ovarian Cancer Predisposition Non-Coding Variants in BRCA1 and BRCA2 Genes: Potential Impact on Breast and Ovarian Cancer Predisposition." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASS027.
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Les cancers de l'ovaire et du sein sont définis par les principales voies impliquées dans la tumorigénèse. Dans les cancers héréditaires du sein/ovaire (HBOC), les tumeurs présentant des variants pathogènes (PV) de BRCA1/2 présentent une altération de la réparation de l'ADN par recombinaison homologue (RH). Des années après la découverte des gènes BRCA1/2, les PV ont été uniquement recherchés sur l'ADN constitutionnel. Aujourd’hui, cette information est également recherchée au niveau tumoral car en plus de leur utilité pour améliorer le conseil génétique, elle est aussi impliquée dans le choix thérapeutique. Cependant, les données recueillies indiquent que les PV inactivant la protéine ne seraient pas l’unique mécanisme d’inactivation de la voie de réparation de l’ADN par RH. Dans ce contexte, l'objectif principal de cette thèse est d'identifier des mécanismes alternatifs d'inactivation de la voie HR pour améliorer à la fois: le conseil génétique et la prise en charge thérapeutique. À cette fin, nous avons tenté de contribuer à la classification de variants non-codants et faux-sens (autre que provoquant un stop prématuré) de BRCA1/2 et également recherché de nouveaux biomarqueurs de réponse thérapeutique dans d’autres gènes de la voie de HR.Nous avons décrit des variants constitutionnels dans des régions potentiellement importantes de régulation des gènes BRCA1 et BRCA2, et démontré qu'une partie d'entre eux étaient fonctionnellement actifs à mettre en lien avec la pathogénicité. Nous avons également exploré les caractéristiques moléculaires des tumeurs du sein et de l'ovaire des porteurs des variants BRCA1 et observé une prédominance de la perte de l'allèle sauvage pour les tumeurs des porteurs de variants pathogènes. Etant donné ces résultats, nous proposons d’intégrer les informations de LOH dans le modèle multifactoriel de classification des variants BRCA1. Enfin, nous avons mis en évidence des mécanismes alternatifs d'inactivation de la voie RH, dans une cohorte de patientes avec un cancer de l'ovaire présentant une excellente réponse aux platines, y compris des mutations constitutionnelles et somatiques des gènes BRCA1/2, l'hyperméthylation du promoteur BRCA1 ainsi que des mutations dans d'autres gènes de la voie RHOvarian and breast cancers are currently defined by the main pathways involved in the tumorigenesis. In hereditary breast/ovarian cancers (HBOC), tumors with BRCA1/2 pathogenic variants (PV) present an impairment of DNA repair by homologous recombination (HR). For many years, BRCA1/2 PV were only searched on germline DNA. Currently, this information is also searched at tumor level to personalize treatment. Even so, the reason of the inactivation of this pathway remains uncertain for most cases, even in the presence of HR deficient signature.Gathered evidence indicates that protein inactivating PV may not be the only mechanism of HR dysfunction. In this context, the main objective of this thesis is to identify alternative mechanisms of HR inactivation to improve both: genetic counseling and therapeutic response. For this purpose, we have attempted to contribute to non-coding and missense (other than premature stop codon) BRCA1/2 variant classification and searched for new biomarkers of therapeutic response to DNA damage agents in other HR genes.We identified germline variants in key transcriptional regulatory elements of BRCA1 and BRCA2, and demonstrated that part of them were functionally active and had additional arguments suggesting pathogenicity. We also explored molecular features of breast and ovarian tumors from BRCA1 variant carriers and observed a predominance of loss of the wild-type allele. Conforming to this evidence, we propose to incorporate LOH information, into the multifactorial model for BRCA1 variant classification. Finally, besides the enrichment of BRCA1/2 germline and somatic PV, we described alternative mechanisms of HR inactivation in a OC population presenting optimal response to platinum-based chemotherapy, including BRCA1 promoter hypermethylation and also mutations in other genes of HR pathway
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Deming, Brenda Boon. "Evaluating the role of lymphocyte radiosensitivity and variants in double-strand break repair genes, checkpoint kinase 2 (CHEK2) and nibrin (NBN), in the predisposition to prostate cancer : a dissertation /." San Antonio : UTHSC, 2007. http://proquest.umi.com/pqdweb?did=1425298611&sid=1&Fmt=2&clientId=70986&RQT=309&VName=PQD.
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Vuorela, M. (Mikko). "Role of the RNF8, UBC13, MMS2 and RAD51C DNA damage response genes and rare copy number variants in hereditary predisposition to breast cancer." Doctoral thesis, Oulun yliopisto, 2013. http://urn.fi/urn:isbn:9789526203096.
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Abstract Mutations in the currently known breast cancer susceptibility genes account for only 25–30% of all familial cases. Novel susceptibility genes can be identified by several methods, including candidate gene re-sequencing and genome-wide microarrays. We have applied microarrays for the detection of a new genomic variation class, copy number variants (CNVs), which potentially could disrupt genes in multiple pathways related to breast cancer susceptibility. The aim of the current study was to evaluate the role of the RNF8, UBC13, MMS2 and RAD51C DNA damage response genes in breast cancer susceptibility as well as to study if rare CNVs are associated with the predisposition to this disease. The analysis of 123 familial breast cancer cases revealed altogether nine different changes in the RNF8 and UBC13 candidate genes. However, none of the observed alterations were considered pathogenic. No alterations were observed in MMS2. The obtained results suggest that breast cancer predisposing alterations in RNF8, UBC13 and MMS2 are rare, or even absent. The RAD51C mutation screening of 147 familial breast cancer cases and 232 unselected ovarian cancer cases revealed two deleterious mutations: c.-13_14del27 was observed in a breast cancer case with familial history of ovarian cancer and c.774delT in an ovarian cancer case. Both mutations were absent in the control cohort. The results of the study support the hypothesis that rare variants of RAD51C predispose predominantly to ovarian cancer. A genome-wide scan of CNVs was performed for 103 familial breast cancer cases and 128 controls. The biological networks of the genes disrupted by CNVs were different between the two groups. In familial breast cancer cases, the observed mutations disrupted genes, which were significantly overrepresented in cellular functions related to maintenance of genomic integrity (P=0.0211). Biological network analysis showed that the disrupted genes were closely related to estrogen signaling and TP53-centered tumor suppressor network, and this result was confirmed by the analysis of an independent young breast cancer cohort of 75 cases. These results suggest that rare CNVs represent an alternative source of genetic variation contributing to hereditary risk for breast cancerTiivistelmä Tunnetut rintasyöpäalttiusgeenien mutaatiot selittävät vain 25–30 prosenttia kaikista perinnöllisistä rintasyöpätapauksista. Uusia alttiusgeenejä voidaan tunnistaa useilla eri menetelmillä, kuten kandidaattigeenien mutaatiokartoituksella ja genomin-laajuisilla mikrosirutekniikoilla. Tässä tutkimuksessa sovelsimme mikrosirutekniikkaa uuden geneettisen variaatioluokan, kopiolukuvariaation (CNV), tutkimiseen. CNV:t voivat vaurioittaa lukuisia rintasyöpäalttiuteen liittyviä biokemiallisia reittejä. Tämän tutkimuksen tarkoitus oli arvioida RNF8-, UBC13-, MMS2- ja RAD51C -DNA- vauriovastegeenien sekä harvinaisten CNV:iden yhteyttä rintasyöpä-alttiuteen. 123 familiaalisen rintasyöpätapauksen analyysissä löytyi yhteensä yhdeksän muutosta RNF8- ja UBC13-geeneistä, joista yksikään ei osoittautunut patogeeniseksi. MMS2-geenissä ei havaittu muutoksia. Tulosten perusteella rintasyövälle altistavat muutokset RNF8-, UBC13- ja MMS2- geeneissä ovat joko erittäin harvinaisia tai niitä ei esiinny lainkaan. RAD51C-geenin mutaatiokartoitus 147 familiaalisesta rintasyöpätapauksesta sekä 232 valikoimattomasta munasarjasyöpätapauksesta paljasti kaksi haitallista mutaatiota. c.-13_14del27 havaittiin rintasyöpäpotilaalla, jonka suvussa esiintyi munasarjasyöpää, ja c.774delT todettiin munasarjasyöpäpotilaalta. Kumpaakaan mutaatiota ei havaittu verrokkiaineistossa. Tulokset vahvistavat hypoteesia RAD51C-geenin harvinaisten varianttien yhteydestä pääasiassa munasarjasyöpäriskiin. CNV:iden genomin-laajuinen skannaaminen suoritettiin 103 familiaaliselle rintasyöpätapaukselle ja 128 verrokille. CNV:iden häiritsemien geenien muodostamat biologiset verkostot olivat erilaiset näiden kahden ryhmän välillä. Familiaalisilla rintasyöpätapauksilla havaitut CNV:t vaikuttivat geeneihin, jotka olivat voimakkaasti korostuneita genomin eheyttä ylläpitävissä tehtävissä (P=0.0211). Biologisten verkostojen analyysi paljasti, että CNV:iden vahingoittamat geenit liittyivät läheisesti estrogeenisignalointiin sekä TP53-tuumorisupressoriverkostoon, ja tämä tulos vahvistettiin analysoimalla riippumatonta nuorista rintasyöpäpotilaista koostuvaa kohorttia (N=75). Tutkimuksen tulosten mukaan harvinaiset CNV:t ovat vaihtoehtoinen geneettisen variaation lähde perinnölliseen rintasyöpäalttiuteen
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Schmidt, Xenia. "TOX3 : a candidate breast cancer predisposition gene." Thesis, University of St Andrews, 2012. http://hdl.handle.net/10023/3104.
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Schmidt, Xénia. "TOX3 – A candidate breast cancer predisposition gene." Thesis, Bordeaux 2, 2011. http://www.theses.fr/2011BOR21831/document.
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Deux tiers des cancers du sein expriment le récepteur à l’estrogène alpha (REα) et leur croissance dépend des estrogènes alors que l’expression de REα induit la différenciation et la sénescence des cellules humaines mammaires épithéliales normales. Le développement embryonnaire et la différenciation de la glande mammaire adulte sont contrôlés par des facteurs de transcription, dont beaucoup sont aussi impliqués dans la tumorigenèse. Plusieurs études d'association pan-génomiques ont identifié le putatif facteur de transcription TOX high mobility group box family member 3 (TOX3) comme un nouveau gène de prédisposition au cancer du sein.L’objectif de cette étude était la caractérisation fonctionelle de TOX3 dans l’épithélium mammaire normal et le cancer du sein.J’ai examiné l’expression de TOX3 dans des tumeurs du sein humaines et dans le sein normal par analyse des données d’expression issues de puces à ADN. L’effet de TOX3 sur la différenciation des cellules épithéliales mammaires était analysé par des assays CFC et FACS. De plus, j’ai effectué une analyse microarray des cellules luminales cancéreuses MCF-7 exprimant TOX3 afin d’identifier les gènes cibles de TOX3 ainsi que la méthode de purification d’affinité en tandem (TAP) combinée à la spectrométrie de masse afin d’identifier des protéines interactants de TOX3. Finalement, j’ai étudié le potentiel oncogénique de TOX3 dans un modèle de xénogreffeTwo thirds of breast cancers express the estrogen receptor alpha (ERα) and are estrogen-dependent for growth. In contrast, expression of ERα induces differentiation and senescence in normal human mammary epithelial cells. Both embryonic development and lineage commitment in the adult mammary gland are governed by transcriptional regulators, many of which have also been implicated in tumourigenesis. Genome-wide association studies have identified the previously uncharacterised putative transcription factor TOX high mobility group box family member 3 (TOX3) as a new candidate breast cancer susceptibility gene.In the present study, I aimed to characterise TOX3 function in the normal human mammary epithelium and in breast cancer.I have examined TOX3 expression in primary breast tumours and in the normal mammary gland using micorarray data. The influence of TOX3 expression on lineage commitment was investigated using the colony forming cell (CFC) assay and FACS analysis. I further carried out microarray analysis of luminal breast cancer cells ectopically expressing TOX3 to identify TOX3 target genes as well as tandem affinity purification of TOX3 to identify TOX3 interacting proteins. Finally, the oncogenic potential of TOX3 was investigated in a human-in-mouse xenograft model
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Torkko, Kathleen Carroll. "Vitamin D receptor gene polymorphisms and prostate cancer /." Connect to full text via ProQuest. IP filtered, 2005.
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Thesis (Ph.D. in Epidemiology) -- University of Colorado at Denver and Health Sciences Center, 2005.Typescript. Includes bibliographical references (leaves 95-118). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;
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TORCHARD, DELPHINE. "Recherches sur la predisposition aux cancers du sein et de l'ovaire : le gene brca1." Paris 7, 1997. http://www.theses.fr/1997PA077306.
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Le cancer du sein est le cancer le plus frequent chez les femmes et affecte 10% d'entre elles au cours de leur vie. La plupart de ces cancers sont sporadiques. Neanmoins, environ 5% d'entre eux sont attribuables a la transmission autosomale dominante d'une predisposition genetique. L'heterogeneite des familles dans lesquelles apparait un exces de cancers du sein est le reflet d'une heterogeneite genetique. En effet, la responsabilite de mutations des genes brca1, brca2, p53 et du recepteur aux androgenes, dans le cancer du sein, est maintenant bien etablie. Le cancer de l'ovaire, quant a lui, est plus rare. Comme pour le cancer du sein, la plupart des cas sont sporadiques. Une faible fraction de ces cancers de l'ovaire, apparaissant souvent en association avec des cancers du sein dans des familles a risque, sont egalement attribuables a une predisposition genetique dont des mutations dans le gene brca1 sont principalement responsables. La finalite de mon projet de recherche etait, au depart, de cloner, par etude de genes candidats, le gene brca1 responsable du syndrome du cancer du sein et/ou de l'ovaire familial, localise en 17q21. Au cours de ce projet, l'etude d'une famille dans laquelle ce syndrome cosegrege avec la keratose palmoplantaire epidermolytique (kpp) a permis d'etablir, pour la premiere fois, la responsabilite de la keratine 9 dans la kpp. Par contre, la responsabilite de ce gene dans le syndrome du cancer du sein et/ou de l'ovaire familial a ete ecartee. Un autre gene candidat, le gene de la plakoglobine, a egalement fait l'objet d'une recherche d'alterations dans les familles de cancer du sein et/ou de l'ovaire, sans succes. Neanmoins, plusieurs donnees genetiques et biologiques suggerent l'implication de ce gene dans la tumorigenese mammaire. Le gene brca1 ayant ete clone en 1994 par une equipe americaine, nous avons recherche des mutations dans 20 familles ou la maladie est liee a ce gene. Des mutations ont ete detectees dans 17 familles; elles aboutissent, pour la plupart, a l'arret premature de la traduction. Une d'entre elles est originale : l'exon 17 du gene brca1 est delete, probablement par recombinaison homologue entre deux sequences alu situees de part et d'autre de celui-ci, dans les introns 16 et 17. Alors que l'implication du gene brca1 dans le cancer du sein et/ou de l'ovaire familial ne fait plus aucun doute, il reste de nombreuses donnees controversees. Bien que la plupart des auteurs s'accordent pour dire que la localisation de la proteine brca1 est nucleaire, certains la decrivent cytoplasmique. Les mutations du gene brca1 sont rares dans les cancers de l'ovaire sporadiques et absentes dans les cancers du sein sporadiques, mettant en doute son role de gene suppresseur de tumeur. Si brca1 joue un role dans le developpement d'une tumeur sporadique, il le fait donc indirectement. Certaines donnees, qui restent fortement a preciser, suggerent que brca1 serait un facteur de transcription. Il parait, neanmoins, evident qu'il soit implique dans le cycle cellulaire et la meiose.
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Lawrence, Kirsty Josephine. "Breast cancer predisposition gene BRCA1, pathogenic C61G mutation in mice : synthetic viability in DNA repair and tumour development." Thesis, University of Birmingham, 2016. http://etheses.bham.ac.uk//id/eprint/7000/.
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The N-terminus of BRCA1 is clinically important as inheritance of a mutation in this region correlates to an increased risk is breast and ovarian cancer. Whilst this is fairly clear, what specific mutations do and the aetiology of the disease is not clear. This thesis investigates N-terminal BRCA1 mutations using both in vitro and cell-based methods with a focus on DNA repair, mainly double-strand break and DNA crosslink repair. The use of chemotherapy agents is used with specific mutations to look at the individual phenotypes these create to each drug or radiation. This thesis also provides evidence on haploinsufficient or dominant negative effects of N-terminal mutations. Overall, the N-terminus of BRCA1 can affect DNA repair and increase genome instability that may lead to tumour development.
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Zhou, Jeff Xiwu, Xiaoyan Yang, Shunbin Ning, Ling Wang, Kesheng Wang, Yanbin Zhang, Fenghua Yuan, et al. "Identification of KANSARL as the First Cancer Predisposition Fusion Gene Specific to the Population of European Ancestry Origin." Digital Commons @ East Tennessee State University, 2017. https://dc.etsu.edu/etsu-works/6528.
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Gene fusion is one of the hallmarks of cancer. Recent advances in RNA-seq of cancer transcriptomes have facilitated the discovery of fusion transcripts. In this study, we report identification of a surprisingly large number of fusion transcripts, including six KANSARL (KANSL1-ARL17A) transcripts that resulted from the fusion between the KANSL1 and ARL17A genes using a RNA splicingcode model. Five of these six KANSARL fusion transcripts are novel. By systematic analysis of RNA-seq data of glioblastoma, prostate cancer, lung cancer, breast cancer, and lymphoma from different regions of the World, we have found that KANSARL fusion transcripts were rarely detected in the tumors of individuals from Asia or Africa. In contrast, they exist in 30 - 52% of the tumors from North Americans cancer patients. Analysis of CEPH/Utah Pedigree 1463 has revealed that KANSARL is a familially-inherited fusion gene. Further analysis of RNA-seq datasets of the 1000 Genome Project has indicated that KANSARL fusion gene is specific to 28.9% of the population of European ancestry origin. In summary, we demonstrated that KANSARL is the first cancer predisposition fusion gene associated with genetic backgrounds of European ancestry origin.
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LIDEREAU, WEINSTEIN ROSETTE. "La variabilite genetique des proto-oncogenes ras, myc et mos comme marqueur de predisposition et d'evolution dans le cancer du sein." Paris 7, 1987. http://www.theses.fr/1987PA077129.
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Magdinier, Frédérique. "Expression du gène de prédisposition au cancer du sein, BRCA1, dans les tissus humains normaux et pathologiques : implication de la méthylation dans le contrôle de son expression." Lyon 1, 1999. http://www.theses.fr/1999LYO1T128.
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Mantere, T. (Tuomo). "DNA damage response gene mutations and inherited susceptibility to breast cancer." Doctoral thesis, Oulun yliopisto, 2017. http://urn.fi/urn:isbn:9789526216416.
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Abstract Breast cancer is the most common malignancy in women and it is strongly influenced by hereditary risk factors. So far, most of the breast cancer-associated genes, including BRCA1/2, have been identified among those that encode proteins involved in DNA damage response (DDR) pathways. However, known genetic risk factors explain less than half of the familial risk of breast cancer. Identification of novel genes and mutations that predispose to breast cancer is important for the understanding of the mechanisms that contribute to the disease development and also for the identification of those individuals who are at high risk. The first aim of this study was to resolve the complementation groups of Finnish patients with Fanconi anemia (FA), which is a rare genetic disease caused by defects in a specific DDR pathway, and to study the role of the causative gene mutations in breast cancer predisposition. The second aim of this study was to identify novel breast cancer susceptibility genes and alleles by targeted next-generation sequencing (NGS) of multiple (~800) DDR related genes. In both approaches, the identified gene mutations were subjected to case-control association analysis utilizing DNA samples of over 1,000 breast cancer cases and 1,000 healthy controls. Investigation of the Finnish FA patients revealed six different disease-causing mutations in three different genes (FANCA, FANCG and FANCI). All of the studied mutations were recurrent in the Finnish population but did not associate with breast cancer. Targeted NGS identified three novel potential breast cancer susceptibility genes. A significant enrichment of TEX15 c.7253dupT and FANCD2 c.2715+1G>A mutations was observed among the hereditary breast cancer cases (P = 0.018 and P = 0.036, respectively). The strongest evidence was found for a Finnish founder mutation in MCPH1 (c.904_916del), which associated with breast cancer susceptibility both in familial (P = 0.003, OR 8.3) and unselected (P = 0.016, OR 3.3) patient cohorts. The tumor suppressive function of MCPH1 was indicated by the loss of the wild-type allele of MCPH1 in 40% of the studied carrier tumors. Furthermore, carriers exhibited a significant increase in genomic instability measured by spontaneous chromosomal rearrangements in peripheral blood lymphocytesTiivistelmä Rintasyöpä on naisten yleisin syöpä. Sairastumisriskiin vaikuttavat voimakkaasti perinnölliset alttiustekijät, ja suurin osa tähän asti tunnistetuista rintasyöpäalttiusgeeneistä, kuten BRCA1/2, koodaa DNA-vauriovasteessa (DDR) toimivia proteiineja. Tunnistetut tekijät selittävät yhä kuitenkin vain alle puolet rintasyövän perinnöllisestä alttiudesta. Uusien alttiusgeenien tunnistaminen on tärkeää rintasyövän patomekanismien ymmärtämiseksi sekä korkean rintasyöpäriskin omaavien henkilöiden tunnistamiseksi. Tämän tutkimuksen tarkoituksena oli määrittää viallisesta DDR-signaalinsiirtoreitistä johtuvan Fanconin anemian (FA) komplementaatioryhmät suomalaisilta FA-potilailta sekä tutkia sairauden taustalla olevien geenimutaatioden yhteyttä rintasyöpäriskiin. Uusia alttiusgeenejä etsittiin myös kohdennetulla uuden sukupolven sekvensointimenetelmällä, jonka avulla tutkittiin yhtäaikaisesti n. 800 DDR-geeniä. Molemmilla lähestymistavoilla tunnistettujen geenimuutosten yhteyttä rintasyöpään selvitettiin tapaus-verrokkitutkimuksen avulla, jossa tutkittiin DNA-näytteitä yli tuhannelta rintasyöpäpotilaalta sekä yli tuhannelta terveeltä henkilöltä. Suomalaisten FA-potilaiden geenimuutoksia selvittävässä tutkimuksessa tunnistettiin yhteensä kuusi mutaatiota kolmessa eri geenissä (FANCA, FANCG ja FANCI). Kaikki tutkimuksessa tunnistetut mutaatiot olivat toistuvia suomalaisessa väestössä, mutta merkitsevää assosiaatiota näiden mutaatioiden ja rintasyöpäalttiuden välillä ei havaittu. DDR-geenien sekvensoinnin avulla tunnistettiin kolme uutta mahdollista rintasyöpäalttiusgeeniä. Tutkimuksessa havaittiin TEX15 c.7253dupT ja FANCD2 c.2715+1G>A mutaatioiden rikastuminen perinnöllisessä rintasyöpäaineistossa (P = 0.018 ja P = 0.036). Merkittävin yhteys rintasyöpäalttiuden kanssa todettiin MCPH1-geenin perustajamutaatiolle (c.904_916del). Tämä mutaatio assosioitui rintasyöpäalttiuden kanssa sekä perinnöllisessä (P = 0.003, OR 8.3) että valikoimattomassa potilasaineistossa (P = 0.016, OR 3.3). Useissa mutaatiokantajien tuumoreissa (40 %) normaali MCPH1 vastinalleeli oli hävinnyt, mikä viittaisi siihen, että MCPH1 toimii tuumorisuppressorina. Mutaatiokantajilla todettiin myös kohonnut määrä kromosomaalisia muutoksia veren periferaalisissa lymfosyyteissä, mahdollisesti kohonneeseen genomiseen epävakauteen liittyen
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Marlin, Régine. "Apport du séquençage pangénomique pour l'identification des prédispositions héréditaires aux cancers." Thesis, Antilles, 2015. http://www.theses.fr/2015ANTI0005/document.
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Ce travail de thèse illustre l’intérêt d’utiliser le séquençage de nouvelle génération (Next- Generation Sequencing ou NGS) pour améliorer le diagnostic moléculaire des formes de prédispositions aux cancers. Nous avons appliqué deux stratégies différentes, l’une basée sur l’analyse simultanée d’un panel de gènes impliqués dans une pathologie, l’autre sur l’analyse de toutes les parties codante du génome ou exome.Nous avons montré que le développement d’un panel de 10 gènes impliqués dans la carcinogenèse des cancers coliques a permis d’améliorer le diagnostic moléculaire de ces formes de cancers. Cette technologie a diminué le délai de rendu des résultats et est plus sensible que le séquençage Sanger et la QMPSF (Quantitative Multiplex PCR of Short Fragment).L’application d’une stratégie d’analyse d’exomes de trio par NGS, à l’analyse de deux formes de cancers sporadiques de phénotype extrême, cancers du sein et de l’ovaire, a permis la détection de mutations de novo portant sur des gènes impliqués dans l’oncogenèse. Pour mettre en cause ces mutations dans le phénotype, nous avons réalisé des tests fonctionnels et des études de récurrenceThe working thesis Illustre interest of the USE next generation sequencing (NGS Next- Generation Sequencing e) pay Improve Molecular diagnosis of predisposition to cancer forms. Have we applied two different strategies you in June based on the simultaneous analysis of genes not involved in panel A pathology, the Other on the analysis of all the parties of the coding genome e exome.Nous Have Shown que le development of a panel of 10 genes involved in carcinogenesis of colon cancer a Permit to improve the molecular diagnosis of forms of CES dE cancers. This technology has reduced the Delai rendering results and is more reasonable That Sanger sequencing and QMPSF (Quantitative Multiplex PCR of Short Fragment) .The application OF exomes an analysis by NGS trio Strategy at analysis of two forms of sporadic cancer phenotype extreme, breast cancer and ovarian cancer, permit the detection of de novo mutations on genes involved in oncogenesis. For Questioning mutations IN THESE phenotype, We Have made Functional testing and induction studies
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Li, Chunde. "Tracking functional changes in the cancer genome : a molecular genetic analysis of renal and prostatic carcinomas using PCR based techniques by a candidate chromosome and candidate gene approach /." Stockholm, 1999. http://diss.kib.ki.se/1999/19991210li/.
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PRESNEAU, NADEGE. "Recherche de mutations constitutionnelles dans les genes de predispositions hereditaires aux cancers du sein et/ou de l'ovaire : brca-1, brca-2. recherche de nouveaux genes suppresseurs de tumeur impliques dans l'oncogenese mammaire." Clermont-Ferrand 2, 1999. http://www.theses.fr/1999CLF21122.
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Le gene brca-1 (breast cancer n 1), implique principalement dans une predisposition hereditaire au cancer du sein pre menopausique, localise sur le chromosome 17 en 17q12-21, a ete clone en 1994 par l'equipe de mark skolnik. Un deuxieme gene de predisposition hereditaire au cancer du sein, brca-2, a ete localise en 13q12-13 et clone en 1995. Au total, 52% des familles seraient porteuses d'une mutation brca-1, 35% porteuses d'une mutation brca-2 et 13% des familles liees a d'autres genes. Notre travail de these s'est ainsi inscrit dans un contexte general d'etude des predispositions hereditaires aux cancers du sein et/ou de l'ovaire. Cette etude a comporte deux objectifs majeurs. Notre etude a permis d'evaluer la reelle proportion de familles francaises a haut risque de cancers du sein et/ou de l'ovaire porteuse d'une mutation constitutionnelle du gene brca-1. En effet, des mutations germinales dans le gene brca-1 ont ete detectees dans 24% des familles francaises a haut risque de cancers du sein et/ou de l'ovaire, confirmant les resultats deja publies par d'autres equipes francaises. Puisque seulement 17 de nos familles sur les 70 etaient porteuses d'une mutation germinale de brca-1, nous avons recherche pour, ces meme 70 familles, l'eventuelle presence de mutations constitutionnelles dans le gene brca-2. Les premiers resultats de ce travail ont montre que 3 familles etaient porteuses d'une mutation du gene brca-2. Ainsi il apparait maintenant evident qu'il existe plusieurs genes de predispositions hereditaires aux cancers du sein et/ou des ovaires en plus de brca-1 et brca-2. Ainsi, la deuxieme partie de notre travail a consiste a rechercher des nouveaux genes de type oncosuppresseurs pouvant etre implique dans la tumorogenese mammaire. Ces genes peuvent etre impliques de facon indirecte par une eventuelle interaction avec les genes brca mais peuvent etre egalement impliques plus directement en etant eux-memes des genes candidats pour les genes brca-x. Par la technique de ddrt-pcr, nous avons ainsi recherche l'expression differentielle entre le tissu normal mammaire et le tissu tumoral mammaire d'une patiente (mme lp) dont la predisposition hereditaire semblait etre liee ni a brca-1 ni a brca-2. Ainsi, nous avons pu identifier plusieurs sequences differentielles dont une seule pourrait etre interessante a exploiter en clonant son adnc complet via une sequence genomique clone dans un vecteur de type pac (z84477 ncbi) avec la quelle notre sequence presente 100% d'homologie sur la totalite de sa sequence (82 pb).
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Puget, Nadine. "Prédisposition génétique au cancer du sein : recherche de mutations dans les régions régulatrices et de réarrangements structuraux du gène BRCA1." Lyon 1, 1999. http://www.theses.fr/1999LYO1T093.
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Rouleau, Etienne. "Implication des remaniements géniques dans l'inactivation des gènes de prédisposition au cancer du sein." Thesis, Paris 11, 2011. http://www.theses.fr/2011PA11T106.
Full textAbstract:
Parmi les cancers du sein, 5 à 10% serait associé à une prédisposition génétique familiale. La prise en charge des patients prédisposés nécessite une bonne définition des risques de cancer. L’identification de l’altération moléculaire causale dans chacune de ces familles est donc un enjeu essentiel dans la prise en charge médicale. Deux gènes, BRCA1 et BRCA2, sont associés à une prédisposition majeure au cancer du sein et de l’ovaire depuis le milieu des années 1990, expliquant environ 15% des formes héréditaires. L’analyse moléculaire de ces deux gènes est désormais réalisée en routine pour la recherche de variations nucléotidiques et plus récemment de remaniements géniques ce qui a permis d’améliorer le taux de détection de mutations délétères. Cependant, pour près de 85% des familles avec une agrégation familiale ou un âge anormalement jeune de cancer du sein, aucune mutation délétère n’a pu être mise en évidence. Dans ce contexte, mon travail de thèse a eu pour objectif de tester plusieurs hypothèses permettant d’expliquer les risques de cancer du sein observés chez des familles montrant l’absence de mutation des gènes BRCA1 et BRCA2. Nous avons ainsi recherché des mécanismes d’altération rarement explorés pour les gènes BRCA1 et BRCA2, et enfin analysé d’autres gènes candidats dont le gène CDH1 et huit autres gènes impliqués dans la réparation de l’ADN. Nous avons pu mieux caractériser des remaniements sur les gènes BRCA1 et BRCA2. Enfin, nous avons pu évaluer l’impact de variants de signification inconnue et des réarrangements détectés par l’étude de leurs transcrits. Dans un premier temps, nous avons mis en place et validé de nouvelles approches techniques de détection et de caractérisation : la CGH-array dédiée, la qPCR-HRM et le peignage moléculaire. Ces techniques ont ensuite été utilisées pour étudier les remaniements géniques et leur fréquence pour onze gènes candidats à la prédisposition au cancer du sein à partir de 472 familles négatives aux mutations délétères BRCA1 et BRCA2. Parmi ces 11 gènes, nous pouvons conclure que les remaniements géniques détectés concernent principalement les gènes BRCA1 et BRCA2, et à un moindre degré le gène CHEK2. En appliquant ces techniques, nous avons pu décrire de nouveaux événements, deux larges délétions et une duplication intronique, pour les gènes CDH1 et BARD1, ouvrant de nouvelles perspectives sur l’étude des transcrits alternatifs. Nous avons en particulier pu décrire la grande diversité des réarrangements délétères en 5’ du gène BRCA1. L’enjeu est ensuite l’interprétation de ces événements. Notre étude des transcrits a permis de décrire un variant exonique d’épissage entraînant une délétion de l’exon 23 au niveau du transcrit BRCA1. Nous avons aussi validé la pathogénicité d’un réarrangement en phase de l’exon 3 de BRCA2 par une étude quantitative du transcrit et une évaluation de la coségrégation. Au final, moins de 1% de nouveaux remaniements ont été mis en évidence. Ce travail est riche d’enseignement pour les nouvelles investigations à mettre en place pour les familles prédisposées. En dehors de la technique d’identification, il est nécessaire de développer des stratégies de validation basées principalement sur la quantification des effets de ces altérations au niveau de l’ARN et des protéines. Cependant, il manque encore de nombreux chaînons pour expliquer l’héritabilité des cancers du sein. Les études sur les nouveaux gènes candidats et l’avènement des techniques de séquençage pangénome à haut débit, devraient permettre d’avoir une meilleure vision des phénomènes pathobiologiques liés à la prédisposition au cancer du seinFive to 10% of breast cancers are linked to a genetic predisposition. The management of patients at risk requires a good definition in the risk of cancer. The identification of causal molecular alterations in each of these families is a key issue in medical care. Two genes, BRCA1 and BRCA2, are related with the greatest susceptibility to breast cancer and ovarian cancer since the mid-1990s, accounting for about 15% of hereditary forms. Molecular analysis of these two genes is now routinely performed for the detection of nucleotide variations and more recently large rearrangements which have improved the detection rate of deleterious mutations. However, for more than 85% of families, no mutation explains familial aggregation or unusual young age of breast cancer onset. In this context, my thesis aimed at testing several hypotheses to explain the risks of breast cancer observed in families without any identified mutations in the BRCA1 and BRCA2 genes. We investigated some mechanisms of genic rearrangements rarely explored for BRCA1 and BRCA2 genes, and finally investigated other candidate genes, especially CDH1 gene and eight other genes involved in double-strand DNA repair. We have better characterized some rearrangements in the BRCA1 and BRCA2 genes. Finally, we applied RNA quantitative approaches to better assess the impact from variants of unknown significance and detected rearrangements. Initially, we developed and validated new technical approaches for detection and characterization such as dedicated CGH-array, qPCR-HRM and molecular combing. Rare large germline rearrangements and their frequency in eleven candidate genes for susceptibility to breast cancer were studied among 472 families negative by routine testing for BRCA1 and BRCA2 genes. Of these 11 genes, we conclude that genic rearrangements are found then mainly in the BRCA1 and BRCA2 genes, and to a lesser extent in the CHEK2 gene. We were able to describe two large intronic deletions and one duplication for the CDH1 and BARD1 genes, opening new perspectives on the regulation of their alternative transcript. In particular, we described the wide diversity of new rearrangements involving the 5' region of the BRCA1 gene. Then, it is necessary to validate and interpret those new events. Our transcript analysis described a new exonic variant causing the splice deletion of exon 23 in BRCA1 gene. We have developed tools to validate an in-frame large rearrangement of BRCA2 exon 3 with some transcript quantitative approaches and disease cosegregation.Finally, less than 1% of new rearrangements have been identified. This work is instructive for further investigations to establish molecular etiology in those families with breast cancer predisposition. Not only by applying new technologies, it is necessary to develop other strategies based primarily on quantifying effects of these alterations on transcription and traduction. However, it still lacks many links to explain the heritability of breast cancer. The combination of new candidate genes studies and the advent of high-throughput sequencing are expected to give a better vision of pathobiological phenomena related to the breast cancer predisposition
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Chiang, Yu-Chieh, and 江玗潔. "Identify the predisposition genes to endometrial cancer." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/t3akzx.
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Lhotová, Klára. "Analýza hereditárních genetických variant predisponujících ke vzniku familiární formy karcinomu ovaria." Doctoral thesis, 2021. http://www.nusl.cz/ntk/nusl-437901.
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Ovarian cancer (OC) is the deadliest gynecologic malignancy with a substantial proportion of hereditary cases and a frequent association with breast cancer (BC). Genetic testing facilitates preventive management for carriers of mutations in OC-susceptibility genes. However, the prevalence of germline mutations varies among populations and many rarely mutated OC predisposition genes remain to be identified. We analyzed 219 genes in 1333 Czech OC patients and 2278 population-matched controls (PMC) using next-generation sequencing. Altogether, 427/1333 (32%) patients and 58 /2278 (2,5%) PMC carried pathogenic mutations in 18 known/anticipated OC predisposition genes. Mutations in BRCA1, BRCA2, RAD51C, RAD51D, BARD1 and mismatch repair genes conferred a high OC risk (with OR>5). Mutations in BRIP1 and NBN were associated with moderate risk (both OR ≥2 - <5). BRCA1/2 mutations dominated in almost all clinicopathological subgroups including sporadic borderline tumors of ovary (BTO). Analysis of remaining 201 genes revealed somatic mosaics in PPM1D and germline mutations in SHPRH and NAT1 associating with a high/moderate OC risk significantly; however, further studies are warranted to delineate their contribution to OC development in other populations. Results of this study demonstrate the high proportion...
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Yaspan, Brian L. "Genetic predisposition to prostate cancer the contribution of the HPCX locus and TGFB1 gene /." Diss., 2008. http://etd.library.vanderbilt.edu/ETD-db/available/etd-03052008-111718/.
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"Breast cancer susceptibility gene (BRCA1) mutations in Hong Kong Chinese women with breast cancer." 1998. http://library.cuhk.edu.hk/record=b6073102.
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Wang Ya-Ping.Thesis (Ph.D.)--Chinese University of Hong Kong, 1998.
Includes bibliographical references (p. 152-161).
Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web.
Mode of access: World Wide Web.
Abstracts in English and Chinese.
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Yawitch, Tali Michelle. "Inherited predisposition to breast/ovarian cancer : the frequency and nature of BRCA1 gene mutations in South African families." Diss., 2002. http://hdl.handle.net/2263/30470.
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Breast cancer is the most common cancer in South African women. Approximately 5¬10% of all breast cancer cases are due to an inherited predisposition, resulting from mutations in tumour suppressor genes. The BRCA1 gene on chromosome 17q is one such tumour suppressor gene, that when mutated confers an increased risk of breast/ovarian cancer in carriers. To date, more than 500 different BRCA 1 mutations have been reported worldwide. Some of these mutations are frequently reported and others occur commonly in certain population groups. These population-specific differences in mutations represent founder effects, whereby a single ancestral mutation accounts for the majority of breast cancer cases. This study was undertaken as the nature and frequency of BRCA1 mutations in South African breast/ovarian cancer families is unknown. Fifty-one breast/ovarian cancer families were screened for three commonly occurring mutations (185deIAG, 4184del4 and 5382insC) using polymerase chain reaction (PCR) and allele-specific oligonucleotide (ASO) hybridisation. The protein truncation test (PTT) was utilised to detect truncating mutations in the large exon 11, and the remaining coding exons were screened for mutations using exon-by-exon PCR single strand conformation polymorphism/heteroduplex analysis (SSCP/HA). Seven disease-causing mutations were identified in 15 families, consisting of five different frameshift mutations and two different nonsense mutations. Four Ashkenazi Jewish families were found to harbour the 185delAG mutation; the 5382insC mutation was identified in two Afrikaner families and one Ashkenazi Jewish family. Haplotype analysis revealed that the four Ashkenazi families share the common Ashkenazi Jewish haplotype, suggesting a common ancestor for these families. Similarly, the two Afrikaner families share the same haplotype as families of north and east European ancestry with the 5382insC mutation. The haplotype of the Ashkenazi Jewish family with this mutation was however different to the linked haplotype, indicating a recombination event or an independent mutation. Both these mutations are thought to have occurred in or before the medieval period. Furthermore, four Afrikaner families were found to carry the novel E881X nonsense mutation, which has not been previously described. Haplotype analysis of these families suggested that these patients share a common ancestor, and genealogic studies have identified the founding couple for this mutation, who both arrived in the Cape from France in the late 1600s. Four additional families were found to harbour BRCA1 mutations by SSCP/HA. Three of these mutations have not been previously reported - the S451X nonsense mutation (identified in a family of Scottish origin), the 1493delC mutation identified in an Afrikaner family, and the 4957insC mutation identified in an Indian family. The 448insA mutation was identified in a family of German origin, where the patient had cancer of the fallopian tubes. A number of different described polymorphisms and variants of unknown functional significance were also identified. This is the first study to show that BRCA1 is involved in South African breast/ovarian cancer families, to the extent that 29.4% (15/51) of families have BRCA1 mutations. Furthermore, minor founder effects in the Afrikaner population have been demonstrated. These results enable improved genetic counselling and clinical management of mutation positive families as well as subsequent testing of family members.Dissertation (MSc (Human Genetics))--University of Pretoria, 2005.
Genetics
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