Relevant bibliographies by topics / Variante somatica

Academic literature on the topic 'Variante somatica'

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Published: 11 March 2023

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Journal articles on the topic "Variante somatica"

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Bennett, Mark F., Michael S. Hildebrand, Sayaka Kayumi, Mark A. Corbett, Sachin Gupta, Zimeng Ye, Michael Krivanek, et al. "Evidence for a Dual-Pathway, 2-Hit Genetic Model for Focal Cortical Dysplasia and Epilepsy." Neurology Genetics 8, no. 1 (January 25, 2022): e0652. http://dx.doi.org/10.1212/nxg.0000000000000652.

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Background and ObjectivesThe 2-hit model of genetic disease is well established in cancer, yet has only recently been reported to cause brain malformations associated with epilepsy. Pathogenic germline and somatic variants in genes in the mechanistic target of rapamycin (mTOR) pathway have been implicated in several malformations of cortical development. We investigated the 2-hit model by performing genetic analysis and searching for germline and somatic variants in genes in the mTOR and related pathways.MethodsWe searched for germline and somatic pathogenic variants in 2 brothers with drug-resistant focal epilepsy and surgically resected focal cortical dysplasia (FCD) type IIA. Exome sequencing was performed on blood- and brain-derived DNA to identify pathogenic variants, which were validated by droplet digital PCR. In vitro functional assays of a somatic variant were performed.ResultsExome analysis revealed a novel, maternally inherited, germline pathogenic truncation variant (c.48delG; p.Ser17Alafs*70) in NPRL3 in both brothers. NPRL3 is a known FCD gene that encodes a negative regulator of the mTOR pathway. Somatic variant calling in brain-derived DNA from both brothers revealed a low allele fraction somatic variant (c.338C>T; p.Ala113Val) in the WNT2 gene in 1 brother, confirmed by droplet digital PCR. In vitro functional studies suggested a loss of WNT2 function as a consequence of this variant. A second somatic variant has not yet been found in the other brother.DiscussionWe identify a pathogenic germline mTOR pathway variant (NPRL3) and a somatic variant (WNT2) in the intersecting WNT signaling pathway, potentially implicating the WNT2 gene in FCD and supporting a dual-pathway 2-hit model. If confirmed in other cases, this would extend the 2-hit model to pathogenic variants in different genes in critical, intersecting pathways in a malformation of cortical development. Detection of low allele fraction somatic second hits is challenging but promises to unravel the molecular architecture of FCDs.
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Ura, Hiroki, Sumihito Togi, and Yo Niida. "Dual Deep Sequencing Improves the Accuracy of Low-Frequency Somatic Mutation Detection in Cancer Gene Panel Testing." International Journal of Molecular Sciences 21, no. 10 (May 16, 2020): 3530. http://dx.doi.org/10.3390/ijms21103530.

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Cancer gene panel testing requires accurate detection of somatic mosaic mutations, as the test sample consists of a mixture of cancer cells and normal cells; each minor clone in the tumor also has different somatic mutations. Several studies have shown that the different types of software used for variant calling for next generation sequencing (NGS) can detect low-frequency somatic mutations. However, the accuracy of these somatic variant callers is unknown. We performed cancer gene panel testing in duplicate experiments using three different high-fidelity DNA polymerases in pre-capture amplification steps and analyzed by three different variant callers, Strelka2, Mutect2, and LoFreq. We selected six somatic variants that were detected in both experiments with more than two polymerases and by at least one variant caller. Among them, five single nucleotide variants were verified by CEL nuclease-mediated heteroduplex incision with polyacrylamide gel electrophoresis and silver staining (CHIPS) and Sanger sequencing. In silico analysis indicated that the FBXW7 and MAP3K1 missense mutations cause damage at the protein level. Comparing three somatic variant callers, we found that Strelka2 detected more variants than Mutect2 and LoFreq. We conclude that dual sequencing with Strelka2 analysis is useful for detection of accurate somatic mutations in cancer gene panel testing.
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Das, Kingshuk, Amber Carter, Brandie Heald, Scott T. Michalski, Sarah M. Nielsen, Nhu Ngo, Sara Elrefai, et al. "Integrated germline and somatic cancer testing provides opportunity to identify cancer risk and resolve variant origins." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): 10589. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.10589.

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10589 Background: Germline and somatic genetic testing are established tools for the management of cancer patients. Somatic testing is primarily used to inform therapy and germline testing is used to diagnose hereditary cancer predisposition syndromes. While somatic testing can detect germline variants, the interpretation and reporting algorithms are optimized to predict therapeutic efficacy. As a result, germline variants may be missed or only interpreted in context of their potential to act as a therapeutic target. We retrospectively reviewed a series of patients who received both germline and somatic testing to examine the opportunities for concurrent germline testing to improve somatic reporting. Methods: Our study reviewed data from 43 patients with solid cancer diagnoses who were otherwise unselected and underwent testing with a 435-gene somatic genetic test and an 83-gene germline test. The most frequent cancers were pancreatic (18), ovarian (8), and prostate (7). Results: Out of the 43 patients, 7 (16%) harbored a pathogenic or likely pathogenic germline variant (PGV) in a cancer susceptibility gene. PGVs were identified in MLH1, MSH6, CHEK2, PALB2, CDKN2A, NBN, and MUTYH. Notably, 3 of these genes ( CHEK2, PALB2, MUTYH) were not considered therapeutic targets, and therefore were only included as ancillary findings near the end of the preliminary somatic test reports (generated prior to integration of germline test results). In addition, 40 of 43 (93%) patients had at least one variant detected by somatic testing in at least one of the germline panel genes (mean number variant genes = 4.1, maximum = 10); all of these variants were within the reportable range of the germline assay, and therefore germline test results were able to resolve their germline versus somatic origins. The genes that most frequently had somatic variants identified were TP53 (79% of patients), CDKN2A (37%), SMAD4 (30%), and FLCN (21%). Conclusions: Due to the size of commonly ordered somatic gene panels, there is a high probability of detecting variants in hereditary cancer predisposition genes (> 90% of patients in this study) that can provide either therapy or cancer risk information or both. Given that a significant proportion (16% in this study) of cancer patients harbor PGVs (which can further inform treatment, disease surveillance, preventive measures, and risk assessment for family members), it is crucial to resolve the somatic versus germline origin of these variants. Since interpretation and reporting algorithms for somatic testing are optimized for therapy prediction, and variables such as specimen tumor purity, tumor ploidy, and variant allele fraction render estimates of variant origin unreliable for diagnostic purposes, it is important to take advantage of germline testing concurrently in patients receiving somatic testing to glean this critical information.
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Tsuchida, Naomi, Yosuke Kunishita, Yuri Uchiyama, Yohei Kirino, Makiko Enaka, Yukie Yamaguchi, Masataka Taguri, et al. "Pathogenic UBA1 variants associated with VEXAS syndrome in Japanese patients with relapsing polychondritis." Annals of the Rheumatic Diseases 80, no. 8 (March 31, 2021): 1057–61. http://dx.doi.org/10.1136/annrheumdis-2021-220089.

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ObjectivesTo determine clinical and genetic features of individuals with relapsing polychondritis (RP) likely caused by pathogenic somatic variants in ubiquitin-like modifier activating enzyme 1 (UBA1).MethodsFourteen patients with RP who met the Damiani and Levine criteria were recruited (12 men, 2 women; median onset age (IQR) 72.1 years (67.1–78.0)). Sanger sequencing of UBA1 was performed using genomic DNA from peripheral blood leukocytes or bone marrow tissue. Droplet digital PCR (ddPCR) and peptide nucleic acid (PNA)-clamping PCR were used to detect low-prevalence somatic variants. Clinical features of the patients were investigated retrospectively.ResultsUBA1 was examined in 13 of the 14 patients; 73% (8/11) of the male patients had somatic UBA1 variants (c.121A>C, c.121A>G or c.122T>C resulting in p.Met41Leu, p.Met41Val or p.Met41Thr, respectively). All the variant-positive patients had systemic symptoms, including a significantly high prevalence of skin lesions. ddPCR detected low prevalence (0.14%) of somatic variant (c.121A>C) in one female patient, which was subsequently confirmed by PNA-clamping PCR.ConclusionsGenetic screening for pathogenic UBA1 variants should be considered in patients with RP, especially male patients with skin lesions. The somatic variant in UBA1 in the female patient is the first to be reported.
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Fujita, Atsushi, Takefumi Higashijima, Hiroshi Shirozu, Hiroshi Masuda, Masaki Sonoda, Jun Tohyama, Mitsuhiro Kato, et al. "Pathogenic variants of DYNC2H1, KIAA0556, and PTPN11 associated with hypothalamic hamartoma." Neurology 93, no. 3 (June 13, 2019): e237-e251. http://dx.doi.org/10.1212/wnl.0000000000007774.

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ObjectiveIntensive genetic analysis was performed to reveal comprehensive molecular insights into hypothalamic hamartoma (HH).MethodsThirty-eight individuals with HH were investigated by whole exome sequencing, target capture-based deep sequencing, or single nucleotide polymorphism (SNP) array using DNA extracted from blood leukocytes or HH samples.ResultsWe identified a germline variant of KIAA0556, which encodes a ciliary protein, and 2 somatic variants of PTPN11, which forms part of the RAS/mitogen-activated protein kinase (MAPK) pathway, as well as variants in known genes associated with HH. An SNP array identified (among 3 patients) one germline copy-neutral loss of heterozygosity (cnLOH) at 6p22.3–p21.31 and 2 somatic cnLOH; one at 11q12.2–q25 that included DYNC2H1, which encodes a ciliary motor protein, and the other at 17p13.3–p11.2. A germline heterozygous variant and an identical somatic variant of DYNC2H1 arising from cnLOH at 11q12.2–q25 were confirmed in one patient (whose HH tissue, therefore, contains biallelic variants of DYNC2H1). Furthermore, a combination of a germline and a somatic DYNC2H1 variant was detected in another patient.ConclusionsOverall, our cohort identified germline/somatic alterations in 34% (13/38) of patients with HH. Disruption of the Shh signaling pathway associated with cilia or the RAS/MAPK pathway may lead to the development of HH.
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Wu, Yanqing, Wenzhe Fan, Miao Xue, Yiyang Tang, Suo Peisu, Bo Yang, Tanxiao Huang, Jing Zhang, and Jiaping Li. "TP53 pathogenic variants with low allele fraction in germline genetic testing." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): 10600. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.10600.

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10600 Background: Blood or saliva DNA generally considered to be representative of germline genome in genetic cancer risk assessment. However white blood cells from these samples may also include somatic origin DNA due to postzygotic variation or, most commonly, clonal hematopoiesis (CH). Low variant allele fraction (VAF) found in germline genetic testing suggest the possibility of somatic variant and may lead to misinterpretation of genetic risk. TP53, of which germline pathogenic variants are associated with Li-Fraumeni syndrome (LFS), is frequently mutated in CH. This analysis investigated characteristics of TP53 pathogenic variants with low VAF. Methods: We reviewed the prevalence and distribution of TP53 pathogenic variants(PVs) detected in 11,277 advanced cancer patients who underwent clinical testing with a clinical NGS pan-cancer panel. Potential somatic PVs were defined as variants with low VAF from 10% to 35%. The VAF were evaluated in matched tumor tissue samples if available. Results: TP53 pathogenic variants were detected in 36 (0.32%) patients from blood or saliva samples, VAF between 10% and 35% were identified in 8(22.22%) patients and 7 of them were performed NGS sequencing in matched tumor tissue samples. The average VAF of tissue samples were 9.31times lower than blood or saliva samples(21.69% vs 3.88%). Conclusions: TP53 pathogenic variants with low allele fraction in blood or saliva samples indicate the possibility of somatic variant, a reduced VAF in matched tumor tissue samples may contribute to confirmation for suspicion of somatic origin.
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Brown, Natasha J., Zimeng Ye, Chloe Stutterd, Sureshni I. Jayasinghe, Amy Schneider, Saul Mullen, Simone A. Mandelstam, and Michael S. Hildebrand. "Somatic IDH1 variant (p.R132C) in an adult male with Maffucci syndrome." Molecular Case Studies 7, no. 6 (September 29, 2021): a006127. http://dx.doi.org/10.1101/mcs.a006127.

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Maffucci syndrome is a rare, highly variable somatic mosaic condition, and well-known cancer-related gain-of-function variants in either the IDH1 or IDH2 genes have been found in the affected tissues of most reported individuals. Features include benign enchondroma and spindle-cell hemangioma, with a recognized increased risk of various malignancies. Fewer than 200 affected individuals have been reported; therefore, accurate estimates of malignancy risk are difficult to quantify and recommended surveillance guidelines are not available. The same gain-of-function IDH1 and IDH2 variants are also implicated in a variety of other benign and malignant tumors. An adult male presented with several soft palpable lesions on the right upper limb. Imaging and histopathology raised the possibility of Maffucci syndrome. DNA was extracted from peripheral blood lymphocytes and tissue surgically resected from a spindle-cell hemangioma. Sanger sequencing and droplet digital polymerase chain reaction (PCR) analysis of the IDH1 gene were performed. We identified a somatic mosaic c.394C > T (p.R132C) variant in exon 5 of IDH1, in DNA derived from hemangioma tissue at ∼17% variant allele fraction. This variant was absent in DNA derived from blood. This variant has been identified in the affected tissue of most reported individuals with Maffucci syndrome. Although this individual has a potentially targetable variant, and there is a recognized risk of malignant transformation in this condition, a decision was made not to intervene with an IDH1 inhibitor. The reasons and prospects for therapy in this condition are discussed.
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Khanna, Shivani, Steven Brad Maron, Leah Chase, Samantha Lomnicki, Sonia Kupfer, and Daniel V. T. Catenacci. "Suspected and confirmed germline variants from tumor-only somatic sequencing of 864 gastrointestinal malignancies." Journal of Clinical Oncology 37, no. 15_suppl (May 20, 2019): e13131-e13131. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e13131.

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e13131 Background: Targeted tumor-only somatic sequencing informs therapies and is becoming a routine part of cancer care. It also identifies patients with possible germline variants who require confirmatory genetic testing. The aim was to identify patients with suspected and confirmed germline variants whose GI tumors underwent somatic sequencing. Methods: 864 patients with GI tumors who had Foundation One (FO) somatic sequencing from 4/2003-3/2018 were evaluated. Inclusion criteria for suspected germline variants were: a) allele frequency ≥ 35% in hereditary cancer genes and b) pathogenic variants by FO and/or ClinVar. Variants in commonly mutated somatic genes ( TP53, KRAS, CDKN2A) were excluded in patients over age 40. Recommendation of genetic evaluation and germline test results were recorded. Patient, family, and tumor characteristics were compared using univariate analysis. Results: 199 of 864 patients had suspected germline pathogenic variants. 50 patients were recommended genetic evaluation, and 26 patients underwent genetic testing. A germline pathogenic variant was confirmed in 15 patients. Among all patients suspected to have germline variants, 8% were confirmed by genetic testing. Patients under age 40 and those with family cancer history were more often referred for testing (Table). Patients with variants in BRCA1, MLH1, MSH2, PMS2, POLE and TP53 were more often referred for testing. Conclusions: A quarter of patients carried a somatic pathogenic variant with allele frequency ≥35% in a hereditary cancer gene. 25% of these patients were recommended for genetic evaluation. Younger patients and those with family history were more often referred. 8% of patients with suspected germline variants were confirmed by genetic testing. These results provide “real world” experience in using somatic only tumor testing to identify patients with germline pathogenic variants who then might benefit from future cancer screening and genetic testing in family members. Comparison of characteristics by recommendation to undergo genetic testing based on somatic tumor sequencing results. [Table: see text]
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Michalski, Scott T., Daniel Esteban Pineda Alvarez, Meaghan Russell, Shan Yang, Guru Sonpavde, and Edward D. Esplin. "Tumor sequencing with germline genetic testing: Identification of patients with hereditary cancer and precision treatment eligibility." Journal of Clinical Oncology 37, no. 15_suppl (May 20, 2019): 1580. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.1580.

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1580 Background: Cancer is a fundamentally genetic disease, as such, somatic and germline mutation analysis is used in the comprehensive assessment of patients with cancer. Studies report that approximately 10% of patient’s tumors have clinically significant variants known to predispose to hereditary cancer, with medical implications for both patients and family members. We retrospectively reviewed a series of patients where providers suspected a somatic variant also existed in the germline and followed up with clinical germline genetic testing. We report the rate of concordance between germline and somatic results and their clinical impact. Methods: Our study used de-identified data from 1043 consecutive patients who underwent somatic genetic testing followed by germline testing with NGS-based hereditary cancer gene panels. Results: Somatic results most frequently prompting germline testing included variants in BRCA2 (290), BRCA1 (174), TP53 (158), ATM (70), MLH1 (65), APC (65), PMS2 (61), MSH6 (58), PTEN (54) and CDH1 (42). In 364/1043 cases (35%) the variant was detected as likely pathogenic or pathogenic (LP/P) in the germline. Genes confirmed as germline variants in 60-100% of cases included: FANCA, AXIN2, RAD50, MUTYH, BLM, PALB2, CHEK2, FANCD2, MITF, SDHB. Variants in: FH, BRCA2, RET, ATM, SDHA, BRIP1, MSH2, BRCA1, BAP1, EGFR and RAD51D confirmed in the germline in 25-60%. Variants were rarely germline for TP53 (3%), APC (3%), PTEN (2%) and none in CDKN2A, NF1 and STK11. In 24 (2%) cases a LP/P germline variant was detected but not reported in the tumor. Conclusions: Approximately ⅓ of patients suspected to have hereditary risk after tumor testing had LP/P germline variants. Notably, some genes had a high probability of variants occurring in the germline, while others were primarily seen in tumors. Interestingly, 6% of the germline variants were not included on the somatic report due to technical and gene content differences in either assays or due to differences of clinical classification between somatic and germline testing. Adding germline results to somatic testing may inform options for precision treatment, prevention, or early detection of, secondary malignancies and guide genetic counseling of family members.
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Sancho-Galán, Pau, Antonio Amores-Arrocha, Víctor Palacios, and Ana Jiménez-Cantizano. "Preliminary Study of Somatic Variants of Palomino Fino (Vitis vinifera L.) Grown in a Warm Climate Region (Andalusia, Spain)." Agronomy 10, no. 5 (May 4, 2020): 654. http://dx.doi.org/10.3390/agronomy10050654.

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Vegetative propagation of Vitis vinifera cultivars over hundreds of years has led to the accumulation of a large number of somatic variants of the same grapevine variety. These variants are now considered a working tool to cope with changing environmental conditions as a result of, among others, global warming. In this work, three somatic variants of the major grapevine variety of the South West (SW) of Andalusia (Spain), Palomino Fino, have been genetically and morphologically characterized, as well as their grape musts from two different vintages. The genetic analysis at 22 microsatellite loci confirmed the identity of the three somatic variants that presented the same genotype as Palomino Fino, while the morphological study showed differences between the three somatic variants and Palomino Fino, highlighting the somatic variant Palomino Pelusón. Regarding the physicochemical analysis of its musts, differences were also observed between the somatic variants and Palomino Fino. As a result of all of the above, the use of grapes from somatic variants can be a viable and natural alternative for the production of quality wines in warm climate areas. On the other hand, promoting the cultivation of the somatic variants could contribute to preventing the loss of Palomino Fino intraspecific variability.
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Dissertations / Theses on the topic "Variante somatica"

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Vijayan, Vinaya. "Understanding and Improving Identification of Somatic Variants." Diss., Virginia Tech, 2016. http://hdl.handle.net/10919/72969.

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It is important to understand the entire spectrum of somatic variants to gain more insight into mutations that occur in different cancers for development of better diagnostic, prognostic and therapeutic tools. This thesis outlines our work in understanding somatic variant calling, improving the identification of somatic variants from whole genome and whole exome platforms and identification of biomarkers for lung cancer. Integrating somatic variants from whole genome and whole exome platforms poses a challenge as variants identified in the exonic regions of the whole genome platform may not be identified on the whole exome platform and vice-versa. Taking a simple union or intersection of the somatic variants from both platforms would lead to inclusion of many false positives (through union) and exclusion of many true variants (through intersection). We develop the first framework to improve the identification of somatic variants on whole genome and exome platforms using a machine learning approach by combining the results from two popular somatic variant callers. Testing on simulated and real data sets shows that our framework identifies variants more accurately than using only one somatic variant caller or using variants from only one platform. Short tandem repeats (STRs) are repetitive units of 2-6 nucleotides. STRs make up approximately 1% of the human genome and have been traditionally used as genetic markers in population studies. We conduct a series of in silico analyses using the exome data of 32 individuals with lung cancer to identify 103 STRs that could potentially serve as cancer diagnostic markers and 624 STRs that could potentially serve as cancer predisposition markers. Overall these studies improve the accuracy in identification of somatic variants and highlight the association of STRs to lung cancer.
Ph. D.
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Muyas, Remolar Francesc 1992. "Highly accurate variant detection for identification of tumor mutations and mosaic variants." Doctoral thesis, Universitat Pompeu Fabra, 2019. http://hdl.handle.net/10803/668325.

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The rapid development of high-throughput sequencing technologies pushed forward the fields of medical genomics and precision medicine, creating many new applications for diagnostics and clinical studies that require high quality data and highly accurate analysis methods. Distinguishing errors from real variants in Next Generation Sequencing data is a challenge when systematic errors, random sequencing errors, germline variants or somatic variants at very low allele frequency are present in the same data. In the first part of this thesis, we developed a genotype callability filter (ABB) able to identify systematic variant calling errors that were not found by state-of-the art methods. This tool cleans false positive calls from somatic and germline variant callsets, as well as detects false gene-disease associations in case-control studies. Secondly, we developed a set of novel methods able to distinguish and correct sequencing and PCR errors with the use of molecular barcodes, permitting us to build error rate models for the detection of somatic mutations at extremely low allele frequencies in liquid biopsies. As final part of this thesis, we characterized mosaic mutations in a multi-tissue, multi-individual study using a cohort of thousands of samples from hundreds of healthy individuals.
El ràpid desenvolupament de les tecnologies de seqüenciació d’alt rendiment ha impulsat els camps de la genòmica mèdica i la medicina d’alta precisió, creant una gran varietat de noves aplicacions, les quals requereixen dades d’una qualitat excel·lent i mètodes d’anàlisi altament precisos. La distinció entre errors i variants reals en dades de seqüenciació de propera generació (NGS) és un repte quan hi ha errors sistemàtics o aleatoris mesclats amb variants germinals o somàtiques a freqüències al·lèliques molt baixes. En la primera part d'aquesta tesi, hem desenvolupat un filtre per al genotipatge de variants (ABB) capaç d'identificar errors sistemàtics durant el procés de detecció de variants que altres mètodes convencionals no poden trobar. Aquesta eina filtra falsos positius del conjunt de variants finals en estudis de variacions somàtiques i germinals, així com també detecta falses associacions de malalties gèniques en estudis de casos-controls. En segon lloc, hem desenvolupat un conjunt de nous mètodes capaços de distingir i corregir els errors de seqüenciació i PCR amb l’ús d’identificadors moleculars. Aquests ens permeten modelar les taxes d’error i conseqüentment detectar mutacions somàtiques a freqüències al·lèliques extremadament baixes en l’anàlisi de biòpsies líquides. Per finalitzar aquesta tesi, hem caracteritzat les mutacions mosaiques en un estudi multi-teixit multi-individu utilitzant una cohort de centenars d'individus sans amb milers de mostres.
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Demidov, German 1990. "Methods for detection of germline and somatic copy-number variants in next generation sequencing data." Doctoral thesis, Universitat Pompeu Fabra, 2019. http://hdl.handle.net/10803/668208.

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Germline copy-number variants (CNVs), as well as somatic copy-number alterations (CNAs), play an important role in many phenotypic traits, including genetic diseases and cancer. Next Generation Sequencing (NGS) allows accurate detection of short variants, but reliable detection of large-scale CNVs in NGS data remains challenging. In this work, I address this issue and describe a novel statistical method for detection of CNVs and CNAs implemented in the tool called ClinCNV. I present analytical performance measures of “ClinCNV” in different datasets, compare it with the performance of other existing methods, and show the advantages of ClinCNV. ClinCNV is already implemented as a part of the diagnostics pipeline at the Institute of Medical Genetics and Applied Genomics (IMGAG), Tuebingen, Germany. ClinCNV has the potential to facilitate molecular diagnostic of genetic-based diseases as well as cancer through accurate detection of copy-number variants.
Las variantes en el número de copias genéticas, tanto en estado germinal (CNV) como en somático (CNA), juegan un papel muy importante en muchos rasgos fenotípicos y están frecuentemente relacionadas con una gran variedad enfermedades genéticas y cáncer. Aunque la secuenciación de próxima generación (NGS) permite detectar variantes cortas con una gran precisión, la correcta detección de CNVs a gran escala con datos de secuenciación sigue siendo un gran desafío. En esta tesis, me centro en abordar este problema y describo un nuevo método estadístico para la detección de CNV y CNA englobado en una nueva herramienta llamada ClinCNV. Para el análisis del rendimiento de ClinCNV y demostrar las ventajas de este nuevo algoritmo, comparamos nuestra herramienta con otras existentes en distintos conjuntos de datos. Por otra parte, ClinCNV ya está implementado como parte del sistema de trabajo de diagnóstico en el Instituto de Genética Médica y Genómica Aplicada (IMGAG) en Tuebingen (Alemania). En resumen, ClinCNV tiene el potencial de facilitar el diagnóstico molecular de enfermedades genéticas y cáncer mediante la precisa detección de variantes en el número de copias genéticas.
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Lobón, García Irene. "Detection of somatic variants from genomic data and their role in neurodegenerative diseases." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/667569.

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Somatic mutations are those that arise after the zygote is formed and are therefore inherited by a fraction of the cells of an individual. Their relevance in certain skin diseases has been known for almost half a decade and cancer, the most common disease caused by somatic mutations, has been extensively studied. Yet, their prevalence in healthy individuals as well as their putative role in other human disorders such as neurodegenerative diseases are still unanswered questions. Furthermore, accurate detection of somatic variants from bulk sequencing data still poses a technical challenge. This work focuses on detecting and circumventing the biases that hinder their identification. Using this knowledge, we identified somatic point mutations in the exomes of five different tissues from sporadic Parkinson disease patients. We also assessed the detection of somatic copy number variants from array CGH data using two tissues from Alzheimer disease patients. Finally, we participated in the identification of somatic variants in an extensive genomic dataset from a neurotypical individual.
Las mutaciones somáticas son aquellas que surgen tras la formación del cigoto y son, por tanto, heredadas por una fracción de las células de un individuo. Su importancia en algunas enfermedades cutáneas se conoce desde hace casi medio siglo. El cáncer, la enfermedad más común causada por mutaciones somáticas, se ha estudiado extensamente. Sin embargo, su prevalencia en individuos sanos, así como su potencial relevancia en otras afecciones humanas, como las enfermedades neurodegenerativas, son cuestiones todavía por resolver. Asimismo, detectar variantes somáticas con precisión en datos de secuenciación de muestras homogeneizadas sigue siendo complejo técnicamente. Este trabajo se centra en la detección y resolución de los sesgos que dificultan su identificación. Aplicando este conocimiento, identificamos mutaciones somáticas de una sola base en datos de secuenciación del exoma de cinco tejidos diferentes de pacientes de la enfermedad de Parkinson. También evaluamos la detección de variantes de número de copia somáticas en datos de array CGH de dos tejidos de pacientes de Alzheimer. Finalmente, participamos en la identificación de variantes somáticas en un amplio conjunto de datos genómicos de un individuo neurotípico.
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Hasan, Mohammad Shabbir. "Identifying and Analyzing Indel Variants in the Human Genome Using Computational Approaches." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/90797.

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Insertion and deletion (indel), a common form of genetic variation, has been shown to cause or contribute to human genetic diseases and cancer. Despite this importance and being the second most abundant variant type in the human genome, indels have not been studied as much as the single nucleotide polymorphism (SNP). With the advance of next-generation sequencing technology, many indel calling tools have been developed. However, performance comparison of commonly used tools has shown that (1) the tools have limited power in identifying indels and there are significant number of indels undetected, and (2) there is significant disagreement among the indel sets produced by the tools. These findings indicate the necessity of improving the existing tools or developing new algorithms to achieve reliable and consistent indel calling results. Two indels are biologically equivalent if the resulting sequences are the same. Storing biologically equivalent indels as distinct entries in databases causes data redundancy and misleads downstream analysis. It is thus desirable to have a unified system for identifying and representing equivalent indels. This dissertation describes UPS-indel, a utility tool that creates a universal positioning system for indels so that equivalent indels can be uniquely determined by their coordinates in the new system. Results show that UPS-indel identifies more redundant indels than existing algorithms. While mapping short reads to the reference genome, a significant number of short reads are unmapped and excluded from downstream analyses, thereby causing information loss in the subsequent variant calling. This dissertation describes Genesis-indel, a computational pipeline that explores the unmapped reads to identify missing novel indels. Results analyzing sequence alignment of 30 breast cancer patients show that Genesis-indel identifies many novel indels that also show significant enrichment in oncogenes and tumor suppressor genes, demonstrating the importance of rescuing indels hidden in the unmapped reads in cancer and disease studies. Somatic mutations play a vital role in transforming healthy cells into cancer cells. Therefore, accurate identification of somatic mutations is essential. Many somatic mutations callers are available with different strengths and weaknesses. An ensemble approach integrating the power of the callers is warranted. This dissertation describes SomaticHunter, an ensemble of two callers, namely Platypus and VarDict. Results on synthetic tumor data show that for both SNPs and indels, SomaticHunter achieves recall comparable to the state-of-the-art somatic mutation callers and the highest precision, resulting in the highest F1 score.
Doctor of Philosophy
Insertion and deletion (indel), a common form of genetic variation in the human genome, is associated with genetic diseases and cancer. However, indels are heavily understudied due to experimental and computational challenges. This dissertation addresses the computational challenges in three aspects. First, the current approach of representing indels is ambiguous and causes significant database redundancy. A universal positioning system, UPS-indel, is proposed to represent equivalent indels unambiguously and the UPS-indel algorithm is theoretically proven to find all equivalent indels and is thus exhaustive. Second, a significant number of indels are hidden in DNA reads not mapped to the reference genome. Genesis-indel, a computational pipeline that explores the unmapped reads to identify novel indels that are initially missed, is developed. Genesis-indel has been shown to uncover indels that can be important genetic markers for breast cancer. Finally, mutations occurring in somatic cells play a vital role in transforming healthy cells into cancer cells. Therefore, accurate identification of somatic mutation is essential for a better understanding of cancer genomes. SomaticHunter, an ensemble of two sensitive variant callers, is developed. Simulated studies using whole genome and whole exome sequences have shown that SomaticHunter achieves recall comparable to state-of-the-art somatic mutation callers while delivering the highest precision and therefore resulting in the highest F1 score among all the callers compared.
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Lim, Wai Yen Alfred. "Directed evolution of human single-chain variable fragments (scFv) by somatic hypermutation." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.707919.

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Roth, Andrew Justin Latham. "Probabilistic models for the identification and interpretation of somatic single nucleotide variants in cancer genomes." Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/56222.

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Somatic single nucleotide variants (SNVs) are mutations resulting from the substitution of a single nucleotide in the genome of cancer cells. Somatic SNVs are numerous in the genomes of most types of cancers. SNVs can contribute to the malignant phenotype of cancer cells, though many SNVs likely have negligible selective value. Because many SNVs are selectively neutral, their presence in a measurable proportion of cells is likely due to drift or genetic hitchhiking. This makes SNVs an appealing class of genomic aberrations to use as markers of clonal populations and ultimately tumour evolution. Advances in sequencing technology, in particular the development of high throughput sequencing (HTS) technologies, have made it possible to systematically profile SNVs in tumour genomes. We introduce three probabilistic models to solve analytical problems raised by experimental designs that leverage HTS to study cancer biology. The first experimental design we address is paired sequencing of normal and tumour tissue samples to identify somatic SNVs. We develop a probabilistic model to jointly analyse data from both samples, and reduce the number of false positive somatic SNV predictions. The second experimental design we address is the deep sequencing of SNVs to quantify the cellular prevalence of clones harbouring the SNVs. The key challenge we resolve is that allele abundance measured by HTS is not equivalent to cellular prevalence due to the confounding issues of mutational genotype, normal cell contamination and technical noise. We develop a probabilistic model which solves these problems while simultaneously inferring the number of clonal populations in the tissue. The final experimental design we consider is single cell sequencing. Single cell sequencing provides a direct means to measure the genotypes of clonal populations. However, sequence data from a single cell is inherently noisy which confounds accurate measurement of genotypes. To overcome this problem we develop a model to aggregate cells by clonal population in order to pool statistical strength and reduce error. The model jointly infers the assignment of cells to clonal populations, the genotype of the clonal populations, and the number of populations present.
Science, Faculty of
Graduate
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Cai, Xuyu. "Single-Neuron Sequencing to Explore Somatic Genetic Variants in Normal and Pathological Human Brain Development." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10858.

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The human brain is one of the most exquisite structures in nature, featuring extreme functional complexity and capacities that allow for advanced cognitive abilities. During the development of the human brain, neural progenitors undergo massive proliferation, which is known to inevitably result in spontaneous mutations; yet the degree of somatic mosaicism within the human brain is unexplored. Several hypotheses have been proposed that various types of somatic mosaicism may serve as an adaptive mechanism to diversify neurons and thereby promote the functional complexity of human brains. Previously proposed mechanisms to increase somatic mosaicism within the brain include elevated somatic LINE-1 element retrotransposition, and the creation of somatic aneuploidy during neurogenesis. On the other hand, genomic diversity needs to be balanced by genomic stability, in order to protect against deleterious mutations that reduce the fitness of the cells, or oncogenic mutations that might promote cancers. In fact, brain-specific somatic mutations have also been proposed to contribute to the unexplained burden of neurological diseases. To directly study genomic variability from cell-to-cell within the human brain, we developed a method to isolate and amplify single neuronal genomes from postmortem and surgically resected human brain tissues. We quantified the frequency of somatic LINE-1 retrotransposition events and aneuploidy in human cortical neurons, and found that the frequencies of both are low, with no sign of brain-specific elevation, arguing against the hypotheses that these two mutational sources are obligate generators of neuronal diversity. Additionally, aneuploidy analysis was performed on bulk and single cortical cells from a hemimegalencephaly brain. Hemimegalencephaly is an asymmetrical brain overgrowth syndrome caused by somatic mutations in brain. Single-cell analysis identified an unexpected mosaic tetrasomy of chromosome 1q, affecting both neuronal and glial populations, as a genetic cause of hemimegalencephaly. These results demonstrate that single-neuron sequencing allows systematic assessment of genomic diversity in the human brain and the identification and characterization of pathogenic somatic mutations underlying neurological disorders.
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Planas, Fèlix Mercè. "Detection and classification of somatic structural variants, and its application in the study of neuronal development." Doctoral thesis, Universitat de Barcelona, 2020. http://hdl.handle.net/10803/672163.

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The identification and analysis of genomic variation across individuals has been central in biology, first through comparative genomics to answer evolutionary questions, and then in the context of biomedicine, where it is actually becoming central to the study of most diseases. Next generation sequence technologies are allowing the systematic analysis of thousands of different types of genetic variation, enhancing the identification of disease markers and the understanding of the molecular basis of disease. For the past years, there has been a burst of new methodology for genome analysis around diseases coming from hundreds of groups around the world. Specific computational methods and strategies are being designed and improved around the identification and interpretation of genomic variation. The identification and classification of different types of genomic variants in the context of biomedicine is a key and foundational step for the development of a personalized medicine. This has been particularly central in the field of cancer genomics, which has based the research of the past ten to fifteen years in the sequencing of genomic DNA, and the identification and interpretation of (mostly) somatic and germline variation. Throughout these years, a large number of methods for variant detection have been developed with different action ranges. Despite all these developments, the identification of genomic variants has still room for improvement, not only at the level of sensitivity and specificity, but also at the computational level. Given the emergence of many initiatives for personalized medicine around the world, and the expected number of genomes that will have to be analyzed within health care systems, we require robust algorithms, designed together with a matching implementation that will minimize the computational costs of the analysis. With this aim, during this thesis, I have pushed and designed and implemented an algorithm for the efficient processing of genomic data, in close collaboration with computer scientists of our center that defined the implementation, focusing on lowering the energy and the time of the analysis. This methodology, which relies on a reference free approach of read classification, has been protected with a patent, and is being used as the foundation for the development of SMuFin2, a more accurate and computationally efficient version of the initial SMuFin from 2014. We here show that our method is able to process whole genome sequences very fast and with a minimal energy consumption, compared with existing methods, and that has great potential for the identification of all ranges of variants, including insertions of non-human DNA. Further developments on SMuFin2 are needed to finally assess its full variant calling capabilities. Despite their great importance and their clear role in the biology of the cell, somatic variation that occurs in healthy tissues has remained diffuse in their roles. In the case of development, some hypotheses have been proposed to explain the observed somatic DNA damage that occurs during brain development (e.g., replication stress). But the real impact and the underlying mechanisms of this somatic variation are not yet understood. In order to seed light on the type and potential functional impact of somatic variation in brain development, we established a new collaboration to identify, and describe somatic DNA rearrangements induced by Pgbd5 during brain development and adult state in 36 mice neural tissue samples. The detection of somatic variants in healthy tissues presents more challenges than in the cancer scenario, where a variant is present in a significant number of cells and is easier to detect. We have identified, classified and interpreted the landscape of somatic variation in neural development and identified interesting differences between adult and embryonic variation load, and specific types of variants, as the potential result of the activity of these transposase-like genes.
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Melloni, G. E. M. "COMPUTATIONAL FRAMEWORKS FOR THE IDENTIFICATION OF SOMATIC AND GERMLINE VARIANTS CONTRIBUTING TO CANCER PREDISPOSITION AND DEVELOPMENT." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/462986.

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The most recent cancer classification from NIH includes ~200 types of tumor that originates from several tissue types (http://www.cancer.gov/types). Although macroscopic and microscopic characteristics varies significantly across subtypes, the starting point of every cancer is believed to be a single cell that acquires DNA somatic alterations that increases its fitness over the surrounding cells and makes it behave abnormally and proliferate uncontrollably. Somatic mutations are the consequence of many possible defective processes such as replication deficiencies, exposure to carcinogens, or DNA repair machinery faults. Mutation development is a random and mostly natural process that frequently happens in every cell of an individual. Only the acquisition of a series of subtype-specific alterations, including also larger aberrations such as translocations or deletions, can lead to the development of the disease and this is a long process for the majority of adult tumor types. However, genetic predisposition for certain cancer types is epidemiologically well established. In fact, several cancer predisposing genes where identified in the last 30 years with various technologies but they characterize only a small fraction of familial cases. This work will therefore cover two main steps of cancer genetics and genomics: the identification of the genes that somatically changes the behavior of a normal human cell to a cancer cell and the genetic variants that increase risk of cancer development. The use of publicly available datasets is common to all the three results sections that compose this work. In particular, we took advantage of several whole exome sequencing databases (WES) for the identification of both driver mutations and driver variants. In particular, the use of WES in cancer predisposition analysis represents one of the few attempts of performing such analysis on genome-wide sequencing germline data.
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Books on the topic "Variante somatica"

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Quain, Angela, and Anne M. Comi. Sturge-Weber Syndrome and Related Cerebrovascular Malformation Syndromes. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0112.

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Sturge-Weber syndrome is a rare disorder presenting with a capillary malformation, better known as a port-wine birthmark, on the upper face, glaucoma, and a leptomeningeal angioma. Most children develop seizures and strokes, with variable degrees of neurodevelopmental impairments including hemiparesis, visual field deficits, cognitive deficits, epilepsy, and migraines. In 2013, a somatic activating mutation in GNAQ was identified in the capillary malformations and leptomeningeal angiomas of Sturge-Weber patients. In the diagnosis of Sturge-Weber syndrome, contrast-enhanced imaging is essential to the diagnosis of brain involvement. Functional imaging has demonstrated impaired venous drainage and a role for seizures in exacerbating perfusion deficits. Aggressive seizure management is fundamental to treatment. Some data supports the use of low-dose aspirin to reduce the occurrence of strokelike episodes and seizures.
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Van den Bergh, Omer, Nadia Zacharioudakis, and Sibylle Petersen. Interoception, categorization, and symptom perception. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198811930.003.0011.

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Medical practice and the disease model importantly rely on the accuracy assumption of symptom perception: patients’ symptom reports are a direct and accurate reflection of physiological dysfunction. This implies that symptoms can be used as a read-out of dysfunction and that remedying the dysfunction removes the symptoms. While this assumption is viable in many instances of disease, the relationship between symptoms and physiological dysfunction is highly variable and, in a substantial number of cases, completely absent. This chapter considers symptom perception as a form of unconscious inferential somatic decision-making that compellingly produces consciously experienced symptoms. At a mechanistic level, this perspective removes the categorical distinction between symptoms that are closely associated with physiological dysfunction and those that are not. In addition, it brings symptom perception in accordance with general theories of perception. Some clinical implications to understand and treat symptoms poorly related to physiological dysfunction are discussed.
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DeRubeis, Robert J., and Daniel R. Strunk, eds. The Oxford Handbook of Mood Disorders. Oxford University Press, 2015. http://dx.doi.org/10.1093/oxfordhb/9780199973965.001.0001.

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Mood disorders are a pressing societal problem, with depression alone now constituting a leading cause of disability in Western Europe and the United States. In the most comprehensive volume of its kind, the Oxford Handbook of Mood Disorders provides detailed coverage of the characterization, understanding, and treatment of mood disorders. Chapters are written by the world’s leading experts in their respective areas. The Handbook provides coverage of unipolar depression, bipolar disorder, and variants of these disorders. Current approaches to classifying the mood disorders are reviewed, and contemporary controversies are placed in historical context. Chapter authors offer a variety of approaches to understanding the heterogeneity of the experiences of those who meet criteria for mood disorders, both within and across cultures. The role of genetic and environmental risk factors as well as premorbid personality and cognitive processes in the development of mood pathology are detailed. Interpersonal, neurobiological, and psychological factors also receive detailed consideration. The volume reviews mood disorders in special populations (e.g., postpartum and seasonal mood disorders) as well as common comorbidities (e.g., anxiety, substance use disorders). Somatic and psychosocial treatment approaches receive in-depth coverage with chapters that describe and review empirical evidence regarding each of the most influential treatment approaches. The depth and breadth offered by the Oxford Handbook of Mood Disorders make it an invaluable resource for clinicians and researchers, as well as for scholars and students.
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Zachar, Peter, and Kenneth S. Kendler. A DSM insiders’ history of premenstrual dysphoric disorder. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780198725978.003.0041.

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Chapter 41 discusses a kind of in vivo case study of the interactions between science and extra-scientific processes involved in the construction of nosological categories of psychiatry. The very first medical report on a cluster of symptoms, regularly affecting some women over their menstrual cycle, the so-called syndrome of premenstrual tension, appeared in 1931. The name changed with time to premenstrual syndrome, subsequently renamed as late luteal phase dysphoric disorder (LLPDD) and is currently known as premenstrual dysphoric disorder (PMDD). It was listed as a psychiatric disorder in the DSM-III, but was later moved to the section on the condition deserving further study (aka the “appendix”). In the DSM-5, PMDD returned to the main section of the manual devoted to depressive disorders as a diagnosis approved for routine clinical use. The PDD is an ideal-type condition to stimulate a controversy about its justification as a psychiatric disorder. By its nature it affects only females (here, feminist issues may arise); it is clearly linked to physiological rhythm (is it not a somatic issue?); does it exist as a distinct behavioral abnormality or is it just a variant of female experience?: does it need to be treated pharmacologically? (the issues of medicalization and “big pharma”). It provides a detailed narrative on the vicissitudes of this psychiatric nosological category, which is not only based on a careful study by interested outsiders but is crucially enriched by the insights of one of the participants of the very process of DSM construction.
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Book chapters on the topic "Variante somatica"

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An, Jisong, Kyoung Il Min, and Young Seok Ju. "Identifying Somatic Mitochondrial DNA Mutations." In Variant Calling, 153–65. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2293-3_10.

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Huang, Weitai, Ngak Leng Sim, and Anders J. Skanderup. "Accurate Ensemble Prediction of Somatic Mutations with SMuRF2." In Variant Calling, 53–66. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2293-3_4.

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Garofoli, Andrea, Désirée Schnidrig, and Charlotte K. Y. Ng. "PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data." In Variant Calling, 195–204. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2293-3_12.

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Bahonar, Sajedeh, and Hesam Montazeri. "Somatic Single-Nucleotide Variant Calling from Single-Cell DNA Sequencing Data Using SCAN-SNV." In Variant Calling, 267–77. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2293-3_17.

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Li, Minghao, Ting He, Chen Cao, and Quan Long. "An Individualized Approach for Somatic Variant Discovery." In Bioinformatics for Cancer Immunotherapy, 11–36. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0327-7_2.

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Dienstmann, Rodrigo. "Standardized Decision Support in NGS Reports of Somatic Cancer Variants." In Next Generation Sequencing in Cancer Research, Volume 2, 67–80. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-15811-2_5.

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Chang, Ti-Cheng, Ke Xu, Zhongshan Cheng, and Gang Wu. "Somatic and Germline Variant Calling from Next-Generation Sequencing Data." In Advances in Experimental Medicine and Biology, 37–54. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-91836-1_3.

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Moriyama, Takuya, Seiya Imoto, Satoru Miyano, and Rui Yamaguchi. "Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection." In Mathematical and Computational Oncology, 87–101. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-64511-3_9.

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Nicora, Giovanna, Simone Marini, Ivan Limongelli, Ettore Rizzo, Stefano Montoli, Francesca Floriana Tricomi, and Riccardo Bellazzi. "A Semi-supervised Learning Approach for Pan-Cancer Somatic Genomic Variant Classification." In Artificial Intelligence in Medicine, 42–46. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-21642-9_7.

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Ziebarth, Jesse D., Anindya Bhattacharya, and Yan Cui. "Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources." In Methods in Molecular Biology, 101–20. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9207-2_8.

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Conference papers on the topic "Variante somatica"

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Arslanturk, Suzan, and Sorin Draghici. "Disease Subtyping using Somatic Variant Data." In BCB '18: 9th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. New York, NY, USA: ACM, 2018. http://dx.doi.org/10.1145/3233547.3233565.

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Norris, Alexis L., Rachael E. Workman, Yunfan Fan, James R. Eshleman, and Winston Timp. "Abstract 3608: Detection of somatic structural variants using nanopore sequencing." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-3608.

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Lai, Zhongwu, Brad Chapman, Miika Ahdesmäki, Oliver Hofmann, Justin Johnson, and Jonathan Dry. "Abstract 166: Optimizing the detection of subclonal somatic variants with VarDict." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-166.

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Harley, Alena S., Corine K. Lau, and Eve Shinbrot. "Abstract 2474: Automated somatic variant classifier to reduce false positives identified by tumor normal variant callers." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-2474.

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Harley, Alena S., Corine K. Lau, and Eve Shinbrot. "Abstract 2474: Automated somatic variant classifier to reduce false positives identified by tumor normal variant callers." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-2474.

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Lee, Joyce, Andy Wing Chun PANG, Caspar Groß, Jakob Admard, Elena Buena-Atienza, Stephan Ossowski, Thomas Anantharaman, Mark Oldakowski, Sven Bocklandt, and Alex Hastie. "Abstract 1329: Identifying low allele frequency somatic variants using the Saphyr System." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-1329.

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Merino, Maria J., Esra Dikoglu, Sandeep Gurram, Marston Linehan, and Ramaprasad Srinivasan. "Abstract 2556: The somatic variant of HLRCC, an unrecognized type of RCC." In Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-2556.

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Boyle, Sean M., Michael J. Clark, Ravi Alla, Shujun Luo, Deanna M. Church, Elena Helman, Parin Sripakdeevong, John West, and Rich Chen. "Abstract 533: Accurately identifying expressed somatic variants for neoantigen detection and immuno-oncology." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-533.

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Dias-Santagata, Dora, David G. McFadden, Lindsay A. Bernardo, Kerry D. Lynch, A. John Iafrate, Peter M. Sadow, and Gilbert H. Daniels. "Abstract 1191: Somatic mutation profiling of the follicular variant of papillary thyroid cancer." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-1191.

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Stratford, Jeran, Gunjan Hariani, Jeff Jasper, Chad Brown, Wendell Jones, and Victor J. Weigman. "Abstract 5276: Impact of duplicate removal on low frequency NGS somatic variant calling." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-5276.

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Reports on the topic "Variante somatica"

1

Weller, Joel I., Derek M. Bickhart, Micha Ron, Eyal Seroussi, George Liu, and George R. Wiggans. Determination of actual polymorphisms responsible for economic trait variation in dairy cattle. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600017.bard.

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The project’s general objectives were to determine specific polymorphisms at the DNA level responsible for observed quantitative trait loci (QTLs) and to estimate their effects, frequencies, and selection potential in the Holstein dairy cattle breed. The specific objectives were to (1) localize the causative polymorphisms to small chromosomal segments based on analysis of 52 U.S. Holstein bulls each with at least 100 sons with high-reliability genetic evaluations using the a posteriori granddaughter design; (2) sequence the complete genomes of at least 40 of those bulls to 20 coverage; (3) determine causative polymorphisms based on concordance between the bulls’ genotypes for specific polymorphisms and their status for a QTL; (4) validate putative quantitative trait variants by genotyping a sample of Israeli Holstein cows; and (5) perform gene expression analysis using statistical methodologies, including determination of signatures of selection, based on somatic cells of cows that are homozygous for contrasting quantitative trait variants; and (6) analyze genes with putative quantitative trait variants using data mining techniques. Current methods for genomic evaluation are based on population-wide linkage disequilibrium between markers and actual alleles that affect traits of interest. Those methods have approximately doubled the rate of genetic gain for most traits in the U.S. Holstein population. With determination of causative polymorphisms, increasing the accuracy of genomic evaluations should be possible by including those genotypes as fixed effects in the analysis models. Determination of causative polymorphisms should also yield useful information on gene function and genetic architecture of complex traits. Concordance between QTL genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects that are segregating in the U.S. Holstein population; a probability of <10²⁰ was used to accept the null hypothesis that no segregating gene within the chromosomal segment was affecting the trait. Genotypes for 83 grandsires and 17,217 sons were determined by either complete sequence or imputation for 3,148,506 polymorphisms across the entire genome. Variant sites were identified from previous studies (such as the 1000 Bull Genomes Project) and from DNA sequencing of bulls unique to this project, which is one of the largest marker variant surveys conducted for the Holstein breed of cattle. Effects for stature on chromosome 11, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met 3 criteria: (1) complete or nearly complete concordance, (2) nominal significance of the polymorphism effect after correction for all other polymorphisms, and (3) marker coefficient of determination >40% of total multiple-regression coefficient of determination for the 30 polymorphisms with highest concordance. The missense polymorphism Phe279Tyr in GHR at 31,909,478 base pairs on chromosome 20 was confirmed as the causative mutation for fat and protein concentration. For effect on fat percentage, 12 additional missensepolymorphisms on chromosome 14 were found that had nearly complete concordance with the suggested causative polymorphism (missense mutation Ala232Glu in DGAT1). The markers used in routine U.S. genomic evaluations were increased from 60,000 to 80,000 by adding markers for known QTLs and markers detected in BARD and other research projects. Objectives 1 and 2 were completely accomplished, and objective 3 was partially accomplished. Because no new clear-cut causative polymorphisms were discovered, objectives 4 through 6 were not completed.
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