Artigos de revistas: "Association copy"

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Teare, Brian. "from Association Copy". New England Review 43, n.º 3 (2022): 107–13. http://dx.doi.org/10.1353/ner.2022.0089.

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Brezina, Stefanie, Moritz Feigl, Tanja Gumpenberger, Ricarda Staudinger, Andreas Baierl e Andrea Gsur. "Genome-wide association study of germline copy number variations reveals an association with prostate cancer aggressiveness". Mutagenesis 35, n.º 3 (7 de abril de 2020): 283–90. http://dx.doi.org/10.1093/mutage/geaa010.

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Abstract Prostate cancer is a major health burden, being the second most commonly diagnosed malignancy in men worldwide. Overtreatment represents a major problem in prostate cancer therapy, leading to significant long-term quality-of-life effects for patients and a broad socio-ecological burden. Biomarkers that could facilitate risk stratification of prostate cancer aggressiveness at the time of diagnosis may help to guide clinical treatment decisions and reduce overtreatment. Previous research on genetic variations in prostate cancer has shown that germline copy number variations as well as somatic copy number alterations are commonly present in cancer patients, altering a greater portion of the cancer genome than any other type of genetic variation. To investigate the effect of germline copy number variations on cancer aggressiveness we have compared genome-wide screening data from genomic DNA isolated from the blood of 120 patients with aggressive prostate cancer, 231 patients with non-aggressive prostate cancer and 87 controls with benign prostatic hyperplasia from the Prostate Cancer Study of Austria biobank using the Affymetrix SNP 6.0 array. We could show that patients with an aggressive form of prostate cancer had a higher frequency of copy number variations [mean count of copy number segments (CNS) = 12.9, median count of CNS = 9] compared to patients with non-aggressive prostate cancer (mean count of CNS = 10.4, median count of CNS = 8) or control patients diagnosed with benign prostatic hyperplasia (mean count of CNS = 9.3, median count of CNS = 8). In general, we observed that copy number gain is a rarer event, compared to copy number loss within all three patient groups. Furthermore, we could show a significant effect of copy number losses located on chromosomes 8, 9 and 10 on prostate cancer aggressiveness (P = 0.040, P = 0.037 and P = 0.005, respectively). Applying a cross-validation analysis yielded an area under the curve of 0.63. Our study reports promising findings suggesting that copy number losses might play an important role in the establishment of novel biomarkers to predict prostate cancer aggressiveness at the time of diagnosis. Such markers could be used to facilitate risk stratification to reduce overtreatment of prostate cancer patients.

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Ai, Zhen, Ming Li, Wenting Liu, Jia-Nee Foo, Omniah Mansouri, Peiran Yin, Qian Zhou et al. "Low α-defensin gene copy number increases the risk for IgA nephropathy and renal dysfunction". Science Translational Medicine 8, n.º 345 (29 de junho de 2016): 345ra88. http://dx.doi.org/10.1126/scitranslmed.aaf2106.

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Although a major source of genetic variation, copy number variations (CNVs) and their involvement in disease development have not been well studied. Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis worldwide. We performed association analysis of the DEFA1A3 CNV locus in two independent IgAN cohorts of southern Chinese Han (total of 1189 cases and 1187 controls). We discovered three independent copy number associations within the locus: DEFA1A3 [P = 3.99 × 10−9; odds ratio (OR), 0.88], DEFA3 (P = 6.55 × 10−5; OR, 0.82), and a noncoding deletion variant (211bp) (P = 3.50 × 10−16; OR, 0.75) (OR per copy, fixed-effects meta-analysis). While showing strong association with an increased risk for IgAN (P = 9.56 × 10−20), low total copy numbers of the three variants also showed significant association with renal dysfunction in patients with IgAN (P = 0.03; hazards ratio, 3.69; after controlling for the effects of known prognostic factors) and also with increased serum IgA1 (P = 0.02) and galactose-deficient IgA1 (P = 0.03). For replication, we confirmed the associations of DEFA1A3 (P = 4.42 × 10−4; OR, 0.82) and DEFA3 copy numbers (P = 4.30 × 10−3; OR, 0.74) with IgAN in a Caucasian cohort (531 cases and 198 controls) and found the 211bp variant to be much rarer in Caucasians. We also observed an association of the 211bp copy number with membranous nephropathy (P = 1.11 × 10−7; OR, 0.74; in 493 Chinese cases and 500 matched controls), but not with diabetic kidney disease (in 806 Chinese cases and 786 matched controls). By explaining 4.96% of disease risk and influencing renal dysfunction in patients with IgAN, the DEFA1A3 CNV locus may be a potential therapeutic target for developing treatments for this disease.

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ZHANG, XueGong, e XueYa ZHOU. "Copy number variation based genetic association studies". Chinese Science Bulletin 56, n.º 6 (1 de março de 2011): 370–82. http://dx.doi.org/10.1360/972010-1759.

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Nygaard, Sune Boris, Maria Unni Rømer, Ib Jarle Christensen, Signe Lykke Nielsen, David Hersi Smith, Kirsten Vang Nielsen, Sven Müller, Ben Vainer, Hans J. Nielsen e Nils Brünner. "TOP1 gene copy number in stage III colorectal cancer (CRC) samples: Association to prognosis." Journal of Clinical Oncology 30, n.º 4_suppl (1 de fevereiro de 2012): 475. http://dx.doi.org/10.1200/jco.2012.30.4_suppl.475.

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475 Background: TOP1 inhibitor treatment is frequently being used in combination therapy of metastatic CRC. This study aims to reveal whether TOP1 gene copy number associates with patient prognosis, since such a relationship may have significant implications for future studies aiming at validating the predictive value of TOP1 gene copy number. Methods: The study included TOP1 and CEN-20 FISH analyses (DAKO A/S Denmark) on FFPE tissue sections from 154 stage III CRC patients who did not receive adjuvant chemotherapy. TOP1 gene copy number, CEN-20 copy number and the TOP1/CEN-20 ratios were analyzed and correlated to overall survival (OS), to time to recurrence (TTR) of patients with CRC and to local recurrence (LR) in patients with rectal cancer (RC). Results: TOP1 copy number counts and the TOP1/CEN-20 ratios, age, gender and primary tumor location were separately added into a multivariate analysis as continuous variables. For OS and LR, TOP1 copy number was significant and the ratio was borderline significant with higher copy number associated with longer OS or longer time to LR. When the patients were dichotomized using the TOP1 median copy number, we found that patients with high TOP1 copy number in their tumor cells had a significant longer OS (HR: 0.68; 95% CI: 0.47-0.98; p = 0.04) compared to patients with low TOP1 copy number. Using the median TOP1/CEN-20 ratio to dichotomize, no significant differences were observed between patients with levels above or below the median ratio number for OS (HR: 0.76; 95% CI: 0.53-1.10; p = 0.14). TOP1 copy number divided the RC patients into two groups with a trend towards a significant difference in time to LR (HR: 0.56; 95% CI: 0.27-1.16; p = 0.11) with higher copy number. If the median ratio was used, a significant association with longer time to LR (HR: 0.43; 95% CI: 0.20-0.92; p = 0.03) was found. No significant associations between TOP1 copy number or ratio and TTR were observed. Conclusions: Increased TOP1 copy number is associated with longer OS in CRC patients and fewer LR in RC patients. Thus, future studies analyzing the association between TOP1 copy number and response to therapy in CRC patients should be planned in such a way that a prognostic and a predictive value of TOP1 can be separated.

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Valla, Marit, Signe Opdahl, Borgny Ytterhus e Anna Mary Bofin. "DTX3 copy number increase in breast cancer: a study of associations to molecular subtype, proliferation and prognosis". Breast Cancer Research and Treatment 187, n.º 1 (22 de fevereiro de 2021): 57–67. http://dx.doi.org/10.1007/s10549-021-06138-2.

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Abstract Purpose The degree of cell proliferation is important for subclassification of breast cancers into prognostic and therapeutic groups. DTX3 has been identified as a driver of proliferation in luminal breast cancer. In this study, we describe DTX3 copy number in breast cancer primary tumours and corresponding axillary lymph node metastases, and studied associations with molecular subtype, proliferation and prognosis. Methods Using fluorescence in situ hybridization, we assessed DTX3 and chromosome 12 centromere (CEP12) copy number in 542 primary breast cancers and 117 lymph node metastases, from a well-described cohort of Norwegian breast cancer patients. Proliferation was expressed as mitotic counts and Ki67 score. Associations between DTX3 copy number and molecular subtype and proliferation were assessed using Pearson’s χ2 test. We studied the effect of copy number increase on prognosis estimating cumulative incidence of breast cancer death and hazard ratios. Results Mean DTX3 copy number ≥ 4 was found in 23 tumours (4%), and mean ≥ 5 in 9 tumours (1.7%). Copy number increase was found within all molecular subtypes except the 5 negative phenotype and the Luminal B (HER2 +) subtype. DTX3 copy number increase was not accompanied by an increase in CEP12. Point estimates showed that there were associations between DTX3 copy number increase and high proliferation and poor prognosis; however, precision depended on copy number cut-off. Conclusions DTX3 copy number increase was present in a small proportion of breast cancer cases. There was an association between copy number increase and high tumour cell proliferation and poor prognosis.

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Whitman, Mary C., Sherin Shaaban, Sarah MacKinnon, Wai-Man Chan, David A. Mackey, David G. Hunter e Elizabeth C. Engle. "Genetic associations in esotropia: genome-wide association study and copy number variation". Journal of American Association for Pediatric Ophthalmology and Strabismus 23, n.º 4 (agosto de 2019): e63. http://dx.doi.org/10.1016/j.jaapos.2019.08.231.

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Jiang, Rui, Jie Cheng, Xiu-Kai Cao, Yi-Lei Ma, Buren Chaogetu, Yong-Zhen Huang, Xian-Yong Lan, Chu-Zhao Lei, Lin-Yong Hu e Hong Chen. "Copy Number Variation of the SHE Gene in Sheep and Its Association with Economic Traits". Animals 9, n.º 8 (6 de agosto de 2019): 531. http://dx.doi.org/10.3390/ani9080531.

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Copy number variation (CNV) caused by gene rearrangement is an important part of genomic structural variation. We found that the copy number variation region of the Src Homology 2 Domain Containing E (SHE) gene correlates with a quantitative trait locus of sheep related to milk fat percentage and bone density. The aim of our study was to detect the copy number variation of the SHE gene in four sheep breeds and to conduct a correlation analysis with economic traits, hoping to provide some reference for sheep breeding. In this study, we examined 750 sheep from four Chinese breeds: Chaka sheep (CKS), Hu sheep (HS), Large Tail Han sheep (LTHS) and Small Tail Han sheep (STHS). We used qPCR to evaluate the copy number of the SHE gene, and then used general linear models to analyze the associations between CNV and economic traits. The results showed that there were more individuals with SHE copy number loss in CKS and HS than in STHS and LTHS individuals. Association analyses showed that gain and normal copy number types were correlated to body length, circumference of cannon bone, heart girth, chest width and high at the cross in CKS, HS and STHS (p < 0.05), but this association was not observed for LTHS. Chi-square values (χ2) found prominent differences in CNV distribution among the studied breeds. Overall, the CNV of the SHE gene may be an important consideration for sheep molecular breeding.

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León-Mimila, Paola, Hugo Villamil-Ramírez, Blanca López-Contreras, Sofía Morán-Ramos, Luis Macias-Kauffer, Víctor Acuña-Alonzo, Blanca del Río-Navarro et al. "Low Salivary Amylase Gene (AMY1) Copy Number Is Associated with Obesity and Gut Prevotella Abundance in Mexican Children and Adults". Nutrients 10, n.º 11 (1 de novembro de 2018): 1607. http://dx.doi.org/10.3390/nu10111607.

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Genome-wide association studies (GWAS) have identified copy number variants (CNVs) associated with obesity in chromosomal regions 1p31.1, 10q11.22, 11q11, 16p12.3, and recently 1p21.1, which contains the salivary amylase gene (AMY1). Recent evidence suggests this enzyme may influence gut microbiota composition through carbohydrate (mainly starch) degradation. The role of these CNVs in obesity has been scarcely explored in the Latino population, and thus the aim of our study was to evaluate the association of 1p31.1, 10q11.22, 11q11, 16p12.3 and 1p21.1 CNVs with obesity in 921 Mexican children, to replicate significant associations in 920 Mexican adults, and to analyze the association of AMY1 copy number with gut microbiota in 75 children and 45 adults. Of the five CNVs analyzed, 1q11 CNV was significantly associated with obesity in children, but not in adults. Only AMY1 CNV was significantly associated with obesity in both age groups. Moreover, gut microbiota analyses revealed a positive correlation between AMY1 copy number and Prevotella abundance. This genus has enzymes and gene clusters essential for complex polysaccharide degradation and utilization. To our knowledge, this is the first study to analyze the association of these five CNVs in the Mexican population and to report a correlation between AMY1 CN and gut microbiota in humans.

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Venkatapoorna, Chandra, Priscilla Ayine, Emily Parra, Taylor Koenigs, Megan Phillips, Jeganathan Babu, Maninder Sandey e Thangiah Geetha. "Association of Salivary Amylase (AMY1) Gene Copy Number with Obesity in Alabama Elementary School Children". Nutrients 11, n.º 6 (19 de junho de 2019): 1379. http://dx.doi.org/10.3390/nu11061379.

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Salivary amylase (AMY1) is the most abundant enzyme in human saliva, responsible for the hydrolysis of α-1,4 glycosidic linkages that aids in the digestion of starch. Recently studies have shown that the copy number of AMY1 is associated with obesity; however, the data varies with location. One-third of children are overweight/obese in Alabama. In this study, we aim to determine the relationship between the copy number of AMY1 gene and obesity measurements in children from Alabama. One hundred twenty-seven children aged between 6 to 10 years participated in this study. Anthropometric measurements were measured using WHO recommendations. Genomic DNA was extracted from saliva, and the copy number of the AMY1 gene was estimated by digital PCR. The association between AMY1 copy number and obesity measurements was analyzed by linear regression. The mean AMY1 copy number significantly decreased in overweight/obese (6.21 ± 1.48) compared to normal weight (7.97 ± 2.35) children. AMY1 copy number inversely associated with the obesity measurements. African Americans had a stronger association between low AMY1 copy number and obesity compared to white/European Americans. Our findings suggest that overweight/obese children have a low AMY1 copy number and the effect is more prominent in African Americans.

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Muir, Scott P., e Sara Dallas. "ALA Committee on Professional Ethics". Journal of Intellectual Freedom and Privacy 1, n.º 2-3 (30 de dezembro de 2016): 13. http://dx.doi.org/10.5860/jifp.v1i2-3.6167.

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The Committee on Professional Ethics (COPE) is an American Library Association (ALA) Council Committee. COPE’s charge is to augment the ALA Code of Ethics by explanatory interpretations and additional statements, prepared by the committee or elicited from other units of ALA. When units of the Association develop statements dealing with ethical issues, a copy is sent to the Committee on Professional Ethics for review so that it may be compared to the existing ALA Code of Ethics in order to determine whether or not conflicts are present. COPE then offers non-binding opinions on issues before the ALA Council.

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Wang, Xiang, Ding Zhang, Guoqiang Wang, Anqi Duan, Xiang Ruan e Teng Zhao. "Association between PD-L1 variants and PD-L1 expression: A pan-cancer analysis." Journal of Clinical Oncology 38, n.º 15_suppl (20 de maio de 2020): e13661-e13661. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e13661.

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e13661 Background: Programmed cell death-1 (PD-L1) expression has become a predictive biomarker of response to immune checkpoint inhibitors (ICIs) in several types of solid tumors. Patients with high expression of PD-L1 can benefit more from immunotherapy. However, whether PD-L1 variants would influence the PD-L1 expression has not been fully studied. Methods: Patients with both mutation and immunohistochemistry results for PD-L1 expression from our dataset was analyzed. Patients with both mutation and RNA expression data were obtained from The Cancer Genome Atlas (TCGA) and also analyzed. Results: In our dataset, 10002 patients were included in the analysis. 101 (1%) patients harbored PD-L1 variants, including 24 with single nucleotide variant (SNV), 1 with fusion, 3 with copy-number reduction, 59 with copy-number gain, and 16 germline SNV. The PD-L1 positive rate was 42% in patients with SNV, 100% in fusion, 0% in copy-number reduction, 78% in copy-number gain, 19% in germline SNV and 39% in patients without PD-L1 variants. 32 studies of 10071 patients from TCGA were included for analysis. 244 (2.22%) patients harboring PD-L1 variants, including 2 with frame shift mutations, 3 with nonsense mutations, 38 with missense mutations, 2 with splices, 3 with fusions, 83 with copy-number reduction and 118 with copy-number amplification. The PD-L1 expression in patients with PD-L1 variants was significantly higher than patients without PD-L1 variants (P < 0.001). Further analysis among PD-L1 variants groups showed that PD-L1 fusion and amplification were associated with higher PD-L1 expression. Conclusions: Our results suggested that the PD-L1 expression was associated with PD-L1 variants. Patients with PD-L1 fusion and copy-number amplification was associated with higher PD-L1 expression, while PD-L1 germline SNV and copy-number deletion was associated with lower PD-L1 expression.Our results suggested that the PD-L1 expression was associated with PD-L1 variants. Patients with PD-L1 fusion and copy-number amplification was associated with higher PD-L1 expression, while PD-L1 germline SNV and copy-number deletion was associated with lower PD-L1 expression.

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McDermott, Mary M., Charlotte A. Peterson, Robert Sufit, Luigi Ferrucci, Jack M. Guralnik, Melina R. Kibbe, Tamar S. Polonsky et al. "Peripheral artery disease, calf skeletal muscle mitochondrial DNA copy number, and functional performance". Vascular Medicine 23, n.º 4 (8 de maio de 2018): 340–48. http://dx.doi.org/10.1177/1358863x18765667.

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In people without lower extremity peripheral artery disease (PAD), mitochondrial DNA copy number declines with aging, and this decline is associated with declines in mitochondrial activity and functional performance. However, whether lower extremity ischemia is associated with lower mitochondrial DNA copy number and whether mitochondrial DNA copy number is associated with the degree of functional impairment in people with PAD is unknown. In people with and without PAD, age 65 years and older, we studied associations of the ankle–brachial index (ABI) with mitochondrial DNA copy number and associations of mitochondrial DNA copy number with functional impairment. Calf muscle biopsies were obtained from 34 participants with PAD (mean age: 73.5 years (SD 6.4), mean ABI: 0.67 (SD 0.15), mean 6-minute walk distance: 1191 feet (SD 223)) and 10 controls without PAD (mean age: 73.1 years (SD 4.7), mean ABI: 1.14 (SD 0.07), mean 6-minute walk distance: 1387 feet (SD 488)). Adjusting for age and sex, lower ABI values were associated with higher mitochondrial DNA copy number, measured in relative copy number (ABI<0.60: 914, ABI 0.60–0.90: 731, ABI 0.90–1.50: 593; p trend=0.016). The association of mitochondrial DNA copy number with the 6-minute walk distance and 4-meter walking velocity differed significantly between participants with versus without PAD ( p-value for interaction=0.001 and p=0.015, respectively). The correlation coefficient between mitochondrial DNA copy number and the 6-minute walk distance was 0.653 ( p=0.056) among people without PAD and –0.254 ( p=0.154) among people with PAD and ABI < 0.90. In conclusion, lower ABI values are associated with increased mitochondrial DNA copy number. Associations of mitochondrial DNA copy number with the 6-minute walk distance and 4-meter walking velocity significantly differed between people with versus without PAD, with stronger positive associations observed in people without PAD than in people with PAD. The cross-sectional and exploratory nature of the analyses precludes conclusions regarding causal inferences. ClinicalTrials.gov Identifier: NCT02246660

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Aslam, M. Muaaz, Peter John, Kang-Hsien Fan, Javaid Mehmood Malik, Eleanor Feingold, F. Yesim Demirci e M. Ilyas Kamboh. "Association of Fc Gamma Receptor 3B Gene Copy Number Variation with Rheumatoid Arthritis Susceptibility". Genes 13, n.º 12 (29 de novembro de 2022): 2238. http://dx.doi.org/10.3390/genes13122238.

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Structural variations such as copy number variants (CNVs) have been associated with multiple autoimmune diseases. In this study, we explored the association of the Fc gamma receptor 3B gene (FCGR3B) copy number variation (CNV) with rheumatoid arthritis (RA) susceptibility and related serological traits in the Pakistani population. We also performed a meta-analysis of four published FCGR3B CNV studies along with the current study. A total of 927 subjects (597 RA cases, 330 healthy controls) were recruited from three rheumatology centers in Pakistan. Anti-cyclic citrullinated peptide (anti-CCP) antibodies and rheumatoid factor (RF) were measured in RA patients. FCGR3B copy number was assayed using the TaqMan® CN assay (Hs04211858_cn, Applied Biosystems, Foster City, CA, USA) and the copy number was estimated by using CopyCaller® software (version 2.1; Applied Biosystems, USA). Logistic regression was applied to calculate the odds ratio (OR) of RA risk associated with FCGR3B CNV using sex and age as covariates in R. Meta-analysis on four previously published studies and the current study was performed using the random-effect model. We observed a significant association between FCGR3B copy number < 2 and RA susceptibility (OR = 1.53; 95% CI: 1.05 to 2.22; p = 0.0259) and anti-CCP seropositivity (OR 2.56; 95% CI: 1.34 to 4.89; p = 0.0045). A non-significant association of FCGR3B copy number < 2 was also observed between increased rheumatoid factor (RF) seropositivity (OR = 1.74; 95% CI:0.93 to 3.26; p = 0.0816). Meta-analysis on 13,915 subjects (7005 RA cases and 6907 controls) also showed significant association of copy number < 2 with the increased risk of RA (OR = 1.30; 95% CI: 1.07 to 1.56; p = 0.00671). FCGR3B copy number < 2 is associated with increased RA risk and anti-CCP seropositivity.

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Li, Xing, Chenling Qu, Yan Wang, Zhenxing Mao, Chongjian Wang, Wenjie Li e Songcheng Yu. "Associations of CYP24A1 copy number variation with vitamin D deficiency and insulin secretion". Applied Physiology, Nutrition, and Metabolism 44, n.º 12 (dezembro de 2019): 1367–70. http://dx.doi.org/10.1139/apnm-2019-0193.

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Vitamin D plays an important role in insulin secretion. As the enzyme that initiates degradation of the active metabolite of vitamin D (1,25-(OH)2 vitamin D), 24-hydroxylase encoded by CYP24A1 may be associated with insulin secretion. In this study, we aimed at investigating the association between copy number of CYP24A1 and the concentration of insulin. Included in the study were 1528 rural people from Henan Province of China. The copy number of CYP24A1 and the concentrations of serum 25(OH) vitamin D3 and insulin were determined. Association between copy number of CYP24A1 and vitamin D deficiency was investigated with logistic regression model. Correlation between copy number of CYP24A1 and serum insulin was observed by Spearman correlation. The results suggested that copy number variation of CYP24A1 was associated with vitamin D deficiency. Higher copy number of CYP24A1 was a risk factor for vitamin D deficiency (adjusted odds ratio: 1.199; 95% confidence interval: 1.028–1.397; P = 0.021). Furthermore, copy number of CYP24A1 was positive correlated with the concentration of serum insulin (r = 0.115; P < 0.001), regardless of vitamin D status, age, and body mass index (BMI). Increased copy number of CYP24A1 is associated with not only vitamin D deficiency but also increased serum insulin. Vitamin D supplement may be beneficial to individuals with high copy number of CYP24A1. Novelty Increased copy number of CYP24A1 was a risk factor of vitamin D deficiency. Increased copy number of CYP24A1 was associated with increased serum concentration of insulin independent of age, BMI, and vitamin D status.

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Breheny, Patrick, Prabhakar Chalise, Anthony Batzler, Liewei Wang e Brooke L. Fridley. "Genetic Association Studies of Copy-Number Variation: Should Assignment of Copy Number States Precede Testing?" PLoS ONE 7, n.º 4 (6 de abril de 2012): e34262. http://dx.doi.org/10.1371/journal.pone.0034262.

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Skuratovskaia, D. A., J. K. Sofronova, P. A. Zatolokin, M. A. Vasilenko, L. S. Litvinova e I. O. Mazunin. "The association of the mitochondrial DNA oriB variants with metabolic syndrome". Biomeditsinskaya Khimiya 63, n.º 6 (2017): 533–38. http://dx.doi.org/10.18097/pbmc20176306533.

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Different genes are involved in the development of pathology and formation the metabolic syndrome (MS) phenotype. In the literature, there is a data connection to the site oriB polymorphisms of mitochondrial DNA (mtDNA), known as 16184-16193 polycytosine tract, with insulin resistance, type 2 diabetes (T2DM) and other metabolic abnormalities in different ethnic populations. It is supposed that for certain polymorphisms at this site decreases mtDNA copy number in the cells. In this study, we have identified different allelic variants of the mtDNA oriB site in MS patients (n=106) and healthy individuals (n=71) using capillary sequencing, and determined the amount of mtDNA copy blood leukocytes by droplet digital polymerase chain reaction (ddPCR). The continuous polycytosine tract was significantly more common in MS patients, and such a link was particularly strong in MS patients with type 2 diabetes (p<0.01). No significant correlation has been found between mtDNA copy number and the oriB site variants, but in general there is a tendency to decreased mtDNA copy number in MS patients.

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Chen, Rene, Esther Thorson e Stephen Lacy. "The Impact of Newsroom Investment on Newspaper Revenues and Profits: Small and Medium Newspapers, 1998–2002". Journalism & Mass Communication Quarterly 82, n.º 3 (setembro de 2005): 516–32. http://dx.doi.org/10.1177/107769900508200303.

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This study used Inland Press Association data from 1998 to 2002 for newspapers with less than 85,000 circulation and found a positive relationship between newsroom investment and circulation revenue per copy, advertising revenue per copy, total revenue per copy, and gross profit per copy. The strongest relationships were between newsroom investment and total revenue per copy and advertising revenue per copy. For both variables and for all five years, newsroom investment accounted for at least 20% of the variance in these financial performance variables.

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Yang, Peng, Zijing Zhang, Jiawei Xu, Kaixing Qu, Shijie Lyv, Xianwei Wang, Cuicui Cai et al. "The Association of the Copy Number Variation of the MLLT10 Gene with Growth Traits of Chinese Cattle". Animals 10, n.º 2 (5 de fevereiro de 2020): 250. http://dx.doi.org/10.3390/ani10020250.

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Copy number variation is a part of genomic structural variation and has caused widespread concern. According to the results of high-throughput screening of the MLLT10 gene, we found that the copy number variation region of the MLLT10 gene was correlated with bovine growth traits. We aimed to detect the MLLT10 gene copy number variation and provide materials for the Chinese yellow cattle breed. In this study, the SPSS software was used to analyze the correlation among the copy number type of six different cattle breeds (i.e., Qinchuan, Xianan, Jiaxian, Yanbian, Sinan, Yunling) and the corresponding growth traits. The results showed the following: In Qinchuan cattle, the copy number duplication type was greater than the deletion and normal types; in Xianan cattle, the copy number duplication and normal types were less as compared with the deletion type; and in Yunling cattle, the frequency of the duplication type was dominant among the three types of copy number variants. The correlation analysis result showed that there is a significant correlation between the copy number variation (CNV) of the MLLT10 gene and the growth traits of three cattle breeds. Furthermore, correlation analysis showed that MLLT10 CNV had positive effects on growth traits such as hip width, rump length, hucklebone width, and cannon bone circumference (p < 0.05). This study provides a basis for the molecular-assisted marker breeding of cattle and contributes to the breeding of cattle.

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Ahumada, Viviana A., Kristen McEachern, Kristy Kuplast-Barr e Kurt Alex Schalper. "Abstract 2508: Clinical significance of PARP7 (TIPARP) gene copy number alterations in human non-small cell and head & neck carcinomas". Cancer Research 83, n.º 7_Supplement (4 de abril de 2023): 2508. http://dx.doi.org/10.1158/1538-7445.am2023-2508.

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Abstract Introduction: PARP7, encoded by the TIPARP gene, is a monoART involved in cellular stress responses and with immunomodulatory functions in cancer. The PARP7 gene is amplified in a subset of squamous cell carcinomas and ongoing clinical studies are assessing its role as anti-cancer therapeutic target (NCT04053673, NCT05127590) Here, we analyzed the frequency of PARP7 copy number alterations and its association with tumor immune microenvironment (TIME) features and outcomes in non-small cell lung cancer (NSCLC) and head & neck squamous-cell carcinoma (HNSCC) cohorts. Methods: The PARP7 gene copy number and amplification was analyzed using a dual probe fluorescence in situ hybridization (FISH) assay in two retrospective cohorts of NSCLC (Cohort #1, n=124) and HNSCC (Cohort #2, n=83) represented in tissue microarray format. In a subset of cases, the PARP7 copy number was also studied using whole exome DNA sequencing. The TIME was assessed on consecutive tumor sections using a multiplexed quantitative immunofluorescence panel including the markers DAPI, cytokeratin, CD4, CD8 and PD-L1 coupled to computational pathology analysis. The association between the markers, with clinicopathologic variables and survival was studied. Results: Increased PARP7 copy number (>2 copies/cell) was identified in 55% of NSCLCs (85% of them of squamous-cell histology) and 76% of HNSCCs. A high copy number (>3 copies/cell) was identified in 22% cases from both tumor type cohorts. After adjustment of the PARP7 gene copy number by the chromosome 3 centromeric probe (CEN3) signal, PARP7 amplification (>1.5 PARP7/CEN3 signal) was detected in 22% of NSCLC cases and 34% of HNSCC. A higher number of cases with PARP7 copy number gains were identified using FISH than with whole exome DNA sequencing. No significant associations between the PARP7 gains/losses and major clinicopathologic variables were found. However, higher PARP7 copy number was associated with reduced CD8+ or CD4+ tumor infiltrating lymphocytes (TILs) and a numerically lower tumor PD-L1 protein levels in HNSCC. Elevated PARP7 copy number was associated with shorter overall survival in both studied tumor types. Conclusion: Elevated PARP7 gene copy number identifies a subset of lung and head & neck squamous-cell carcinomas with unfavorable TIME features and adverse prognosis. Detection of PARP7 gene abnormalities using FISH in tumor biopsy samples is sensitive and has potential as a predictive biomarker. Citation Format: Viviana A. Ahumada, Kristen McEachern, Kristy Kuplast-Barr, Kurt Alex Schalper. Clinical significance of PARP7 (TIPARP) gene copy number alterations in human non-small cell and head & neck carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2508.

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Karimi, Leila, Lies Lahousse, Mohsen Ghanbari, Natalie Terzikhan, André G. Uitterlinden, Johan van der Lei, Guy G. Brusselle, Bruno H. Stricker e Katia M. C. Verhamme. "β2-Adrenergic Receptor (ADRB2) Gene Polymorphisms and Risk of COPD Exacerbations: The Rotterdam Study". Journal of Clinical Medicine 8, n.º 11 (1 de novembro de 2019): 1835. http://dx.doi.org/10.3390/jcm8111835.

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The role of the β2-adrenergic receptor (ADRB2) gene in patients with chronic obstructive pulmonary disease (COPD) is unclear. We investigated the association between ADRB2 variants and the risk of exacerbations in COPD patients treated with inhaled β2-agonists. Within the Rotterdam Study, a population-based cohort study, we followed 1,053 COPD patients until the first COPD exacerbation or end of follow-up and extracted rs1042713 (16Arg > Gly) and rs1042714 (27Gln > Glu) in ADRB2. Exposure to inhaled β2-agonists was categorised into current, past or non-use on the index date (date of COPD exacerbation for cases and on the same day of follow-up for controls). COPD exacerbations were defined as acute episodes of worsening symptoms requiring systemic corticosteroids and/or antibiotics (moderate exacerbations), or hospitalization (severe exacerbations). The associations between ADRB2 variants and COPD exacerbations were assessed using Cox proportional hazards models, adjusting for age, sex, use of inhaled corticosteroids, daily dose of β2-agonists, and smoking. In current users of β2-agonists, the risk of COPD exacerbation decreased by 30% (hazard ratio (HR); 0.70, 95% CI: 0.59–0.84) for each copy of the Arg allele of rs1042713 and by 20% (HR; 0.80, 95% CI: 0.69–0.94) for each copy of the Gln allele of rs1042714. Furthermore, current users carrying the Arg16/Gln27 haplotype had a significantly lower risk (HR; 0.70, 95% CI: 0.59–0.85) of COPD exacerbation compared to the Gly16/Glu27 haplotype. In conclusion, we observed that the Arg16/Gln27 haplotype in ADRB2 was associated with a reduced risk of COPD exacerbation in current users of inhaled β2-agonists.

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SUN, Yu-Lin, Fei LIU e Xiao-Hang ZHAO. "Genome-wide Association Analysis Based on Copy Number Variations*". PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 36, n.º 8 (16 de outubro de 2009): 968–77. http://dx.doi.org/10.3724/sp.j.1206.2008.00881.

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Liu, Xue, Ryan J. Longchamps, Kerri L. Wiggins, Laura M. Raffield, Lawrence F. Bielak, Wei Zhao, Achilleas Pitsillides et al. "Association of mitochondrial DNA copy number with cardiometabolic diseases". Cell Genomics 1, n.º 1 (outubro de 2021): 100006. http://dx.doi.org/10.1016/j.xgen.2021.100006.

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McCarroll, Steven A., e David M. Altshuler. "Copy-number variation and association studies of human disease". Nature Genetics 39, S7 (27 de junho de 2007): S37—S42. http://dx.doi.org/10.1038/ng2080.

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McCarroll, S. A. "Extending genome-wide association studies to copy-number variation". Human Molecular Genetics 17, R2 (15 de outubro de 2008): R135—R142. http://dx.doi.org/10.1093/hmg/ddn282.

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Plagnol, Vincent. "Association tests and software for copy number variant data". Human Genomics 3, n.º 2 (2009): 191. http://dx.doi.org/10.1186/1479-7364-3-2-191.

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Lin, Peng, Sarah M. Hartz, Jen-Chyong Wang, Robert F. Krueger, Tatiana M. Foroud, Howard J. Edenberg, John I. Nurnberger, Jr et al. "Copy Number Variation Accuracy in Genome-Wide Association Studies". Human Heredity 71, n.º 3 (2011): 141–47. http://dx.doi.org/10.1159/000324683.

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Lee, Jae-Ho, e Dae-Kwang Kim. "Association between Mitochondrial D-loop Polymorphism and Copy Number". Korean Journal of Physical Anthropology 27, n.º 3 (2014): 131. http://dx.doi.org/10.11637/kjpa.2014.27.3.131.

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Ashar, Foram N., Yiyi Zhang, Ryan J. Longchamps, John Lane, Anna Moes, Megan L. Grove, Josyf C. Mychaleckyj et al. "Association of Mitochondrial DNA Copy Number With Cardiovascular Disease". JAMA Cardiology 2, n.º 11 (1 de novembro de 2017): 1247. http://dx.doi.org/10.1001/jamacardio.2017.3683.

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Baker, William. "King Poppy : An Association Copy: An Addendum to McCormack". Victorian Poetry 61, n.º 1 (março de 2023): 129–30. http://dx.doi.org/10.1353/vp.2023.a905524.

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Kumar, Bhupender, Zafar Iqbal Bhat, Savita Bansal, Sunil Saini, Afreen Naseem, Khushnuma Wahabi, Archana Burman, Geeta Trilok Kumar, Sundeep Singh Saluja e M. Moshahid Alam Rizvi. "Association of mitochondrial copy number variation and T16189C polymorphism with colorectal cancer in North Indian population". Tumor Biology 39, n.º 11 (novembro de 2017): 101042831774029. http://dx.doi.org/10.1177/1010428317740296.

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Globally, colorectal cancer is the third most common type of cancer. Genetic instability leading to cancer development is one of the major causes for development of cancer. Alterations in mitochondrial genome, that is, mutations, single-nucleotide polymorphisms, and copy number variations are known to contribute in cancer development. The aim of our study was to investigate association of mitochondrial T16189C polymorphism and copy number variation with colorectal cancer in North Indian population. DNA isolated from peripheral blood of 126 colorectal cancer patients and 114 healthy North Indian subjects was analyzed for T16189C polymorphism and half of them for mitochondrial copy number variation. Genotyping was done using polymerase chain reaction–restriction fragment length polymorphism, and copy number variation was estimated using real-time polymerase chain reaction, numbers of mitochondrial copies and found to be significantly higher in colorectal cancer patients than healthy controls (88 (58–154), p = 0.001). In the regression analysis, increased mitochondrial copy number variation was associated with risk of colorectal cancer (odds ratio = 2.885, 95% confidence interval = 1.3–6.358). However, T16189C polymorphism was found to be significantly associated with the risk of rectal cancer (odds ratio = 5.213, p = 0.001) and non-significantly with colon cancer (odds ratio = 0.867, p = 0.791). Also, false-positive report probability analysis was done to validate the significant findings. Our results here indicate that mitochondrial copy number variation may be playing an important role in the development of colorectal cancer, and detection of mitochondrial copy number variation can be used as a biomarker for predicting the risk of colorectal cancer in North Indian subjects.

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Watson, R. G., F. Muhale, L. Thorne, J. Yu, B. O’Neil, J. M. Hoskins, M. O. Myers, H. L. McLeod e J. T. Auman. "Association of copy number variants in colorectal liver metastases with 5-fluorouracil resistance". Journal of Clinical Oncology 27, n.º 15_suppl (20 de maio de 2009): e14502-e14502. http://dx.doi.org/10.1200/jco.2009.27.15_suppl.e14502.

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e14502 Background: Resistance to 5-fluorouracil (5-FU) represents a major contributor to cancer-related mortality in advanced colorectal cancer patients. Previous work has shown that thymidylate synthase (TYMS) copy gains were associated with significantly shorter survival, while increased expression of thymidine phosphorylase (TP) led to greater sensitivity to 5-FU in vitro. We assessed TYMS and TP copy number in colorectal liver metastases from untreated patients and patients treated with 5-FU in an effort to elucidate the underlying molecular mechanisms for 5-FU resistance. Methods: Liver metastases were procured from 59 patients who had received 5-FU within 6 months preceding liver resection (treated samples) and from 46 patients who had received no 5-FU treatment in the 6 months prior to their liver resections (untreated samples). DNA copy number of TYMS and TP was evaluated in frozen colorectal liver metastases using quantitative real time PCR. Results: For TYMS, 8.9% of the treated samples showed copy number gain, as compared to 4.8% of the untreated samples. Loss of TYMS was rare, with only 1 and 2 occurrences seen in the treated and untreated samples, respectively. For TP, both groups exhibited similar copy number gains (25% for treated, 29% for untreated); however, a greater proportion of the treated samples exhibited loss of TP (20% vs. 10%). Collectively, the treated samples have a much higher incidence of genetic alterations potentially associated with resistance (TYMS gain or TP loss) than untreated samples (30% vs. 10%, p = 0.03 Fisher exact test). Conclusions: Colorectal liver metastases treated with 5-FU exhibit DNA copy variants that may reduce 5- FU's efficacy. Our data suggest that these genetic alterations may have important implications for the management of advanced colorectal cancer patients with recurrent disease. No significant financial relationships to disclose.

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Brucker, Amanda, Wenbin Lu, Rachel Marceau West, Qi-You Yu, Chuhsing Kate Hsiao, Tzu-Hung Hsiao, Ching-Heng Lin et al. "Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis". PLOS Computational Biology 16, n.º 5 (4 de maio de 2020): e1007797. http://dx.doi.org/10.1371/journal.pcbi.1007797.

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Li, LiJuan, Peng Yang, ShuYue Shi, ZiJing Zhang, QiaoTing Shi, JiaWei Xu, Hua He et al. "Association Analysis to Copy Number Variation (CNV) of Opn4 Gene with Growth Traits of Goats". Animals 10, n.º 3 (6 de março de 2020): 441. http://dx.doi.org/10.3390/ani10030441.

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Extensive research has been carried out regarding the correlation between the growth traits of livestock and genetic polymorphisms, including single nucleotide polymorphisms and copy number variations (CNV). The purpose of this study was to analyze the CNV and its genetic effects of the Opn4 gene in 284 Guizhou goats (Guizhou black goat: n = 186, Guizhou white goat: n = 98). We used qPCR to detect the CNV of the Opn4 gene in Guizhou goats, and the classification results were correlated with the corresponding individual growth traits by SPSS software. The results showed that the Opn4 gene had a superior effect on growth traits with multiple copy variants in Guizhou black goats, and there was a significant correlation between copy number variation sites and body length traits. Contrary to the former conclusion, in Guizhou white goats, individuals with the Normal copy number type showed superior growth traits and copy number variant sites were significantly associated with body weight traits. Therefore, the CNV of the Opn4 gene can be used as a candidate molecular genetic marker to improve goat growth traits, speeding up the breeding process of goat elite varieties.

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Cai, Meiying, Na Lin, Linjuan Su, Xiaoqing Wu, Xiaorui Xie, Ying Li, Yuan Lin, Hailong Huang e Liangpu Xu. "Prenatal diagnosis of 22q11.2 copy number abnormalities in fetuses via single nucleotide polymorphism array". Molecular Biology Reports 47, n.º 10 (15 de setembro de 2020): 7529–35. http://dx.doi.org/10.1007/s11033-020-05815-7.

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Abstract The q11.2 region on chromosome 22 contains numerous low-copy repeats that lead to deleted or duplicated regions in the chromosome, thereby resulting in different syndromes characterized by intellectual disabilities or congenital anomalies. The association between patient phenotypes and 22q11.2 copy number abnormalities has been previously described in postnatal cases; however, these features have not been systematically evaluated in prenatal cases because of limitations in phenotypic identification in prenatal testing. In this study, we investigated the detection rate of 22q11.2 copy number abnormalities in 2500 fetuses using single nucleotide polymorphism (SNP) array and determined the common abnormal ultrasound findings in fetuses carrying the 22q11.2 copy number abnormalities. The 22q11.2 copy number abnormalities were identified in 13 fetuses with cardiovascular malformations (6/13), kidney malformations (3/13), isolated ultrasound markers (3/13), or high-risk Down syndrome based on maternal serum screening (1/13). Approximately 0.5% (13/2500) of the fetuses harbored 22q11.2 copy number abnormalities. The most frequent ultrasound findings in fetuses with these abnormalities were cardiovascular malformations, followed by kidney malformations and isolated ultrasound markers. Prenatal diagnosis of these genetic abnormalities allows for the delineation of differential diagnoses, characterization of a wide spectrum of associated malformations, and determination of associations that exist between prenatal diagnosis and obstetrical outcomes.

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Dunstan, Emma, Sue Lester, Rachel Black, Maureen Rischmueller, Helen Chan, Alex W. Hewitt e Catherine L. Hill. "No Association between FCγR3B Copy Number Variation and Susceptibility to Biopsy-Proven Giant Cell Arteritis". Arthritis 2013 (20 de agosto de 2013): 1–4. http://dx.doi.org/10.1155/2013/514914.

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Objective. To determine the relationship between FCGR3B gene copy number variation (CNV) and biopsy proven giant cell arteritis (GCA). Methods. FCGR3B CNV was determined in 139 Australian biopsy proven GCA patients and 162 population matched controls, using a duplex qPCR assay and RNase P as the reference gene. Copy number was determined using Copy Caller software (v.1.0, Applied Biosystems, USA). CNV genotypes were classified into 3 groups (<2, 2, 3+) for analysis purposes, and analysis was performed using logistic regression. Results. All GCA patients had a positive temporal artery biopsy, and the most common presenting symptoms were visual disturbance and temporal headache. The mean age of patients at biopsy was 74 years (range 51–94) and 88/139 (63%) were female. The frequency of low (<2) FCGR3B copy number was comparable between GCA patients (9/139=6.5%) and controls (10/162=6.2%), as was the frequency of high (3+) FCGR3B copy number (15/130 (10.8%) in GCA patients versus 13/162 (8.0%) in controls). Overall there was no evidence that FCGR3B CNV frequencies differed between GCA patients and controls (χ2=0.75, df=2, P=0.69). Conclusion. FCGR3B CNV is not associated with GCA; however, replicate studies are required.

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Golubovic, Milica. "Judicial Professional Associations: Fostering Judicial Reform Through Civil Society Development". Southeastern Europe 33, n.º 1 (2009): 48–62. http://dx.doi.org/10.1163/187633309x421157.

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AbstractThis article documents the history of judicial professional associations (the Judges' Association of Serbia, Prosecutors' Association of Serbia, and Magistrates' Association of Serbia) in Serbia from their early development in the mid-1990s through the present day. With a close focus on the associations' relationship with USAID implementing partner American Bar Association/Central Europe and Eurasian Law Initiative (ABA/CEELI), the article identifies the challenges to establishing sustainable judicial professional associations. These challenges include a lack of secure funding, low organizational and administrative capacity, a high turnover rate of volunteers and employees, reliance on foreign-generated 'copy-and-paste' activities that do not take local needs into account, and uneasy relationships with the local and central governments. Successes of the fledgling judicial professional associations are also noted, including the implementation of continuing legal education (CLE) seminars.

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Wong, Jason Yat-Yang, Richard Cawthon, Wei Hu, Somayina Ezennia, Shahinaz Gadalla, Charles Breeze, Batel Blechter et al. "Abstract 2251: Alu retroelement copy number, leukocyte telomere length, and lung cancer risk in the prospective Prostate, Lung, Colorectal and Ovarian Cancer (PLCO) Screening Trial". Cancer Research 82, n.º 12_Supplement (15 de junho de 2022): 2251. http://dx.doi.org/10.1158/1538-7445.am2022-2251.

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Abstract Prospective cohort and genome-wide association studies have found consistent associations between longer leukocyte telomere length (LTL) and increased lung cancer risk. These findings present a paradox in the traditional expectations of telomere dynamics in cancer development, as longer telomeres are generally considered to be reflective of less advanced age and greater genomic stability. We posited that longer LTL may reflect or lead to delayed cellular senescence allowing cells to accumulate genomic abnormalities that drive lung carcinogenesis. Furthermore, increased copy number of Alu retroelements, repetitive mobile DNA sequences that are approximately 300 base pairs in length, could also reflect genomic instability. We previously found that exposure to diesel exhaust, a known lung carcinogen, was associated with increased Alu copy number and suspect that increased Alu retrotransposition could influence lung carcinogenesis. However, the interrelationship between Alu retroelements, LTL, and lung cancer is unknown. Therefore, we investigated associations between Alu copy number, LTL, and lung cancer risk in the prospective Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. We conducted a nested case-control study of 410 confirmed incident lung cancer cases and 416 controls individually matched on age, sex, race/ethnicity, study center, and blood draw date. Quantitative PCR was used to measure Alu copy number and telomere length relative to albumin (Alb) copy number (Alu/Alb and T/S ratio, respectively) in pre-diagnostic leukocytes. Conditional logistic regression was used to estimate associations between quartiles (Q) of Alu/Alb ratio (reference=Q1) and lung cancer risk, adjusted for matching factors, smoking status and packyears, and LTL. Additionally, we dichotomized Alu/Alb ratio and LTL at their medians and created a cross-combination variable to assess combined effects. We found a positive dose-response relationship between Alu/Alb ratio and lung cancer risk (odds ratio (OR), 95% confidence intervals (CI): Q2: 1.34 (0.73, 2.48); Q3:1.89 (0.94, 3.84); Q4: 2.66 (1.03, 5.63); p-trendordinal=0.02). The association was apparent for lung adenocarcinoma (LUAD) (Q2: 1.32 (0.46, 3.77); Q3: 2.88 (0.90, 9.25); Q4: 5.07 (1.29, 19.87); p-trendordinal=0.02). We have previously reported that longer measured LTL was also associated with an increased risk of LUAD (Q4: 2.82 (1.16-6.85); p-trend=0.011). The combined effect of both a higher Alu/Alb ratio and longer LTL was 6.07 (1.75, 21.04; p=4.5x10-3) for LUAD compared with lower/shorter levels of both. Higher Alu copy number and longer LTL were associated with increased risk of lung cancer, especially LUAD. Our findings require replication. If confirmed, evaluation of Alu copy number and LTL in risk stratification and prediction analyses is warranted. Citation Format: Jason Yat-Yang Wong, Richard Cawthon, Wei Hu, Somayina Ezennia, Shahinaz Gadalla, Charles Breeze, Batel Blechter, Neal Freedman, Wen-Yi Huang, H. Dean Hosgood, Wei Jie Seow, Bryan Bassig, Mohammad Rahman, Richard Hayes, Nathaniel Rothman, Qing Lan. Alu retroelement copy number, leukocyte telomere length, and lung cancer risk in the prospective Prostate, Lung, Colorectal and Ovarian Cancer (PLCO) Screening Trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2251.

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Xiong, Lie, Pei-Fen Kuan, Jianan Tian, Sunduz Keles e Sijian Wang. "Multivariate Boosting for Integrative Analysis of High-Dimensional Cancer Genomic Data". Cancer Informatics 13s7 (janeiro de 2014): CIN.S16353. http://dx.doi.org/10.4137/cin.s16353.

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In this paper, we propose a novel multivariate component-wise boosting method for fitting multivariate response regression models under the high-dimension, low sample size setting. Our method is motivated by modeling the association among different biological molecules based on multiple types of high-dimensional genomic data. Particularly, we are interested in two applications: studying the influence of DNA copy number alterations on RNA transcript levels and investigating the association between DNA methylation and gene expression. For this purpose, we model the dependence of the RNA expression levels on DNA copy number alterations and the dependence of gene expression on DNA methylation through multivariate regression models and utilize boosting-type method to handle the high dimensionality as well as model the possible nonlinear associations. The performance of the proposed method is demonstrated through simulation studies. Finally, our multivariate boosting method is applied to two breast cancer studies.

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Hu, Wei. "Abstract 2255: Alu retroelement copy number alterations and non-Hodgkin lymphoma". Cancer Research 82, n.º 12_Supplement (15 de junho de 2022): 2255. http://dx.doi.org/10.1158/1538-7445.am2022-2255.

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Abstract Background: Alu retrotransposons are repetitive DNA elements that make up nearly 10% of the human genome and reflect genomic instability. Genomic instability plays an important role in the pathogenesis of non-Hodgkin lymphoma (NHL). However, the relationship between Alu retrotransposons and future risk of NHL is unclear. Methods: We conducted a nested case-control study of NHL risk and Alu retroelement copy number within the Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) study, a prospective cohort with prediagnostic blood samples from 29,133 male Finnish smokers. We measured Alu copy number in 107 incident NHL cases and 1:1 matched controls (± 5 years age). DNA samples extracted from blood were assayed in triplicate using a monochrome multiplex quantitative polymerase chain reaction. We used the albumin gene for the single copy gene to control for genome content in samples. The odds ratios (OR) and 95% confidence intervals (CI) for all NHL were estimated using conditional logistic regression models, adjusting for age at randomization, number of cigarettes smoked per day and smoking duration. Polytomous logistic regression models were fit to compute ORs with Alu copy number for NHL subtypes. To determine if the association might be driven in part by elevated Alu copy number among undiagnosed cases at the time of blood sample collection, we excluded cases diagnosed within the first two years of follow-up. Results: Higher Alu copy number (using the median as the cut-point) was associated with an increased risk of NHL, both overall [OR, 95% CI=3.80 (1.76-8.17)] as well as for the diffuse large B-cell lymphoma [OR, 95% CI=4.83 (1.50-15.55)] and chronic lymphocytic leukemia/small lymphocytic lymphoma (SLL) [OR, 95% CI=2.66 (1.10-6.40)] subtypes. These associations were similar after excluding individuals diagnosed with NHL within two years after blood draw. Conclusions: These findings, which require replication, suggest that higher Alu copy number in prediagnostic leukocytes may play a role in the pathogenesis of NHL. Citation Format: Wei Hu. Alu retroelement copy number alterations and non-Hodgkin lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2255.

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Gu, Wenjuan, Hyungwon Choi e Debashis Ghosh. "Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study". Cancer Informatics 6 (janeiro de 2008): CIN.S342. http://dx.doi.org/10.4137/cin.s342.

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With an increasing number of cancer profiling studies assaying both transcript mRNA and copy number expression levels, a natural question then involves the potential to combine information across the two types of genomic data. In this article, we perform a study to assess the nature of association between the two types of data across several experiments. We report on several interesting findings: 1) global correlation between gene expression and copy number is relatively weak but consistent across studies; 2) there is strong evidence for a cis-dosage effect of copy number on gene expression; 3) segmenting the copy number levels helps to improve correlations.

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Huang, Liansha, Dacai Teng, Hao Wang, Guoqing Sheng e Tonghua Liu. "Association of copy number variation in the AHI1 gene with risk of obesity in the Chinese population". European Journal of Endocrinology 166, n.º 4 (abril de 2012): 727–34. http://dx.doi.org/10.1530/eje-11-0999.

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ObjectiveThe prevalence of obesity has increased dramatically over the past decade. Gene copy number variants (CNVs) have been recognized as a hereditable source of susceptibility in human complex diseases including obesity. Recent studies have shown that Abelson helper integration site 1 (Ahi1) gene has a significant contribution in the homeostasis regulation in mouse models of obesity. A study was therefore carried out to investigate whether CNVs inAHI1gene contribute to human obesity.Subjects and methodsWe analyzed samples from 70 Chinese overweight adults and 74 healthy controls for DNA copy number change using the Affymetrix single-nucleotide polymorphism (SNP) 6.0 array. Validation of CNVs ofAHI1was achieved by real-time PCR using the ΔΔCtmethod.ResultsCopy number gain analysis revealed significant gains (P=0.0017) ofAHI1gene copy number in 17 of 70 (24.3%) samples but only four of 74 (5.4%) controls overall. Then we studied the frequency distribution of CNVs inAHI1gene according to body mass index (BMI) grade. Five out of 28 (18.5%) at-risk obese, six out of 26 (26.9%) moderate obese, and six out of 17 (29.4%) severe obese subjects studied showed increasedAHI1gene copy number.ConclusionsThe result suggested that there was a significant linear trend for increasingAHI1gene copy number frequencies with increasing BMI.

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Lanktree, M., e R. A. Hegele. "COPY NUMBER VARIATION IN METABOLIC SYNDROME". Clinical & Investigative Medicine 31, n.º 4 (1 de agosto de 2008): 15. http://dx.doi.org/10.25011/cim.v31i4.4812.

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Metabolic syndrome (MetS) is defined by the presence of abdominal obesity, hypertension, dysglycemia, and dyslipidemia. Many mutations have been discovered that cause rare monogenic components of metabolic syndrome, and association studies have linked common variants with increased risk of MetS and its components. Despite successes in identifying genetic contributors to metabolic syndrome, unexplained heritability exists and copy number variation (CNV) could be responsible for a portion of this variation. As observed with single nucleotide changes, it is likely that both rare and common CNVs will contribute to MetS disease susceptibility. Recent efforts to map CNVs in control populations have given insight into their size, frequency and distribution. However, despite being observed in controls, the reported CNVs could still modulate susceptibility for late-onset complex traitsor produce subtle metabolic phenotypes. Here we examine the overlap between CNVs found in control datasets and genes with functional hypotheses or evidence of previous association to MetS. Secondly, we present the results and methodology of a search for a rare CNV in a high-penetrance Mendelian disorder, namely familial partial lipodystrophy. As methods to identify CNVs increase in precision and accuracy, the prospect of identifying their role in both rare Mendelian and common complex diseases is exciting.

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Glessner, Joseph T., Jin Li e Hakon Hakonarson. "ParseCNV integrative copy number variation association software with quality tracking". Nucleic Acids Research 41, n.º 5 (3 de janeiro de 2013): e64-e64. http://dx.doi.org/10.1093/nar/gks1346.

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Li, Man, Jacob Carey, Stephen Cristiano, Katalin Susztak, Josef Coresh, Eric Boerwinkle, Wen Hong L. Kao, Terri H. Beaty, Anna Köttgen e Robert B. Scharpf. "Genome-Wide Association of Copy Number Polymorphisms and Kidney Function". PLOS ONE 12, n.º 1 (30 de janeiro de 2017): e0170815. http://dx.doi.org/10.1371/journal.pone.0170815.

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Sebat, J., B. Lakshmi, D. Malhotra, J. Troge, C. Lese-Martin, T. Walsh, B. Yamrom et al. "Strong Association of De Novo Copy Number Mutations with Autism". Science 316, n.º 5823 (20 de abril de 2007): 445–49. http://dx.doi.org/10.1126/science.1138659.

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Bentley, Robert W., John Pearson, Richard B. Gearry, Murray L. Barclay, Cushla McKinney, Tony R. Merriman e Rebecca L. Roberts. "Association of Higher DEFB4 Genomic Copy Number With Crohnʼs Disease". American Journal of Gastroenterology 105, n.º 2 (fevereiro de 2010): 354–59. http://dx.doi.org/10.1038/ajg.2009.582.

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Eleftherohorinou, H., J. C. Andersson-Assarsson, R. G. Walters, J. S. El-Sayed Moustafa, L. Coin, P. Jacobson, L. M. S. Carlsson et al. "famCNV: copy number variant association for quantitative traits in families". Bioinformatics 27, n.º 13 (5 de maio de 2011): 1873–75. http://dx.doi.org/10.1093/bioinformatics/btr264.

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Serrano, Nicholas Anthony, Chang Xu, John Houck, Pei Wang, Wenhong Fan, Yan Liu e Pawadee Lohavanichbutr. "Association of DNA Copy Number and miRNA Expression in OSCC". Otolaryngology–Head and Neck Surgery 145, n.º 2_suppl (agosto de 2011): P60. http://dx.doi.org/10.1177/0194599811416318a63.

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Thyagarajan, Bharat, Weihua Guan, Veronika Fedirko, Helene Barcelo, Huakang Tu, Myron Gross, Michael Goodman e Roberd M. Bostick. "No association between mitochondrial DNA copy number and colorectal adenomas". Molecular Carcinogenesis 55, n.º 8 (10 de agosto de 2015): 1290–96. http://dx.doi.org/10.1002/mc.22370.

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