Comparative analysis of genome-wide copy number variations between Tibetan sheep and White Suffolk sheep

2021 ◽

Vol 11 (1) ◽

pp. 33

Author(s):

Nayoung Han ◽

Jung Mi Oh ◽

In-Wha Kim

Keyword(s):

Copy Number ◽

Genome Wide Association Study ◽

Copy Number Gain ◽

Copy Number Variations ◽

Gene Gain ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Haplotype Blocks ◽

Genome Wide ◽

Control And Prevention

For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (N = 72,299) and CNV data (N = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. CYP2D6 rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. DMD ranked the highest in frequency for gene gain (64.52%), while TPMT ranked the highest in frequency for gene loss (51.80%). Copy number gain of CYP4F2 was observed in 22 subjects; 13 of those subjects were carriers with CYP4F2*3 gain. In the case of TPMT, approximately one-half of the participants (N = 308) had loss of the TPMT*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.

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Genome-wide copy number variations as molecular diagnostic tool for cutaneous intermediate melanocytic lesions: a systematic review and individual patient data meta-analysis

Virchows Archiv ◽

10.1007/s00428-021-03095-5 ◽

2021 ◽

Author(s):

Chiel F. Ebbelaar ◽

Anne M. L. Jansen ◽

Lourens T. Bloem ◽

Willeke A. M. Blokx

Keyword(s):

Systematic Review ◽

Sensitivity And Specificity ◽

Copy Number ◽

Individual Patient Data ◽

Meta Analysis ◽

Copy Number Variations ◽

Patient Data ◽

Melanocytic Lesions ◽

Genome Wide ◽

Malignant Lesions

AbstractCutaneous intermediate melanocytic neoplasms with ambiguous histopathological features are diagnostically challenging. Ancillary cytogenetic techniques to detect genome-wide copy number variations (CNVs) might provide a valuable tool to allow accurate classification as benign (nevus) or malignant (melanoma). However, the CNV cut-off value to distinguish intermediate lesions from melanoma is not well defined. We performed a systematic review and individual patient data meta-analysis to evaluate the use of CNVs to classify intermediate melanocytic lesions. A total of 31 studies and 431 individual lesions were included. The CNV number in intermediate lesions (median 1, interquartile range [IQR] 0–2) was significantly higher (p<0.001) compared to that in benign lesions (median 0, IQR 0–1) and lower (p<0.001) compared to that in malignant lesions (median 6, IQR 4–11). The CNV number displayed excellent ability to differentiate between intermediate and malignant lesions (0.90, 95% CI 0.86–0.94, p<0.001). Two CNV cut-off points demonstrated a sensitivity and specificity higher than 80%. A cut-off of ≥3 CNVs corresponded to 85% sensitivity and 84% specificity, and a cut-off of ≥4 CNVs corresponded to 81% sensitivity and 91% specificity, respectively. This individual patient data meta-analysis provides a comprehensive overview of CNVs in cutaneous intermediate melanocytic lesions, based on the largest pooled cohort of ambiguous melanocytic neoplasms to date. Our meta-analysis suggests that a cut-off of ≥3 CNVs might represent the optimal trade-off between sensitivity and specificity in clinical practice to differentiate intermediate lesions from melanoma.

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High-resolution genome-wide array-CGH reveals copy number variations associated with premature ovarian failure

Placenta ◽

10.1016/j.placenta.2011.07.029 ◽

2011 ◽

Vol 32 ◽

pp. S282

Author(s):

Paola Scaruffi ◽

Sara Stigliani ◽

Annamaria Jane Nicoletti ◽

Pier Luigi Venturini ◽

Gian Paolo Tonini ◽

...

Keyword(s):

High Resolution ◽

Premature Ovarian Failure ◽

Copy Number ◽

Array Cgh ◽

Copy Number Variations ◽

Ovarian Failure ◽

Genome Wide

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Genome-wide burden and association analyses implicate copy number variations in asthma risk among children and young adults from Latin America

Scientific Reports ◽

10.1038/s41598-018-32837-w ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 3

Author(s):

Pablo Oliveira ◽

Gustavo N. O. Costa ◽

Andresa K. A. Damasceno ◽

Fernando P. Hartwig ◽

George C. G. Barbosa ◽

...

Keyword(s):

Young Adults ◽

Latin America ◽

Copy Number ◽

Copy Number Variations ◽

Association Analyses ◽

Asthma Risk ◽

Genome Wide ◽

Children And Young Adults

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Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content

BMC Genomics ◽

10.1186/1471-2164-15-517 ◽

2014 ◽

Vol 15 (1) ◽

pp. 517 ◽

Cited By ~ 16

Author(s):

Hui Zhang ◽

Zhi-Qiang Du ◽

Jia-Qiang Dong ◽

Hai-Xia Wang ◽

Hong-Yan Shi ◽

...

Keyword(s):

Copy Number ◽

Copy Number Variations ◽

Abdominal Fat ◽

Fat Content ◽

Genome Wide

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P1-258: Genome-Wide Analysis of Large Rare Copy Number Variations in Alzheimer Disease Among Caribbean Hispanics

Alzheimer s & Dementia ◽

10.1016/j.jalz.2011.05.538 ◽

2011 ◽

Vol 7 ◽

pp. S193-S194

Author(s):

Ekaterina Rogaeva ◽

Mahdi Ghani ◽

Dalila Pinto ◽

Joseph Lee ◽

Christiane Reitz ◽

...

Keyword(s):

Alzheimer Disease ◽

Copy Number ◽

Copy Number Variations ◽

Genome Wide Analysis ◽

Genome Wide

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Genome-Wide Copy Number Variation Association Study of Atrial Fibrillation Related Thromboembolic Stroke

Journal of Clinical Medicine ◽

10.3390/jcm8030332 ◽

2019 ◽

Vol 8 (3) ◽

pp. 332 ◽

Cited By ~ 4

Author(s):

Chia-Shan Hsieh ◽

Pang-Shuo Huang ◽

Sheng-Nan Chang ◽

Cho-Kai Wu ◽

Juey-Jen Hwang ◽

...

Keyword(s):

Atrial Fibrillation ◽

Signaling Pathway ◽

Copy Number ◽

Genetic Factors ◽

Copy Number Variations ◽

Nucleotide Polymorphisms ◽

Thromboembolic Stroke ◽

Genome Wide ◽

A Genome ◽

The Impact

Atrial fibrillation (AF) is a common cardiac arrhythmia and is one of the major causes of ischemic stroke. In addition to the clinical factors such as CHADS2 or CHADS2-VASC score, the impact of genetic factors on the risk of thromboembolic stroke in patients with AF has been largely unknown. Single-nucleotide polymorphisms in several genomic regions have been found to be associated with AF. However, these loci do not contribute to all the genetic risks of AF or AF related thromboembolic risks, suggesting that there are other genetic factors or variants not yet discovered. In the human genome, copy number variations (CNVs) could also contribute to disease susceptibility. In the present study, we sought to identify CNVs determining the AF-related thromboembolic risk. Using a genome-wide approach in 109 patients with AF and thromboembolic stroke and 14,666 controls from the Taiwanese general population (Taiwan Biobank), we first identified deletions in chromosomal regions 1p36.32-1p36.33, 5p15.33, 8q24.3 and 19p13.3 and amplifications in 14q11.2 that were significantly associated with AF-related stroke in the Taiwanese population. In these regions, 148 genes were involved, including several microRNAs and long non-recoding RNAs. Using a pathway analysis, we found deletions in GNB1, PRKCZ, and GNG7 genes related to the alpha-adrenergic receptor signaling pathway that play a major role in determining the risk of an AF-related stroke. In conclusion, CNVs may be genetic predictors of a risk of a thromboembolic stroke for patients with AF, possibly pointing to an impaired alpha-adrenergic signaling pathway in the mechanism of AF-related thromboembolism.

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