scholarly journals Next generation sequencing‐based copy number analysis reveals low prevalence of deletions and duplications in 46 genes associated with genetic cardiomyopathies

2015 ◽  
Vol 4 (2) ◽  
pp. 143-151 ◽  
Author(s):  
Ozge Ceyhan‐Birsoy ◽  
Trevor J. Pugh ◽  
Mark J. Bowser ◽  
Elizabeth Hynes ◽  
Ashley L. Frisella ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Next Generation ◽  
Copy Number Analysis ◽  
Low Prevalence ◽  
Generation Sequencing

scholarly journals Allele-Specific Droplet Digital PCR Combined with a Next-Generation Sequencing-Based Algorithm for Diagnostic Copy Number Analysis in Genes with High Homology: Proof of Concept Using Stereocilin

2018 ◽  
Vol 64 (4) ◽  
pp. 705-714 ◽  
Author(s):  
Sami S Amr ◽  
Elissa Murphy ◽  
Elizabeth Duffy ◽  
Rojeen Niazi ◽  
Jorune Balciuniene ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
High Homology ◽  
Next Generation ◽  
Copy Number Analysis ◽  
Confirmatory Testing ◽  
Allele Specific ◽  
Generation Sequencing

Abstract BACKGROUND Copy number variants (CNVs) can substantially contribute to the pathogenic variant spectrum in several disease genes. The detection of this type of variant is complicated in genes with high homology to other genomic sequences, yet such genomics regions are more likely to lead to CNVs, making it critical to address detection in these settings. METHODS We developed a copy number analysis approach for high homology genes/regions that consisted of next-generation sequencing (NGS)-based dosage analysis accompanied by allele-specific droplet digital PCR (ddPCR) confirmatory testing. We applied this approach to copy number analysis in STRC, a gene with 98.9% homology to a nonfunctional pseudogene, pSTRC, and characterized its accuracy in detecting different copy number states by use of known samples. RESULTS Using a cohort of 517 patients with hearing loss, we prospectively demonstrated the clinical utility of the approach, which contributed 30 of the 122 total positives (6%) to the diagnostic yield, increasing the overall yield from 17.6% to 23.6%. Positive STRC genotypes included homozygous (n = 15) or compound heterozygous (n = 8) deletions, or heterozygous deletions in trans with pathogenic sequence variants (n = 7). Finally, this approach limited ddPCR testing to cases with NGS copy number findings, thus markedly reducing the number of costly and laborious, albeit specific, ddPCR tests. CONCLUSIONS NGS-based CNV detection followed by allele-specific ddPCR confirmatory testing is a reliable and affordable approach for copy number analysis in medically relevant genes with homology issues.

scholarly journals Next-Generation Sequencing–Based Assessment of JAK2, PD-L1, and PD-L2 Copy Number Alterations at 9p24.1 in Breast Cancer

2019 ◽  
Vol 21 (2) ◽  
pp. 307-317 ◽  
Author(s):  
Sounak Gupta ◽  
Chad M. Vanderbilt ◽  
Paolo Cotzia ◽  
Javier A. Arias-Stella ◽  
Jason C. Chang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Next Generation Sequencing ◽  
Copy Number ◽  
Copy Number Alterations ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Use of next-generation sequencing to detectLDLRgene copy number variation in familial hypercholesterolemia

2017 ◽  
Vol 58 (11) ◽  
pp. 2202-2209 ◽  
Author(s):  
Michael A. Iacocca ◽  
Jian Wang ◽  
Jacqueline S. Dron ◽  
John F. Robinson ◽  
Adam D. McIntyre ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number Variation ◽  
Familial Hypercholesterolemia ◽  
Copy Number ◽  
Next Generation ◽  
Number Variation ◽  
Generation Sequencing

scholarly journals Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing

2020 ◽  
Author(s):  
Hao Bai ◽  
Yanghua He ◽  
Yi Ding ◽  
Huanmin Zhang ◽  
Jilan Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Marek's Disease ◽  
Neoplastic Disease ◽  
Marek’S Disease ◽  
Next Generation ◽  
Qrt Pcr ◽  
Genome Wide ◽  
A Genome ◽  
Generation Sequencing

Abstract Background: Marek’s disease (MD) is a highly neoplastic disease primarily affecting chickens, and remains as a chronic infectious disease that threatens the poultry industry. Copy number variation (CNV) has been examined in many species and is recognized as a major source of genetic variation that directly contributes to phenotypic variation such as resistance to infectious diseases. Two highly inbred chicken lines 63 (MD-resistant) and 72 (MD-susceptible), as well as their F1 generation and six recombinant congenic strains (RCSs) with varied susceptibility to MD, are considered as ideal models to identify the complex mechanisms of genetic and molecular resistance to MD.Results: In the present study, to unravel the potential genetic mechanisms underlying resistance to MD, we performed a genome-wide CNV detection using next generation sequencing on the inbred chicken lines with the assistance of CNVnator. As a result, a total of 1,649 CNV regions (CNVRs) were successfully identified after merging all the nine datasets, of which 90 CNVRs were overlapped across all the chicken lines. Within these shared regions, 1,360 harbored genes were identified. In addition, 55 and 44 CNVRs with 62 and 57 harbored genes were specifically identified in line 63 and 72, respectively. Bioinformatics analysis showed that the nearby genes were significantly enriched in 36 GO terms and 6 KEGG pathways including JAK/STAT signaling pathway. Ten CNVRs (nine deletions and one duplication) involved in 10 disease-related genes were selected for validation by using qRT-PCR, all of which were successfully confirmed. Finally, qRT-PCR was also used to validate two deletion events in line 72 that were definitely normal in line 63. One high-confidence gene, IRF2 was identified as the most promising candidate gene underlying resistance and susceptibility to MD in view of its function and overlaps with data from previous study.Conclusions: Our findings provide valuable insights for understanding the genetic mechanism of resistance to MD and the identified gene and pathway could be considered as the subject of further functional characterization.

scholarly journals Comprehensive Assessment of Somatic Copy Number Variation Calling Using Next-Generation Sequencing Data

2021 ◽  
Author(s):  
Yun-Ching Chen ◽  
Fayaz Seifuddin ◽  
Cu Nguyen ◽  
Zhaowei Yang ◽  
Wanqiu Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number Variation ◽  
Cancer Progression ◽  
Copy Number ◽  
Tissue Sample ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Dna Amount ◽  
Number Variation ◽  
Generation Sequencing

AbstractCopy number variation (CNV) is a common type of mutation that often drives cancer progression. With advances in next-generation sequencing (NGS), CNVs can be detected in a detailed manner via newly developed computational tools but quality of such CNV calls has not been carefully evaluated. We analyzed CNV calls reported by 6 cutting-edge callers for 91 samples which were derived from the same cancer cell line, prepared and sequenced by varying the following factors: type of tissue sample (Fresh vs. Formalin Fixed Paraffin Embedded (FFPE)), library DNA amount, tumor purity, sequencing platform (Whole-Genome Sequencing (WGS) versus Whole-Exome Sequencing (WES)), and sequencing coverage. We found that callers greatly determined the pattern of CNV calls. Calling quality was drastically impaired by low purity (<50%) and became variable when WES, FFPE, and medium purity (50%-75%) were applied. Effects of low DNA amount and low coverage were relatively minor. Our analysis demonstrates the limitation of benchmarking somatic CNV callers when the real ground truth is not available. Our comprehensive analysis has further characterized each caller with respect to confounding factors and examined the consistency of CNV calls, thereby providing guidelines for conducting somatic CNV analysis.

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