29. CHROMOSOMAL COPY NUMBER ANALYSIS OF CHORIONIC VILLUS FROM SPONTANEOUS ABORTION BY NEXT GENERATION SEQUENCING

2019 ◽  
Vol 39 ◽  
pp. e44-e45
Author(s):  
Y. Tamura ◽  
M. Santo ◽  
Y. Araki ◽  
H. Matsubayashi ◽  
Y. Takaya ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Spontaneous Abortion ◽  
Copy Number ◽  
Chorionic Villus ◽  
Next Generation ◽  
Copy Number Analysis ◽  
Chromosomal Copy Number ◽  
Chromosomal Copy ◽  
Generation Sequencing

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
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