Full metadata record
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Charles Lee | * |
dc.date.accessioned | 2023-10-23T16:30:46Z | - |
dc.date.available | 2023-10-23T16:30:46Z | - |
dc.date.issued | 2022 | * |
dc.identifier.issn | 1672-0229 | * |
dc.identifier.issn | 2210-3244 | * |
dc.identifier.other | OAK-33862 | * |
dc.identifier.uri | https://dspace.ewha.ac.kr/handle/2015.oak/266439 | - |
dc.description.abstract | We aimed to develop a whole-genome sequencing (WGS)-based copy number variant (CNV) calling algorithm with the potential of replacing chromosomal microarray assay (CMA) for clinical diagnosis. JAX-CNV is thus developed for CNV detection from WGS data. The performance of this CNV calling algorithm was evaluated in a blinded manner on 31 samples and compared to the 112 CNVs reported by clinically validated CMAs for these 31 samples. The result showed that JAX-CNV recalled 100% of these CNVs. Besides, JAX-CNV identified an average of 30 CNVs per individual, representing an approximately seven-fold increase compared to calls of clinically validated CMAs. Experimental validation of 24 randomly selected CNVs showed one false positive, i.e., a false discovery rate (FDR) of 4.17%. A robustness test on lower-coverage data revealed a 100% sensitivity for CNVs larger than 300 kb (the current threshold for College of American Pathologists) down to 10x coverage. For CNVs larger than 50 kb, sensitivities were 100% for coverages deeper than 20x, 97% for 15x, and 95% for 10x. We developed a WGS-based CNV pipeline, including this newly developed CNV caller JAX-CNV, and found it capable of detecting CMA-reported CNVs at a sensitivity of 100% with about a FDR of 4%. We propose that JAX-CNV could be further examined in a multi-institutional study to justify the transition of first-tier genetic testing from CMAs to WGS. JAX-CNV is available at https://github.com/TheJacksonLaboratory/JAX-CNV. | * |
dc.language | English | * |
dc.publisher | ELSEVIER | * |
dc.subject | Copy number variant | * |
dc.subject | Chromosomal microarray assay | * |
dc.subject | Whole-genome sequencing | * |
dc.subject | JAX-CNV | * |
dc.subject | Genetic testing | * |
dc.title | JAX-CNV: A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level | * |
dc.type | Article | * |
dc.relation.issue | 6 | * |
dc.relation.volume | 20 | * |
dc.relation.index | SCIE | * |
dc.relation.index | SCOPUS | * |
dc.relation.startpage | 1197 | * |
dc.relation.lastpage | 1206 | * |
dc.relation.journaltitle | GENOMICS PROTEOMICS & BIOINFORMATICS | * |
dc.identifier.doi | 10.1016/j.gpb.2021.06.003 | * |
dc.identifier.wosid | WOS:001034927200002 | * |
dc.author.google | Lee, Wan-Ping | * |
dc.author.google | Zhu, Qihui | * |
dc.author.google | Yang, Xiaofei | * |
dc.author.google | Liu, Silvia | * |
dc.author.google | Cerveira, Eliza | * |
dc.author.google | Ryan, Mallory | * |
dc.author.google | Mil-Homens, Adam | * |
dc.author.google | Bellfy, Lauren | * |
dc.author.google | Ye, Kai | * |
dc.author.google | Lee, Charles | * |
dc.author.google | Zhang, Chengsheng | * |
dc.contributor.scopusid | Charles Lee(23980489900;57290864600) | * |
dc.date.modifydate | 20231123120503 | * |