Academic Journal
A robust benchmark for detection of germline large deletions and insertions
| Title: | A robust benchmark for detection of germline large deletions and insertions |
|---|---|
| Authors: | Justin M. Zook, Nancy F. Hansen, Nathan D. Olson, Lesley Chapman, James C. Mullikin, Chunlin Xiao, Stephen Sherry, Sergey Koren, Adam M. Phillippy, Paul C. Boutros, Sayed Mohammad E. Sahraeian, Vincent Huang, Alexandre Rouette, Noah Alexander, Christopher E. Mason, Iman Hajirasouliha, Camir Ricketts, Joyce Lee, Rick Tearle, Ian T. Fiddes, Alvaro Martinez Barrio, Jeremiah Wala, Andrew Carroll, Noushin Ghaffari, Oscar L. Rodriguez, Ali Bashir, Shaun Jackman, John J. Farrell, Aaron M. Wenger, Can Alkan, Arda Soylev, Michael C. Schatz, Shilpa Garg, George Church, Tobias Marschall, Ken Chen, Xian Fan, Adam C. English, Jeffrey A. Rosenfeld, Weichen Zhou, Ryan E. Mills, Jay M. Sage, Jennifer R. Davis, Michael D. Kaiser, John S. Oliver, Anthony P. Catalano, Mark J. P. Chaisson, Noah Spies, Fritz J. Sedlazeck, Marc Salit |
| Contributors: | Alkan, Can |
| Source: | Nat Biotechnol Nature Biotechnology Nature Biotechnology, vol 38, iss 11 |
| Publisher Information: | Springer Science and Business Media LLC, 2020. |
| Publication Year: | 2020 |
| Subject Terms: | 0301 basic medicine, 1.1 Normal biological development and functioning, Human Genome, 0206 medical engineering, Bioinformatics and Computational Biology, Molecular Sequence Annotation, DNA, Sequence Analysis, DNA, 02 engineering and technology, Biological Sciences, Diploidy, Article, 3. Good health, 03 medical and health sciences, INDEL Mutation, Underpinning research, Genomic Structural Variation, Genetics, Humans, Generic health relevance, Sequence Analysis, Germ-Line Mutation |
| Description: | New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping. |
| Document Type: | Article Other literature type |
| File Description: | application/pdf |
| Language: | English |
| ISSN: | 1546-1696 1087-0156 |
| DOI: | 10.1038/s41587-020-0538-8 |
| Access URL: | http://repository.bilkent.edu.tr/bitstream/11693/75718/1/A_robust_benchmark_for_detection_of_germline_large_deletions_and_insertions.pdf https://pubmed.ncbi.nlm.nih.gov/32541955 https://escholarship.org/uc/item/83j0h3ws https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8454654 https://www.nature.com/articles/s41587-020-0538-8 http://www-nature-com-443.webvpn.bjmu.tsg211.com/articles/s41587-020-0538-8 https://www.ncbi.nlm.nih.gov/pubmed/32541955 https://escholarship.org/content/qt83j0h3ws/qt83j0h3ws.pdf?t=r0sukl https://hdl.handle.net/11693/75718 https://escholarship.org/uc/item/83j0h3ws |
| Rights: | Springer TDM |
| Accession Number: | edsair.doi.dedup.....3325cb1708ed88a941f9d1750f6d61e6 |
| Database: | OpenAIRE |
| ISSN: | 15461696 10870156 |
|---|---|
| DOI: | 10.1038/s41587-020-0538-8 |