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Article: INDELseek: Detection Of Complex Insertions And Deletions From Next-generation Sequencing Data
Title | INDELseek: Detection Of Complex Insertions And Deletions From Next-generation Sequencing Data |
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Authors | |
Keywords | Bioinformatics Complex indel Next-generation sequencing Variant calling |
Issue Date | 2017 |
Publisher | BioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/ |
Citation | BMC Genomics, 2017, v. 18, p. 16:1-7 How to Cite? |
Abstract | BACKGROUND: Complex insertions and deletions (indels) from next-generation sequencing (NGS) data were prone to escape detection by currently available variant callers as shown by large-scale human genomics studies. Somatic and germline complex indels in key disease driver genes could be missed in NGS-based genomics studies. RESULTS: INDELseek is an open-source complex indel caller designed for NGS data of random fragments and PCR amplicons. The key differentiating factor of INDELseek is that each NGS read alignment was examined as a whole instead of 'pileup' of each reference position across multiple alignments. In benchmarking against the reference material NA12878 genome (n = 160 derived from high-confidence variant calls), GATK, SAMtools and INDELseek showed complex indel detection sensitivities of 0%, 0% and 100%, respectively. INDELseek also detected all known germline (BRCA1 and BRCA2) and somatic (CALR and JAK2) complex indels in human clinical samples (n = 8). Further experiments validated all 10 detected KIT complex indels in a discovery cohort of clinical samples. In silico semi-simulation showed sensitivities of 93.7-96.2% based on 8671 unique complex indels in >5000 genes from dbSNP and COSMIC. We also demonstrated the importance of complex indel detection in accurately annotating BRCA1, BRCA2 and TP53 mutations with gained or rescued protein-truncating effects. CONCLUSIONS: INDELseek is an accurate and versatile tool for complex indel detection in NGS data. It complements other variant callers in NGS-based genomics studies targeting a wide spectrum of genetic variations. |
Persistent Identifier | http://hdl.handle.net/10722/245310 |
ISSN | 2023 Impact Factor: 3.5 2023 SCImago Journal Rankings: 1.047 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Au, CH | - |
dc.contributor.author | Leung, AYH | - |
dc.contributor.author | Kwong, A | - |
dc.contributor.author | Chan, TL | - |
dc.contributor.author | Ma, ESK | - |
dc.date.accessioned | 2017-09-18T02:08:21Z | - |
dc.date.available | 2017-09-18T02:08:21Z | - |
dc.date.issued | 2017 | - |
dc.identifier.citation | BMC Genomics, 2017, v. 18, p. 16:1-7 | - |
dc.identifier.issn | 1471-2164 | - |
dc.identifier.uri | http://hdl.handle.net/10722/245310 | - |
dc.description.abstract | BACKGROUND: Complex insertions and deletions (indels) from next-generation sequencing (NGS) data were prone to escape detection by currently available variant callers as shown by large-scale human genomics studies. Somatic and germline complex indels in key disease driver genes could be missed in NGS-based genomics studies. RESULTS: INDELseek is an open-source complex indel caller designed for NGS data of random fragments and PCR amplicons. The key differentiating factor of INDELseek is that each NGS read alignment was examined as a whole instead of 'pileup' of each reference position across multiple alignments. In benchmarking against the reference material NA12878 genome (n = 160 derived from high-confidence variant calls), GATK, SAMtools and INDELseek showed complex indel detection sensitivities of 0%, 0% and 100%, respectively. INDELseek also detected all known germline (BRCA1 and BRCA2) and somatic (CALR and JAK2) complex indels in human clinical samples (n = 8). Further experiments validated all 10 detected KIT complex indels in a discovery cohort of clinical samples. In silico semi-simulation showed sensitivities of 93.7-96.2% based on 8671 unique complex indels in >5000 genes from dbSNP and COSMIC. We also demonstrated the importance of complex indel detection in accurately annotating BRCA1, BRCA2 and TP53 mutations with gained or rescued protein-truncating effects. CONCLUSIONS: INDELseek is an accurate and versatile tool for complex indel detection in NGS data. It complements other variant callers in NGS-based genomics studies targeting a wide spectrum of genetic variations. | - |
dc.language | eng | - |
dc.publisher | BioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/ | - |
dc.relation.ispartof | BMC Genomics | - |
dc.rights | BMC Genomics. Copyright © BioMed Central Ltd. | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | Bioinformatics | - |
dc.subject | Complex indel | - |
dc.subject | Next-generation sequencing | - |
dc.subject | Variant calling | - |
dc.title | INDELseek: Detection Of Complex Insertions And Deletions From Next-generation Sequencing Data | - |
dc.type | Article | - |
dc.identifier.email | Kwong, A: avakwong@hku.hk | - |
dc.identifier.authority | Kwong, A=rp01734 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1186/s12864-016-3449-9 | - |
dc.identifier.scopus | eid_2-s2.0-85008354482 | - |
dc.identifier.hkuros | 275663 | - |
dc.identifier.volume | 18 | - |
dc.identifier.spage | 16:1 | - |
dc.identifier.epage | 7 | - |
dc.identifier.isi | WOS:000391333100002 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 1471-2164 | - |