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Article: INDELseek: Detection Of Complex Insertions And Deletions From Next-generation Sequencing Data

TitleINDELseek: Detection Of Complex Insertions And Deletions From Next-generation Sequencing Data
Authors
Issue Date2017
PublisherBioMed 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?
AbstractBACKGROUND: 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 Identifierhttp://hdl.handle.net/10722/245310
ISSN
2017 Impact Factor: 3.73
2015 SCImago Journal Rankings: 2.343
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorAu, CH-
dc.contributor.authorLeung, AYH-
dc.contributor.authorKwong, A-
dc.contributor.authorChan, TL-
dc.contributor.authorMa, ESK-
dc.date.accessioned2017-09-18T02:08:21Z-
dc.date.available2017-09-18T02:08:21Z-
dc.date.issued2017-
dc.identifier.citationBMC Genomics, 2017, v. 18, p. 16:1-7-
dc.identifier.issn1471-2164-
dc.identifier.urihttp://hdl.handle.net/10722/245310-
dc.description.abstractBACKGROUND: 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.languageeng-
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/-
dc.relation.ispartofBMC Genomics-
dc.rightsBMC Genomics. Copyright © BioMed Central Ltd.-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleINDELseek: Detection Of Complex Insertions And Deletions From Next-generation Sequencing Data-
dc.typeArticle-
dc.identifier.emailKwong, A: avakwong@hku.hk-
dc.identifier.authorityKwong, A=rp01734-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/s12864-016-3449-9-
dc.identifier.hkuros275663-
dc.identifier.volume18-
dc.identifier.spage16:1-
dc.identifier.epage7-
dc.identifier.isiWOS:000391333100002-
dc.publisher.placeUnited Kingdom-

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