Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort

We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor-Hopkins Center for...

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Published inNucleic acids research Vol. 45; no. 4; pp. gkw1237 - 1648
Main Authors Gambin, Tomasz, Akdemir, Zeynep C., Yuan, Bo, Gu, Shen, Chiang, Theodore, Carvalho, Claudia M.B., Shaw, Chad, Jhangiani, Shalini, Boone, Philip M., Eldomery, Mohammad K., Karaca, Ender, Bayram, Yavuz, Stray-Pedersen, Asbjørg, Muzny, Donna, Charng, Wu-Lin, Bahrambeigi, Vahid, Belmont, John W., Boerwinkle, Eric, Beaudet, Arthur L., Gibbs, Richard A., Lupski, James R.
Format Journal Article
LanguageEnglish
Published England Oxford University Press 28.02.2017
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Online AccessGet full text
ISSN0305-1048
1362-4962
1362-4962
DOI10.1093/nar/gkw1237

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Abstract We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17-50% of pathogenic CNVs in different disease cohorts where 7.1-11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.
AbstractList We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor–Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17–50% of pathogenic CNVs in different disease cohorts where 7.1–11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.
We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17-50% of pathogenic CNVs in different disease cohorts where 7.1-11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17-50% of pathogenic CNVs in different disease cohorts where 7.1-11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.
Author Yuan, Bo
Eldomery, Mohammad K.
Belmont, John W.
Beaudet, Arthur L.
Gibbs, Richard A.
Chiang, Theodore
Karaca, Ender
Boone, Philip M.
Bayram, Yavuz
Akdemir, Zeynep C.
Gu, Shen
Shaw, Chad
Bahrambeigi, Vahid
Muzny, Donna
Boerwinkle, Eric
Jhangiani, Shalini
Charng, Wu-Lin
Lupski, James R.
Gambin, Tomasz
Carvalho, Claudia M.B.
Stray-Pedersen, Asbjørg
AuthorAffiliation 5 Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
6 Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
8 Texas Children's Hospital, Houston, TX 77030, USA
2 Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665 Warsaw, Poland
3 Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
7 Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
1 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
4 Norwegian National Unit for Newborn Screening, Division for Pediatric and Adolescent Medicine, Oslo University Hospital, N-0424 Oslo, Norway
AuthorAffiliation_xml – name: 2 Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665 Warsaw, Poland
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Snippet We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions...
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StartPage gkw1237
SubjectTerms Algorithms
Alternative Splicing
Cohort Studies
Computational Biology
Computational Biology - methods
Consanguinity
Datasets as Topic
DNA Copy Number Variations
Exome
Genetic Diseases, Inborn - diagnosis
Genetic Diseases, Inborn - genetics
Hemizygote
High-Throughput Nucleotide Sequencing
Homozygote
Humans
Inheritance Patterns
Models, Genetic
Pedigree
Reproducibility of Results
Sequence Deletion
Workflow
Title Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort
URI https://www.ncbi.nlm.nih.gov/pubmed/27980096
https://www.proquest.com/docview/1852687141
https://pubmed.ncbi.nlm.nih.gov/PMC5389578
Volume 45
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