Secondary findings and carrier test frequencies in a large multiethnic sample

Tomasz Gambin, Shalini N. Jhangiani, Jennifer E. Below, Ian M. Campbell, Wojciech Wiszniewski, Donna M. Muzny, Jeffrey Staples, Alanna C. Morrison, Matthew N. Bainbridge, Samantha Penney, Amy L. McGuire, Richard A. Gibbs, James R. Lupski, Eric Boerwinkle

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

Background: Besides its growing importance in clinical diagnostics and understanding the genetic basis of Mendelian and complex diseases, whole exome sequencing (WES) is a rich source of additional information of potential clinical utility for physicians, patients and their families. We analyzed the frequency and nature of single nucleotide variants (SNVs) considered secondary findings and recessive disease allele carrier status in the exomes of 8554 individuals from a large, randomly sampled cohort study and 2514 patients from a study of presumed Mendelian disease having undergone WES. Methods: We used the same sequencing platform and data processing pipeline to analyze all samples and characterized the distributions of reported pathogenic (ClinVar, Human Gene Mutation Database (HGMD)) and predicted deleterious variants in the pre-specified American College of Medical Genetics and Genomics (ACMG) secondary findings and recessive disease genes in different ethnic groups. Results: In the 56 ACMG secondary findings genes, the average number of predicted deleterious variants per individual was 0.74, and the mean number of ClinVar reported pathogenic variants was 0.06. We observed an average of 10 deleterious and 0.78 ClinVar reported pathogenic variants per individual in 1423 autosomal recessive disease genes. By repeatedly sampling pairs of exomes, 0.5 % of the randomly generated couples were at 25 % risk of having an affected offspring for an autosomal recessive disorder based on the ClinVar variants. Conclusions: By investigating reported pathogenic and novel, predicted deleterious variants we estimated the lower and upper limits of the population fraction for which exome sequencing may reveal additional medically relevant information. We suggest that the observed wide range for the lower and upper limits of these frequency numbers will be gradually reduced due to improvement in classification databases and prediction algorithms.

Original languageEnglish (US)
Article number54
JournalGenome Medicine
Volume7
Issue number1
DOIs
StatePublished - Jun 13 2015
Externally publishedYes

Fingerprint

Exome
Recessive Genes
Genomics
Databases
Medical Genetics
Ethnic Groups
Genes
Cohort Studies
Nucleotides
Alleles
Physicians
Mutation
Population

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics
  • Molecular Biology
  • Molecular Medicine

Cite this

Gambin, T., Jhangiani, S. N., Below, J. E., Campbell, I. M., Wiszniewski, W., Muzny, D. M., ... Boerwinkle, E. (2015). Secondary findings and carrier test frequencies in a large multiethnic sample. Genome Medicine, 7(1), [54]. https://doi.org/10.1186/s13073-015-0171-1

Secondary findings and carrier test frequencies in a large multiethnic sample. / Gambin, Tomasz; Jhangiani, Shalini N.; Below, Jennifer E.; Campbell, Ian M.; Wiszniewski, Wojciech; Muzny, Donna M.; Staples, Jeffrey; Morrison, Alanna C.; Bainbridge, Matthew N.; Penney, Samantha; McGuire, Amy L.; Gibbs, Richard A.; Lupski, James R.; Boerwinkle, Eric.

In: Genome Medicine, Vol. 7, No. 1, 54, 13.06.2015.

Research output: Contribution to journalArticle

Gambin, T, Jhangiani, SN, Below, JE, Campbell, IM, Wiszniewski, W, Muzny, DM, Staples, J, Morrison, AC, Bainbridge, MN, Penney, S, McGuire, AL, Gibbs, RA, Lupski, JR & Boerwinkle, E 2015, 'Secondary findings and carrier test frequencies in a large multiethnic sample', Genome Medicine, vol. 7, no. 1, 54. https://doi.org/10.1186/s13073-015-0171-1
Gambin, Tomasz ; Jhangiani, Shalini N. ; Below, Jennifer E. ; Campbell, Ian M. ; Wiszniewski, Wojciech ; Muzny, Donna M. ; Staples, Jeffrey ; Morrison, Alanna C. ; Bainbridge, Matthew N. ; Penney, Samantha ; McGuire, Amy L. ; Gibbs, Richard A. ; Lupski, James R. ; Boerwinkle, Eric. / Secondary findings and carrier test frequencies in a large multiethnic sample. In: Genome Medicine. 2015 ; Vol. 7, No. 1.
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AU - Muzny, Donna M.

AU - Staples, Jeffrey

AU - Morrison, Alanna C.

AU - Bainbridge, Matthew N.

AU - Penney, Samantha

AU - McGuire, Amy L.

AU - Gibbs, Richard A.

AU - Lupski, James R.

AU - Boerwinkle, Eric

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N2 - Background: Besides its growing importance in clinical diagnostics and understanding the genetic basis of Mendelian and complex diseases, whole exome sequencing (WES) is a rich source of additional information of potential clinical utility for physicians, patients and their families. We analyzed the frequency and nature of single nucleotide variants (SNVs) considered secondary findings and recessive disease allele carrier status in the exomes of 8554 individuals from a large, randomly sampled cohort study and 2514 patients from a study of presumed Mendelian disease having undergone WES. Methods: We used the same sequencing platform and data processing pipeline to analyze all samples and characterized the distributions of reported pathogenic (ClinVar, Human Gene Mutation Database (HGMD)) and predicted deleterious variants in the pre-specified American College of Medical Genetics and Genomics (ACMG) secondary findings and recessive disease genes in different ethnic groups. Results: In the 56 ACMG secondary findings genes, the average number of predicted deleterious variants per individual was 0.74, and the mean number of ClinVar reported pathogenic variants was 0.06. We observed an average of 10 deleterious and 0.78 ClinVar reported pathogenic variants per individual in 1423 autosomal recessive disease genes. By repeatedly sampling pairs of exomes, 0.5 % of the randomly generated couples were at 25 % risk of having an affected offspring for an autosomal recessive disorder based on the ClinVar variants. Conclusions: By investigating reported pathogenic and novel, predicted deleterious variants we estimated the lower and upper limits of the population fraction for which exome sequencing may reveal additional medically relevant information. We suggest that the observed wide range for the lower and upper limits of these frequency numbers will be gradually reduced due to improvement in classification databases and prediction algorithms.

AB - Background: Besides its growing importance in clinical diagnostics and understanding the genetic basis of Mendelian and complex diseases, whole exome sequencing (WES) is a rich source of additional information of potential clinical utility for physicians, patients and their families. We analyzed the frequency and nature of single nucleotide variants (SNVs) considered secondary findings and recessive disease allele carrier status in the exomes of 8554 individuals from a large, randomly sampled cohort study and 2514 patients from a study of presumed Mendelian disease having undergone WES. Methods: We used the same sequencing platform and data processing pipeline to analyze all samples and characterized the distributions of reported pathogenic (ClinVar, Human Gene Mutation Database (HGMD)) and predicted deleterious variants in the pre-specified American College of Medical Genetics and Genomics (ACMG) secondary findings and recessive disease genes in different ethnic groups. Results: In the 56 ACMG secondary findings genes, the average number of predicted deleterious variants per individual was 0.74, and the mean number of ClinVar reported pathogenic variants was 0.06. We observed an average of 10 deleterious and 0.78 ClinVar reported pathogenic variants per individual in 1423 autosomal recessive disease genes. By repeatedly sampling pairs of exomes, 0.5 % of the randomly generated couples were at 25 % risk of having an affected offspring for an autosomal recessive disorder based on the ClinVar variants. Conclusions: By investigating reported pathogenic and novel, predicted deleterious variants we estimated the lower and upper limits of the population fraction for which exome sequencing may reveal additional medically relevant information. We suggest that the observed wide range for the lower and upper limits of these frequency numbers will be gradually reduced due to improvement in classification databases and prediction algorithms.

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