Exome sequencing of a multigenerational human pedigree

Dale Hedges, Dan Burges, Eric Powell, Cherylyn Almonte, Jia Huang, Stuart Young, Benjamin Boese, Mike Schmidt, Margaret A Pericak-Vance, Eden R Martin, Xinmin Zhang, Timothy T. Harkins, Stephan L Zuchner

Research output: Contribution to journalArticle

63 Citations (Scopus)

Abstract

Over the next few years, the efficient use of next-generation sequencing (NGS) in human genetics research will depend heavily upon the effective mechanisms for the selective enrichment of genomic regions of interest. Recently, comprehensive exome capture arrays have become available for targeting approximately 33 Mb or,180,000 coding exons across the human genome. Selective genomic enrichment of the human exome offers an attractive option for new experimental designs aiming to quickly identify potential disease-associated genetic variants, especially in family-based studies. We have evaluated a 2.1 M feature human exome capture array on eight individuals from a three-generation family pedigree. We were able to cover up to 98% of the targeted bases at a long-read sequence read depth of $3, 86% at a read depth of $10, and over 50% of all targets were covered with $20 reads. We identified up to 14,284 SNPs and small indels per individual exome, with up to 1,679 of these representing putative novel polymorphisms. Applying the conservative genotype calling approach HCDiff, the average rate of detection of a variant allele based on Illumina 1 M BeadChips genotypes was 95.2% at $10x sequence. Further, we propose an advantageous genotype calling strategy for low covered targets that empirically determines cut-off thresholds at a given coverage depth based on existing genotype data. Application of this method was able to detect.99% of SNPs covered $8x. Our results offer guidance for ''real-world'' applications in human genetics and provide further evidence that microarray-based exome capture is an efficient and reliable method to enrich for chromosomal regions of interest in next-generation sequencing experiments.

Original languageEnglish
Article numbere8232
JournalPLoS One
Volume4
Issue number12
DOIs
StatePublished - Dec 1 2009

Fingerprint

Exome
Pedigree
pedigree
Genotype
genotype
Microarrays
Polymorphism
Design of experiments
Medical Genetics
Exons
Genes
Single Nucleotide Polymorphism
genomics
application coverage
Genetic Research
Inborn Genetic Diseases
application methods
exons
Human Genome
experimental design

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Hedges, D., Burges, D., Powell, E., Almonte, C., Huang, J., Young, S., ... Zuchner, S. L. (2009). Exome sequencing of a multigenerational human pedigree. PLoS One, 4(12), [e8232]. https://doi.org/10.1371/journal.pone.0008232

Exome sequencing of a multigenerational human pedigree. / Hedges, Dale; Burges, Dan; Powell, Eric; Almonte, Cherylyn; Huang, Jia; Young, Stuart; Boese, Benjamin; Schmidt, Mike; Pericak-Vance, Margaret A; Martin, Eden R; Zhang, Xinmin; Harkins, Timothy T.; Zuchner, Stephan L.

In: PLoS One, Vol. 4, No. 12, e8232, 01.12.2009.

Research output: Contribution to journalArticle

Hedges, D, Burges, D, Powell, E, Almonte, C, Huang, J, Young, S, Boese, B, Schmidt, M, Pericak-Vance, MA, Martin, ER, Zhang, X, Harkins, TT & Zuchner, SL 2009, 'Exome sequencing of a multigenerational human pedigree', PLoS One, vol. 4, no. 12, e8232. https://doi.org/10.1371/journal.pone.0008232
Hedges D, Burges D, Powell E, Almonte C, Huang J, Young S et al. Exome sequencing of a multigenerational human pedigree. PLoS One. 2009 Dec 1;4(12). e8232. https://doi.org/10.1371/journal.pone.0008232
Hedges, Dale ; Burges, Dan ; Powell, Eric ; Almonte, Cherylyn ; Huang, Jia ; Young, Stuart ; Boese, Benjamin ; Schmidt, Mike ; Pericak-Vance, Margaret A ; Martin, Eden R ; Zhang, Xinmin ; Harkins, Timothy T. ; Zuchner, Stephan L. / Exome sequencing of a multigenerational human pedigree. In: PLoS One. 2009 ; Vol. 4, No. 12.
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