Targeted Capture and Massively Parallel Sequencing of Twelve Human Exomes

By Sarah B. H. Ng, Emily H. Turner, P. Robertson, Steven Flygare, Abigail W. Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam K Bhattacharjee, Evan E. Eichler and 3 more. 2009

1,836 citations recorded by the source corpus.

Genome-wide association studies suggest that common genetic variants explain only a modest fraction of heritable risk for common diseases, raising the question of whether rare variants account for a significant fraction of unexplained heritability. Although DNA sequencing costs have fallen markedly, they remain far from what is necessary for rare and novel variants to be routinely identified at a genome-wide scale in large cohorts. We have therefore sought to develop second-generation methods for targeted sequencing of all protein-coding regions (‘exomes’), to reduce costs while enriching for discovery of highly penetrant variants. Here we report on the targeted capture and massively parallel sequencing of the exomes of 12 humans. These include eight HapMap individuals representing three populations, and four unrelated individuals with a rare dominantly inherited disorder, Freeman–Sheldon syndrome (FSS). We demonstrate the sensitive and specific identification of rare and common variants in over 300 megabases of coding sequence. Using FSS as a proof-of-concept, we show that candidate genes for Mendelian disorders can be identified by exome sequencing of a small number of unrelated, affected individuals. This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of non-synonymous variants by predicted functional impact.

Subfields: Genetics

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Citations in the corpus

CADD: predicting the deleteriousness of variants throughout the human genome (2018, positive): “In addition, our SNV scores are available through a number of third-party sources, such as dbNSFP (48), as a plug-in for Ensembl VEP, ANNOVAR (49), SeattleSeq (50), ExAC / gnomAD (8) and PopViz (51).”
SIFT web server: predicting effects of amino acid substitutions on proteins (2012, background): “The majority of SNVs found in a human are common among the population, but disease-causing variants are typically private or rare, and tend to occur in protein coding regions which constitute only 1% (30 megabases) of the total genome (2,3).”
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries (2011, background): “Key applications for targeted approaches include sequencing of exons or sets of protein-coding genes implicated in specific diseases [18-21], whole human exome sequencing (for example, in cancer or disease cohorts) [22-24] (reviewed in [25]), and resequencing of specific regions as a follow-up to ge”
Genomic responses in mouse models poorly mimic human inflammatory diseases (2013, background): “Furthermore, new genomic information, such as the availability of personal genomes (32) or exomes (33) to capture the disease heterogeneity directly from patients or systematic interpretation of genome-wide signatures in human diseases (34, 35), will likely complement or short circuit the need for m”
Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study (2011, methodology): “Indel calling in the Bowtie/in-house pipeline was adapted with minor modifications(18).”
Natural genetic variation caused by small insertions and deletions in the human genome. (2011, result): “In further support of this conclusion, exome re-sequencing projects and the 1000 Genomes Project also have identified coding INDELs (Ng et al. 2009; Ng et al. 2010; 1000 Genomes Project Consortium 2010).”
The Human Phenotype Ontology (2010, background): “It is now in principle possible to identify disease genes by exome sequencing of a small number of unrelated affected individuals (4), and similar methodologies are likely to transform investigations of cancer (5) and potentially even polygenic disorders.”
Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches (2015, neutral): “Targeted enrichment, or sequence capture, was originally done with hybridization of sheared whole genomic DNAs to microarrays containing conserved sequences derived from either EST libraries or transcriptomes of species that bracketed the species of interest (Ng et al., 2009).”
Pooled association tests for rare variants in exon-resequencing studies. (2010, positive): “We have shown that this approach performs well on simulated and empirical data, relative to other methods, and demonstrated that the incorporation of computational predictions of functional effects provides a further improvement in power, concordant with recent work.(11,19) The variable-threshold ap”
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. (2012, background): “Sequencing coverage is nonuniform across targeted regions and from one sample to the next (Ng et al. 2009; Bainbridge et al. 2010; Teer et al. 2010).”
Deep mutational scanning: assessing protein function on a massive scale (2011, background): “Genomic technologies, which are rapidly increasing in scale, are identifying large numbers of candidate mutations for a wide variety of diseases [3].”
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data (2010, methodology): “Since exome data for four Freeman–Sheldon cases were not available to us, we downloaded the exome data for eight HapMap subjects reported in (11).”