Faculty Opinions recommendation of Targeted capture and massively parallel sequencing of 12 human exomes.

By E. Shore. 2009

357 citations recorded by the source corpus.

Subfields: Cancer Research, Genetics, Public Health, Environmental and Occupational Health

View Paper: https://www.semanticscholar.org/paper/efc88b2e7cc275e3fb3d927f46e1b3617030592e

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Citations in the corpus

The impact of next-generation sequencing on genomics (2011, background): “NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge (2014, methodology): “There were a large variety of annotation sources (see Table 4), including but not limited to: OMIM [50], Uniprot [51], SeattleSeq [52], SNPedia [53], NCBI ClinVar, PharmGKB [54], Human Gene Mutation Database [55], dbNSFP [56], and in-house annotations.”
A survey of tools for variant analysis of next-generation genome sequencing data (2013, neutral): “quences [2, 3].”
DNA sequencing at 40: past, present and future (2017, neutral): “In this period, whole-genome sequencing (WGS) remained too expensive for most groups to scale, motivating the development of targeted capture methods 93–96 and then whole-exome sequencing (WES), that is, selective sequencing of the 1–2% of the genome that is encodes proteins 97 .”
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data (2011, neutral): “…defined by Genomic Evolutionary Rate Profiling (GERP) 17,67,72 , for non-synonymous variants in human exome data that were reported Ng et al. 8 These data are meant to provide a general sense for the effects of variant filtering with commonly used definitions of deleteriousness, and other…”
Applications of next-generation sequencing to phylogeography and phylogenetics. (2013, methodology): “, 2009), most applications have been directed at human disease genes and exomes (Albert et al., 2007; Hodges et al., 2007; Ng et al., 2009; Tewhey et al., 2009a).”
CONTRA: copy number analysis for targeted resequencing (2012, neutral): “Our method calls copy number gains and losses for each target region based on normalized depth of coverage.”
Exome sequencing reveals VCP mutations as a cause of familial ALS (2010, neutral): “Our data broaden the phenotype of IBMPFD to include motor neuron degeneration, suggest that VCP mutations may account for 1%–2% of familial ALS, and provide evidence directly implicating defects in the ubiquitination/protein degradation pathway inmotor neuron degeneration.”
Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations (2011, neutral): “In this study, we sequenced the protein-coding regions of the genome (the exome) 8 to test the hypothesis that de novo protein-altering mutations substantially contribute to the genetic basis of sporadic ASD.”
M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity (2016, methodology): “Each individual can be thought of as a patient with a Mendelian disease for whom the causative variant has been removed from the genome.”