Exome sequencing as a tool for Mendelian disease gene discovery

By Michael Bamshad, Sarah B. H. Ng, Abigail W. Bigham, H. Tabor, M. Emond, Deborah A. Nickerson, Jay Shendure. 2011

1,755 citations recorded by the source corpus.

Subfields: Genetics, Pathology and Forensic Medicine, Computational Biology & Bioinformatics

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Citations in the corpus

Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2 (2013, background): “Uses in recent research include identifying rare alleles that cause Mendelian disease (Bamshad et al., 2011), scanning for potentially medically actionable alleles in an individual’s genome (Ashley et al., 2010), and proﬁling the spectrum of rare variation uncovered by deep sequencing of large…”
Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions (2016, neutral): “Exome capture approaches require a large initial investment in capture probe design (Bamshad et al. 2011; Schlötterer et al. 2014; Jones and Good 2016).”
A practical guide to environmental association analysis in landscape genomics (2015, methodology): “To identify such genes, two types of approaches are currently used (Barrett & Hoekstra 2011).”
A SPECTRAL APPROACH INTEGRATING FUNCTIONAL GENOMIC ANNOTATIONS FOR CODING AND NONCODING VARIANTS (2016, background): “Therefore, despite their potential to be useful for identifying functional variants, most of these annotations tend to be used in a subjective manner [13, 14, 15].”
The Next-Generation Sequencing Revolution and Its Impact on Genomics (2013, positive): “Although this limits the types of mutations that can be discovered, rare coding variants that are predicted to have significant functional consequences can be discovered (Bamshad et al., 2011).”
Phosphoinositide 3-kinase δ gene mutation predisposes to respiratory infection and airway damage (2013, positive): “Recent improvements in DNA sequencing technology provide an opportunity to study the patient’s whole genome or its coding part, known as the exome (4).”
Toward better understanding of artifacts in variant calling from high-coverage samples (2014, background): “…been widely used for personal and cancer genomics (Watson et al., 2013), for the discovery of de novo mutations associated with Mendelian diseases (Bamshad et al., 2011), for the reconstruction of human population history (Li and Durbin, 2011) and for the understanding of mutation processes…”
Three-dimensional reconstruction of protein networks provides insight into human genetic disease (2012, background): “Moreover, with the development of exome sequencing, many mutations are being discovered in every study 44 .”
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs (2020, methodology): “Whole-exome sequencing (WES) and whole-genome sequencing (WGS) have been increasingly used in human disease studies in the research and clinical setting [1 – 3].”