Genetic diagnosis by whole exome capture and massively parallel DNA sequencing
Murim Choi,Ute I. Scholl,Weizhen Ji,Tiewen Liu,Irina Tikhonova,Paul Zumbo,Ahmet Nayir,Ayșin Bakkaloğlu,Seza Ozen,Sami A. Sanjad,Carol Nelson-Williams,Anita Farhi,Shrikant Mane,Richard P. Lifton +13 more
TLDR
A method for whole-exome sequencing coupling Roche/NimbleGen whole exome arrays to the Illumina DNA sequencing platform is reported, demonstrating the ability to capture approximately 95% of the targeted coding sequences with high sensitivity and specificity for detection of homozygous and heterozygous variants.Abstract:
Protein coding genes constitute only approximately 1% of the human genome but harbor 85% of the mutations with large effects on disease-related traits. Therefore, efficient strategies for selectively sequencing complete coding regions (i.e., “whole exome”) have the potential to contribute to the understanding of rare and common human diseases. Here we report a method for whole-exome sequencing coupling Roche/NimbleGen whole exome arrays to the Illumina DNA sequencing platform. We demonstrate the ability to capture approximately 95% of the targeted coding sequences with high sensitivity and specificity for detection of homozygous and heterozygous variants. We illustrate the utility of this approach by making an unanticipated genetic diagnosis of congenital chloride diarrhea in a patient referred with a suspected diagnosis of Bartter syndrome, a renal salt-wasting disease. The molecular diagnosis was based on the finding of a homozygous missense D652N mutation at a position in SLC26A3 (the known congenital chloride diarrhea locus) that is virtually completely conserved in orthologues and paralogues from invertebrates to humans, and clinical follow-up confirmed the diagnosis. To our knowledge, whole-exome (or genome) sequencing has not previously been used to make a genetic diagnosis. Five additional patients suspected to have Bartter syndrome but who did not have mutations in known genes for this disease had homozygous deleterious mutations in SLC26A3. These results demonstrate the clinical utility of whole-exome sequencing and have implications for disease gene discovery and clinical diagnosis.read more
Citations
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Predicting the Functional Effect of Amino Acid Substitutions and Indels
TL;DR: A new algorithm, PROVEAN (Protein Variation Effect Analyzer), is developed, which provides a generalized approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions, and in-frame insertions and deletions.
Journal ArticleDOI
Exome sequencing identifies the cause of a Mendelian disorder
Sarah B H Ng,Kati J. Buckingham,Choli Lee,Abigail W. Bigham,Holly K. Tabor,Holly K. Tabor,Karin M. Dent,Chad D. Huff,Paul Shannon,Ethylin Wang Jabs,Ethylin Wang Jabs,Deborah A. Nickerson,Jay Shendure,Michael J. Bamshad,Michael J. Bamshad +14 more
TL;DR: Exome sequencing of a small number of unrelated affected individuals is a powerful, efficient strategy for identifying the genes underlying rare mendelian disorders and will likely transform the genetic analysis of monogenic traits.
Journal ArticleDOI
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.
Michael A. Quail,Miriam Smith,Paul Coupland,Thomas D. Otto,Simon R. Harris,Thomas R. Connor,Anna Bertoni,Harold Swerdlow,Yong Gu +8 more
TL;DR: All three fast turnaround sequencers evaluated here were able to generate usable sequence, however there are key differences between the quality of that data and the applications it will support.
Journal ArticleDOI
Exome sequencing as a tool for Mendelian disease gene discovery
Michael J. Bamshad,Sarah B. Ng,Abigail W. Bigham,Abigail W. Bigham,Holly K. Tabor,Holly K. Tabor,Mary J. Emond,Deborah A. Nickerson,Jay Shendure +8 more
TL;DR: Experimental and analytical approaches relating to exome sequencing have established a rich framework for discovering the genes underlying unsolved Mendelian disorders and set the stage for applying exome and whole-genome sequencing to facilitate clinical diagnosis and personalized disease-risk profiling.
Journal ArticleDOI
Ten years of next-generation sequencing technology.
TL;DR: An overview of the evolution of NGS is provided and the most significant improvements in sequencing technologies and library preparation protocols are discussed and the current landscape of N GS applications is explored to provide a perspective for future developments.
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