A low-cost exon capture method suitable for large-scale screening of genetic deafness by the massively-parallel sequencing approach

Genetic Testing and Molecular Biomarkers
Wenxue TangXi Lin

Abstract

Current major barriers for using next-generation sequencing (NGS) technologies in genetic mutation screening on an epidemiological scale appear to be the high accuracy demanded by clinical applications and high per-sample cost. How to achieve high efficiency in enriching targeted disease genes while keeping a low cost/sample is a key technical hurdle to overcome. We validated a cDNA-probe-based approach for capturing exons of a group of genes known to cause deafness. Polymerase chain reaction amplicons were made from cDNA clones of the targeted genes and used as bait probes in hybridization for capturing human genomic DNA (gDNA) fragments. The cDNA library containing the clones of targeted genes provided a readily available, low-cost, and regenerable source for producing capture probes with standard molecular biology equipment. Captured gDNA fragments by our method were sequenced by the Illumina NGS platform. Results demonstrated that targeted exons captured by our approach achieved specificity, multiplexicity, uniformity, and depth of coverage suitable for accurate sequencing applications by the NGS systems. Reliable genotype calls for various homozygous and heterozygous mutations were achieved. The results were confirmed inde...Continue Reading

References

Oct 9, 2012·Current Opinion in Pediatrics·A Eliot Shearer, Richard J H Smith
Jun 28, 2013·Journal of Medical Genetics·A Eliot ShearerRichard J H Smith
May 31, 2014·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Barbara VonaThomas Haaf
Aug 16, 2015·Otolaryngologic Clinics of North America·Kay W Chang
Sep 15, 2012·Hearing Research·Robert W EppsteinerRichard J H Smith
Dec 19, 2015·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Trevor J PughMatthew S Lebo
Dec 5, 2012·American Journal of Medical Genetics. Part a·Isabelle SchrauwenMatthew J Huentelman
Oct 15, 2013·Molecular Ecology·Ke BiCraig Moritz
Sep 25, 2015·BMC Medical Genetics·Maria Carolina Costa Melo SvidnickiEdi Lúcia Sartorato
Jun 9, 2017·Expert Review of Molecular Diagnostics·Manou SommenGuy Van Camp
Mar 20, 2015·The Annals of Otology, Rhinology, and Laryngology·Shin-Ya Nishio, Shin-Ichi Usami
Jun 19, 2015·Otolaryngology--head and Neck Surgery : Official Journal of American Academy of Otolaryngology-Head and Neck Surgery·A Eliot Shearer, Richard J H Smith
Jan 1, 2014·Personalized Medicine·Mark E SamuelsGuy Van Vliet
Oct 22, 2015·Current Opinion in Otolaryngology & Head and Neck Surgery·Kayla M JasperBrian K Reilly
Nov 13, 2020·Clinical and Experimental Otorhinolaryngology·Doo-Yi Oh, Byung Yoon Choi

Citations

Oct 18, 2002·Human Genetics·Xue Zhong LiuLi Rong Xu
Aug 19, 2003·Ear and Hearing·Eugene H ChangRichard J H Smith
Feb 27, 2004·Journal of Medical Genetics·K CrynsGuy Van Camp
Mar 9, 2005·Lancet·Richard J H SmithKarl R White
May 19, 2006·The New England Journal of Medicine·Cynthia C Morton, Walter E Nance
Oct 16, 2007·Nature Methods·Thomas J AlbertRichard A Gibbs
Oct 16, 2007·Nature Methods·Gregory J PorrecaJay Shendure
Oct 16, 2007·Nature Methods·David T OkouMichael E Zwick
Jan 30, 2008·Bioinformatics·Ruiqiang LiJun Wang
Sep 17, 2008·Nature Methods·David W CraigMatthew J Huentelman
Oct 11, 2008·Nature Biotechnology·Jay Shendure, Hanlee Ji
Apr 17, 2009·Bioinformatics·Hua BaoSuhua Shi
Nov 17, 2010·Proceedings of the National Academy of Sciences of the United States of America·A Eliot ShearerRichard J H Smith

Related Concepts

Exons
Nucleic Acid Hybridization Procedure
Genetic Screening Method
Polymerase Chain Reaction Analysis
Sequencing
Massively-Parallel Sequencing
Genomic DNA
Sequence Determinations, DNA
Hearing Screening
High-Throughput Nucleotide Sequencing

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