Solution-based targeted genomic enrichment for precious DNA samples.

BMC Biotechnology
A Eliot ShearerRichard J H Smith

Abstract

Solution-based targeted genomic enrichment (TGE) protocols permit selective sequencing of genomic regions of interest on a massively parallel scale. These protocols could be improved by: 1) modifying or eliminating time consuming steps; 2) increasing yield to reduce input DNA and excessive PCR cycling; and 3) enhancing reproducible. We developed a solution-based TGE method for downstream Illumina sequencing in a non-automated workflow, adding standard Illumina barcode indexes during the post-hybridization amplification to allow for sample pooling prior to sequencing. The method utilizes Agilent SureSelect baits, primers and hybridization reagents for the capture, off-the-shelf reagents for the library preparation steps, and adaptor oligonucleotides for Illumina paired-end sequencing purchased directly from an oligonucleotide manufacturing company. This solution-based TGE method for Illumina sequencing is optimized for small- or medium-sized laboratories and addresses the weaknesses of standard protocols by reducing the amount of input DNA required, increasing capture yield, optimizing efficiency, and improving reproducibility.

References

Oct 16, 2007·Nature Methods·Thomas J AlbertRichard A Gibbs
Jan 30, 2010·Nature Methods·Lira MamanovaDaniel J Turner
Jul 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Tom WalshMary-Claire King
Sep 18, 2010·Human Molecular Genetics·Sarah B NgJay Shendure
Oct 19, 2010·Nature Methods·Isaäc J NijmanEdwin Cuppen
Nov 17, 2010·Proceedings of the National Academy of Sciences of the United States of America·A Eliot ShearerRichard J H Smith
Sep 29, 2011·Nature Reviews. Genetics·Michael J BamshadJay Shendure
Sep 29, 2011·Nature Biotechnology·Michael J ClarkMichael Snyder

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Citations

May 29, 2012·Asian Journal of Andrology·Brian J Morris, Jake H Waskett
Jun 28, 2013·Journal of Medical Genetics·A Eliot ShearerRichard J H Smith
Apr 9, 2014·BMC Genomics·Jeffrey M KiddBrenna M Henn
Jun 29, 2015·Nucleic Acids Research·Dhawal JainPeter B Becker
Mar 20, 2015·The Annals of Otology, Rhinology, and Laryngology·Naoko SakumaShin-Ichi Usami
Mar 20, 2015·The Annals of Otology, Rhinology, and Laryngology·Hideaki MotekiShin-Ichi Usami
Mar 21, 2015·The Annals of Otology, Rhinology, and Laryngology·Kentaro MoriShin-Ichi Usami
Mar 21, 2015·The Annals of Otology, Rhinology, and Laryngology·Hideaki MotekiShin-Ichi Usami
Mar 7, 2015·The Annals of Otology, Rhinology, and Laryngology·Hideaki MotekiShin-Ichi Usami
Sep 14, 2013·Journal of the American Society of Nephrology : JASN·Fengxiao BuRichard J H Smith

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Methods Mentioned

BETA
exome sequencing
PCR
Illumina sequencing
sample pooling

Software Mentioned

MORL
SOLiD
SureSelect
Covaris

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