Solution-based targeted genomic enrichment for precious DNA samples

Aiden Eliot Shearer; Michael S Hildebrand; Richard JH Smith

doi:10.1186/1472-6750-12-20

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Solution-based targeted genomic enrichment for precious DNA samples

Journal article

Open access

Peer reviewed

Solution-based targeted genomic enrichment for precious DNA samples

Aiden Eliot Shearer, Michael S Hildebrand and Richard JH Smith

BMC biotechnology, Vol.12(1), pp.20-20

05/04/2012

DOI: 10.1186/1472-6750-12-20

PMCID: PMC3561655

PMID: 22559009

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https://doi.org/10.1186/1472-6750-12-20View

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Abstract

Background: 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. Results: 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. Conclusions: 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.

Targeted genomic enrichment

Massively parallel sequencing

Methodology

Sequence capture

Illumina

Details

Title: Subtitle: Solution-based targeted genomic enrichment for precious DNA samples
Creators: Aiden Eliot Shearer - Department of Otolaryngology—Head & Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
Michael S Hildebrand - Department of Otolaryngology—Head & Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
Richard JH Smith - Department of Otolaryngology—Head & Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
Resource Type: Journal article
Publication Details: BMC biotechnology, Vol.12(1), pp.20-20
DOI: 10.1186/1472-6750-12-20
PMID: 22559009
PMCID: PMC3561655
NLM abbreviation: BMC Biotechnol
ISSN: 1472-6750
eISSN: 1472-6750
Publisher: BioMed Central
Language: English
Date published: 05/04/2012
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Molecular Physiology and Biophysics; Anatomy and Cell Biology; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Otolaryngology; Internal Medicine
Record Identifier: 9984007298302771

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