Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection.

Hdl Handle:
http://hdl.handle.net/10147/238815
Title:
Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection.
Authors:
Kenny, Elaine M; Cormican, Paul; Gilks, William P; Gates, Amy S; O'Dushlaine, Colm T; Pinto, Carlos; Corvin, Aiden P; Gill, Michael; Morris, Derek W
Affiliation:
Trinity Genome Sequencing Laboratory, Neuropsychiatric Genetics Research Group, Department of Psychiatry, Institute of Molecular Medicine, Trinity College Dublin, Ireland. elaine.kenny@tcd.ie
Citation:
Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection. 2011, 18 (1):31-8 DNA Res.
Journal:
DNA research : an international journal for rapid publication of reports on genes and genomes
Issue Date:
Feb-2011
URI:
http://hdl.handle.net/10147/238815
DOI:
10.1093/dnares/dsq029
PubMed ID:
21163834
Abstract:
Screening large numbers of target regions in multiple DNA samples for sequence variation is an important application of next-generation sequencing but an efficient method to enrich the samples in parallel has yet to be reported. We describe an advanced method that combines DNA samples using indexes or barcodes prior to target enrichment to facilitate this type of experiment. Sequencing libraries for multiple individual DNA samples, each incorporating a unique 6-bp index, are combined in equal quantities, enriched using a single in-solution target enrichment assay and sequenced in a single reaction. Sequence reads are parsed based on the index, allowing sequence analysis of individual samples. We show that the use of indexed samples does not impact on the efficiency of the enrichment reaction. For three- and nine-indexed HapMap DNA samples, the method was found to be highly accurate for SNP identification. Even with sequence coverage as low as 8x, 99% of sequence SNP calls were concordant with known genotypes. Within a single experiment, this method can sequence the exonic regions of hundreds of genes in tens of samples for sequence and structural variation using as little as 1 μg of input DNA per sample.
Item Type:
Article
Language:
en
MeSH:
DNA; Exons; High-Throughput Nucleotide Sequencing; Polymorphism, Single Nucleotide; RNA, Complementary
ISSN:
1756-1663

Full metadata record

DC FieldValue Language
dc.contributor.authorKenny, Elaine Men_GB
dc.contributor.authorCormican, Paulen_GB
dc.contributor.authorGilks, William Pen_GB
dc.contributor.authorGates, Amy Sen_GB
dc.contributor.authorO'Dushlaine, Colm Ten_GB
dc.contributor.authorPinto, Carlosen_GB
dc.contributor.authorCorvin, Aiden Pen_GB
dc.contributor.authorGill, Michaelen_GB
dc.contributor.authorMorris, Derek Wen_GB
dc.date.accessioned2012-08-15T14:20:04Z-
dc.date.available2012-08-15T14:20:04Z-
dc.date.issued2011-02-
dc.identifier.citationMultiplex target enrichment using DNA indexing for ultra-high throughput SNP detection. 2011, 18 (1):31-8 DNA Res.en_GB
dc.identifier.issn1756-1663-
dc.identifier.pmid21163834-
dc.identifier.doi10.1093/dnares/dsq029-
dc.identifier.urihttp://hdl.handle.net/10147/238815-
dc.description.abstractScreening large numbers of target regions in multiple DNA samples for sequence variation is an important application of next-generation sequencing but an efficient method to enrich the samples in parallel has yet to be reported. We describe an advanced method that combines DNA samples using indexes or barcodes prior to target enrichment to facilitate this type of experiment. Sequencing libraries for multiple individual DNA samples, each incorporating a unique 6-bp index, are combined in equal quantities, enriched using a single in-solution target enrichment assay and sequenced in a single reaction. Sequence reads are parsed based on the index, allowing sequence analysis of individual samples. We show that the use of indexed samples does not impact on the efficiency of the enrichment reaction. For three- and nine-indexed HapMap DNA samples, the method was found to be highly accurate for SNP identification. Even with sequence coverage as low as 8x, 99% of sequence SNP calls were concordant with known genotypes. Within a single experiment, this method can sequence the exonic regions of hundreds of genes in tens of samples for sequence and structural variation using as little as 1 μg of input DNA per sample.en_GB
dc.language.isoenen
dc.rightsArchived with thanks to DNA research : an international journal for rapid publication of reports on genes and genomesen_GB
dc.subject.meshDNA-
dc.subject.meshExons-
dc.subject.meshHigh-Throughput Nucleotide Sequencing-
dc.subject.meshPolymorphism, Single Nucleotide-
dc.subject.meshRNA, Complementary-
dc.titleMultiplex target enrichment using DNA indexing for ultra-high throughput SNP detection.en_GB
dc.typeArticleen
dc.contributor.departmentTrinity Genome Sequencing Laboratory, Neuropsychiatric Genetics Research Group, Department of Psychiatry, Institute of Molecular Medicine, Trinity College Dublin, Ireland. elaine.kenny@tcd.ieen_GB
dc.identifier.journalDNA research : an international journal for rapid publication of reports on genes and genomesen_GB
dc.description.provinceLeinsteren

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