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Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection

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...

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Autores principales: 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.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041504/
https://www.ncbi.nlm.nih.gov/pubmed/21163834
http://dx.doi.org/10.1093/dnares/dsq029
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author 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.
author_facet 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.
author_sort Kenny, Elaine M.
collection PubMed
description 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.
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spelling pubmed-30415042011-02-24 Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection 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. DNA Res Full Papers 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. Oxford University Press 2011-02 2010-12-16 /pmc/articles/PMC3041504/ /pubmed/21163834 http://dx.doi.org/10.1093/dnares/dsq029 Text en © The Author 2010. Published by Oxford University Press on behalf of Kazusa DNA Research Institute http://creativecommons.org/licenses/by-nc/2.5/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Full Papers
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.
Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection
title Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection
title_full Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection
title_fullStr Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection
title_full_unstemmed Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection
title_short Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection
title_sort multiplex target enrichment using dna indexing for ultra-high throughput snp detection
topic Full Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041504/
https://www.ncbi.nlm.nih.gov/pubmed/21163834
http://dx.doi.org/10.1093/dnares/dsq029
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