Cargando…
Solution-based targeted genomic enrichment for precious DNA samples
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 excessi...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561655/ https://www.ncbi.nlm.nih.gov/pubmed/22559009 http://dx.doi.org/10.1186/1472-6750-12-20 |
_version_ | 1782257996469895168 |
---|---|
author | Shearer, Aiden Eliot Hildebrand, Michael S Smith, Richard JH |
author_facet | Shearer, Aiden Eliot Hildebrand, Michael S Smith, Richard JH |
author_sort | Shearer, Aiden Eliot |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3561655 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35616552013-02-05 Solution-based targeted genomic enrichment for precious DNA samples Shearer, Aiden Eliot Hildebrand, Michael S Smith, Richard JH BMC Biotechnol Methodology Article 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. BioMed Central 2012-05-04 /pmc/articles/PMC3561655/ /pubmed/22559009 http://dx.doi.org/10.1186/1472-6750-12-20 Text en Copyright ©2012 Shearer et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Shearer, Aiden Eliot Hildebrand, Michael S Smith, Richard JH Solution-based targeted genomic enrichment for precious DNA samples |
title | Solution-based targeted genomic enrichment for precious DNA samples |
title_full | Solution-based targeted genomic enrichment for precious DNA samples |
title_fullStr | Solution-based targeted genomic enrichment for precious DNA samples |
title_full_unstemmed | Solution-based targeted genomic enrichment for precious DNA samples |
title_short | Solution-based targeted genomic enrichment for precious DNA samples |
title_sort | solution-based targeted genomic enrichment for precious dna samples |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561655/ https://www.ncbi.nlm.nih.gov/pubmed/22559009 http://dx.doi.org/10.1186/1472-6750-12-20 |
work_keys_str_mv | AT sheareraideneliot solutionbasedtargetedgenomicenrichmentforpreciousdnasamples AT hildebrandmichaels solutionbasedtargetedgenomicenrichmentforpreciousdnasamples AT smithrichardjh solutionbasedtargetedgenomicenrichmentforpreciousdnasamples |