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  Exome sequencing from nanogram amounts of starting DNA: comparing three approaches

Rykalina, V., Shadrin, A., Amstislavskiy, V., Rogaev, E. I., Lehrach, H., & Borodina, T. A. (2014). Exome sequencing from nanogram amounts of starting DNA: comparing three approaches. PLoS One, 9(7): e101154. doi:10.1371/journal.pone.0101154.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0026-AA94-E Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0026-AA95-C
Genre: Journal Article

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 Creators:
Rykalina, Vera1, Author              
Shadrin, Alexey1, Author              
Amstislavskiy, Vyacheslav2, Author              
Rogaev, Evgeny I. , Author
Lehrach, Hans3, Author              
Borodina, Tatiana A.1, Author              
Affiliations:
1Technology Development(Alexey Soldatov), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479657              
2Human Chromosome 21 (Marie-Laure Yaspo), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479652              
3Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              

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 Abstract: Hybridization-based target enrichment protocols require relatively large starting amounts of genomic DNA, which is not always available. Here, we tested three approaches to pre-capture library preparation starting from 10 ng of genomic DNA: (i and ii) whole-genome amplification of DNA samples with REPLI-g (Qiagen) and GenomePlex (Sigma) kits followed by standard library preparation, and (iii) library construction with a low input oriented ThruPLEX kit (Rubicon Genomics). Exome capture with Agilent SureSelectXT2 Human AllExon v4+UTRs capture probes, and HiSeq2000 sequencing were performed for test libraries along with the control library prepared from 1 µg of starting DNA. Tested protocols were characterized in terms of mapping efficiency, enrichment ratio, coverage of the target region, and reliability of SNP genotyping. REPLI-g- and ThruPLEX-FD-based protocols seem to be adequate solutions for exome sequencing of low input samples.

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Language(s): eng - English
 Dates: 2014-07-03
 Publication Status: Published online
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 Rev. Method: Peer
 Identifiers: DOI: 10.1371/journal.pone.0101154
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Title: PLoS One
Source Genre: Journal
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Publ. Info: San Francisco, CA : Public Library of Science
Pages: - Volume / Issue: 9 (7) Sequence Number: e101154 Start / End Page: - Identifier: ISSN: 1932-6203
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000277850