title: Exome sequencing from nanogram amounts of starting DNA: comparing three approaches.
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.
authors.affiliation: Max-Planck Institute for Molecular Genetics, Berlin, Germany; AlacrisTheranostics GmbH, Berlin, Germany; Freie Universität Berlin, Berlin, Germany.
authors.forename: Vera N
authors.initials: VN
authors.lastname: Rykalina
authors.affiliation: Max-Planck Institute for Molecular Genetics, Berlin, Germany; Freie Universität Berlin, Berlin, Germany.
authors.forename: Alexey A
authors.initials: AA
authors.lastname: Shadrin
authors.affiliation: Max-Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Vyacheslav S
authors.initials: VS
authors.lastname: Amstislavskiy
authors.affiliation: Vavilov Institute of General Genetics, Moscow, Russia.
authors.forename: Evgeny I
authors.initials: EI
authors.lastname: Rogaev
authors.affiliation: Max-Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.affiliation: Max-Planck Institute for Molecular Genetics, Berlin, Germany; AlacrisTheranostics GmbH, Berlin, Germany.
authors.forename: Tatiana A
authors.initials: TA
authors.lastname: Borodina
mesh_terms: D004247:DNA / Q000097:blood / Q000235:genetics*; D059472:Exome; D015723:Gene Library; D023281:Genomics / Q000379:methods; D060005:Genotyping Techniques / Q000379:methods; D006801:Humans; D018401:Sample Size; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA