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Nucleic Acids Research Advance Access published online on July 8, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn345
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

SNP-specific extraction of haplotype-resolved targeted genomic regions

Johannes Dapprich1,*, Deborah Ferriola1, Eleni E. Magira2,3, Mark Kunkel1 and Dimitri Monos2,3

1Generation Biotech, Lawrenceville, NJ 08648, 2Department of Pediatrics, University of Pennsylvania, School of Medicine and 3Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA

*To whom correspondence should be addressed. Tel: +1 609 637 0878; Fax: +1 609 637 9483; Email: jdapprich{at}generationbiotech.com Correspondence may also be addressed to Dimitri Monos. Tel: +1 215 590 1449; Fax: +1 215 590 2930; Email: monosd{at}email.chop.edu The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Received February 8, 2008. Revised May 13, 2008. Accepted May 13, 2008.

The availability of genotyping platforms for comprehensive genetic analysis of complex traits has resulted in a plethora of studies reporting the association of specific single-nucleotide polymorphisms (SNPs) with common diseases or drug responses. However, detailed genetic analysis of these associated regions that would correlate particular polymorphisms to phenotypes has lagged. This is primarily due to the lack of technologies that provide additional sequence information about genomic regions surrounding specific SNPs, preferably in haploid form. Enrichment methods for resequencing should have the specificity to provide DNA linked to SNPs of interest with sufficient quality to be used in a cost-effective and high-throughput manner. We describe a simple, automated method of targeting specific sequences of genomic DNA that can directly be used in downstream applications. The method isolates haploid chromosomal regions flanking targeted SNPs by hybridizing and enzymatically elongating oligonucleotides with biotinylated nucleotides based on their selective binding to unique sequence elements that differentiate one allele from any other differing sequence. The targeted genomic region is captured by streptavidin-coated magnetic particles and analyzed by standard genotyping, sequencing or microarray analysis. We applied this technology to determine contiguous molecular haplotypes across a ~150 kb genomic region of the major histocompatibility complex.


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