SNP discovery performance of two second generation sequencing platforms in the NOD2 gene region

Espen Melum (1, 2) , Sandra May (1) , Markus Schilhabel (1) , Ingo Thomsen (1) , Tom H. Karlsen (2) , Philip Rosenstiel (1) , Stefan Schreiber (1, 3) , Andre Franke (1)

1 Institute of Clinical Molecular Biology
2 Medical Department
3 1st Medical Department

A potentially important application of second generation sequencing technologies is to identify disease-associated variation. For comparison of the performance in SNP detection, the Crohn's disease (CD) associated NOD2 gene was subjected to targeted resequencing using two different second generation sequencing technologies. Eleven CD patients were selected based on their haplotype background at the NOD2 locus. The 40 kb large NOD2 gene region was amplified using long-range PCR (LR-PCR), and sequenced with the Roche 454/FLX system, an Applied Biosystems SOLiD mate-pair library (2x25 bp), and a SOLiD fragment (50 bp) library. The entire NOD2 region was also sequenced using conventional Sanger technology. Four-hundred and forty-two SNPs were discovered with the SOLiD mate-pair library, 454 with the fragment library and 441 with the 454/FLX. For the homozygous SNPs, 98% were confirmed by Sanger for the mate-pair library, 100% for the fragment library and 99% for the 454/FLX. Ninety-six percent of the heterozygous SNPs detected with the SOLiD mate-pair library, 91% with the fragment library and 96% with the 454/FLX were confirmed by Sanger. In a simulation, the SNP detection performance fell rapidly when the achieved coverage was below 40x. Due to uneven representation of the target region when using LR-PCR, oversequencing of other regions is necessary.

Mots clés: Life Sciences

Espen Melum, Sandra May, Markus Schilhabel, Ingo Thomsen, Tom H. Karlsen, et al.. SNP discovery performance of two second generation sequencing platforms in the NOD2 gene region. Human Mutation, 2010, 31 (7), pp.875. ⟨10.1002/humu.21276⟩. ⟨hal-00552394⟩