• Streptococcus pneumoniae
• Genotyping and SNP detection of Streptococcus pneumoniae
• S. pneumoniae Sequence Download Tool
• Francisella tularensis
• Genotyping and SNP detection of Francisella tularensis
• F. tularensis Comparative Analysis Tool
• Haemophilus influenzae
• Genome Sequencing and Species Microarray for H. influenzae
• High Throughput Genotyping using Human DNA Isolated from Stored Serum Specimens
• Bioinformatic SNP Filter Scripts
• Poster Presentations

Identification of Novel Susceptibility Loci to Human Pathogens Using the Affymetrix® Human SNP 6.0 Array

Project Abstract

This clinical genomics project was done in collaboration with Dr. John Belmont of Baylor College of Medicine. The objective of this project was to develop expertise and resources for the scientific community to understand variability of host-pathogen interactions due to host genetic polymorphisms for infectious agents using the Affymetrix® genome-wide human SNP 6.0 array platform. The SNP 6.0 array features more than 1.8 million markers of genetic variation chosen from the public and Perlegen SNP databases, including more than 906,000 SNPs and more than 946,000 probes for the detection of copy number variation. These SNPs are present on 200 to 1100 bp Nsp I or Sty I digested fragments in the human genome, and are amplified using the Affymetrix® genome-wide human SNP Nsp/Sty assay kit. The amplified products from each restriction enzyme digest are combined, purified, fragmented, labeled and hybridized to the SNP 6.0 array. The genotype calls (CHP files) are generated using the Affymetrix® Genotyping Console™ software from the scanned arrays (CEL) files.

We assessed the utility of whole-genome amplified (WGA) serum DNA for array based high-throughput genotyping using the human DNA isolated from serum samples from an influenza surveillance study. WGA DNA samples from 45 archived serum replicates and 5 fresh sera paired with non-amplified genomic DNA were genotyped on SNP6.0. The raw data (.CEL) files of this project are available.

This study is the first to demonstrate the performance of WGA DNA from 20-year old archived serum samples using the SNP 6.0 platform. A manuscript entitled, “Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping” has been submitted to BMC Genetics for publication.

A list of the samples examined in this study is available below. Additionally, the raw data, in the form of Affymetrix® CEL files, is available for download below. This download is in the form of a compressed archive containing the individual CEL files and the sample list. Please note that this archive file is quite large.

Data and Resources