Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing
1 Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
2 Cancer Vaccine Center, DanaFarber Cancer Institute, Boston, MA, USA
3 Department of Medicine, Harvard Medical School, Boston, MA, USA
4 Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
BMC Genomics 2012, 13:378 doi:10.1186/1471-2164-13-378Published: 6 August 2012
Additional file 1: Table S1:
In silico model of typing resolution for standard SBT genotyping assays which assess exons 2,3, exons 2,3,4 (class I) or exon 2 (DRB). Table S2 - Primer sequences used for additional HLA class II loci typing. Table S3 - Primers used. Table S4 - Read numbers recovered per sample and amplicon in both genotyping experiments. Table S5 - Read numbers recovered per sample and amplicon in preliminary class II additional loci experiment. Table S6 - Class I genotyping results from the second experiment. Table S7 - DRB genotyping results from the second experiment. Table S8 - Additional class II amplicon genotyping results. Table S9 - Primers used for Sanger sequencing of novel KTS02 HLA-C allele. Table S10 - Cost estimate for cSBT at a variety of multiplexing levels.
Format: XLS Size: 282KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 2: File 1:
Galaxy workflow and custom tools/scripts used (zip archive).
Format: ZIP Size: 83KB Download file
Additional file 3: File 2:
Novel sequences identified during sequencing (fasta file).
Format: FASTA Size: 3KB Download file