Open Access Highly Accessed Methodology article

Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

Simon M Lank1, Brittney A Golbach1, Hannah M Creager1, Roger W Wiseman1, Derin B Keskin23, Ellis L Reinherz23, Vladimir Brusic23 and David H O’Connor14*

Author Affiliations

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

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BMC Genomics 2012, 13:378  doi:10.1186/1471-2164-13-378

Published: 6 August 2012

Additional files

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.

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Additional file 2: File 1:

Galaxy workflow and custom tools/scripts used (zip archive).

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Additional file 3: File 2:

Novel sequences identified during sequencing (fasta file).

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Additional file 4: Figure 1:

Formation of abortive, short DNA products during emPCR.

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