Genotyping HLA and KIR from NGS data

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Presentation transcript:

Genotyping HLA and KIR from NGS data NGS Data Consortium Meeting: ASHI 2012

Main considerations per read Quality Specificity Novel Mutation Depth (post-filter)

FASTQ sequence read format Quality FASTQ sequence read format Minimum Quality Requirement? Per base ? per read ? Vs read depth ?

Specificity Filtering Strategy (e.g. HLA-A)

Filtering Strategy (e.g. HLA-A) Specificity Filtering Strategy (e.g. HLA-A)

Pipeline aligns and correctly identifies new alleles Specificity Pipeline aligns and correctly identifies new alleles

Depth HLA: Alignment Reference Sequence Crucial

Read depth required for calling zygosity ? WGS ~ 20x (with 99% accuracy) Diagnostic HLA =? Allele drop out ? (PCR & capture methods)

KIR gene-content by read depth (WGS data))

Denisovan had a KIR2DL4/3DS1-duplication haplotype

2DS4 in/del genotype based on read-depth

KIR: 21 New Alleles Discovered from 8 individuals

HLA haplotypes from 8 KhoeSan

Summary SOS ver. II

Acknowledgements Meeting Organizers Life Technologies Peter Parham DNA Samples And Whole-Exome Data Brenna Henn Jeffrey Kidd Jeff Wall Carlos Bustamente Arnav Moudgil Neda Nemat-Gorgani Laurent Abi-Rached Meeting Organizers Life Technologies