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Genotyping HLA and KIR from NGS data

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Presentation on theme: "Genotyping HLA and KIR from NGS data"— Presentation transcript:

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

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

3

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

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

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

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

8 Depth HLA: Alignment Reference Sequence Crucial

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

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

11 Denisovan had a KIR2DL4/3DS1-duplication haplotype

12 2DS4 in/del genotype based on read-depth

13 KIR: 21 New Alleles Discovered from 8 individuals

14 HLA haplotypes from 8 KhoeSan

15 Summary SOS ver. II

16 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

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