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Genotyping HLA and KIR from NGS data

Genotyping HLA and KIR from NGS data. NGS Data Consortium Meeting: ASHI 2012. Main considerations per read. Quality Specificity Novel Mutation Depth (post-filter). Quality. FASTQ sequence read format. Minimum Quality Requirement? Per base ? per read ? Vs read depth ?. Specificity.

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Genotyping HLA and KIR from NGS data

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

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

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

  6. Specificity Pipeline aligns and correctly identifies new alleles

  7. Depth HLA: Alignment Reference Sequence Crucial

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

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

  10. Denisovan had a KIR2DL4/3DS1-duplication haplotype

  11. 2DS4 in/del genotype based on read-depth

  12. KIR: 21 New Alleles Discovered from 8 individuals

  13. HLA haplotypes from 8 KhoeSan

  14. Summary SOS ver. II

  15. Acknowledgements Peter Parham DNA Samples And Whole-Exome Data Brenna Henn Jeffrey Kidd Jeff Wall Carlos Bustamente • ArnavMoudgil NedaNemat-Gorgani Laurent Abi-Rached • Meeting Organizers • Life Technologies

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