Genotyping HLA and KIR from NGS data
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Genotyping HLA and KIR from NGS data
NGS Data Consortium Meeting: ASHI 2012
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Main considerations per read
• Quality• Specificity
• Novel Mutation• Depth (post-filter)
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FASTQ sequence read format
Minimum Quality Requirement?• Per base ? per read ?• Vs read depth ?
Quality
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Specificity Filtering Strategy (e.g. HLA-A)
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Specificity Filtering Strategy (e.g. HLA-A)
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Pipeline aligns and correctly identifies new allelesSpecificity
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HLA: Alignment Reference Sequence CrucialDepth
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Read depth required for calling zygosity ?
• WGS ~ 20x (with 99% accuracy)• Diagnostic HLA =?• Allele drop out ? (PCR & capture methods)
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KIR gene-content by read depth
(WGS data))
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Denisovan had a KIR2DL4/3DS1-duplication haplotype
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2DS4 in/del genotype based on read-depth
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KIR: 21 New Alleles Discovered from 8 individuals
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HLA haplotypes from 8 KhoeSan
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SOS ver. II
Summary
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Peter Parham
Acknowledgements
DNA SamplesAnd Whole-Exome Data
Brenna HennJeffrey KiddJeff WallCarlos Bustamente
Neda Nemat-Gorgani
• Arnav Moudgil
Laurent Abi-Rached
• Meeting Organizers• Life Technologies