KIR copy number, allele, and haplotype imputation system
Project leaders: Katsushi Tokunaga, Mary Carrington, Seik-Soon Khor (Charles)
Detailed project description:
With recent advances in next-generation sequencing (NGS) technology, KIR can now be characterized at a higher resolution, including KIR gene copy number (CN), allele, and complete KIR haplotype phasing. However, there are few SNPs in the KIR region due to difficulties in designing unique probes to tag each of the KIR genes. Thus, we developed a new methodology designated KIBAG (KIR Genotype Imputation with Attribute Bagging), which enables rapid and inexpensive determination of KIR types from a GWAS dataset by utilizing SNPs outside the KIR region to impute KIR CN, alleles, and haplotypes. To date, we have generated population-specific KIR references for 25 distinct populations around the world.
This work is part of the on-going HKimpNet (HLA & KIR Imputation Network) project, which aims to provide population-specific HLA & KIR imputation systems to the research community.
Milestones by year:
2019-2020: Registration of participants
2021: Raw data generation & HLA/KIR reference building
2022: HLA/KIR references QC & HKimpNet imputation service
Data required (number, type of data, inclusion/exclusion criteria):
- SNPs dataset (genotyping array/WES/WGS)
- HLA/KIR genotyping data (PCR-SSO, PCR-SSOP, NGS-capture, NGS-full length)