Papers › Family based HLA imputation and optimization of haplo-identical transplants
Family based HLA imputation and optimization of haplo-identical transplants
Zuriya Ansbacher-Feldman, Sapir Israeli, Martin Maiers, Loren Gragert, Dianne De Santis, Moshe Israeli, yoram louzoun
Recently, haplo-identical transplantation with multiple HLA mismatches has become a viable option for system cell transplants. Haplotype sharing detection requires imputation of donor and recipient. We show that even in high-resolution typing when all alleles are known, there is a 15% error rate in haplotype phasing, and even more in low resolution typings. Similarly, in related donors, parents haplotypes should be imputed to determine what haplotype each child inherited. We propose GRAMM (GRaph bAsed FaMilly iMputation) to phase alleles in family pedigree HLA typing data, and in mother-cord blood unit pairs. We show that GRAMM has practically no phasing errors when pedigree data are available. We apply GRAMM to simulations with different typing resolutions as well as paired cord-mother typings, and show very high phasing accuracy, and improved alleles imputation accuracy. We use GRAMM to detect recombination events and show that the rate of falsely detected recombination events (False Positive Rate) in simulations is very low. We then apply recombination detection to typed families to estimate the recombination rate in Israeli and Australian population datasets. The estimated recombination rate has an upper bound of 10-20% per family (1-4% per individual). GRAMM is available at: https://gramm.math.biu.ac.il/.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Tasks
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections