HLA Allelic and Genotypic Ambiguity Reduction in ImmPort

1. HLA Allelic and Genotypic Ambiguity Reduction in ImmPort Paula Guidry, Ph.D. BISC Team – UT Southwestern

2. HLA Typing Platforms and Ambiguity • HLA Typing Platforms • SSOP – single-stranded oligonucleotide probe • SSP – sequence-specific priming • SBT – sequence-based typing • SSCP – single-stranded conformation polymorphism • Allelic Ambiguity • Typing methodology cannot distinguish between a set of alleles • Polymorphisms that distinguish these alleles are not interrogated by the method • Outside of exon 2 (class II) or exons 2 and 3 (class I) • Sections of these exons not covered by the probes/primers • Genotypic Ambiguity • Inability to determine phase in heterozygous samples

3. Ambiguity in HLA Typing Data

4. Ambiguity in HLA Typing Data Allelic Ambiguity Reduction Genotypic Ambiguity Reduction

5. Ambiguity Reduction Principles CWD Alleles • Common and Well-Documented (CWD) HLA Alleles • Allele has an estimated frequency of at least 0.001 in any reference population • Accurate frequency estimates require an allele to be observed 3+ times • Studies with 1500 unrelated individuals (2n = 3000 chromosomes) can only accurately detect allele frequencies ≥ 0.001 OR • Allele has been detected unambiguously in at least three unrelated individuals but gene frequencies have not been estimated accurately • Rare HLA Alleles • Alleles that are not CWD Cano et al (2007). Common and Well-Documented HLA Alleles. Human Immunology 68: 392-417.

6. Ambiguity Reduction Principles Regional CWD • Meta-Analysis to Determine Worldwide HLA Allele Frequencies • Data sources • 13th IHW Anthropology/Human Genetic Diversity component • 12th IHW Anthropology component • Literature • 8 journals • Every issue from 1990 – 2007 • 4 studies from other journals • AlleleFrequencies.net • ≥ 20 individuals per population sample • 497 population samples from around the world • Total of 66,800 individuals Solberg et al (2008). Balancing Selection and Heterogeneity Across the Classical Human Leukocyte Antigen Loci: A Meta-Analytic Review of 497 Population Studies. Human Immunology 69: 443-464.

7. Ambiguity Reduction Principles Regional CWD • Reg-CWD HLA Alleles • Allele is common and well-documented in a particular world region* OTH – significantly admixed populations * Ignoring the past 1000 years of human migration • Reg-Rare HLA Alleles • Not reg-CWD • Not detected in other world regions • Neither Reg-CWD nor Reg-Rare • Not reg-CWD • Detected in other world regions

8. HLA Allelic Ambiguity Reduction Heuristic Steve Mack, Glenys Thomson, Rich Single

9. Allelic Ambiguity Reduction Allelic Ambiguity Reduction

10. Allelic Ambiguity Reduction Phase 1 Elimination of less-probable alleles by CWD status Are any of the alleles reg-CWD? Are any of the alleles CWD? Are any of the alleles reg-Rare? no no yes yes yes Eliminate others Eliminate others Eliminate others Possible results: single allele call or multiple allele possibilities

11. Allelic Ambiguity Reduction Phase 2 Reduction of multiple alleles to G- or P-codes Do any alleles belong to a common G-code? Do any alleles or G-codes belong to a common P-code? Do the alleles contain any G- or P-codes? no yes yes yes Combine to G-code Combine to P-code Eliminate rare alleles Possible results: single G- or P- call, multiple G- or P- calls or multiple alleles not related by G- or P- code

12. Allelic Ambiguity Reduction Phase 3 Reduction of alleles in the same family by frequency Are the alleles part of the same allele family? Is the ratio of MRWAFs* for any pair of these alleles > 9.49999? Keep the allele/code with the lowest 2nd field (third and fourth digits) yes no yes no yes Are there still multiple alleles in the set? User determines most likely allele Eliminate the lower frequency alleles *MRWAF is the mean regional weighted allele frequency: mean frequency for an allele in a given region, weighted by sample sizes (2n)

13. Outcome of HLA Allelic Ambiguity Reduction

14. HLA Genotypic Ambiguity Reduction Heuristic Steve Mack, Glenys Thomson, Rich Single

15. Genotypic Ambiguity Reduction Genotypic Ambiguity Reduction

16. Genotypic Ambiguity Reduction Phase 1 Reduction of sub-genotypes by CWD status Are any sub-genotypes reg-CWD/reg-CWD? Are any sub-genotypes reg-CWD/CWD or CWD/CWD? Are any G/G, P/P, G/P, G/reg-CWD, G/CWD, P/reg-CWD, P/CWD? no no no yes yes yes Eliminate others Eliminate others Eliminate others

17. Genotypic Ambiguity Reduction Phase 1, continued Reduction of sub-genotypes by CWD status Are any reg-CWD/reg-Rare, CWD/reg-Rare, G/reg-Rare or P/reg-Rare? Are any sub-genotypes reg-Rare/reg-Rare? no yes yes Eliminate others Eliminate others

18. Genotypic Ambiguity Reduction Phase 2 Reduction of sub-genotypes by zygosity and allele numbers Are any of the sub-genotypes homozygous? Keep the sub-genotype with the lowest sum of the 2nd field (third and fourth digits) no yes Keep homozygous sub-genotypes and sub-genotypes containing these alleles

19. Outcome of HLA Allelic and Genotypic Ambiguity Reduction Allelic Ambiguity Reduction Genotypic Ambiguity Reduction

20. ImmPortHLA Ambiguity Reduction Tool www.ImmPort.org

24. Example HLA Typing Results File Ready for Ambiguity Reduction in ImmPort

28. Ambiguity Reduction Input File Allelic Ambiguity Reduction Output Genotypic Ambiguity Reduction Output

29. Acknowledgements Steven J. Mack , Ph.D.(CHORI) Glenys Thomson, Ph.D. (Berkeley) Richard Single, Ph.D. (UVM) Nishanth Marthandan Thomas Smith, Ph.D. Patrick Dunn, Ph.D. John Campbell Jeff Wiser Richard Scheuermann, Ph.D. David Karp, M.D., Ph.D.

30. www.ImmPort.org

31. Allelic Ambiguity Reduction MRWAF Analysis MRWAF is the mean regional weighted allele frequency: mean frequency for an allele in a given region, weighted by sample sizes (2n) If all alleles have MRWAF = 0 or all pairs have MRWAF ratio ≤ 9.49999, then these are passed to the next step