Royal Liverpool University Hospital & University of Liverpool ALLELE FREQUENCIES.NET DATABASE (AFND) TO SUPPORT H&I Derek Middleton Royal Liverpool University Hospital & University of Liverpool

DATABASE POPULATIONS 1/5/2016 Polymorphic Region Population Studies Gene/Allele Data Haplotype Data Genotype Data HLA 1050 1035 426 - KIR 238 237 154 Cytokine 121 MIC 62 21 Totals 1,471 1,455 447

1 2

1 2

IMGT/HLA alleles 7,527 alleles Release 3.8.0 - April 2012

RARE ALLELE SEARCH

INFORMATION PROVIDED BY INDIVIDUAL LAB ON RARE ALLELE

HISTOGRAMS OF FINDING OF HLA ALLELES

Rare HLA alleles detector (RHAD)

Study of Rare & Novel HLA Alleles by NGS HLA . Study of Rare & Novel HLA Alleles by NGS HLA Non-CWD based on Mack et al to confirm and further characterize these alleles in multiple populations and when possible determine their haplotype association. The subjects and families should be previously HLA typed at any level (serology, DNA). Investigators may submit Samples NGS data Family members

KIR GENE, ALLELE FREQUENCIES

KIR GENOTYPES

GENOTYPES FOUND IN ONLY ONE POPULATION (n=166) Number of Pops Number of Genotypes 1 12 2 11 9 7 3 6 5 4 20 150 genotypes found in only 1 individual 1 genotype in 4 individuals 12 genotypes in 2 individuals 1 genotype in 5 individuals 2 genotype in 3 individuals

KDDB query page www.allelefrequencies.net/diseases

KDDB query page www.allelefrequencies.net/diseases

CRITERIA FOR DEFINING GOLD,SILVER,BRONZE DATASETS Gold standard Silver standard Bronze standard Allele frequency Allele frequencies sum to 1 (± 0.015)  Allele frequencies sum to 1 (± 0.015) Any that do not match to gold and silver criteria Allele name resolution All allele names are at least two fields long. Allele name lengths are mixed between one field and two or more fields long.   Sample size ≥50 individuals Any

Number of alleles, datasets and individuals (by 10x4) by loci in Gold standard datasets .

STANDARDISED Reporting of Genotyping Results The HLA community focuses on allele names, often to the exclusion of the primary data. No/little information is available about intron/exons interrogated, primer sequences, or informatics. Reference database versioning is poorly documented. An HLA genotype that represented a unique diploid sequence under one database release might represent multiple diploid sequences in later releases, as new polymorphism is identified in other regions of the gene. The result is that genotyping results are static, and cannot easily be re-evaluated in the context of reference database updates. The equivalence of genotyping results generated using different references or different platforms cannot easily be determined. We’re left throwing out a lot of data

HUMAN IMMUNOLOGY/AFND Short Population Reports: HLA; KIR; MIC; Cytokine Demographic information Typing methods/Kits; alleles able to be detected Raw/individual ambiguous genotype data Data after ambiguity resolution (and how) Analysis H-W; allele frequencies; estimation of haplotype frequencies

CHECKING OF DATA Data automatically checked for errors: correct nomenclature reported ambiguities resolved frequencies reported complete and consistent with data Tool will immediately highlight to the User any problems Once validated, one click to send data to AFND

www.allelefrequencies.net Look at donor registries - practical

www.allelefrequencies.net

HLA−A and −B Epitope Frequencies in World Populations Epitope Frequencies were obtained from raw genotyping data

Human Immunology, 2016, 77, Issue 3 Special Issue: Histocompatibility and Immunogenetics Data Resources Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data 238-48 ACKNOWLEDGEMENTS Eduardo dos Santos, Tony McCabe, Andy Jones, James Jones Faviel F. Gonzalez-Galarza Steve Mack, Alicia Sanchez-Mazas