Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data

Santos, E.; McCabe, Antony; Gonzalez-Galarza, Faviel F.; Jones, Andrew R.; Middleton, Derek

doi:10.1016/j.humimm.2015.11.013

Cited by 108 publications

(41 citation statements)

References 18 publications

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“…Population allele frequencies and location coordinates were downloaded from allelefrequencies.net [70]. Only anthropologically well-characterized populations of >50 individuals were included.…”

Section: Methodsmentioning

confidence: 99%

Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles

et al. 2017

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HLA class I glycoproteins contain the functional sites that bind peptide antigens and engage lymphocyte receptors. Recently, clinical application of sequence-based HLA typing has uncovered an unprecedented number of novel HLA class I alleles. Here we define the nature and extent of the variation in 3,489 HLA-A, 4,356 HLA-B and 3,111 HLA-C alleles. This analysis required development of suites of methods, having general applicability, for comparing and analyzing large numbers of homologous sequences. At least three amino-acid substitutions are present at every position in the polymorphic α1 and α2 domains of HLA-A, -B and -C. A minority of positions have an incidence >1% for the ‘second’ most frequent nucleotide, comprising 70 positions in HLA-A, 85 in HLA-B and 54 in HLA-C. The majority of these positions have three or four alternative nucleotides. These positions were subject to positive selection and correspond to binding sites for peptides and receptors. Most alleles of HLA class I (>80%) are very rare, often identified in one person or family, and they differ by point mutation from older, more common alleles. These alleles with single nucleotide polymorphisms reflect the germ-line mutation rate. Their frequency predicts the human population harbors 8–9 million HLA class I variants. The common alleles of human populations comprise 42 core alleles, which represent all selected polymorphism, and recombinants that have assorted this polymorphism.

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Section: Methodsmentioning

confidence: 99%

Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles

et al. 2017

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“…Significant differences in the HLA‐A alleles between the two regions were seen in A*01:01:01G ( P < 0.0001) and A*11:01:01G ( P = 0.0001). These alleles are also frequently seen in other Arab populations like Sudanese, Tunisian and Moroccans . The most common HLA‐B allele in the Eastern region were B*52:01:01G (8.79%), B*18:01:01G (8.07%) B*51:01:01G (5.88%) and B*58:01:01G (5.28%), while the most common HLA‐B allele within the Central region were B*50:01:01 (15.82%), B*51 :01:01 (13.61%), B*08:01:01 (8.54%) and B*53:01:01 (6.33%) .…”

Section: Hla‐a Hla‐b Hla‐c Hla‐drb1 and Hla‐dqb1 Allele Group Freqmentioning

confidence: 99%

“…The differences between the two regions were significant in the following HLA‐B alleles, B*52:01:01G ( P < 0.0001), B*18:01:01G ( P = 0.0001) and B*51:01:01G ( P < 0.0001). B*51 is a very frequently seen allele in Arabs such as Saudis, Emiratis and Omanis . However, B*52 and B*18 are more frequently seen in Chinese, Malaysians, and Japanese .…”

Section: Hla‐a Hla‐b Hla‐c Hla‐drb1 and Hla‐dqb1 Allele Group Freqmentioning

confidence: 99%

“…Significant difference between the two region were seen in C*04:01:01G ( P = 0.0001), C*12:03:01G ( P < 0.0001), C*06:02:01G ( P < 0.0001) and C*12:02:01G ( P < 0.0001). C*04:01:01 is mostly seen in Indians and Moroccans . However, C*12:03:01G is more frequently seen in Chinese and Indians .…”

Section: Hla‐a Hla‐b Hla‐c Hla‐drb1 and Hla‐dqb1 Allele Group Freqmentioning

confidence: 99%

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HLA‐A, B, C, DRB1 and DQB1 allele and haplotype frequencies in volunteer bone marrow donors from Eastern Region of Saudi Arabia

Jawdat

Alzahrani

Alaskar

et al. 2019

HLA

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We analyzed HLA allele and haplotype frequencies from donors from the Eastern region of Saudi Arabia. A cross‐sectional study was performed on 2405 bone marrow donors from the Eastern region. HLA typing was carried out by sequencing. The most common HLA allele groups were HLA‐A*02:01:01G (11.08%), A*01:01:01G (10.40%), HLA‐B*52:01:01G (8.79%), B*18:01:01G (8.07%), HLA‐C*04:01:01G (17.88%), C*12:03:01G (10.23%), HLA‐DRB1*10:01 (14.89%), DRB1*03:01:01G (14.10%), HLA‐DQB1*02:01:01G (24.53%) and DQB1*05:01:01G (20.17%). The most frequent HLA‐A~C~B~DRB1~DQB1 haplotypes were HLA‐A*01:03~C*15:05:01G~B*73:01~DRB1*10:01:01~DQB1*05:01:01G (3.11%) and HLA‐A*01:01:01G~C*12:02:01G~B*52:01:01G~DRB1*15:02:01~DQB1*06:01:01G (2.25%). When comparing the allele and haplotype frequencies of the Eastern regions' population to those from the Central region we found significant differences in several allele frequencies including A*01:01:01G (P ≤ 0.0001), B*52:01:01G (P ≤ 0.0001), B*18:01:01G (P = 0.0001), C*12:03:01G (P < 0.0001), DRB1*10:01:01 (P < 0.0001) and DQB1*05:01:01G (P < 0.0001). Our data confirms genetic heterogeneity among the Saudi population.

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“…For bone marrow and other donor registries, population level HLA allele frequency data is available for diverse ethnic groups worldwide through the International HLA and Immunogenetics Workshop [2], [3] and Allele Frequencies Net Database (AFND) [4], [5], [6]. These include high resolution HLA haplotype frequencies in US populations for the entire US donor registry [7] and large scale data for German donors [8], [9] while databases of allelic reference sequences and nomenclature are maintained by IPD-IMGT/HLA (http://www.ebi.ac.uk/imgt/hla) [10].…”

Section: Introductionmentioning

confidence: 99%

High resolution HLA haplotyping by imputation for a British population bioresource

et al. 2017

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This study aimed to establish the occurrence and frequency of HLA alleles and haplotypes for a healthy British Caucasian population bioresource from Oxfordshire. We present the results of imputation from HLA SNP genotyping data using SNP2HLA for 5553 individuals from Oxford Biobank, defining one- and two-field alleles together with amino acid polymorphisms. We show that this achieves a high level of accuracy with validation using sequence-specific primer amplification PCR. We define six- and eight-locus HLA haplotypes for this population by Bayesian methods implemented using PHASE. We determine patterns of linkage disequilibrium and recombination for these individuals involving classical HLA loci and show how analysis within a haplotype block structure may be more tractable for imputed data. Our findings contribute to knowledge of HLA diversity in healthy populations and further validate future large-scale use of HLA imputation as an informative approach in population bioresources.

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Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data

Cited by 108 publications

References 18 publications

Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles

Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles

HLA‐A, B, C, DRB1 and DQB1 allele and haplotype frequencies in volunteer bone marrow donors from Eastern Region of Saudi Arabia

High resolution HLA haplotyping by imputation for a British population bioresource

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