High-resolution HLA allele and haplotype frequencies in several unrelated populations determined by next generation sequencing: 17th International HLA and Immunogenetics Workshop joint report.

The primary goal of the unrelated population HLA diversity (UPHD) component of the 17th International HLA and Immunogenetics Workshop was to characterize HLA alleles at maximum allelic-resolution in worldwide populations and re-evaluate patterns of HLA diversity across populations. The UPHD project included HLA genotype and sequence data, generated by various next-generation sequencing methods, from 4,240 individuals collated from 12 different countries. Population data included well-defined large datasets from the USA and smaller samples from Europe, Australia, and Western Asia. Allele and haplotype frequencies varied across populations from distant geographical regions. HLA genetic diversity estimated at 2- and 4-field allelic resolution revealed that diversity at the majority of loci, particularly for European-descent populations, was lower at the 2-field resolution. Several common alleles with identical protein sequences differing only by intronic substitutions were found in distinct haplotypes, revealing a more detailed characterization of linkage between variants within the HLA region. The examination of coding and non-coding nucleotide variation revealed many examples in which almost complete biunivocal relations between common alleles at different loci were observed resulting in higher linkage disequilibrium. Our reference data of HLA profiles characterized at maximum resolution from many populations is useful for anthropological studies, unrelated donor searches, transplantation, and disease association studies.

Molecular analysis of HLA Class I and Class II genes in five different South Indian linguistic groups.

South Indians are a heterogeneous population who speak different languages and differ in their life style and physical appearance. Major population movements, social structure and caste endogamy have influenced the genetic structure of Indian populations. The human leukocyte antigen (HLA) system of populations is highly informative because of the high level of polymorphisms. Knowledge of allele and haplotype frequencies of the HLA system is important in the search for unrelated bone marrow donors. We investigated the distribution of HLA A, B, C, DRB1 and DQB1 loci in five linguistic groups from South India. HLA-A*01:01:01~B*57:01:01:01~C*06:02:01~DRB1*07:01:01~DQB1*03:03:02 was the common haplotype with highest frequency in all the five populations studied. A few relevant haplotypes were identified as most common haplotypes in each linguistic group. Comparison of HLA-A, -B and -DRB1 allele distribution in these five linguistic groups with the other Asian population showed that the South Indian populations were closely related to Sri Lankan populations. A large South Indian donor registry might serve as good source of donors for patients from Sri Lanka and vice versa.

Association of HLA-A, -B, -C, -DRB1 and -DQB1 alleles at amino acid level in individuals with schizophrenia: A study from South India.

BACKGROUND: Schizophrenia, a chronic severe psychiatric illness of unknown aetiology, has been shown to be associated with HLA alleles but at varied degree in different population. The present study has focussed on analysing the frequency of HLA class I and class II alleles in persons with schizophrenia from South India. METHODS: Ninety seven individuals with schizophrenia and 103 age- and gender-matched controls were typed for HLA- A, B, C, DRB1 and DQB1 loci by next-generation sequencing in Illumina MiniSeq using MIA FORA NGS FLEX HLA typing kit. RESULTS: The results showed that HLA-A*01:01:01, B*37:01:01 and C*01:02:01 were positively associated with schizophrenia while HLA-B*35:03:01 and DRB1*04:03:01 were negatively associated. Gender-specific associations revealed that DRB1*10:01:01 and DQB1*05:01:01 were positively associated while DQB1*03:02:01 was negatively associated with female subjects with schizophrenia. A*24:02:01~B*37:01:01~C*06:02:01~DRB1*10:01:01~DQB1*05:01:01 is the predominant haplotype in schizophrenia population when compared to healthy controls. Amino acid association in susceptible and protective alleles has shown that the presence of peptide in the peptide-binding groves of mature HLA-A protein (K, M, V, R and V at 44th, 67th, 150th, 156th and 158th position), HLA-B protein (D and S at 77th and 99th position) and HLA-C protein (M at 99th position) confer susceptibility to the disease, only in the absence of E (Glutamic acid) at 74th position in mature HLA-DRB1 protein. Interaction of amino acids in protective alleles namely B*35:01:01 and DRB1*04:03:01 has revealed that aspartic acid at 114th (D) position in mature HLA-B protein and glutamic acid (E) at 74th position of mature HLA-DRB1 protein have a combined effect in protecting against the disease. CONCLUSION: The study has revealed the HLA association with schizophrenia in south Indian population. The amino acid interaction with the disease needs to be confirmed in a larger population.

Application of high-throughput next-generation sequencing for HLA typing of DNA extracted from postprocessing cord blood units.

Cord blood has become an acceptable source of hematopoietic stem cells for transplantation. HLA plays a major role in hematopoietic stem cell transplantation (HSCT). Typing of cord blood samples for HLA alleles has been performed based on the serological and molecular methods. However, with the advent of next-generation sequencing technology, HLA typing becomes more accurate and unambiguous (upto intron level). Contamination of cord blood cells with erythropoietic cells poses a challenge in DNA extraction and downstream application. In the present study, DNA extracted from buffy coat of cord blood samples was typed for HLA-A, -B, -C, DRB1, and DQB1 alleles by Illumina miniseq and the sequences were aligned, phased, and mapped by MIA FORA software algorithms. Most frequent alleles found were HLA A*01:01:01 (17%), A*24:02:01 (15.1%), A*11:01:01 (13.6%), B*40:06:01 (10.7%), C*06:02:01 (17.7%), C*04:01:01 (14.2%), C*15:02:01 (11.4%), C*07:02:01 (10.7%), DRB1*07:01:01 (15.9%), DRB1*10:01:01 (10.2%), DQB1*06:01:01 (17.4%), DQB1*05:01:01 (12.4%), and DQB1*05:03:01 (10.4%). One null allele (A*24:11N), two novel alleles in B loci and three rare alleles (B*40:06:04, B*51:01:05, and C*01:44) were also identified in the present study. This study shows that high-throughput, unambiguous (third-field resolution) HLA typing can be performed on cord blood samples. In order to preserve the precious sample for future use, minimal amount of cord blood samples (postprocessing) could be used for HLA typing purpose.

Human leucocyte antigen (HLA)-A, -B, -C, -DRB1 and -DQB1 haplotype frequencies from 2491 cord blood units from Tamil speaking population from Tamil Nadu, India.

The Public Cord Blood Bank of Jeevan Stem Cell Foundation was established in 2008 to harvest cord blood units and make them available to treat multiple blood disorders through Hematopoietic Stem Cell Transplants. We studied Human Leucocyte Antigen (HLA)-A, -B, -C, -DRB1 and -DQB1 allele and haplotype diversity in a sample of 2491 unrelated cord-blood units from Jeevan's Public Cord Blood Bank (part of Be The Cure Registry) in the Tamil Nadu state in the Indian Peninsula.