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.

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.

Identification of the novel HLA allele, HLA-B*35:03:23, by next-generation sequencing.

The novel HLA-B allele, HLA-B*35:03:23, differs from B*35:03:01 by a single-nucleotide mismatch in exon 1.

Identification of the novel allele, HLA-B*40:379, by next-generation sequencing.

Identification of the novel allele HLA-B*40:379 carrying polymorphisms in an intron, exon and the 3' untranslated region.

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 leukocyte antigen A, B and Hepatitis B infection outcome: A meta-analysis.

AIM: To evaluate the association between HLA A, B with chronic Hepatitis B by comprehensive meta-analysis. METHODS: We searched PubMed and Cochrane databases, identified relevant studies, evaluated these for quality by New Castle Ottawa scale (NOS) and further analyzed the qualified data sets. Heterogeneity analyses were performed by Cochrane's Q test and I2 tests. Pooled Odds ratio (OR) & 95% Confidence Interval (CI) were obtained by fixed effects, using Mantel-Haenszel's method for homogenous studies, and by using DerSimonian and Laird's method for heterogenous studies. Publication bias was determined by the Beggs test and Eggers test and all tests were two tailed to evaluate their significance. RESULTS: The meta-analyses on 1652 healthy controls and 659 Chronic Hepatitis B (CHB) patients from 8 studies from various continents revealed a HLA B*07 (p value of Odds ratio (pOR)=0.004; OR Fixed effects=0.480 with 95%CI 0.290-0.794) and B*58 (pOR=0.029; OR Fixed Effects=0.020 with 95%CI 0.381-0.949) associated protection for CHB. The identified HLA B*35 associated risk (pOR 0.009; OR Fixed effect 1.445; 95% confidence interval 1.094-1.907) however did not stand the test of random effect model. CONCLUSION: While HLA B*07 and B*58 are protective against CHB. The HLA B*35 associated marginal risk need to be further validated in well-designed global study on larger cohorts, considering the population, ethnic, epidemiological and HLA diversity at the sequence level: these may throw further light to utilize these markers in predictive medicine.

Next Generation Sequencing in HLA haplotype distribution among Telugu speaking population from Andhra Pradesh, India.

HLA A: B:C:DRB1:DQB1 allele and haplotype frequencies were determined among India, Andhra Pradesh, Telugu speaking population from South India by Next Generation Sequencing. 180 bone marrow registry donors and 6 cord blood units from Jeevan Stem Cell Foundation (part of Be The Cure Registry), Chennai, Tamilnadu state were included in the study.