Complexities and similarities of HLA antigen distribution in Asian subcontinent

Shankarkumar, U

doi:10.4103/0971-6866.73397

Cited by 17 publications

(13 citation statements)

References 5 publications

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“…Genetic factors include a strong association with the HLA class II alleles DRB1*16 and DQB1*5, initially reported in a Taiwanese cohort, and DRB1*15, later reported in Thai patients [5–7]. We did not perform HLA analysis in our patient, but previous large-scale population studies have shown DRB1*15 as a common allele among individuals from Asian countries, including India, Taiwan, and Thailand [8].…”

Section: Discussionmentioning

confidence: 94%

Disseminated Nontuberculous Mycobacterial Infection Associated With Acquired Immunodeficiency Due to Anti–Interferon γ Autoantibodies

Yerramilli

Huang

Griffin

et al. 2019

Open Forum Infectious Diseases

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Section: Discussionmentioning

confidence: 94%

Disseminated Nontuberculous Mycobacterial Infection Associated With Acquired Immunodeficiency Due to Anti–Interferon γ Autoantibodies

Yerramilli

Huang

Griffin

et al. 2019

Open Forum Infectious Diseases

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“…On the other hand, the maximum population coverage of MHC II (78.93%) resulted from YLKAIKERL that bound to the largest number of MHC II alleles. When we calculated the population coverage of the proposed MHC I and MHC II epitopes in China, Indonesia, and Philippines 'the place where S. japonicum is endemic' different coverage of each epitope resulted in each country as there was a difference in the frequency distribution of human leukocyte antigen (HLA) class I and II alleles in those countries (75,76). In the case of MHC I Epitopes, FRENGVTPY is a most promising one in China with population coverage 54.46%, while epitopes VVYEVDANF with population coverage 37.53%, and YEHYIGESM with coverage 65.31% are the most promising epitopes in Indonesia and Philippines respectively.…”

Section: Discussionmentioning

confidence: 99%

Translationally Controlled Tumor ProteinTCTPas Peptide Vaccine againstSchistosoma japonicum: an Immunoinformatics Approach

Abdalrahman¹,

Ahmed²,

Elnaeem³

et al. 2018

Preprint

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Schistosoma japonicum is the most pathogenic causative form of schistosomiasis that causes a major health problem in its endemic countries. Until now, praziquantel is the only drug used to treat Schistosomiasis, but it does not prevent re-infection. So, repetition of the treatment is needed. Moreover, there is no effective vaccine against S. japonicum. Therefore, an urgent need for the development of vaccines is mandatory. This study aimed to analyze an immunogenic protein, Transitionally Controlled Tumor Protein (TCTP) using an immunoinformatics approach to design a universal peptide vaccine against Schistosoma japonicum. A set of 22 of TCTP sequences were retrieved from NCBI database. Conservancy of these sequences was tested and then conserved B cell and T cell epitopes were predicted using different tools available in IEBD. Epitopes having high scores in both B and T cell predicting tools were proposed. An epitope 129 YEHYI 133 was predicted as a most promising epitope with good prediction scores in surface accessibility and antigenicity. Besides that, epitopes 129 YEHYIGESM 137 and 92 YLKAIKERL 100 were predicted as the most promising epitopes concerning their binding to MHC I and MHC II allele respectively. The study revealed that our predicted epitopes could be used to develop an efficacious vaccine against Schistosoma japonicum in the future especially epitope YEHYIGESM as it is shared between MHC I and II alleles and overlapped with the most promising B cell epitope. Both in vitro and in vivo studies is recommended to confirm the efficacy of YEHYIGESM as a peptide vaccine.

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“…Balakrishnan et al [20] have previously reported that HLA-DRB1 * 15 allele was the most frequent in Kani tribe (45.19%) and less frequent in Narikkuravars (1.02%) from Tamil Nadu and Kerela, respectively. Additionally, HLA-DRB1 * 10 and DRB1 * 07 were found to be most common alleles in South Indian populations, whereas Caucasians DRB1 * 01 allele was also reported in the Namboothiris of Kerala, Narikkuravars of Tamil Nadu and Maratha of Maharastra [14,20]. Mehra et al [21] reported that HLA-A * 02 was the most frequently occuring HLA allele in North Indian populations.…”

Section: Discussionmentioning

confidence: 99%

“…Its 1 billion people are categorized into 3824 castes, 25,000 sub-castes and 461 tribes [14]. Thus, India is generally considered a living laboratory for human genetic and genomic studies [15].…”

Section: Introductionmentioning

confidence: 99%

Comparative Analyses of Low, Medium and High-Resolution HLA Typing Technologies for Human Populations

Gowda¹,

Ambardar²,

Dighe³

et al. 2016

J Clin Cell Immunol

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Human Leukocyte Antigen (HLA) encoding genes are part of the major histocompatibility complex (MHC) on human chromosome 6. This region is one of the most polymorphic regions in the human genome. Prior knowledge of HLA allelic polymorphisms is clinically important for matching donor and recipient during organ/tissue transplantation. HLA allelic information is also useful in predicting immune responses to various infectious diseases, genetic disorders and autoimmune conditions. India harbors over a billion people and its population is untapped for HLA allelic diversity. In this study, we explored and compared three HLA typing methods for South Indian population, using Sequence-Specific Primers (SSP), NGS (Roche/454) and single-molecule sequencing (PacBio RS II) platforms. Over 1020 DNA samples were typed at low resolution using SSP method to determine the major HLA alleles within the South Indian population. These studies were followed up with medium resolution HLA typing of 80 samples based on exonic sequences on the Roche/454 sequencing system and high-resolution (6-8 digit) typing of 8 samples for HLA alleles of class I genes (HLA-A, B and C) and class II genes (HLA-DRB1 and DQB1) using PacBio RS II platform. The long reads delivered by SMRT technology, covered the full-length class I and class II genes/alleles in contiguous reads including untranslated regions, exons and introns, which provided phased SNP information. We have identified three novel alleles from PacBio data that were verified by Roche 454 sequencing. This is the first case study of HLA typing using second and third generation NGS technologies for an Indian population. The PacBio platform is a promising platform for large-scale HLA typing for establishing an HLA database for the untapped ethnic populations of India.

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Complexities and similarities of HLA antigen distribution in Asian subcontinent

Cited by 17 publications

References 5 publications

Disseminated Nontuberculous Mycobacterial Infection Associated With Acquired Immunodeficiency Due to Anti–Interferon γ Autoantibodies

Disseminated Nontuberculous Mycobacterial Infection Associated With Acquired Immunodeficiency Due to Anti–Interferon γ Autoantibodies

Translationally Controlled Tumor ProteinTCTPas Peptide Vaccine againstSchistosoma japonicum: an Immunoinformatics Approach

Comparative Analyses of Low, Medium and High-Resolution HLA Typing Technologies for Human Populations

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