HLA A*02 allele and B-associated haplotype diversity in Indians

British Journal of Biomedical Science, 2003 by Shankarkumar, U

ABSTRACT

Human leucocyte antigen (HLA) A2 is the most heterogeneous allele at the HLA A locus, with approximately 56 different subtypes. Substantial heterogeneity in A*02 distribution has been observed in populations worldwide. HLA A2 allele distribution varies (4-25%) in different Indian populations and castes. HLA B40 is the most common allele associated with A2 haplotypes. In this study, molecular A*02 subtyping in Maratha (western Indian - Aryan) and Nadar (south Indian - Dravidian) caste groups using high-resolution polymerase chain reaction/reverse line strip/sequencespecific oligonucleotide hybridisation (PCR-RLS-SSOP) indicates the presence of 10 subtypes (A*02011, A*0203, A*0205, A*0206, A*0207, A*0208, A*0209, A*0211, A*0222 and A*0236) in variable frequencies. Moreover, A*0211B*4006 was commonly observed among the north Indian Maratha caste and A*02011-B*4006 among the south Indian Nadar caste groups. HLA A*0211 is found frequently in this population and in Asian Indians, and has been reported with low frequencies in many other populations worldwide. A*0222 has been observed among Hispanics, while A*0236 has been observed exclusively among members of the Maratha caste. The findings demonstrate a substantial heterogeneity among the groups studied that may be a consequence of founder effect, racial admixture or selection pressure due to environmental factors.

KEY WORDS: Founder effect. Haplotypes. HLA-A2 antigens. HLA-B antigens

Introduction

Human leucocyte antigen (HLA) A*02 is the most heterogeneous allele family at the HLA A locus, comprising some 56 different alleles. Most of the nucleotide differences in subtypes occur in the [alpha]1 and [alpha]2 domains responsible for peptide binding and HLA-restricted recognition by the T-cell receptor. This is consistent with the view that positive selection for polymorphism is a major factor in the fixation of this allele.1 Furthermore, HLA A2 has also been implicated in a number of diseases including Alzheimer's,2 psoriatic arthritis,3 vitiligo4 and pulmonary tuberculosis5.

Substantial heterogeneity in A2 subtype distribution has been observed in populations worldwide. HLA A2 occurs with varying frequency in north Indians (17.33%),6 south Indians (15.06%),7 Marathi-speaking Hindus (14.4%),8 Gujarathi Hindus (12.43%)9 and Uttar Pradesh Indians (10.99%).10 Distribution of A2 among the different caste groups also shows heterogeneity.11,12 In addition, substantial A*02 subtype distribution has been observed in populations worldwide,6,13 with HLA A*02011 showing the highest frequency in most populations.14-18

A*0211 is the most frequent allele reported among north Indians but it is a relatively rare allele in populations elsewhere around the world.14,18-21 A*0206 and A*0203 are common alleles in most Asian populations, while A*0205 occurs in Caucasians and Negroes. Recently, A*0209 has been reported in north Indians.13

In view of the these observations, and the A19 allelic diversity among Western populations,22 this study aims to determine the molecular diversity of the A*02 allele and its B* allele haplotype associations in the western Indian Maratha caste (Aryan descent) from the Maharastra state and the south Indian Nadar caste (originally Dravidian) from the Tamil Nadu state, using a high-resolution polymerase chain reaction (PCR)-based reverse blot sequence-specific oligonucleotide hybridisation technique.

Materials and methods

Subjects

A total of 2908 unrelated healthy individuals belonging to different population and caste groups (Table 1) were studied and the A2 allele was determined by serology. In order to study the different A*02 subtypes, 61 healthy individuals from the Nadar caste group in the southern Indian state of Tamil Nadu,23 and 93 healthy individuals from the Maratha caste group in the western Indian state of Maharastra24 were studied. A total of 51 A*02-positive samples belonging to the Maratha (n = 38) and Nadar (n = 13) castes were studied for molecular subtypes and their B* allele-associated haplotypes.

HLA A*02 and B*40 molecular typing

DNA was obtained from EDTA-anticoagulated peripheral mononuclear cells using standard methods.25 Genomic DNA from 51 A2-positive samples was selected and genotyped for A*02 and B* allele subtypes by PCR/reverse line strip/ sequence-specific oligonucleotide hybridisation (PCR-RLS-SSOP) strips (Roche Molecular, Oakland CA, USA). Each HLA A typing strip contained 57 immobilised sequencespecific oligos (SSOs), while the HLA B typing strip contained 84 immobilised SSOs.

Genomic DNA was amplified using HLA A or HLA B locus-specific biotinylated primers and hybridised with the SSO strips. Alkaline phosphatase-conjugated streptavidin was responsible for the positive colour development, using bromochloroindolyl phosphate/nitro blue tetrazolium (BICP/NBT) in dimethylformamide (DMF) as substrate.

Alleles were determined using the pattern interpretation software supplied with the kit.

Results

Of the 56 A*02 alleles known, 10 subtypes (A*02011, A*0203, A*0205, A*0206, A*0207, A*0208, A*0209, A*0211, A*0222 and A*0236) were identified in the Indian populations studied (Table 2). A high frequency of A*0211 was found among members of the Maratha caste, which corroborates earlier observations among north Indians (Aryans), while the high frequency of A*02011 in the south Indian Nadar caste (Dravidian) was observed for the first time.