The frequency of HLA alleles in a population of Inuit women of northern Quebec

Background Human leukocyte antigen (HLA) alleles code for proteins that are involved in the recognition of foreign antigens and activation of the immune system. The frequency of HLA alleles varies across different populations. Objective To describe the frequency of HLA alleles in a population of Inuit women of Nunavik, Quebec, Canada. Design A cohort of women was recruited from 4 different communities between January 2002 and December 2007. HLA-B*07, HLA-DQB1*03, DQB1*06:02, DRB1*13 and DRB1*15:01 alleles were typed by PCR sequence-specific primers (PCR-SSP) and HLA-E and G alleles were type by DNA-sequencing procedures. Results We obtained data on 524 participants. The most frequent HLA alleles in this population were HLA-E*01:03, HLA-G*01:04:01 and HLA-DQB1*03, and they were found in 89, 75 and 94% of the population, respectively. Conclusions The distribution of HLA alleles in Nunavik, Quebec is unique when compared to other populations in Canada or around the world.

N unavik is the arctic and sub-arctic region of Northern Quebec, Canada. For 4,000 years this region has been inhabited by nomads, the first residents of Nunavik travelled from Asia to North America via the Bering Strait. The Inuit people are descendants of the Thule, who appeared in the western part of Northern Canada around 1,000 AD. The earliest archaeological evidence of the Thule people in Nunavik dates back to around the thirteenth century (1,2). Today, Nunavik's population of 11,000 lives in 14 communities along the coast of Hudson Bay, Hudson Straight and Ungava Bay. Ninety percent of the population of Nunavik self-identifies as Inuit. This population is not only geographically isolated but has a unique cultural and socio-demographic make-up (1,3) (Fig. 1).
Human leukocyte antigens (HLA) are part of the major histocompatibility complex (MHC) in humans. The HLA family of genes code for cell surface proteins, which present antigens (foreign or self) to immune cells, and other proteins involved in internal processing of antigens (4Á6). HLA class I proteins include HLA-A, B, C, E, F and G and are expressed on all nucleated cells. Class II proteins include HLA-DP, DQ and DR and are expressed on immune cells (lymphocytes and macrophages) (4).
HLA genes are highly polymorphic allowing HLA proteins to bind to and present a variety of antigenic proteins to immune cells (4). Determining which HLA alleles are present in a population (and their frequencies) could provide insights into the origin of Native American groups, the evolution of HLA polymorphisms (a point in a DNA sequence where there is variation), and the population's genetic susceptibility to disease. Polymorphisms in various HLA genes have been linked with susceptibility to viral infections such as HPV, HIV, HBV and HCV (4Á8). It is hypothesised that individuals with HLA polymorphisms with a higher binding affinity to a particular viral antigen are better at clearing the infection.
An allele is an alternative form or version of a gene. An individual's genotype is the 2 alleles inherited for a particular gene.  A haplotype is a set of DNA polymorphisms along a chromosome that tend to be inherited together (9). HLA alleles are named in this way: HLAÁlocus name*allele number. The first 2 numbers after the asterisk (*) are the allele number and any numbers after that are the allele subtype (10). For example HLA-G*01:04:01, 01 is the allele number and 04:01 is the allele subtype.

Methods
The data used for this analysis were taken from a prospective cohort of Inuit women used to study the prevalence, incidence and determinants of human papillomavirus (HPV) infection. Details of this study have been previously published (11). Nurse practitioners systematically asked women aged 15Á69 presenting for a regularly scheduled Pap test at a clinic in one of the 4 participating communities between January 2002 and December 2007 if they wanted to participate. All eligible women provided written consent, and ethics approval was obtained from the McGill Institutional Review Board and the Tulattavik Health Center.
At enrolment, cervical specimens were collected and used for HLA typing. Low-resolution typing was used to determine the presence of HLA-B*07 and 4 class II alleles: HLA-DQB1*03, DQB1*06:02, DRB1*13 and DRB1*15:01 (these alleles were associated with cervical cancer in previous literature and were chosen a priori). They were typed using a PCR technique that used sequence-specific primers (PCR-SSP), according to a well-established procedure where pairs of oligonucleotides were used as primers for amplification of the HLA alleles (12,13). Class I HLA-E and G alleles were typed using high-resolution DNA typing; therefore, all of the alleles present in the population were captured. HLA-G and HLA-E alleles were determined through direct DNA sequencing of the nucleotide regions encompassing the HLA-E exon 3 (218bp) and HLA-G exons 2Á4 (1718bp) using purified DNA from cervical samples (14).

Discussion
This is the first known study to determine the frequency of HLA alleles in the Inuit of Nunavik, Quebec. A study by Leffell et al. investigated the frequency of HLA alleles in the Yup'ik Inuit population of Alaska in which HLA-B*07:02, DRB1*15:01, DRB1*13:01 and DQB1*06:02 were present in less than 2% of the population and DQB1*03:01 had a frequency 61.7% (15). On the basis of the distribution of these 5 alleles, the Yup'ik population of Alaska and the Inuits of Nunavik are somewhat similar. Unfortunately, the Alaskan study did not type for HLA-E or G.
In women living in Montreal, Quebec, the HLAB*07, HLA-DQB1*06:02, DRB1*13 and DRB1*15:01 alleles were all more frequent than in Nunavik. In 2 Montreal populations, their frequencies were 15, 20, 20 and 23%, respectively (13,16). HLA-DQB1*03 was found in around 60% of the Montreal populations, whereas it was found in almost all of the Inuit women (94%). The reported haplotypes of these 5 alleles were again found in a greater proportion of the Montreal population than the Nunavik population (13,16).
Limitations to this study include the possibility of regional differences of HLA frequencies within the Nunavik territory and non-random recruitment. In conclusion, the frequency of HLA alleles in Nunavik, Quebec is different from that found in other Canadian populations and other populations around the world. Two alleles in particular, HLA-G*01:04:01 and HLA-DQB1*03 (found in 76 and 94% of individuals, respectively) were found more frequently in the Nunavik population than in other populations which have been studied. Clinical significance of these findings in terms of the potential impact on HPV prevalence or persistence will be subsequently explored. These regional variations could have an impact on disease outcome including not only HPV but also other morbidities such as autoimmune disorders and vaccine efficacy.