title: SNP variants associated with non-Hodgkin lymphoma (NHL) correlate with human leukocyte antigen (HLA) class II expression.
abstract: Large consortia efforts and genome-wide association studies (GWASs) have linked a number of genetic variants within the 6p21 chromosomal region to non-Hodgkin lymphoma (NHL). Complementing these efforts, we genotyped previously reported SNPs in the human leukocyte antigen (HLA) class I (rs6457327) and class II (rs9271100, rs2647012 and rs10484561) regions in a total of 1,145 subjects (567 NHL cases and 578 healthy controls) from two major ethnic groups in Malaysia, the Malays and the Chinese. We identified a NHL-associated (PNHL_add= 0.0008; ORNHL_add= 0.54; 95% CI = 0.37-0.77) and B-cell associated (PBcell_add= 0.0007; ORBcell_add= 0.51; 95% CI = 0.35-0.76) SNP rs2647012 in the Malaysian Malays. In silico cis-eQTL analysis of rs2647012 suggests potential regulatory function of nearby HLA class II molecules. Minor allele rs2647012-T is linked to higher expression of HLA-DQB1, rendering a protective effect to NHL risk. Our findings suggest that the HLA class II region plays an important role in NHL etiology.
authors.affiliation: Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Lik-Chin
authors.initials: LC
authors.lastname: Ten
authors.affiliation: Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Yoon-Ming
authors.initials: YM
authors.lastname: Chin
authors.affiliation: Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Mei-Chee
authors.initials: MC
authors.lastname: Tai
authors.affiliation: Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Edmund Fui-Min
authors.initials: EF
authors.lastname: Chin
authors.affiliation: Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Yat-Yuen
authors.initials: YY
authors.lastname: Lim
authors.affiliation: Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Sujatha
authors.initials: S
authors.lastname: Suthandiram
authors.affiliation: Hematology Unit, Ampang Hospital, Kuala Lumpur, Malaysia.
authors.forename: Kian-Meng
authors.initials: KM
authors.lastname: Chang
authors.affiliation: Hematology Unit, Ampang Hospital, Kuala Lumpur, Malaysia.
authors.forename: Tee-Chuan
authors.initials: TC
authors.lastname: Ong
authors.affiliation: Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Ping-Chong
authors.initials: PC
authors.lastname: Bee
authors.affiliation: Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Zahurin
authors.initials: Z
authors.lastname: Mohamed
authors.affiliation: Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Gin-Gin
authors.initials: GG
authors.lastname: Gan
authors.affiliation: Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Ching-Ching
authors.initials: CC
authors.lastname: Ng
mesh_terms: D000328:Adult; D003710:Demography; D005260:Female; D005786:Gene Expression Regulation; D020022:Genetic Predisposition to Disease; D004854:Herpesvirus 4, Human / Q000502:physiology; D000949:Histocompatibility Antigens Class II / Q000235:genetics*; D006801:Humans; D008214:Lymphocytes / Q000821:virology; D008228:Lymphoma, Non-Hodgkin / Q000235:genetics*; D008296:Malaysia; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics
chemical_list: D000949:Histocompatibility Antigens Class II