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Open Access Research article

A meta-analysis of genome-wide association studies of follicular lymphoma

Christine F Skibola1*, Lucia Conde1, Jia-Nee Foo2, Jacques Riby1, Keith Humphreys3, Fenna CM Sillé1, Hatef Darabi3, Sylvia Sanchez1, Henrik Hjalgrim4, Jianjun Liu2, Paige M Bracci5 and Karin E Smedby6

Author affiliations

1 School of Public Health, Division of Environmental Health Sciences, University of California, Berkeley, 94720, CA, USA

2 Human Genetics, Genome Institute of Singapore, A*STAR, 138673, Singapore

3 Dept of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden

4 Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark

5 Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94143, USA

6 Unit of Clinical Epidemiology, Dept of Medicine Solna, Karolinska Institutet, Stockholm, Sweden

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Citation and License

BMC Genomics 2012, 13:516  doi:10.1186/1471-2164-13-516

Published: 1 October 2012

Abstract

Background

B-cell non-Hodgkin lymphoma represents a diverse group of hematological malignancies, of which follicular lymphoma (FL) is one of the most common subtypes. Family and epidemiological studies suggest an important genetic role in the etiology of FL. In recent genome-wide association studies (GWAS) of FL, several genetic susceptibility loci have been identified on chromosome 6p21.33 (rs6457327) and 6p21.32 (rs10484561, rs2647012) in the human leukocyte antigen class I and class II regions. To identify new genetic variants and further elucidate the genetic basis of FL, a meta-analysis was performed of the top 1000 SNPs associated with FL risk from two GWAS in the US, Denmark and Sweden (592 cases, 1541 controls), with independent validation in 107 cases and 681 controls.

Results

rs9275517 and rs3117222 in the HLA class II region were validated and inversely associated with FL risk (rs9275517: OR = 0.63, 95% CI = 0.55-0.73, p = 4.03 × 10-11; rs3117222: OR = 0.66, 95% CI = 0.57-0.77, p = 1.45 × 10-7). rs9275517, which is in high linkage disequilibrium with rs2647012 (r2 = 0.9), was no longer associated with FL after conditioning on rs2647012. The rs3117222 association was independent of established FL SNPs, but not of the HLA-DPB1*0301 allele. Using publicly available gene expression profiles with matching genotype information, we found that rs3117222 also was significantly correlated with increased HLA-DPB1 expression.

Conclusions

By performing a meta-analysis of two GWAS of FL, we further validated the relevance of HLA-DPB1*0301 as a protective allele in the pathogenesis of FL. Moreover, the protective rs3117222 A allele correlated with increased levels of HLA-DPB1, suggesting a possible disease mechanism involving HLA-DPB1 expression regulation. Our results add further support to the major role of HLA genetic variation in the pathogenesis of FL.

Keywords:
Follicular lymphoma (FL); Genome-wide association studies (GWAS); Human leukocyte antigen (HLA); Meta-analysis