Abstract 4730: Integrating pathway analysis and genetics of gene expression for genome-wide association study on basal cell carcinoma

Clinical Research Program, Department of Dermatology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA.
Human Genetics (Impact Factor: 4.82). 10/2011; 131(4):615-23. DOI: 10.1007/s00439-011-1107-5
Source: PubMed


Genome-wide association studies (GWASs) have primarily focused on marginal effects for individual markers and have incorporated external functional information only after identifying robust statistical associations. We applied a new approach combining the genetics of gene expression and functional classification of genes to the GWAS of basal cell carcinoma (BCC) to identify potential biological pathways associated with BCC. We first identified 322,324 expression-associated single-nucleotide polymorphisms (eSNPs) from two existing GWASs of global gene expression in lymphoblastoid cell lines (n = 955), and evaluated the association of these functionally annotated SNPs with BCC among 2,045 BCC cases and 6,013 controls in Caucasians. We then grouped them into 99 KEGG pathways for pathway analysis and identified two pathways associated with BCC with p value <0.05 and false discovery rate (FDR) <0.5: the autoimmune thyroid disease pathway (mainly HLA class I and II antigens, p < 0.001, FDR = 0.24) and Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway (p = 0.02, FDR = 0.49). Seventy-nine (25.7%) out of 307 significant eSNPs in the JAK-STAT pathway were associated with BCC risk (p < 0.05) in an independent replication set of 278 BCC cases and 1,262 controls. In addition, the association of JAK-STAT signaling pathway was marginally validated using 16,691 eSNPs identified from 110 normal skin samples (p = 0.08). Based on the evidence of biological functions of the JAK-STAT pathway on oncogenesis, it is plausible that this pathway is involved in BCC pathogenesis.

Download full-text


Available from: Peter Kraft, Oct 04, 2015
29 Reads
  • Source
    • "In a recent study, it was estimated that 70% of cis-eQTLs in LCLs are shared with skin (Ding et al., 2010). In our study, we also marginally validated the findings on the JAK-STAT signaling pathway using the skin eQTLs (Zhang et al., 2011a). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Genome-wide association studies (GWAS) have become a widely used approach for genetic association studies of various human traits. A few GWAS have been conducted with the goal of identifying novel loci for pigmentation traits, melanoma, and non-melanoma skin cancer. Nevertheless, the phenotype variation explained by the genetic markers identified so far is limited. In this review, we discuss the GWAS study design and its application in pigmentation and skin cancer research. Furthermore, we summarize recent developments in post-GWAS activities such as meta-analysis, pathway analysis, and risk prediction.
    Pigment Cell & Melanoma Research 07/2012; 25(5):612-7. DOI:10.1111/j.1755-148X.2012.01023.x · 4.62 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Nucleotide excision repair (NER) is responsible for protecting DNA in skin cells against UVR-induced damage. Using a candidate pathway approach, a matched case-control study nested within a prospective, community-based cohort was carried out to test the hypothesis that single-nucleotide polymorphisms (SNPs) in NER genes are associated with susceptibility to non-melanoma skin cancer (NMSC). Histologically confirmed cases of NMSC (n=900) were matched to controls (n=900) on the basis of age, gender, and skin type. Associations were measured between NMSC and 221 SNPs in 26 NER genes. Using the additive model, two tightly linked functional SNPs in ERCC6 were significantly associated with increased risk of NMSC: rs2228527 (odds ratio (OR) 1.57, 95% confidence interval (CI) 1.20-2.05) and rs2228529 (OR 1.57, 95% CI 1.20-2.05). These associations were confined to basal cell carcinoma (BCC) of the skin (rs2228529, OR 1.78, 95% CI 1.30-2.44; rs2228527, OR 1.78, 95% CI 1.31-2.43). These hypothesis-generating findings suggest that functional variants in ERCC6 may be associated with an increased risk of NMSC that may be specific to BCC.
    Journal of Investigative Dermatology 02/2012; 132(5):1354-62. DOI:10.1038/jid.2012.4 · 7.22 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Dermatologists have been placed in a prime position to make new genetic discoveries. Tissue is easily obtained from the skin or mucosa for the study of germline and somatic mosaic disorders. This, along with the recent development of next-generation sequencing, makes dermatology an exciting field with essentially endless possibilities for discovering genes responsible for disease, better understanding complex molecular pathways, and eventually developing targeted therapies. To take advantage of this great opportunity, a basic understanding of the advances in genetic testing is vital. Herein we give an overview of next-generation sequencing, including some of the applications it may be used for. We also review various study designs for genetic discovery, each of their benefits and downfalls, and how they may be applied to the study of dermatologic disease.
    Pediatric Dermatology 12/2012; 30(4). DOI:10.1111/pde.12062 · 1.02 Impact Factor
Show more