Search

Inherited polymorphisms in immuno-modulatory genes may contribute to variations in immune function and genetic susceptibility for complex diseases, including cancer. We report results from a comprehensive study to discover novel single nucleotide polymorphisms (SNPs) and to estimate allelic frequency for both novel and known coding and regulatory region SNPs in genes encoding proteins that have been implicated in the immune response to tumors. We identified 12 novel nucleotide substitution variants and one deletion variant in 17 genes analyzed (TGFβR, β2M, IFNγ, TNFα, TNFαR, LTα, IL-6, IL-12, IL-2, IL-1α, IL-1β, IL-1RN, IL-10, CTLA4, CD40L, Fasand FasL). We determined the frequency of these novel polymorphisms, as well as 17 previously identified polymorphisms, in a control sample of 158 individuals, approximately half of which were Caucasian (n = 74) and half of which were African American (n = 84). Significant differences in allele frequencies were observed between the two racial groups for 13/17 genes tested. These allelic variations maybe associated with alterations in immune function and thus susceptibility to a number of complex disease states such as cancer.

Numerous single nucleotide polymorphisms (SNPs) have been identified in the human genome, yet the functional significance of most is unknown. CYP3A4 is a key enzyme in the metabolism of numerous compounds. An A→G substitution 290 bp upstream of the CYP3A4transcription start site (CYP3A4*1B) has been associated with cancer phenotypes, but its phenotypic effects are unclear. To investigate the functional significance of CYP3A4*1B, we generated two luciferase reporter constructs: 1‐kb (denoted L, long) and 0.5‐kb (denoted S, short) promoter fragments containing either the variant (VL,VS) or the wild‐type (WL, WS) sequences. We evaluated the effect of the variant sequence in the HepG2 and MCF‐7 cell lines, and in primary human hepatocytes from three donors. Reporter constructs with the variant sequence had 1.2‐ to 1.9‐fold higher luciferase activity than constructs with wild‐type sequence in the cell lines (P< 0.0001) and hepatocytes (P= 0.021, P= 0.027, P= 0.061). The ratio of transcriptional activity for VS:WSwas similar to the VL:WLratio in HepG2 cells, but the VS:WSratio was consistently less than the VL:WLratio in MCF‐7 cells. This suggests that CYP3A4expression is higher from the variant promoter and that a repressor sequence may exist in the longer constructs. Electrophoretic mobility shift assays demonstrated specific binding of a component of HepG2 nuclear extract to both wild‐type and variant promoters with consistently higher binding affinities to the wild‐type sequence. This suggests the existence of a transcriptional repressor responsible for the lower CYP3A4*1Aactivity. Therefore, the phenotypic effects of the variant CYP3A4*1Bmay be associated with enhanced CYP3A4 expression due to reduced binding of a transcriptional repressor. Environ. Mol. Mutagen. 42:299–305, 2003. © 2003 Wiley‐Liss, Inc.

We apply a method proposed by Rogatko et al. [1995: Am J Med Genet 59:24–32] to estimate carrier risks using genetic linkage data. The method is illustrated for X-linked ocular albinism. Linkage data from pedigrees were combined with genome mapping data to compute carrier risks for individuals with unknown carrier status based on pedigree data alone. We considered two situations. First, a linkage map with some ambiguity in the gene order was considered. This analysis allows us to examine the effect of incomplete genetic map information on risk computations. Second, published physical and meiotic mapping information was used to derive a linkage map that could be assumed known without ambiguity. In both situations, the mean and median estimate of carrier risk differed significantly from that obtained using pedigree relationships only, in that the computed risk was significantly different from the a priori value of 0.5. The 95% CI's associated with point estimates of risk made using the known map or a map with ambiguity did not overlap in some cases. These results suggest that the risk estimate and the confidence with which a risk estimate can be imparted may depend on the genetic map and marker data used in the risk estimation procedure. We conclude that the method presented here can be used to estimate genetic risk under a variety of analytical conditions. Am. J. Med. Genet. 70: 58–66, 1997. © Wiley-Liss, Inc.

Germline mutations in PTEN are the underlying genetic defect in Cowden disease, which is associated with a lifetime risk of 25-50% of developing breast cancer. To investigate the role of PTEN in inherited breast cancer in the absence of manifestations of Cowden disease, we screened 177 unrelated subjects with breast cancer who also had a family history of breast cancer in at least one relative. We found no disease associated PTEN mutations in this cohort, supporting previous studies suggesting that PTEN mutations do not contribute to inherited susceptibility to breast cancer without associated manifestations of Cowden disease. We did identify an association between a common polymorphism in intron 4 and lower mean age of diagnosis of breast cancer. While preliminary, these findings suggest that further study is warranted to determine whether this allelic variant of PTEN could function as a low penetrance breast cancer susceptibility allele.