Each SNP was assayed with two independent cDNA preparations, each in duplicate so that the ASE was calculated as the average of 4 different ratios. The diagnostic criteria for the TGFBR1 ASE phenotype were the same as in our prior report, i.e. a ratio of cDNA/gDNA either ≥ 1.5 or ≤ 0.67[14]. Selection of SNPs Using phase II HapMap data for the HapMap European (CEU) sample for TGFBR1, we selected 18 tag SNPs in addition Selleckchem ZIETDFMK to TGFBR1*6A and genotyped the 19 variants in all colorectal cancer cases. The tag SNPs were designed to give pairwise r2 > 0.8 for all common SNPs in the TGFBR1 region. A check using release 22 (April 2007) of the HapMap Phase

II data showed that this pairwise r2 value was achieved for 57 of 58 common SNPs identified in HapMap Phase II. The remaining common SNP was tagged successfully (r2 > 0.8) using a haplotype of two of the tag SNPs. The mean r2 for the 58 SNPs was 0.967 indicating excellent coverage of this region with our 18 tag SNPs. Statistical analyses

We used standard www.selleckchem.com/products/wnt-c59-c59.html chi-square tests to assess the significance of allele frequency differences between ASE individuals (>1.5 or <0.67; N = 11) and the remainder of the cohort. Results Frequency of the TGFBR1 ASE phenotype In this cross sectional study of 118 consecutively-recruited patients with colorectal cancer 74 (62.7%) individuals were heterozygous for informative TGFBR1 SNPs. Eleven (9.3%) patients had evidence of constitutively decreased TGFBR1 allelic expression, https://www.selleckchem.com/products/AZD1480.html i.e. a ratio of cDNA/gDNA either ≥ 1.5 or ≤ 0.67[14]. Median age at diagnosis was 60 years in subjects with TGFBR1 ASE and in those without and the sex distribution was similar as well (Table 1). The frequency of constitutively decreased TGFBR1 allelic expression among Caucasian patients was 10.2% (10/98)and 7.1% (1/14) in the African-American population. None of the patients with self-described Hispanic (3) or Asian (3) ethnicity had decreased TGFBR1 allelic expression. Fifty-five percent of the patients with decreased TGFBR1 allelic expression had a primary colon cancer. This was similar to the 66% with primary colon cancer in patients Cyclooxygenase (COX) with normal TGFBR1 allelic

expression (p = 0.507; Fisher’s Exact Test). The stage at diagnosis was equivalent in both groups with only 9% presenting with stage I disease and 27% of those with normal TGFBR1 allelic expression having stage IV disease, similar to the 36% in those patients with decreased TGFBR1 allelic expression (p = 0.498; Fisher’s Exact Test). A family history of colorectal cancer in a first or second degree relative was present in 29% of all patients and was comparable between the two groups (Table 1). Table 1 Demographics and clinical characteristics of patients with and without constitutively decreased TGFBR1 allelic expression (TGFBR1 ASE).   All patients TGFBR1 ASE + TGFBR1 ASE – Age, years No % No % No % Median age 59.5   64.0   59   Range 35-84   52-77   35-84   Sex             Female 55 46.6 4 3.4 51 43.2 Male 63 53.4 7 5.