ABSTRACT
BACKGROUND: Prostate cancer is a genetically complex disease with locus and disease heterogeneity. The RNASEL gene and HPCX locus have been implicated in hereditary prostate cancer; however, their contributions to sporadic forms of this malignancy remain uncertain. METHODS: Associations of prostate cancer with two variants in the RNASEL gene (a founder mutation, 471delAAAG, and a non-synonymous SNP, rs486907), and with five microsatellite markers in the HPCX locus, were examined in 979 cases and 1,251 controls of Ashkenazi Jewish descent. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using logistic regression models. RESULTS: There was an inverse association between RNASEL rs486907 and prostate cancer in younger men (<65 years) and those with a first-degree relative with prostate cancer; men with AA genotype had ORs of 0.64 and 0.47 (both P < 0.05), respectively, in comparison to men with GG genotype. Within the HPCX region, there were positive associations for allele 135 of bG82i1.1 marker (OR = 1.77, P = 0.01) and allele 188 of DXS1205 (OR = 1.65, P = 0.02). In addition, allele 248 of marker D33 was inversely associated (OR = 0.65, P = 0.05) with Gleason score ≥7 tumors. CONCLUSIONS: Results suggest that variants in RNASEL contribute to susceptibility to early onset and familial forms of prostate cancer, whereas HPCX variants are associated with prostate cancer risk and tumor aggressiveness. The observation that a mutation predicted to completely inactivate RNASEL protein was not associated with prostate cancer, but that a missense variant was associated, suggests that the effect is due to either partial inactivation of the protein, and/or acquisition of a new protein activity.
Subject(s)
Adenocarcinoma/genetics , Endoribonucleases/genetics , Prostatic Neoplasms/genetics , Aged , Aged, 80 and over , Case-Control Studies , Chi-Square Distribution , DNA, Neoplasm/chemistry , DNA, Neoplasm/genetics , Genetic Predisposition to Disease , Genetic Variation , Genotype , Humans , Jews , Male , Microsatellite Repeats/genetics , Middle Aged , Polymerase Chain Reaction , Polymorphism, Single NucleotideABSTRACT
BACKGROUND: Hair is a DNA source that can be collected easily and inexpensively from participants in epidemiological studies. However, there is concern about DNA quality and quantity. Therefore, we assessed genotyping performance of whole genome amplified (WGA)-DNA extracted from hair using the GenomePlex method and evaluated its agreement with genotyping results of buccal cell DNA from the same individuals, using the Illumina GoldenGate platform. METHODS: The Illumina DNA test panel includes 360 highly validated single nucleotide polymorphisms (SNPs) selected from the Linkage IV Panel that are distributed across the entire genome. DNA was extracted from both archived hair and buccal cell samples obtained from 44 randomly selected subjects participating in a large cohort study in Canada. RESULTS: The genotyping success rate was 97.7% for 44 paired samples. However, WGA-DNA from hair failed more during genotyping in comparison to buccal cell DNA. Hair samples with a pre-WGA-DNA>or=1 ng/microL quantified using the PicoGreen assay (n=33) showed an average genotyping completion rate of 98.8% and SNP concordance of 91.2% with genotyping performance of buccal cell DNA. In contrast, samples with a pre-WGA-DNA<1 ng/microL had lower genotyping completion rate (94%) and poor SNP concordance (49%). CONCLUSIONS: Results suggest that WGA-DNA obtained from hair can produce excellent genotyping call rates and show relatively good SNP concordance with results from buccal cell DNA using high-throughput technology. DNA quantity obtained from hair samples is a crucial determinant of genotyping performance. Larger studies are needed to examine the utility of hair DNA with different genotyping platforms.
Subject(s)
DNA/genetics , Genome, Human , Hair/chemistry , Mouth Mucosa , Nucleic Acid Amplification Techniques/methods , Polymorphism, Single Nucleotide , Cohort Studies , DNA/isolation & purification , Female , Genotype , Humans , Male , Middle Aged , Mouth Mucosa/cytology , Pilot Projects , Prospective Studies , Sensitivity and Specificity , Specimen HandlingABSTRACT
BACKGROUND: Because of concerns regarding the quality and quantity of DNA isolated from human hair, such samples are often overlooked as a source of DNA for molecular epidemiological studies. Nevertheless, there are many potential benefits to using hair: it is easily self-collected; it does not require costly collection kits; it can be mailed for a nominal fee; and the hair specimens can be stored at room temperature. However, the amount of DNA that can be extracted from hair samples is somewhat limited. Therefore, we assessed the feasibility of using whole genome amplification (WGA) on genomic DNA extracted from archived human hairs (stored for 7 to 11 years) to increase the quantity of DNA available for genotyping analysis. METHODS: We evaluated two methods of WGA, multiple displacement amplification and the Genomeplex method. Both WGA methods were performed on each of 44 DNA samples isolated from archived human hair specimens. The resulting WGA products where then screened for the presence of three single nucleotide polymorphisms. The genotyping results were compared to genotyping data obtained from DNA isolated from mouthwash samples collected from the same individuals. RESULTS: When we focused on DNA extracted from the hair root, we observed excellent agreement between the genotypes determined from both the hair (pre-WGA) samples and Genomeplex WGA when compared to their corresponding mouthwash DNA samples (kappa=0.83-0.91 and 0.79-0.92, respectively); whereas the agreement between the MDA samples and mouthwash DNA samples was poor (kappa=0.27-0.51). CONCLUSIONS: Our data suggest that, when combined with Genomeplex WGA, hair specimens containing the root portion can serve as a reliable and renewable source of DNA.
