Obtained Genotype Data Research Articles

Clinical results on single cells from 470 embryos using 23-chromosome single nucleotide polymorphism (SNP) microarray preimplantation genetic screening (PGS) from 45 patients

OBJECTIVE: We amplified DNA from a single blastomere or trophectoderm cells and performed complex SNP microarray genetic analyses. DESIGN: Prospective study. MATERIALS AND METHODS: PGS patients between 12/1/09 and 4/25/10 were analyzed. 45 patients underwent embryo biopsy by laser and SNP microarray PGS primarily due to > 2 spontaneous miscarriages. 3 of these patients were tested for translocation abnormalities and aneuploidy. The maternal ages ranged from 34 to 44yrs. 398 embryos from 37 patients underwent day-3 biopsies, whereas 72 embryos from 8 patients underwent blastocyst trophectoderm biopsies. We amplified the DNA using a modified whole genome amplification (WGA) protocol. We used the Illumina Cyto-12 microarray to determine chromosome aberrations and to obtain genotype data for ∼300K SNPs. A high-resolution copy-number profile was used to identify copy number variations (CNVs). Parental DNA was simultaneously analyzed with embryo DNA for CNVs. Data was analyzed with Illumina GenomeStudio software. RESULTS: 45 patients and 470 embryos were tested. 37 patients undergoing a day-3 biopsy were considered for embryo transfer along with 1 patient undergoing a blastocyst biopsy. All embryos from an additional 7 patients undergoing blastocyst biopsies and PGS were frozen. 59% (277/470) of the embryos were abnormal. Many embryos with CNVs were considered normal because of parental CNV analysis. 3.1 ± 2 euploid embryos were identified per patient/cycle. The overall clinical pregnancy rate was 62%. The blastocyst biopsy transferred patient is pregnant.Tabled 1Clinical Pregnancy by Age GroupAgeClinical PregnancyMiscarriageNo TransferFrozen〈3556% (5/9)4% (1/23)0235-3763% (5/8)01038-4075% (9/12)004〉4044% (4/9)041 Open table in a new tab CONCLUSION: 23-chromosome SNP microarray PGS is a valuable technology in an effort to optimize the transfer of euploid embryos and to increase the delivery rates of couples undergoing in vitro fertilization (IVF) due to repeat miscarriages.

Polymorphisms in the Vitamin D Receptor and Risk of Ovarian Cancer in Four Studies

Prior studies have suggested that vitamin D may reduce ovarian cancer risk. Thus, we examined whether three single nucleotide polymorphisms (SNP) in the vitamin D receptor (VDR) gene (Fok1, Bsm1, Cdx2) were associated with risk of epithelial ovarian cancer in a retrospective case-control study (New England Case-Control study, NECC) and a nested case-control study of three prospective cohort studies: the Nurses' Health Study (NHS), NHSII, and the Women's Health Study. Data from the cohort studies were combined and analyzed using conditional logistic regression and pooled with the results from the NECC, which were analyzed using unconditional logistic regression, using a random effects model. We obtained genotype data for 1,473 cases and 2,006 controls. We observed a significant positive association between the number of Fok1 f alleles and ovarian cancer risk in the pooled analysis (P(trend) = 0.03). The odds ratio (OR) for the ff versus FF genotype was 1.26 [95% confidence interval (CI) = 1.01-1.57]. Neither the Bsm1 (P(trend) = 0.96) or Cdx2 (P(trend) = 0.13) SNPs were significantly associated with ovarian cancer risk. Among the prospective studies, the risk of ovarian cancer by plasma vitamin D levels did not clearly vary by any of the genotypes. For example, among women with the Fok1 FF genotype, the OR comparing plasma 25-hydroxyvitamin D >or=32 ng/mL versus <32 ng/mL was 0.66 (95% CI, 0.34-1.28), and among women with the Ff or ff genotype the OR was 0.71 (95% CI, 0.43-1.18). Our results of an association with the Fok1 VDR polymorphism further support a role of the vitamin D pathway in ovarian carcinogenesis.

Catechol-O-methyltransferase genotype is associated with plasma total homocysteine levels and may increase venous thrombosis risk

A disturbed methylation has been proposed as a mechanism via which homocysteine is associated with diseases like vascular disease, neural tube defects and mental disorders. Catechol-O-methyltransferase (COMT) is involved in the S-adenosylmethionine-dependent methylation of catecholamines and catecholestrogens and in this way contributes to homocysteine synthesis. COMT dysfunction has been related to schizophrenia and breast cancer. We hypothesized that COMT dysfunction by virtue of functional genetic polymorphisms may affect plasma total homocysteine (tHcy). Our primary objective was to study the association between common COMT polymorphisms and tHcy. Secondly, we evaluated these polymorphisms as a risk factor for recurrent venous thrombosis. We obtained genotype data from four polymorphisms in the COMT gene (rs2097603, rs4633, rs4680 [324G>A] and rs174699) from 401 population-based controls. We performed haplotype analysis to investigate the association between common haplotypes and tHcy. In addition, we assessed the rs4680 variant as a genetic risk factor in a case-control study on recurrent venous thrombosis (n = 169). We identified a common haplotype that was significantly associated with tHcy levels. This effect was largely explained by the rs4680 variant, resulting in an increase in tHcy of 10.4% (95% CI 0.01 to 0.21, p = 0.03) for 324AA compared with 324GG subjects. Interestingly, we found that the 324AA genotype was more common in venous thrombosis patients (OR 1.61 [95% CI 0.97 to 2.65], p = 0.06) compared to control subjects. We show that the COMT rs4680 variant modulates tHcy, and might be associated with venous thrombosis risk as well.