Sequenom Assay Research Articles

Association of SERPINC1 Gene Polymorphism (rs2227589) With Pulmonary Embolism Risk in a Chinese Population

Background and Aims: Genetic variants in the gene SERPINC1 have been shown to be associated with antithrombin deficiency, which subsequently contributes to the susceptibility to venous thrombosis. However, several other studies have shown conflicting results regarding the association of SERPINC1 gene polymorphisms (rs2227589) with the risk of thrombosis. Hence, in the present study, we conducted a case-control study to further evaluate the association between the variant rs2227589 with antithrombin deficiency in pulmonary embolism (PTE). A pooled systematic analysis was also conducted to evaluate the risk of rs2227589 in venous thromboembolism (VTE) among multiple populations.Methods: This case-control study involved 101 patients and 199 healthy controls. The allele frequency of SERPINC1 variant rs2227589 was analyzed by Sequenom assay. Antithrombin anticoagulant activity was detected using an automatic coagulation analyzer. In addition, a pooled systematic analysis on 10 cohorts consisting of 5,518 patients with VTE and 8,935 controls was performed.Results: In total, 27 (26.7%) PTE subjects were diagnosed as having antithrombin deficiency. Our results showed that antithrombin plasma activity was slightly lower in T allele carriers than that in C allele carriers. However, there was no significant correlation between rs2227589 genotype and antithrombin anticoagulant activity. The recessive model showed that rs2227589 was significantly associated (p = 0.026) with an increased risk {odds ratio [OR]: 2.31, 95% confidence interval [CI] (1.09–4.89)} of Chinese PTE. The pooled systematic analysis of all case-control study and meta-analysis showed that rs2227589 polymorphism was associated with an increased risk of VTE in the additive model [OR: 1.09, 95% CI (1.01–1.18), P = 0.029] and dominant model [OR: 1.10, 95% CI (1.01–1.20), P = 0.034].Conclusions: Our study demonstrated that variant rs2227589 is associated with an increased risk of PTE in a Chinese population but no correlation with antithrombin anticoagulant activity. However, pooled systematic analysis of multiple populations showed a significant association between rs2227589 and the risk of VTE in the additive and dominant genetic model.

Gene-by-Activity Interactions on Obesity Traits of 6-Year-Old New Zealand European Children: A Children of SCOPE Study.

The decline of physical activity in children is considered an important determinant to explain the rising rates of obesity. However, this risk may be augmented in children who are genetically susceptible to increased weight gain. We hypothesized that a sedentary lifestyle and moderate activity will interact with genetic loci, resulting in differential effects in relation to obesity risk. We recruited 643 European children born to participants in the New Zealand-based Screening for Pregnancy Endpoints (SCOPE) study. Seventy gene variants were evaluated by the Sequenom assay. Interaction analyses were performed between the genetic variants and the activity type derived from actigraphy, in relation to percentage body fat. We found a statistically significant association between increased proportions of sedentary activity with increased percentage body fat scores (P = .012). The OLFM4-9568856 (P = .01) and GNPDA2-rs10938397 (P = .044) gene variants showed genotype differences with proportions of sedentary activity. Similarly, the OLFM4-9568856 (P = .021), CLOCK-rs4864548 (P = .029), and LEPR-1045895 (P = .047) showed genotype differences with proportions of moderate activity. We found evidence for unadjusted gene-by-activity interactions of SPACA3/SPRASA-rs16967845, PFKP-rs6602024, and SH2B1-rs7498665 on percentage body fat scores. These findings indicate a differential effect of physical activity in relation to obesity risk, suggesting that children genetically predisposed to increased weight gain may benefit from higher levels of moderate activity.

Gene-by-environment interactions of the CLOCK, PEMT, and GHRELIN loci with average sleep duration in relation to obesity traits using a cohort of 643 New Zealand European children

ObjectivesModern technology may have desensitised the ‘biological clock’ to environmental cues, disrupting the appropriate co-ordination of metabolic processes. Susceptibility to misalignment of circadian rhythms may be partly genetically influenced and effects on sleep quality and duration could predispose to poorer health outcomes. Shorter sleep duration is associated with obesity traits, which are brought on by an increased opportunity to eat and/or a shift of hormonal profile promoting hunger. We hypothesised that increased sleep duration will offset susceptible genetic effects, resulting in reduced obesity risk. MethodsWe recruited 643 (male: 338; female: 305) European children born to participants in the New Zealand centre of the International Screening for Pregnancy Endpoints sleep study. Ten genes directly involved in the circadian rhythm machinery and a further 20 genes hypothesised to be driven by cyclic oscillations were evaluated by Sequenom assay. Multivariable regression was performed to test the interaction between gene variants and average sleep length (derived from actigraphy), in relation to obesity traits (body mass index (BMI) z-scores and percentage body fat (PBF)). ResultsNo association was found between average sleep length and BMI z-scores (p = 0.056) or PBF (p = 0.609). Uncorrected genotype associations were detected between STAT-rs8069645 (p = 0.0052) and ADIPOQ-rs266729 (p = 0.019) with differences in average sleep duration. Evidence for uncorrected gene-by-sleep interactions of the CLOCK-rs4864548 (p = 0.0039), PEMT-936108 (p = 0.016) and GHRELIN-rs696217 (p = 0.046) were found in relation to BMI z-scores but not for PBF. ConclusionOur results indicate that children may have different genetic susceptibility to the effects of sleep duration on obesity. Further confirmatory studies are required in other population cohorts of different age groups.

Genetic variants of 20q12 contributed to non-syndromic orofacial clefts susceptibility.

Previous genomewide association studies (GWAS) identified a region near MAFB at chr20q12 associated with non-syndromic orofacial clefts (NSOC) susceptibility. However, whether other SNPs in this area could independently contribute to non-syndromic orofacial clefts in Chinese populations remained obscure. We selected 24 SNPs based on a haplotype-tagging SNP strategy and evaluated their associations with risk of non-syndromic orofacial clefts in a large-scale two-stage case-control study with 1278 cases and 1295 controls. Genotyping was performed with Sequenom and TaqMan assay. Associations between the SNPs and risk of non-syndromic orofacial clefts were estimated from unconditional logistic regression analyses. Overall, six SNPs were found to be the susceptible factors of non-syndromic orofacial clefts. The most significant and independent SNP was rs6129653 (additive model of P value=1.4E-06). In subgroup analysis, its significant associations with cleft lip only (CLO) and cleft lip and palate (CLP) were observed. Furthermore, in silico bioinformatics analysis indicated that rs6129653 was located in the transcriptionally active region and associated with MAFB expression in human brain tissues. Rs6129653 was an independent locus of non-syndromic orofacial clefts among Chinese populations possibly due to its potential of distal transcriptional regulation of MAFB expression.

Abstract 806: SNPs in vitamin D-related genes are associated with prostate cancer aggressiveness in the North Carolina-Louisiana Prostate Cancer Project (PCaP)

Abstract Introduction: African Americans have higher incidence of, and mortality from, prostate cancer (PCa) compared to other racial/ethnic groups. Frequency of polymorphisms in genes involved in vitamin D metabolism, transport, and activity differ by race/ethnicity. Examining the association between polymorphisms in vitamin D-related genes and PCa aggressiveness may explain differing susceptibility to aggressive PCa among individuals and across different racial/ethnic groups. Methods: TagSNPs (n = 315) in 13 genes (VDR, GC, CYP24A1, CYP27A1, CYP27B1, CYP2R1, CYP3A4, DHCR7, CASR, NADSYN1, RXRA, RXRB, RXRG) were genotyped using Illumina GoldenGate or Sequenom assays in 524 African-American and 657 European-American men with newly-diagnosed PCa from PCaP. DNA extracted from blood samples collected at enrollment was stored at -80C prior to analyses. Research subjects were classified as high aggressive if Gleason sum ≥8, or Gleason score (4+3), or PSA >20 ng/ml, or Gleason score (3+4) AND clinical stage = T3-T4. The comparison group (low aggressive) included research subjects with Gleason sum <7 AND Stage T1-T2 AND PSA < 9 ng/ml. Odds ratios (OR) and 95% confidence intervals (95%CI) were calculated for high aggressive PCa for each SNP using logistic regression with adjustment for age and proportion of African ancestry. Associations were considered statistically significant at p<0.05. A polygenic score based on a previous study of SNP predictors of serum 25-hydroxy-vitamin D levels was calculated utilizing SNPs in the GC, CYP24A1, CYP2R1, and NADSYN1 genes. Results: Among African Americans, 21 SNPs were associated with PCa aggressiveness. The variant allele was associated negatively or positively with high aggressive PCa in eleven and ten SNPs, respectively. For example, two SNPs in the vitamin D binding protein gene known as GC, were inversely associated (rs222054: OR, 0.55, 95%CI, 0.38-0.80; and rs16847028: OR, 0.61, 95%CI, 0.39-0.94). Among European Americans, the variant allele was inversely associated with high aggressive PCa for four SNPs in three genes (CASRrs3863977; CYP24A1rs4809960; RXRArs1007971; and RXRArs3118526), and positively associated with high aggressive PCa for three SNPs in the CYP27B1 gene (rs703842, rs4646536, and rs10877013). There was no association between higher number of ‘low vitamin D’ alleles in the four SNPs that comprised the polygenic score and PCa aggressiveness for either race. Conclusions: Polymorphisms in genes involved in vitamin D etabolism and activity, the vitamin D binding protein and calcium sensing receptor were associated with PCa aggressiveness, and there was no overlap in SNPs between race groups. Our ongoing work will examine interaction between polymorphisms of vitamin D-related genes and vitamin D metabolite levels on PCa aggressiveness. Citation Format: Susan E. Steck, Anna Woloszynska-Read, Samuel Antwi, Hongmei Zhang, Lenore Arab, Elizabeth T.H. Fontham, James Mohler, L. Joseph Su, Feifei Xiao, Gary Smith, Donald Trump, Candace Johnson, Jeannette Bensen. SNPs in vitamin D-related genes are associated with prostate cancer aggressiveness in the North Carolina-Louisiana Prostate Cancer Project (PCaP). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 806.

Multicenter Feasibility Study of Tumor Molecular Profiling to Inform Therapeutic Decisions in Advanced Pediatric Solid Tumors: The Individualized Cancer Therapy (iCat) Study.

Pediatric cancers represent a unique case with respect to cancer genomics and precision medicine, as the mutation frequency is low, and targeted therapies are less available. Consequently, it is unknown whether clinical sequencing can be of benefit. To assess the feasibility of identifying actionable alterations and making individualized cancer therapy (iCat) recommendations in pediatric patients with extracranial solid tumors. Clinical sequencing study at 4 academic medical centers enrolling patients between September 5, 2012, and November 19, 2013, with 1 year of clinical follow-up. Participants were 30 years or younger with high-risk, recurrent, or refractory extracranial solid tumors. The data analysis was performed October 28, 2014. Tumor profiling performed on archived clinically acquired specimens consisted of mutation detection by a Sequenom assay or targeted next-generation sequencing and copy number assessment by array comparative genomic hybridization. Results were reviewed by a multidisciplinary expert panel, and iCat recommendations were made if an actionable alteration was present, and an appropriate drug was available. Feasibility was assessed using a 2-stage design based on the proportion of patients with recommendations. Of 100 participants (60 male; median [range] age, 13.4 [0.8-29.8] years), profiling was technically successful in 89 (89% [95% CI, 83%-95%]). Median (range) follow-up was 6.8 (2.0-23.6) months. Overall, 31 (31% [95% CI, 23%-41%]) patients received an iCat recommendation and 3 received matched therapy. The most common actionable alterations leading to an iCat recommendation were cancer-associated signaling pathway gene mutations (n = 10) and copy number alterations in MYC/MYCN (n = 6) and cell cycle genes (n = 11). Additional alterations with implications for clinical care but not resulting in iCat recommendations were identified, including mutations indicating the possible presence of a cancer predisposition syndrome and translocations suggesting a change in diagnosis. In total, 43 (43% [95% CI, 33%-53%]) participants had results with potential clinical significance. A multi-institution clinical genomics study in pediatric oncology is feasible and a substantial proportion of relapsed or refractory pediatric solid tumors have actionable alterations. clinicaltrials.gov Identifier: NCT01853345.

Rare and Common Germline Variants Contribute to Occurrence of Myelodysplastic Syndrome

Background: Majority of MDS cases appear to be sporadic in nature, but 10-15% have clear familial basis due to predisposing mutations in genes such as RUNX1, GATA2, CEBPA and DDX41. Contribution of germline variants in sporadic MDS is not studied. This study attempts to address the contribution of germline variants in MDS pathogenesis.Methods: We performed amplicon-based massively parallel sequencing (AmpliSeq custom panel adapted for Illumina HiSeq2500 sequencing) on all coding regions of 29 myeloid genes for 144 MDS samples. After identifying the variants in five genes (TET2, MET, GATA2, ASXL1, NOTCH1), we tested an additional 96 MDS samples including therapy-related myeloid neoplasm (T-MN) using a Sequenom assay. We also analyzed WES data for these variants in 178 AML samples and 758 normal controls and AmpliSeq data for ASXL1 and TET2 variants in 655 CML samples.Results: Collation of all coding variants in the 29 myeloid genes sequenced identified germline variants occurring in primary MDS at frequencies significantly higher than expected when compared to the normal population (ExAC and matched cohort were similar) (Table 1). These variants occurred in 5 genes (TET2, MET, GATA2, ASXL1 and NOTCH1) at increased frequencies of 1.5-16.6 fold. Numerous MDS samples had multiple variants (4 with 4 variants, 4 with 3 variants, 18 with 2 variants) while 70 had 1 variant.The 3 germline MET variants have been previously investigated in solid tumorigenesis and likely generate MET variant proteins that contribute to numerous cancer types including MDS. Interestingly, 7/17 (41%) MDS cases with germline MET variants also had other cancers including pancreatic, gastric and laryngeal cancers. Of the TET2 variants, Y867H and P1723S were concurrent in 5 MDS, 5 AML and 6 CML samples indicative of them being on the same allele (i.e. a haplotype). They were seen at higher than normal frequency in MDS and AML, but were not significantly enriched in CML. We are currently confirming their coexistence on the same allele and assaying for decreased TET2 activity to determine whether one or both variants contribute to the phenotype.Other variants identified in MDS include the rare GATA2 (P161A) variant which is present in 1% of the population and the nearby common GATA2 (A164T) allele (~20%). These were mutually exclusive in our cohort and were seen at 3.9 and 1.5-fold, respectively, above the expected population frequency. We generated the P161A variant using site-directed mutagenesis and assayed for GATA2 transactivation activity in HEK293 cells with a GATA2-responsive LYL1 promoter-Luciferase construct (Figure 1). We also included empty vector (EV), wildtype (WT) GATA2 and T354M which is the most common highly penetrant autosomal dominant mutation leading to familial MDS/AML. As expected, T354M displayed a marked decrease in transactivation ability when compared to WT. The P161A variant similarly displayed loss-of-function in this assay, but not to the same magnitude as T354M. This is consistent with the hypothesis that reduced GATA2 function predisposes to myeloid malignancy where decreasing GATA2 activity correlates with increasing risk of developing malignancy. In our study 10/36 (28%) cases harboring these variants were T-MN cases.Apart from MET (E168D) (11.4-fold), the 2 rare variants with highest frequency in MDS versus controls were ASXL1 (N986S) (16.6-fold) and NOTCH1 (R912W) (6.5-fold). ASXL1 is an epigenetic regulator often mutated in hematopoietic malignancy and aberrant NOTCH1 function has been associated with myeloid and lymphoid malignancies.Conclusions: We have identified common and rare germline variants in genes involved in myeloid malignancy that may contribute to MDS pathogenesis. It remains to be seen whether they contribute to initiation, maintenance and/or progression of MDS and other hematopoietic malignancies. This is the first study reporting higher frequency of germline variants in sporadic MDS cases. [Display omitted] [Display omitted] DisclosuresHiwase:Celgene Corporation: Research Funding.

Variant in the RFWD3 gene associated with PATN1, a modifier of leopard complex spotting.

Leopard complex spotting (LP), the result of an incompletely dominant mutation in TRPM1, produces a collection of unique depigmentation patterns in the horse. Although the LP mutation allows for expression of the various patterns, other loci are responsible for modification of the extent of white. Pedigree analysis of families segregating for high levels of patterning indicated a single dominant gene, named Pattern-1 (PATN1), as a major modifier of LP. Linkage analysis in two half-sibling families segregating for PATN1 identified a 15-Mb region on ECA3p that warranted further investigation. Whole transcriptome sequencing of skin samples from horses with and without the PATN1 allele was performed to identify genic SNPs for fine mapping. Two Sequenom assays were utilized to genotype 192 individuals from five LP-carrying breeds. The initial panel highlighted a 1.6-Mb region without a clear candidate gene. In the second round of fine mapping, SNP ECA3:23 658 447T>G in the 3'-UTR of RING finger and WD repeat domain 3 (RFWD3) reached a significance level of P = 1.063 × 10(-39). Sequencing of RFWD3 did not identify any coding polymorphisms specific to PATN1 horses. Genotyping of the RFWD3 3'-UTR SNP in 54 additional LP animals and 327 horses from nine breeds not segregating for LP further supported the association (P = 4.17 × 10(-115)). This variant is a strong candidate for PATN1 and may be particularly useful for LP breeders to select for high levels of white patterning.

Case-control study of ADARB1 and ADARB2 gene variants in migraine.

BackgroundMigraine causes crippling attacks of severe head pain along with associated nausea, vomiting, photophobia and/or phonophobia. The aim of this study was to investigate single nucleotide polymorphisms (SNPs) in the adenosine deaminase, RNA-specific, B1 (ADARB1) and adenosine deaminase, RNA specific, B2 (ADARB2) genes in an Australian case–control Caucasian population for association with migraine. Both candidate genes are highly expressed in the central nervous system and fit criteria for migraine neuropathology. SNPs in the ADARB2 gene were previously found to be positively associated with migraine in a pedigree-based genome wide association study using the genetic isolate of Norfolk Island, Australia. The ADARB1 gene was also chosen for investigation due to its important function in editing neurotransmitter receptor transcripts.MethodsFour SNPs in ADARB1 and nine in ADARB2 were selected by inspecting blocks of linkage disequilibrium in Haploview for genotyping using either TaqMan or Sequenom assays. These SNPs were genotyped in two-hundred and ninety one patients who satisfied the International Classification of Headache Disorders-II 2004 diagnostic criteria for migraine, and three-hundred and fourteen controls, and PLINK was used for association testing.ResultsChi-square analysis found no significant association between any of the SNPs tested in the ADARB1 and ADARB2 genes in this study and the occurrence of migraine.ConclusionsIn contrast to findings that SNPs in the ADARB2 gene were positively associated with migraine in the Norfolk Island population, we find no evidence to support the involvement of RNA editing genes in migraine susceptibility in an Australian Caucasian population.

The Effect of BCMO1 Gene Variants on Macular Pigment Optical Density in Young Healthy Caucasians.

Background: Serum lutein (L) and zeaxanthin (Z) positively correlate with macular pigment optical density (MPOD); hence, the latter is a valuable indirect tool for measuring L and Z content in the macula. L and Z have been attributed antioxidant capacity and protection from certain retinal diseases but their uptake within the eye is thought to depend on genetic, age, and environmental factors. In particular, gene variants within beta-carotene monooxygenase (BCMO1) are thought to modulate MPOD in the macula.Objectives: To determine the effect of BCMO1 single nucleotide polymorphisms (SNPs) rs11645428, rs6420424, and rs6564851 on MPOD in a cohort of young healthy participants of Caucasian origin with normal ocular health.Design: In this cohort study, MPOD was assessed in 46 healthy participants (22 male and 24 female) with a mean age of 23.8 ± 4.0 years (range 19–33). The three SNPs, rs11645428, rs6420424, rs6564851 that have established associations with MPOD were determined using MassEXTEND (hME) Sequenom assay. One-way analysis of variance was performed on groups segregated into homozygous and heterozygous BCMO1 genotypes. Correlations between body mass index (BMI), iris color, gender, central retinal thickness (CRT), diet, and MPOD were investigated.Results: Macular pigment optical density neither significantly varied with BCMO1 rs11645428 (F2,41 = 0.70, p = 0.503), rs6420424 (F2,41 = 0.21, p = 0.801) nor rs6464851 homozygous or heterozygous genotypes (F2,41 = 0,13, p = 0.88), in this young healthy cohort. The combination of these three SNPs into triple genotypes based on plasma conversion efficiency did not affect MPOD (F2,41 = 0.07, p = 0.9). There was a significant negative correlation with MPOD and CRT (r = −0.39, p = 0.01) but no significant correlation between BMI, iris color, gender, and MPOD.Conclusion: Our results indicate that macular pigment deposition within the central retina is not dependent on BCMO1 gene variants in young healthy people. We propose that MPOD is saturated in younger persons and/or other gene variant combinations determine its deposition.

Impact of single nucleotide polymorphism of cyclophosphamide metabolism gene in patients with diffuse large B-cell lymphoma on survival after chemotherapy.

e13519 Background: Cyclophosphamide (Cy) is a prodrug metabolized in liver into active cytotoxin. Cy-containing chemotherapy is often curative for patients with diffuse large B Cell lymphoma (DLBCL); however, 50% of patients relapse. We investigated the association between genetic polymorphisms in Cy metabolism and outcomes after induction chemotherapy for DLBCL Methods: We studied 76 patients with DLBCL treated with standard dose Cy-containing regimens (Cy 500mg/m2) at the University of Minnesota. Somatic DNA was obtained from bone marrow aspirates, and Sequenom and Taqman genotyping assays were used to analyze 22 genes and 38 single nucleotide polymorphisms (SNP) involved in Cy metabolism. Two-year disease free survival (DFS) was compared using a Cox regression model for each SNP, adjusting for age (≥ 65) and gender. The odds of achieving complete remission (CR) were modeled using logistic regression. P-values were corrected for multiple testing using the Holm method. Results: Sixty-one patients (80%) a...

Single-Nucleotide Polymorphisms in the LEPR Gene Are Associated with Divergent Phenotypes for Age at Onset of Puberty in Davisdale Ewes1

Attainment of puberty is a key developmental event influenced by genetic and environmental factors. In examining age at attainment of puberty, we observed closely related rams from the Davisdale line whose daughters differed in age at which they attained puberty. A candidate gene approach was used to identify mutations that may underlie these observed differences. Four rams with divergent phenotypes for their daughter's age at onset of puberty were selected for whole-genome sequencing. The coding regions of genes with known roles in regulating reproductive function were searched for single-nucleotide polymorphisms (SNPs) that altered the amino acid sequence of the protein. Of interest were three SNPs in the leptin receptor gene (LEPR). A Sequenom assay was developed to determine the genotype of these SNPs in daughters of 17 sons of a founding sire. A higher percentage of ewe lambs homozygous for the LEPR mutations failed to undergo puberty before 1 yr of age, and those that did undergo puberty during the first breeding season on average were approximately 17 days older than homozygous wild-type ewes. Heterozygous ewes were intermediate for both measurements. Given the predicted change in protein function produced by the mutation in LEPR and the strong associations between the genotype and onset of puberty phenotypes, we propose that this mutation in LEPR underlies the observed difference in age at onset of puberty in the Davisdale line. Furthermore, these animals will likely provide a useful model to better understand the role of leptin in the regulation of puberty.

A Single Nucleotide Polymorphism in the Cytochrome p450 Gene Positively Impacts Survival Post Cyclophosphamide Conditioning in Autologous Transplants for Lymphoma

Cyclophosphamide (Cy) is a prodrug metabolized by hepatic cytochrome p450 enzymes into active cytotoxin. High dose Cy-containing chemotherapy followed by autologous hematopoietic cell transplant (autoHCT) is often curative for patients with lymphoma; however, relapse occurs in about 50% of patients. We investigated the association between genetic polymorphisms in Cy metabolism and outcomes after autoHCT for lymphoma. We studied lymphoma patients who received myeloablative Cy-containing conditioning between 2004-2012 with available DNA samples. Somatic DNA was obtained from pre-transplant bone marrow aspirates, and Sequenom and Taqman genotyping assays were used to analyze 22 genes and 38 single nucleotide polymorphisms (SNP) involved in Cy metabolism. All patients were followed for at least one year. The association of each SNP with overall survival (OS) and disease-free survival (DFS) following autoHCT was analyzed using multivariable Cox regression, with categorical factors for genotype, age (≥ 55 vs. < 55 years), and gender. A separate model was used for each SNP. P-values were corrected for multiple testing using the Holm method. We studied 93 patients (median age 45 years) with lymphoma (52 Hodgkin, 21 diffuse large B cell, 12 mantle cell, 8 others); 55% were male. Two-thirds received Cy (120 mg/kg) combined with BCNU/etoposide conditioning and a third received Cy (6000 mg/ m2) with total body irradiation (1250 cGy). The majority (96%) had chemosensitive disease with 61% in complete remission pre transplant. Two year DFS and OS for the entire cohort was 60% (95%CI 49-69%) and 86% (95%CI 76-91%), respectively. A single SNP rs3211371 in the CYP2B6 gene significantly impacted survival. This SNP results in Arg487Cys and influences CYP2B6 activity. Adjusted for age and gender, patients heterozygous (CT; n=69) for SNP rs3211371 had significantly better DFS (HR 0.27; 95%CI 0.13- 0.56 ; p=0.024) and OS ( HR 0.09; 95%CI: 0.02-0.35; p=0.03) as compared to homozygous patients (TT; n=21). This association was not confounded by age, gender, disease type, conditioning, or remission status. Our results show a strong association between CYP2B6 rs3211371 SNP and survival in lymphoma patients treated with high-dose Cy and autoHCT. We plan to evaluate serum levels of Cy active metabolites and confirm the potency of this association in a larger study.

ZNF300P1 Encodes a lincRNA that regulates cell polarity and is epigenetically silenced in type II epithelial ovarian cancer

BackgroundWe previously identified that the CpG island-associated promoter of the novel lincRNA ZNF300P1 (also known as LOC134466) is frequently hypermethylated and silenced in ovarian cancer tissues. However, the function of ZNF300P1 was unknown. In this report we demonstrate that ZNF300P1 is involved in the regulation of key cell cycle and cell motility networks in human ovarian surface epithelial cells, and may play a role in promoting metastasis in ovarian cancer cells.MethodsWe applied methylated DNA immunoprecipitation on whole genome promoter tiling arrays and Sequenom assays to examine methylation status of ZNF300P1 in multiple ovarian cancer cell lines, as well as in normal ovarian and ovarian tumor tissues. Transcript profiling was used to investigate the effects of ZNF300P1 suppression in ovarian cancer cells. We utilized siRNA knockdown in normal ovarian surface epithelial cells and performed cellular proliferation, migration and adhesion assays to validate and explore the profiling results.ResultsWe demonstrate that ZNF300P1 is methylated in multiple ovarian cancer cell lines. Loss of ZNF300P1 results in decreased cell proliferation and colony formation. In addition, knockdown of the ZNF300P1 transcript results in aberrant and less persistent migration in wound healing assays due to a loss of cellular polarity. Using an ex vivo peritoneal adhesion assay, we also reveal a role for ZNF300P1 in the attachment of ovarian cancer cells to peritoneal membranes, indicating a potential function of ZNF300P1 expression in metastasis of ovarian cancer cells to sites within the peritoneal cavity.ConclusionOur findings further support ZNF300P1 as frequently methylated in ovarian cancer and reveal a novel function for ZNF300P1 lincRNA expression in regulating cell polarity, motility, and adhesion and loss of expression may contribute to the metastatic potential of ovarian cancer cells.

Haplotype association analysis of genes within the WNT signalling pathways in diabetic nephropathy

BackgroundRenal interstitial fibrosis and glomerular sclerosis are hallmarks of diabetic nephropathy (DN) and several studies have implicated members of the WNT pathways in these pathological processes. This study comprehensively examined common genetic variation within the WNT pathway for association with DN.MethodsGenes within the WNT pathways were selected on the basis of nominal significance and consistent direction of effect in the GENIE meta-analysis dataset. Common SNPs and common haplotypes were examined within the selected WNT pathway genes in a white population with type 1 diabetes, discordant for DN (cases: n = 718; controls: n = 749). SNPs were genotyped using Sequenom or Taqman assays. Association analyses were performed using PLINK, to compare allele and haplotype frequencies in cases and controls. Correction for multiple testing was performed by either permutation testing or using false discovery rate.ResultsA logistic regression model including collection centre, duration of diabetes, and average HbA1c as covariates highlighted three SNPs in GSK3B (rs17810235, rs17471, rs334543), two in DAAM1 (rs1253192, rs1252906) and one in NFAT5 (rs17297207) as being significantly (P < 0.05) associated with DN, however these SNPs did not remain significant after correction for multiple testing. Logistic regression of haplotypes, with ESRD as the outcome, and pairwise interaction analyses did not yield any significant results after correction for multiple testing.ConclusionsThese results indicate that both common SNPs and common haplotypes of WNT pathway genes are not strongly associated with DN. However, this does not completely exclude these or the WNT pathways from association with DN, as unidentified rare genetic or copy number variants could still contribute towards the genetic architecture of DN.

Combined whole genome copy number genotyping and multiplex somatic mutation profiling of FFPE brain tumor specimens for clinical diagnosis and trial selection.

2030 Background: Multi-dimensional cancer genotyping is increasingly needed for clinical diagnostics and trial selection. Whole genome copy number is relevant for glioblastoma and other brain tumors but routine prospective FFPE-based multiplex copy number and somatic mutation genotyping for clinical trials has not been achieved. Methods: Using novel DNA extraction protocols we implemented whole genome copy number (Agilent aCGH stock 1M feature arrays) and somatic mutation profiling (Oncomap v4.4 Sequenom) assays into a CLIA-certified laboratory setting. Twenty-three copy number aberrations (CNAs) relevant to brain tumors were reported from whole genome data and Oncomap results were reported for 471 cancer-related mutations in 41 genes. Results: During the initial eight months of our combined copy number and mutation-testing program, aCGH and Oncomap were performed prospectively on 239 and 157 brain tumor patients respectively. Copy number was reported in 90% of patients (214/239) and failures were due to insufficient DNA from small biopsies. GBMs (n = 94) harbored gains and losses at expected rates and included amplifications of common drug targets (EGFR, EGFRv3, MET, MDM2, MDM4, PDGFRA, CDK4, CDK6). Emerging candidate drug targets were identified including variant EGFR deletions (e.g. EGFRv2) and FGFR3-TACC3 gains for which other clinical tests are not available. Oncomap results for 78 GBMs revealed mutations in TP53, PTEN and IDH1. Less frequent mutations occurred in BRAF, RB1, PIK3CA, PIK3R1 and KRAS. We integrated copy number and mutation data for 27 GBMs, allowing for improved evaluation of tumor suppressor inactivation status (e.g. PTEN mutation with monosomy 10). In combination, our assays reported data on 10 clinically actionable drug targets relevant for 15 clinical trials open at the time of patient testing. Conclusions: We implemented complementary assays for efficiently detecting genome-wide CNAs and mutations on FFPE brain tumor samples in a CLIA-certified environment. Systematic integration of these results broadens the range of diagnostic and actionable data available to identify patients for trials of targeted therapeutics.

Abstract 23: Low incidence of BRAFV600E mutation among melanoma patients in Ireland.

Abstract Background: Aberrant activity of the mitogen-activated protein kinase (MAPK) signalling pathway represents a critical factor in the initiation and development of melanoma. Activation can be the result of largely mutually exclusive somatic mutations of KIT, NRAS, or more frequently, BRAF(V600E). The FDA and EMA approval of a BRAF inhibitor (vemurafenib) that blocks the function of the BRAFV600E protein established a new paradigm for targeted drug development. Currently, BRAF inhibitors are one of the most promising approaches to treat metastatic melanoma. Methods: In this study, we applied mass spectrometry-based SNP genotyping (Sequenom) to detect single nucleotide mutations in 33 cancer-related genes including BRAF, NRAS, KIT, CTNNB1, GNAS, and MET. PCR and extension primers for the multiplexed assay were designed with the Sequenom Assay Design software. Samples were processed as recommended by the manufacturer. Matrix chips were assayed on a Sequenom MassArray MALDI-TOF Mass Array system. Visual inspection and Sequenom Typer software were used to perform genotyping based on mass spectra. We compared two independent melanoma cohorts, one from Ireland (SVUH cohort; n=97) and the other from Belgium (Leuven cohort; n=60). Results: Intriguingly, patients from Ireland showed significant lower BRAFV600E mutation rates (19.0%) when compared to the mutation frequency seen with the Belgian cohort (43.3%) or with the mutation frequency reported by other studies on non-Irish populations (50-70%). In addition, BRAFV600K mutation is rare in the SVUH cohort (1.0%) compared with the Leuven cohort (6.7%). Mutations in BRAFV600M and V600R were &amp;lt;2% in both groups. Although the number of NRASQ61 mutant cases was slightly higher among the Irish melanoma patients compared with Belgium patients (20.6% and 13.3%, respectively), this does not fully account for the difference in BRAFV600E mutation rate. In contrast, many BRAFV600 WT patients in the SVUH cohort carried significantly increased mutation rates in MET (11.4%) compared to the Leuven cohort (0%) and reported elsewhere (2%). c-MET is a receptor tyrosine kinase that activates multiple signal transduction pathways, including MAPK, PI3K, WNT, and Notch. MET inhibitors that are currently in clinical trials include cabozantinib and foretinib and might be a valuable alternative treatment strategy for patients exhibiting this mutation. Mutation rates of the other examined genes were always &amp;lt;5% and did not significantly differ between the groups. Conclusion: Our observation of reduced BRAFV600E mutation rates in Irish patients will directly impact future treatment strategies for these patients. The identification of substantial mutation rates in MET opens up opportunities for targeting a significant subset of melanoma patients with MET inhibitors. Citation Format: Balazs Balint, Karin van den Hurk, Sinead Toomey, Louise Unwin, Kieran Sheahan, Enda McDermott, Ian Murphy, Joost van den Oord, Mairin Rafferty, Bryan Hennessy, William M. Gallagher. Low incidence of BRAFV600E mutation among melanoma patients in Ireland. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 23. doi:10.1158/1538-7445.AM2013-23

Efficient arsenic metabolism--the AS3MT haplotype is associated with DNA methylation and expression of multiple genes around AS3MT.

Arsenic is a very potent toxicant. One major susceptibility factor for arsenic-related toxicity is the efficiency of arsenic metabolism. The efficiency, in turn, is associated with non-coding single nucleotide polymorphisms (SNPs) in the arsenic methyltransferase AS3MT on chromosome 10q24. However, the mechanism of action for these SNPs is not yet clarified. Here, we assessed the influence of genetic variation in AS3MT on DNA methylation and gene expression within 10q24, in people exposed to arsenic in drinking water. DNA was extracted from peripheral blood from women in the Argentinean Andes (N = 103) and from cord blood from new-borns in Bangladesh (N = 127). AS3MT SNPs were analyzed with Sequenom or Taqman assays. Whole genome epigenetic analysis with Infinium HumanMethylation450 BeadChip was performed on bisulphite-treated DNA. Whole genome gene expression analysis was performed with Illumina DirectHyb HumanHT-12 v4.0 on RNA from peripheral blood. Arsenic exposure was assessed by HPLC-ICPMS. In the Argentinean women, the major AS3MT haplotype, associated with more efficient arsenic metabolism, showed increased methylation of AS3MT (p = 10−6) and also differential methylation of several other genes within about 800 kilobasepairs: CNNM2 (p<10−16), NT5C2 (p<10−16), C10orf26 (p = 10−8), USMG5 (p = 10−5), TRIM8 (p = 10−4), and CALHM2 (p = 0.038) (adjusted for multiple comparisons). Similar, but weaker, associations between AS3MT haplotype and DNA methylation in 10q24 were observed in cord blood (Bangladesh). The haplotype-associated altered CpG methylation was correlated with reduced expression of AS3MT and CNNM2 (rs = −0.22 to −0.54), and with increased expression of NT5C2 and USMG5 (rs = 0.25 to 0.58). Taking other possibly influential variables into account in multivariable linear models did only to a minor extent alter the strength of the associations. In conclusion, the AS3MT haplotype status strongly predicted DNA methylation and gene expression of AS3MT as well as several genes in 10q24. This raises the possibility that several genes in this region are important for arsenic metabolism.

Abstract B84: The association between germline genetic variants in the PI3K pathway and PI3K mutations in breast tumors.

Abstract Background: Gene mutations in the PI3K pathway in breast tumors are associated with resistance to tamoxifen and poorer prognosis. Differences in host susceptibility to developing breast cancers with PI3K pathway mutations may explain the heterogeneity in response to tamoxifen for chemoprevention and breast cancer outcomes. The objective of the study was to evaluate the association between host germline single nucleotide polymorphisms (SNPs) and activation of the PI3K pathway in breast tumors. Methods: We extracted tumor and germline DNA from 386 women with stages I-II breast cancer treated at the MD Anderson Cancer Center. Nine PI3K mutation sites were evaluated using the Sequenom assay and 57 tagging single nucleotide polymorphisms (SNPs) of candidate genes in the PI3K pathway were genotyped using the Illumina Golden Gate Platform. Results: 36 patients (10%) had at least one mutation in the PI3K pathway. There was no association between PI3K mutation status by age at diagnosis or ethnicity. In univariate analysis, there was a statistically significant association between PI3K gene mutation status and 3 tagging SNPs in the genes, PTEN (rs123421, rs1234213) and IGF-1 (rs2033178). Conclusion: PI3K mutations are rare in breast tumors but represent a druggable target for prevention and treatment. Host genetics may play a role in contributing to tumor biology and serve to identify individuals at risk for tumors with PI3K pathway activation and tamoxifen resistance. Citation Format: Abenaa M. Brewster, Melissa Bondy, Kim-anh Do, Aysegul Sahin, Katherine Hale, Caimiao Wei, Gordon Mills, Patricia Thompson. The association between germline genetic variants in the PI3K pathway and PI3K mutations in breast tumors. [abstract]. In: Proceedings of the Eleventh Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2012 Oct 16-19; Anaheim, CA. Philadelphia (PA): AACR; Cancer Prev Res 2012;5(11 Suppl):Abstract nr B84.

Comprehensive Study on Associations Between Nine SNPs and Glioma Risk

Glioma cancer is the most common type of adult brain tumor. Recent genome-wide association studies (GWAS) have identified various new susceptibility regions and here we conducted an extensive analysis of associations between 12 single nucleotide polymorphisms (SNPs) and glioma risk. A total of 197 glioma cases and 197 health controls were selected, and 9 SNPs in 8 genes were analyzed using the Sequenom MassARRAY platform and Sequenom Assay Design 3.1 software. We found the MAF among selected controls were consistent with the MAF from the NCBI SNP database. Among 9 SNPs in 8 genes, we identified four significant SNP genotypes associated with the risk of glioma, C/C genotype at rs730437 and T/T genotype at rs1468727 in ERGF were protective against glioma, whereas the T/T genotype at rs1799782 in XRCC1 and C/C genotype at rs861539 in XRCC3 conferred elevated risk. Our comprehensive analysis of nine SNPs in eight genes suggests that the rs730437 and rs1468727 in ERGF, rs1799782 in XRCC1 gene, and rs861539 in XRCC3 gene are associated with glioma risk. These findings indicate that genetic variants of various genes play a complex role in the development of glioma.