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Abstract 4635: Inherited variants affecting RNA editing may contribute to ovarian cancer susceptibility
Permuth‐Wey, Jennifer, Reid, Brett M. , Chen, Zhihua , Gayther, Simon A. , Goode, Ellen L. , Iversen, Edwin S. , Pearce, Leigh, Phelan, Catherine, Rossing, Mary Anne, Schildkraut, Joellen M. , Sellers, Thomas A. , Chen, Y. Ann , Lin, Hui‐Yi , Monteiro, Álvaro N.A. , Berchuck, Andrew , Chenevix‐Trench, Georgia , Doherty, Jennifer A. , Pharoah, Paul D.P. , Ramus, Susan J. , Rossing, Mary Anne

Cancer Research | August 5, 2015 | Volume: 75 | Issue: 15_Supplement | Pages: 4635-4635

10.1158/1538-7445.am2015-4635 Get It

Abstract Background: Recent bioinformatic analyses and high-throughput sequencing efforts have revealed that RNA editing is a widespread post-transcriptional modification that affects non-coding repetitive elements throughout the genome. This modification, which involves the conversion of adenosine into inosine, is mediated by the action of the adenosine deaminases acting on RNA (ADAR) family of enzymes. Based on reports of dysfunctional ADAR expression in epithelial ovarian cancers (EOC), we hypothesized that single nucleotide polymorphisms (SNPs) in five ADAR genes (ADAD1, ADAR1, ADAR2, ADAR3, SND1) may contribute to EOC susceptibility, potentially by altering the expression of corresponding genes in ovarian tissues. Methods: Using directly genotyped and imputed data from 10,891 invasive EOC cases and 21,693 healthy controls of European ancestry represented in the international Collaborative Oncological Gene-environment Study, we evaluated the frequency of 7,133 SNPs in 5 RNA editing genes. Unconditional logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) between genotypes and case status under a log-additive genetic model, with adjustment for the first five principal components representing European ancestry. Subgroup analysis was conducted for the four main histologic sub-types of EOC. We also aggregated SNP-level data and conducted gene-level analyses using the Admixture Maximum Likelihood (AML) test and the Sequence-Kernel Association test for the combined effect of common and rare variants (SKAT-CR). Results: Association analysis revealed a top risk-associated SNP (OR (95% CI) = 1.39 (1.17-1.64)) in ADAR3 with P = 1.3 x10−4, 17 additional SNPs in ADAR1, ADAR3, or SND1 with P = 10−4, and 51 SNPs with P = 10−3; this observed number of statistically-significant SNPs was greater than expected. When restricting to the 6,500 invasive serous adenocarcinomas, the magnitude of association strengthened for numerous SNPs. Exploratory analysis for the less common histologic subtypes (endometrioid (n = 1,439), mucinous (n = 696), and clear cell (n = 660)) revealed SNP-level associations (P<10−3) unique to each sub-type. Gene-level analyses based on AML and SKAT-CR revealed that ADAR1 was globally associated (P<0.10) with susceptibility to invasive EOC, with P = 0.024 and P = 0.023, respectively. Expression quantitative trait locus analysis is underway to evaluate associations between genotype and gene expression in EOC and precursor tissues using data from The Cancer Genome Atlas Project and other sources. Conclusions: Preliminary data from this large-scale collaboration suggest that germline variation involving RNA editing genes may influence susceptibility to EOC. This novel finding warrants further investigation, as inherited and acquired alterations affecting RNA editing may serve as important biological mechanisms that promote the development of EOC and possibly other malignancies. Citation Format: Jennifer Permuth-Wey, Brett M. Reid, Y. Ann Chen, Hui-Yi Lin, Alvaro Monteiro, Zhihua Chen, Andrew Berchuck, Georgia Chenevix-Trench, Jennifer Doherty, Simon Gayther, Ellen Goode, Edwin Iversen, Leigh Pearce, Paul D. P. Pharoah, Catherine Phelan, Susan Ramus, Mary Anne Rossing, Joellen Schildkraut, Thomas Sellers, on behalf of the Ovarian Cancer Association Consortium. Inherited variants affecting RNA editing may contribute to ovarian cancer susceptibility. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4635. doi:10.1158/1538-7445.AM2015-4635
Abstract 4634: Variants within super-enhancer regulatory elements associate with epithelial ovarian cancer risk
Reid, Brett M. , Permuth‐Wey, Jennifer, Chen, Zhihua , Gayther, Simon A. , Goode, Ellen L. , Iversen, Edwin S. , Pearce, Leigh, Phelan, Catherine, Rossing, Mary Anne, Schildkraut, Joellen M. , Sellers, Thomas A. , Chen, Y. Ann , Lin, Hui‐Yi , Monteiro, Álvaro N.A. , Berchuck, Andrew , Chenevix‐Trench, Georgia , Doherty, Jennifer A. , Pharoah, Paul D.P. , Ramus, Susan J.

Cancer Research | August 5, 2015 | Volume: 75 | Issue: 15_Supplement | Pages: 4634-4634

10.1158/1538-7445.am2015-4634 Get It

Abstract Background: Cell-type-specific super enhancers, or large clusters of mediator-rich enhancers, are highly transcribed regions of the genome with key functions in the maintenance of cell identity and control. These regulatory elements are easily perturbed and enriched for disease-associated sequence variation. Identification of disease-associated super-enhancers and investigation of their sequence variants may help identify important, biologically relevant associations previously overlooked by genome-wide studies. Thus, we sought to identify variants within ovarian tissue specific super-enhancers and investigate their association with epithelial ovarian cancer (EOC) susceptibility. Methods: We utilized genotype data from a European population of ∼11,000 invasive EOC cases and 22,000 healthy controls from the Ovarian Cancer Association Consortium. A public catalog of 478 super-enhancers, identified by peak histone H3K27ac ChIP-seq signal in ovarian tissue, was used to identify 72,116 variants located within 344 super-enhancer regions. Unconditional logistic regression (log-additive model) was used to assess individual SNP-EOC risk associations. Additionally, we reviewed associations within 500 kb of super-enhancer regions to identify proximal associated variants. When LD structure indicated, we employed conditional analysis to determine independence of the super-enhancer signal. Gene-EOC risk associations were assessed with the Admixture Maximum Likelihood (AML) test and Sequence-Kernel Association Test (SKAT) for the combined effect of common and rare (MAF<0.01) variants. Models were adjusted for population stratification using the first five principal components. To adjust for multiple comparisons, a false discovery rate of 10% was used. Results: The most significant SNP observed was rs147487657 (p = 7.7×10−6) on locus 2q37.3 in the HDAC4 gene and there were an additional 12 SNPs with p<1.0×10−4, although not significant at 10% FDR. Gene-level analyses identified two super-enhancers significantly associated with EOC risk. An enhancer at the previously reported 2q31 locus, containing HOXD8 and HOXD-AS2, associated (SKAT p = 4.3×10−5; AML p<0.001) with the top SNP located within the 5′UTR of HOXD8 transcription factor (rs847163 (T>C); p<2.08×10−5). Conditional analysis did not identify an independent association within the super-enhancer region. The second EOC-associated super-enhancer identified was at locus 1q32 (SKAT p = 0.00052, AML p = 0.001) containing the CSRP1 gene. There were 6 SNPs with p<0.001 and 16 SNPs with p<0.01, all were inversely associated with risk and consistent with the top hit at rs927901 T>C (OR = 0.94; 95% CI: 0.90-0.97; p = 2.1×10−4). Associations varied by histologic subtype, possibly due to variance in disease relevant super-enhancer cell-type.Conclusion: These findings suggest germline variation within super-enhancer regions may contribute to EOC susceptibility Citation Format: Brett M. Reid, Jennifer Permuth-Wey, Y. Ann Chen, Hui-Yi Lin, Alvaro Monteiro, Zhihua Chen, Andrew Berchuck, Georgia Chenevix-Trench, Jennifer Doherty, Simon Gayther, Ellen L. Goode, Edwin Iversen, Leigh Pearce, Paul Pharoah, Catherine Phelan, Susan Ramus, Mary Anne Rossing, Joellen Schildkraut, Thomas Sellers, on behalf of the Ovarian Cancer Association Consortium. Variants within super-enhancer regulatory elements associate with epithelial ovarian cancer risk. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4634. doi:10.1158/1538-7445.AM2015-4634
Abstract 4633: Evidence that long non-coding RNA variants associate with epithelial ovarian cancer risk
Sellers, Thomas A. , Reid, Brett M. , Richards, Edward J., Teer, Jamie K. , Chen, Zhihua , Goode, Ellen L. , Iverson, Edwin S., Pearce, Leigh, Phelan, Catherine, Rossing, Mary Anne, Schildkraut, Joellen M. , Cheng, Jin Q. , Gayther, Simon A. , Permuth‐Wey, Jennifer, Chen, Y. Ann , Lin, Hui‐Yi , Monteiro, Álvaro N.A. , Berchuck, Andrew , Chenevix‐Trench, Georgia , Doherty, Jennifer A. , Pharoah, Paul D.P. , Ramus, Susan J.

Cancer Research | August 5, 2015 | Volume: 75 | Issue: 15_Supplement | Pages: 4633-4633

10.1158/1538-7445.am2015-4633 Get It

Abstract Background: Genome wide association studies (GWAS) have identified 20 loci associated with epithelial ovarian cancer (EOC) risk. Additional EOC risk loci await identification, and biological approaches may represent a useful strategy for overcoming sample size limitations. The ENCODE project recently concluded that only ∼1.2% of the genome encodes proteins, but at least 20% exhibits biological function and over 80% exhibits biochemical indices of function. Post-GWAS follow-up studies have firmly established that some associations are due to inter-individual differences in non-coding RNAs (ncRNAs). To estimate the magnitude of impact of variants in long non-coding RNAs (lncRNAs), we assessed enrichment of EOC-associated SNPs in lncRNA regions by comparing the density of EOC-associated loci between lncRNA regions, non-lncRNA regions, and the whole genome. Methods: The study population included ∼18,000 invasive EOC cases and 34,000 healthy controls of European ancestry from the Ovarian Cancer Association Consortium with GWAS data imputed to 1000 Genomes Project (1KGP) density. Density was compared with two measures: average chromosome length required for one EOC-associated SNP (kb/locus) and average number of tested SNPs containing one EOC-associated SNP (SNPs/locus). Coordinates and annotation for 13,870 lncRNA genes were downloaded from the publicly available GENCODE (v19) database and were used to annotate SNPs from the 1KGP imputed GWAS data, yielding 13,192 lncRNA genes with biallelic variants imputed at rsquare ≥0.25. A SNP was considered EOC-associated if it reached a significance level of P<10−5. Results: Genome-wide, 11.6% of the 15,123,646 tested SNPs fell within lncRNA regions. Of 5,294 EOC-associated SNPs that were identified, 27.7% were located within lncRNAs, a higher frequency than expected (<v:shape style = “WIDTH: 16.5pt; HEIGHT: 18pt” id = _x0000_i1026 equationxml = ‘14pχ2′ type = “#_x0000_t75”> = 9.35×10−22). Additionally, EOC-associated SNPs were located on average every 237.6 kb (or 1204 tested SNPs) in lncRNA regions versus every 657.7 kb (or 3489 SNPS) in non-lncRNA regions and every 541.5 kb (or 2857 SNPs) in the whole genome, clearly demonstrating an enrichment of EOC-associated loci in lncRNA regions. A total of 1,464 lncRNA SNPs from 53 unique lncRNAs associated with EOC risk (P<10−5); 70 of the identified lncRNA SNPs had P-values between 10−20 and 10−32, and 221 had P-values between 10−10 and 10−15, representing 21 unique regions > 500kb apart. Conclusions: These results justify efforts to integrate functional and population level genetic data on lncRNA regions to explore a new paradigm that addresses the problem of the missing heritability for cancer where restrictions in sample size and statistical power limit the ability to discover additional risk loci. Citation Format: Thomas A. Sellers, Brett M. Reid, Y. Ann Chen, Hui-Yi Lin, Edward Richards, Jamie Teer, Alvaro Monteiro, Zhihua Chen, Andrew Berchuck, Georgia Chenevix-Trench, Jennifer Doherty, Ellen Goode, Edwin Iverson, Leigh Pearce, Paul Pharoah, Catherine Phelan, Susan Ramus, Mary Anne Rossing, Joellen Schildkraut, Jin Cheng, Simon Gayther, Jennifer Permuth-Wey, on behalf of the Ovarian Cancer Association Consortium. Evidence that long non-coding RNA variants associate with epithelial ovarian cancer risk. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4633. doi:10.1158/1538-7445.AM2015-4633
Abstract 3899: Integrating RNA/DNA analysis with a comprehensive cancer panel to improve interpretations of stage four metastatic renal cell carcinoma
Boyle, Sean M. , Clark, Michael , Helman, Elena , Parker, Alexander S. , Luo, Shujun , Kirk, Scott, Sripakdeevong, Parin, Karbelashvili, Mirian, Church, Deanna M. , West, John, Chen, Rich, Ho, Thai H. , Snyder, Michael

Cancer Research | August 5, 2015 | Volume: 75 | Issue: 15_Supplement | Pages: 3899-3899

10.1158/1538-7445.am2015-3899 Get It

Abstract Next-generation sequencing is now commonly applied to measure genomic modifications, providing the opportunity for a more accurate view of cancer progression. That being said, several challenges including tumor purity, heterogeneity and the broad set of cancer associated cellular functions, increase the difficulty of interpreting cancer genomes and make analyzing them distinct from analysis of germline diseases. The ability to detect low allelic mutations in the broad set of cancer-associated genes is critically important. To address these issues, we developed an extended cancer panel, a targeted enrichment sequencing platform that includes over 1,300 cancer genes and 200 miRNAs that improves coverage in traditionally difficult to sequence NGS regions. In this study, we apply an integrated RNA/DNA analysis approach as well as our extended cancer panel to explore mutations in metastatic renal cell carcinoma (RCC) tissue samples before and after treatment. Our goal with this study was to test the importance of integrating DNA and RNA analysis, which allows for detection of mutational events that cannot be observed by either method alone. With RNA analysis it is possible to detect gene fusion events, expression of small variants (SNVs/indels), and gene expression levels while DNA analysis allows for detection of loss of heterozygosity (LOH), copy number variants (CNVs), and small variants. By integrating both the RNA and DNA analysis, it is possible to identify unique variant classes, such as unexpressed variants, allele specific expression (ASE), effects of CNVs on gene expression levels, and how fusion gene integration sites affect CNVs. In our study, each variant class was interpreted pre- and post-treatment, allowing for optimal analysis of treatment effectiveness. By applying both our RNA/DNA integration approach and our extended cancer panel to investigate metastatic RCC samples, we were able to classify many genomic alterations that drive cancer progression. For example, we found that anywhere from 5% to 30% of small variant mutations in driver genes called in the DNA reside in genes that are unexpressed in the RNA. Likewise, we noted multiple cases of ASE, where high profile variants observed in DNA were entirely absent in the RNA despite high expression levels. Strong correlations between CNVs observed in DNA and gene expression changes found in RNA were also detected. We also observed that about half of the RCC samples we tested were biallelic for VHL mutations, suggesting inherited predisposition combined with second hit somatic mutations, facilitating cancer progression. This analysis demonstrates how combining an integrated RNA/DNA approach with a cancer focused augmented enrichment panel allows for detection of both low allelic representation variants and unique variant classes, both of which are critical for accurate interpretation of cancer samples. Citation Format: Sean M. Boyle, Michael J. Clark, Elena Helman, Alexander S. Parker, Thai Ho, Shujun Luo, Scott Kirk, Parin Sripakdeevong, Mirian Karbelashvili, Deanna M. Church, Michael Snyder, John West, Rich Chen. Integrating RNA/DNA analysis with a comprehensive cancer panel to improve interpretations of stage four metastatic renal cell carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3899. doi:10.1158/1538-7445.AM2015-3899
Abstract 2782: Risk loci for a breast-colon cancer phenotype: results from a genome-wide association study
Shete, Sanjay , Brewster, Abenaa M. , Chen, Wei V., Ahsan, Habibul , Andrulis, Irene L. , Lindor, Noralane M. , Lynch, Patrick M. , Pande, Mala , Joon, Aron Y. , Eng, Cathy , John, Esther M. , Lin, Yi , Newcomb, Polly A. , Amos, Christopher I. , Hopper, John L.

Cancer Research | August 5, 2015 | Volume: 75 | Issue: 15_Supplement | Pages: 2782-2782

10.1158/1538-7445.am2015-2782 Get It

Abstract Purpose: Clustering of breast and colorectal cancer has been observed within families in population-based studies giving rise to speculation that there are “breast-colon” cancer susceptibility genes. We performed a genome-wide association study (GWAS) to identify genetic markers associated with a potential breast-colon cancer phenotype. Methods: Cases and controls were ascertained from the Breast and Colon Cancer Family Registries’ (CFR) GWAS subjects. “Breast-colon phenotype” definition was based on 2 or more breast and colon cancer cases diagnosed in first- or second-degree relatives within a family. Cases (n = 985) were women with a history of breast cancer and a family history of colorectal cancer, or persons with colorectal cancer with a family history of breast cancer. Unrelated controls (n = 1769) were frequency matched to cases for age and gender. Following standard quality control measures, 6,220,060 directly measured and imputed single nucleotide polymorphisms (SNPs) were included in the discovery set. SNPs associated at p<1×10−5 were analyzed in a replication dataset of cases (n = 293) and controls (n = 2103) from the Genetics and Epidemiology of Colorectal Cancer Consortium. Results: In a regression model that included gender, age, CFR center and 6 principal components, the top association in the discovery set was in the chromosome 8q22.3 region overlying the BAALC gene (top SNP rs12548629, P = 3.63×10−7). In the replication dataset, of 341 SNPs tested, the top signal was found in multiple correlated SNPs overlying the ROBO1 gene on chromosome 3p12 (rs7429100, P = 2.8×10−3), however, the signal on chromosome 8, the BAALC gene did not replicate. In the discovery set, P values for the SNPs overlaying ROBO1 gene ranged from 2.2×10−5 to 9.7×10−5 (rs7429100, P = 3.9×10−5). The combined meta-analysis showed strongest association at the ROBO1 gene (rs7429100, Pfixed effects 1.84×10−6, Pheterogeneity >0.05 for testing for heterogeneity between the overall discovery set and the replication set). ROBO1 (roundabout, axon guidance receptor, homolog 1) is a transmembrane receptor of the immunoglobulin family and is differentially expressed in human cancers, with a possible role as a tumor suppressor gene. Low ROBO1 expression has been shown to be an adverse prognostic factor for invasive ductal breast cancer and may also play a role in pathogenesis of colorectal cancer. BAALC (brain and acute leukemia, cytoplasmic) is predominantly expressed by neural and blood cells and is largely implicated in acute leukemia. Conclusion: In this exploratory analysis, to elucidate genes/regions associated with pleiotropic effect for breast and colorectal cancer risk we identified germline variation in the region of ROBO1 and BAALC. Validation in a larger dataset and functional characterization of the loci is warranted to elucidate mechanisms by which these genes/SNPs may contribute to the development of breast and colorectal cancer. Citation Format: Mala Pande, Aron Joon, Sanjay Shete, Abenaa M. Brewster, Cathy Eng, Wei V. Chen, Habibul Ahsan, Irene L. Andrulis, Esther M. John, Yi Lin, Polly A. Newcomb, Noralane M. Lindor, Christopher I. Amos, John Hopper, Patrick M. Lynch. Risk loci for a breast-colon cancer phenotype: results from a genome-wide association study. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2782. doi:10.1158/1538-7445.AM2015-2782
Abstract 4636: Investigation of exome variants associated with overall survival in ovarian cancer
Permuth‐Wey, Jenny, Sellers, Thomas A. , Pirie, Ailith, Goode, Ellen L. , Winham, Stacey J. , Fridley, Brooke L. , Larson, Melissa C. , Fogarty, Zachary C. , Berchuck, Andrew , Chen, Y. Ann , Lin, Hui‐Yi , Chenevix‐Trench, Georgia

Cancer Research | August 4, 2015 | Volume: 75 | Issue: 15_Supplement | Pages: 4636-4636

10.1158/1538-7445.am2015-4636 Get It

Abstract Many germline genetic variants have been found to be associated with susceptibility to epithelial ovarian cancer (EOC), but currently few associations have been identified for EOC outcomes such as overall survival. In the absence of evidence for common germline markers, it is possible that rare variants not captured in GWAS arrays may be associated with overall survival. We hypothesize that rare variants, either individually or combined across a gene, may be associated with overall survival in EOC. We utilized data from two genotyping projects of the Ovarian Cancer Association Consortium (OCAC) that used commercial exome-based arrays. The primary sample, genotyped on the Affymetrix Axiom Exome Array at 227,892 standard and custom variants, consisted of 14 independent EOC studies (4293 cases; 2257 deaths). The secondary sample, genotyped on the Illumina Infinium HumanExome BeadChip at 114,620 variants, consisted of six additional EOC studies (1744 cases; 1027 deaths). Both sets were analyzed using Cox proportional hazards regression to determine the association of each variant with overall survival time. Meta-analysis was conducted across samples at 73,203 overlapping variants. Gene-level tests of over 18,000 genes were also conducted using burden tests and Sequencing Kernel Association Tests (SKAT) adapted for Cox proportional hazards models. Gene-level tests were conducted separately for the primary and secondary cases and then were meta-analyzed. Models were adjusted for age, site, and three principle components. Six individual variants had meta-analysis p-values < 1.0E-4, five of which were rare (MAF < 0.003). Common variant rs8170 (MAF = 0.2) in BABAM1 encoding BRISC and BRCA1 A complex member 1 - previously reported to be associated with EOC risk_showed evidence of association with overall survival (Pmeta = 1.5E-5) and consistent estimates of effect size across both samples (HR1 = 1.18, HR2 = 1.19). In imputed genotype data from over 18,000 subjects from OCAC genotyped on the COGS array, this association reaches genome-wide significance (HR = 1.15, P = 4.7E-9). Five genes had gene-level meta-analysis p-values < 1.0E-4, including top ranked ATG2B (p = 1.1E-6), an autophagy gene important for apoptosis; zinc finger protein PEG3 (p = 1.8E-5), playing a role in autophagy and down-regulated in EOC; helicase-like transcription factor HLTF (p = 1.9E-5), involved in post-replication DNA repair; mitochondrial fission regulator 1-like gene FAM54B (p = 3.1E-5); and T-cell surface glycoprotein CD1E (p = 8.8E-5). With over 6000 EOC cases in the primary and secondary samples, this is the largest genome-wide assessment of rare variant genetic associations with EOC overall survival. Variant rs8170 in BABAM1, a necessary component of the BRCA1 complex, is associated with overall survival. Single variant and gene-level analyses provide complementary approaches, suggesting additional candidates that warrant follow-up study. Citation Format: Stacey J. Winham, Brooke L. Fridley, Melissa C. Larson, Zachary Fogarty, Andrew Berchuck, Yian Ann Chen, Hui-Yi Lin, Georgia Chenevix-Trench, Jenny Permuth-Wey, Thomas A. Sellers, Ailith Pirie, Ellen L. Goode, Ovarian Cancer Association Consortium. Investigation of exome variants associated with overall survival in ovarian cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4636. doi:10.1158/1538-7445.AM2015-4636
Network-Based Integration of GWAS and Gene Expression Identifies a HOX -Centric Network Associated with Serous Ovarian Cancer Risk
Kar, Siddhartha , Lawrenson, Kate , Aben, Katja K.H. , Antonenkova, Natalia, Chenevix‐Trench, Georgia , Study, on behalf of the Australian Cancer, Group, and on behalf of the Australian Ovarian Cancer Study, Baker, Helen , Bean, Yukie T., Beckmann, Matthias W. , Bisogna, Maria, Bogdanova, Natalia , Brinton, Louise A. , Campbell, Ian , Carty, Karen , Chang‐Claude, Jenny , Chen, Y. Ann , Chen, Zhihua , Cunningham, Julie M. , Dansonka‐Mieszkowska, Agnieszka , Dicks, Ed , Dörk, Thilo , Eccles, Diana , Easton, Douglas F. , Edwards, Robert P., Ekici, Arif B. , Fasching, Peter A. , Gao, Yu‐Tang , Giles, Graham G. , Glasspool, Rosalind , Goode, Ellen L. , Goodman, Marc T. , Grownwald, Jacek, Harrington, Patricia, Harter, Philipp , Hein, Alexander , Heitz, Florian , Hildebrandt, Michelle A.T., Hillemanns, Peter , Høgdall, Estrid , Høgdall, Claus , Hosono, Satoyo , Iversen, Edwin S., Jakubowska, Anna , Jensen, Allan , Ji, Bu‐Tian , Kjær, Susanne K. , Kelemen, Linda E. , Kellar, Melissa, Kelley, Joseph L., Kiemeney, Lambertus A. , Krakstad, Camilla , Kupryjańczyk, Jolanta , Lambrechts, Diether , Lambrechts, Sandrina, Le, Nhu D. , Lee, Alice W. , Lele, Shashi, Leminen, Arto, Lester, Jenny, Levine, Douglas A. , Liang, Dong , Lissowska, Jolanta , Lu, Karen, Lubiński, Jan , Lundvall, Lene, Massuger, Leon F.A.G. , Matsuo, Keitaro , McGuire, Valerie , McLaughlin, John R., McNeish, Iain A. , Menon, Usha , Moysich, Kirsten B., Narod, Steven A., Nedergaard, Lotte , Ness, Roberta B., Odunsi, Kunle , Olson, Sara H. , Orlow, Irene , Oršulić, Sandra , Weber, Rachel Palmieri , Pearce, Celeste Leigh, Pelttari, Liisa M. , Permuth‐Wey, Jennifer, Phelan, Catherine M., Pike, Malcolm C., Ramus, Susan J. , Rossing, Mary Anne, Rothstein, Joseph H. , Runnebaum, Ingo B. , Rzepecka, Iwona K. , Salvesen, Helga B., Schildkraut, Joellen M. , Schwaab, Ira, Shvetsov, Yurii B. , Sieh, Weiva , Song, Honglin , Southey, Melissa C. , Sucheston‐Campbell, Lara, Tangen, Ingvild L. , Teo, Soo‐Hwang , Terry, Kathryn L. , Thompson, Pamela J., Timorek, Agnieszka, Tworoger, Shelley S. , Altena, Anne M. van , Nieuwenhuysen, Els Van , Vergote, Ignace , Vierkant, Robert A. , Wang‐Gohrke, Shan , Walsh, Christine , Wentzensen, Nicolas, Whittemore, Alice S. , Wicklund, Kristine G. , Woo, Yin Ling , Wu, Xifeng , Wu, Anna H. , Zheng, Wei , Sellers, Thomas A. , Monteiro, Álvaro N.A. , Freedman, Matthew L., Gayther, Simon A. , Lu, Karen H. , Lambrechts, Diether , Tyrer, Jonathan P. , Li, Qiyuan , Anton‐Culver, Hoda , Study, on behalf of the Australian Cancer, Group, and on behalf of the Australian Ovarian Cancer Study, Bandera, Elisa V. , Berchuck, Andrew , Bjørge, Line , Brooks‐Wilson, Angela , Bützow, Ralf C. , Cook, Linda S. , Cramer, Daniel W. , Cybulski, Cezary , Dennis, Joe , Doherty, Jennifer A. , Bois, Andreas du , Dürst, Matthias , Fridley, Brooke L. , Gentry‐Maharaj, Aleksandra , Hildebrandt, Michelle A.T. , Paul, James , Karlan, Beth Y. , Lu, Karen, McLaughlin, John R., Modugno, Francesmary , Nevanlinna, Heli , Pejovic, Tanja B. , Poole, Elizabeth M. , Risch, Harvey A. , Rosen, Barry P. , Rudolph, Anja , Shu, Xiao‐Ou , Siddiqui, Nadeem , Wentzensen, Nicolas , Wilkens, Lynne R. , Yang, Hannah , Ziogas, Argyrios , Pharoah, Paul D.P. , Pelttari, L M , Dörk, Thilo , Lambrechts, Diether , Giles, Graham G , Kiemeney, Lambertus A , Kjaer, Susanne K , McNeish, Iain A , Ramus, Susan J , Teo, Soo H , Tworoger, Shelley S , Hein, Alexander , Hillemanns, Peter , Jensen, Allan , Vierkant, Robert A , Eccles, Diana , Menon, Usha , Lawrenson, Kate , Monteiro, Alvaro N , Moysich, Kirsten , Orlow, Irene , Lissowska, Jolanta , Campbell, Ian G , Southey, Melissa C , Glasspool, Rosalind , Matsuo, Keitaro , Heitz, Florian , Jakubowska, Anna , Kupryjanczyk, Jolanta , Lambrechts, Diether , Sieh, Weiva , Ekici, Arif B , Bogdanova, Natalia V , Chenevix-Trench, Georgia , Zheng, Wei , Høgdall, Estrid , Høgdall, Claus K , Kar, Siddhartha , Lubinski, Jan , Goodman, Marc T

Cancer Epidemiology, Biomarkers & Prevention | July 24, 2015 | Volume: 24 | Issue: 10 | Pages: 1574-1584

10.1158/1055-9965.epi-14-1270 | PMID 26209509 Get It

Abstract Background: Genome-wide association studies (GWAS) have so far reported 12 loci associated with serous epithelial ovarian cancer (EOC) risk. We hypothesized that some of these loci function through nearby transcription factor (TF) genes and that putative target genes of these TFs as identified by coexpression may also be enriched for additional EOC risk associations. Methods: We selected TF genes within 1 Mb of the top signal at the 12 genome-wide significant risk loci. Mutual information, a form of correlation, was used to build networks of genes strongly coexpressed with each selected TF gene in the unified microarray dataset of 489 serous EOC tumors from The Cancer Genome Atlas. Genes represented in this dataset were subsequently ranked using a gene-level test based on results for germline SNPs from a serous EOC GWAS meta-analysis (2,196 cases/4,396 controls). Results: Gene set enrichment analysis identified six networks centered on TF genes (HOXB2, HOXB5, HOXB6, HOXB7 at 17q21.32 and HOXD1, HOXD3 at 2q31) that were significantly enriched for genes from the risk-associated end of the ranked list (P < 0.05 and FDR < 0.05). These results were replicated (P < 0.05) using an independent association study (7,035 cases/21,693 controls). Genes underlying enrichment in the six networks were pooled into a combined network. Conclusion: We identified a HOX-centric network associated with serous EOC risk containing several genes with known or emerging roles in serous EOC development. Impact: Network analysis integrating large, context-specific datasets has the potential to offer mechanistic insights into cancer susceptibility and prioritize genes for experimental characterization. Cancer Epidemiol Biomarkers Prev; 24(10); 1574–84. ©2015 AACR.
Response to Letter Regarding Article, “Effects of Sildenafil on Ventricular and Vascular Function in Heart Failure With Preserved Ejection Fraction”
Borlaug, Barry A. , Chen, Horng, Lin, Grace , Redfield, Margaret M. , Semigran, Marc J., McNulty, Steven E., LeWinter, Martin M. , Lewis, Gregory D. , Deswal, Anita M , Margulies, Kenneth B. , Borlaug, Barry A

Circulation: Heart Failure | July 21, 2015 | Volume: 8 | Issue: 4 | Pages: 840-840

10.1161/circheartfailure.115.002372 | PMID 26405727 Get It

Clinical Outcomes of Cardiac Resynchronization with Epicardial Left Ventricular Lead
Chen, Lu , Fu, Hai‐Xia , Pretorius, Victor , Wiste, Heather J. , Yuan, Hongtao, Feld, Gregory K. , Cha, Yong‐Mei , Birgersdotter‐Green, Ulrika , Fu, Haixia, Yang, Dachun, YANG, DACHUN, Pretorius, Victor

Pacing and Clinical Electrophysiology | July 14, 2015 | Volume: 38 | Issue: 10 | Pages: 1201-1209

10.1111/pace.12687 | PMID 26172535 Get It

BackgroundLeft ventricular (LV) pacing in cardiac resynchronization therapy (CRT) can be achieved via a transvenous or epicardial route. A surgically implanted epicardial LV (eLV) lead is used after a standard transvenous LV (tLV) lead implantation has failed. However, studies of clinical outcomes in patients with eLV leads and comparisons of outcome between tLV and eLV‐CRT are sparse. Therefore, the purpose of this study is to compare clinical response between tLV‐CRT and eLV‐CRT, as well as to understand the differences within the eLV‐CRT population.MethodsForty‐four patients received eLV‐CRT following unsuccessful attempts of tLV‐CRT implantation between 2002 and 2013 at the University of California, San Diego (UCSD) and Mayo Clinics. These patients were matched for age, gender, and etiology of cardiomyopathy in a 1:2 ratio with a cohort of patients who received tLV‐CRT during the same time period.ResultsDuring a mean follow‐up of 57 months, similar clinical outcomes and survival rate were noted between tLV and eLV‐CRT patients (all P > 0.05). Within the eLV‐CRT group, dilated cardiomyopathy patients had significant improvement in New York Heart Association class and ejection fraction (both P < 0.05), while ischemic cardiomyopathy patients did not (both P > 0.05). eLV‐CRT patients with nonanterior lead location had significantly improved survival (P < 0.001). There was also a trend for improved survival in those with nonapical lead location (P = 0.09).ConclusionIn this case‐matched two‐centered study, comparable improvements were noted in patients with tLV‐CRT and eLV‐CRT. Operators should target nonanterior and nonapical locations during eLV‐CRT implantation. Use of eLV‐CRT should be considered a viable alternative for CRT candidates.
Comparison of several von Willebrand factor (VWF) activity assays for monitoring patients undergoing treatment with VWF/FVIII concentrates: improved performance with a new modified automated method
Hillarp, Andreas, Friedman, Kenneth D. , Adcock-Funk, Dorothy M., Tiefenbacher, Stefan, Nichols, William L., Chen, Dong , Stadler, M., Schwartz, Bruce A., Chen, Dong

Haemophilia | July 14, 2015 | Volume: 21 | Issue: 6 | Pages: 837-845

10.1111/hae.12703 | PMID 26172561 Get It

BackgroundThe ability of von Willebrand factor (VWF) to bind platelet GP Ib and promote platelet plug formation is measured in vitro using the ristocetin cofactor (VWF:RCo) assay. Automated assay systems make testing more accessible for diagnosis, but do not necessarily improve sensitivity and accuracy.ObjectiveWe assessed the performance of a modified automated VWF:RCo assay protocol for the Behring Coagulation System (BCS®) compared to other available assay methods.MethodsResults from different VWF:RCo assays in a number of specialized commercial and research testing laboratories were compared using plasma samples with varying VWF:RCo activities (0–1.2 IU mL−1). Samples were prepared by mixing VWF concentrate or plasma standard into VWF‐depleted plasma. Commercially available lyophilized standard human plasma was also studied. Emphasis was put on the low measuring range. VWF:RCo accuracy was calculated based on the expected values, whereas precision was obtained from repeated measurements.ResultsIn the physiological concentration range, most of the automated tests resulted in acceptable accuracy, with varying reproducibility dependent on the method. However, several assays were inaccurate in the low measuring range. Only the modified BCS protocol showed acceptable accuracy over the entire measuring range with improved reproducibility.ConclusionsA modified BCS® VWF:RCo method can improve sensitivity and thus enhances the measuring range. Furthermore, the modified BCS® assay displayed good precision. This study indicates that the specific modifications − namely the combination of increased ristocetin concentration, reduced platelet content, VWF‐depleted plasma as on‐board diluent and a two‐curve calculation mode − reduces the issues seen with current VWF:RCo activity assays.