Citations

Abstract Objective To review and evaluate available software tools for electronic health record–driven phenotype authoring in order to identify gaps and needs for future development. Materials and Methods Candidate phenotype authoring tools were identified through (1) literature search in four publication databases (PubMed, Embase, Web of Science, and Scopus) and (2) a web search. A collection of tools was compiled and reviewed after the searches. A survey was designed and distributed to the developers of the reviewed tools to discover their functionalities and features. Results Twenty-four different phenotype authoring tools were identified and reviewed. Developers of 16 of these identified tools completed the evaluation survey (67% response rate). The surveyed tools showed commonalities but also varied in their capabilities in algorithm representation, logic functions, data support and software extensibility, search functions, user interface, and data outputs. Discussion Positive trends identified in the evaluation included: algorithms can be represented in both computable and human readable formats; and most tools offer a web interface for easy access. However, issues were also identified: many tools were lacking advanced logic functions for authoring complex algorithms; the ability to construct queries that leveraged un-structured data was not widely implemented; and many tools had limited support for plug-ins or external analytic software. Conclusions Existing phenotype authoring tools could enable clinical researchers to work with electronic health record data more efficiently, but gaps still exist in terms of the functionalities of such tools. The present work can serve as a reference point for the future development of similar tools.

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.

Abstract Purpose: Chemotherapy resistance remains a major challenge in the treatment of ovarian cancer. We hypothesize that germline polymorphisms might be associated with clinical outcome. Experimental Design: We analyzed approximately 2.8 million genotyped and imputed SNPs from the iCOGS experiment for progression-free survival (PFS) and overall survival (OS) in 2,901 European epithelial ovarian cancer (EOC) patients who underwent first-line treatment of cytoreductive surgery and chemotherapy regardless of regimen, and in a subset of 1,098 patients treated with ≥4 cycles of paclitaxel and carboplatin at standard doses. We evaluated the top SNPs in 4,434 EOC patients, including patients from The Cancer Genome Atlas. In addition, we conducted pathway analysis of all intragenic SNPs and tested their association with PFS and OS using gene set enrichment analysis. Results: Five SNPs were significantly associated (P ≤ 1.0 × 10−5) with poorer outcomes in at least one of the four analyses, three of which, rs4910232 (11p15.3), rs2549714 (16q23), and rs6674079 (1q22), were located in long noncoding RNAs (lncRNAs) RP11-179A10.1, RP11-314O13.1, and RP11-284F21.8, respectively (P ≤ 7.1 × 10−6). ENCODE ChIP-seq data at 1q22 for normal ovary show evidence of histone modification around RP11-284F21.8, and rs6674079 is perfectly correlated with another SNP within the super-enhancer MEF2D, expression levels of which were reportedly associated with prognosis in another solid tumor. YAP1- and WWTR1 (TAZ)-stimulated gene expression and high-density lipoprotein (HDL)-mediated lipid transport pathways were associated with PFS and OS, respectively, in the cohort who had standard chemotherapy (pGSEA ≤6 × 10−3). Conclusions: We have identified SNPs in three lncRNAs that might be important targets for novel EOC therapies. Clin Cancer Res; 21(23); 5264–76. ©2015 AACR.

Background: The burden associated with caregiving has been well documented. Caregivers have multiple responsibilities, and technology may be accessible as a potential burden-alleviating resource. Materials and Methods: We surveyed cancer caregivers regarding current technology use and willingness to use technology for easing burden or distress. Because age has been associated with technology use, responses were compared between geriatric (≥65 years old) and nongeriatric (18–64 years old) caregivers. Results: We had 112 respondents. Based on nonmissing responses, 66% ( n =71) were women, 95% ( n =106) were white, and 84% ( n =91) had post–high school education. Almost all caregivers reported having Internet (105 [94%]) and e-mail (102 [91%]) access. Nongeriatric caregivers indicated more willingness to access Internet-based tools that help caregivers (54 [93%] versus 41 [76%]; p =0.04) and were more frequent users of social media (37 [64%] versus 16 [30%]; p =0.01), smartphones (33 [57%] versus 16 [30%]; p =0.01), and other mobile wireless devices (42 [72%] versus 19 [35%]; p <0.001) than geriatric caregivers. They also more frequently expected technologies to improve their own quality of life ( p =0.009), increase their feelings of being effective as a caregiver ( p =0.02), and save time ( p =0.003). Regardless of age, a majority of caregivers (67 [62%]) endorsed the potential benefit of caregiving technologies in preventing burnout. Conclusions: Most caregivers have high access to and use of technology. Geriatric and nongeriatric caregivers were receptive to technology-based tools to help with their caregiving roles. Although nongeriatric caregivers expected to derive more benefit from such tools, both groups believed that caregiving technologies could reduce burden.

Primary sclerosing cholangitis (PSC) is a chronic, idiopathic, fibroinflammatory cholangiopathy. The role of the microbiota in PSC etiopathogenesis may be fundamentally important, yet remains obscure. We tested the hypothesis that germ‐free (GF) mutltidrug resistance 2 knockout (mdr2 −/− ) mice develop a distinct PSC phenotype, compared to conventionally housed (CV) mdr2 −/− mice. Mdr2 −/− mice (n = 12) were rederived as GF by embryo transfer, maintained in isolators, and sacrificed at 60 days in parallel with age‐matched CV mdr2 −/− mice. Serum biochemistries, gallbladder bile acids, and liver sections were examined. Histological findings were validated morphometrically, biochemically, and by immunofluorescence microscopy (IFM). Cholangiocyte senescence was assessed by p16 INK4a in situ hybridization in liver tissue and by senescence‐associated β‐galactosidase staining in a culture‐based model of insult‐induced senescence. Serum biochemistries, including alkaline phosphatase, aspartate aminotransferase, and bilirubin, were significantly higher in GF mdr2 −/− ( P < 0.01). Primary bile acids were similar, whereas secondary bile acids were absent, in GF mdr2 −/− mice. Fibrosis, ductular reaction, and ductopenia were significantly more severe histopathologically in GF mdr2 −/− mice ( P < 0.01) and were confirmed by hepatic morphometry, hydroxyproline assay, and IFM. Cholangiocyte senescence was significantly increased in GF mdr2 −/− mice and abrogated in vitro by ursodeoxycholic acid (UDCA) treatment. Conclusions : GF mdr2 −/− mice exhibit exacerbated biochemical and histological features of PSC and increased cholangiocyte senescence, a characteristic and potential mediator of progressive biliary disease. UDCA, a commensal microbial metabolite, abrogates senescence in vitro . These findings demonstrate the importance of the commensal microbiota and its metabolites in protecting against biliary injury and suggest avenues for future studies of biomarkers and therapeutic interventions in PSC. (H epatology 2016;63:185–196)

Background Patient sex and age may influence rates of death after receiving an implantable cardioverter‐defibrillator for primary prevention. Differences in outcomes other than mortality and whether these differences vary by heart failure symptoms, etiology, and left ventricular ejection fraction are not well characterized. Methods and Results We studied 2954 patients with left ventricular ejection fraction ≤0.35 undergoing first‐time implantable cardioverter‐defibrillator for primary prevention within the Cardiovascular Research Network; 769 patients (26%) were women, and 2827 (62%) were aged >65 years. In a median follow‐up of 2.4 years, outcome rates per 1000 patient‐years were 109 for death, 438 for hospitalization, and 111 for heart failure hospitalizations. Procedure‐related complications occurred in 8.36%. In multivariable models, women had significantly lower risks of death (hazard ratio 0.67, 95% CI 0.56 to 0.80) and heart failure hospitalization (hazard ratio 0.82, 95% CI 0.68 to 0.98) and higher risks for complications (hazard ratio 1.38, 95% CI 1.01 to 1.90) than men; patients aged >65 years had higher risks of death (hazard ratio 1.55, 95% CI 1.30 to 1.86) and heart failure hospitalization (hazard ratio 1.25, 95% CI 1.05 to 1.49) than younger patients. Age and sex differences were generally consistent in strata according to symptoms, etiology, and severity of left ventricular systolic dysfunction, except the higher risk of complications in women, which differed by New York Heart Association classification ( P =0.03 for sex–New York Heart Association interaction), and the risk of heart failure hospitalization in older patients, which differed by etiology of heart failure ( P =0.05 for age–etiology interaction). Conclusions The burden of adverse outcomes after receipt of an implantable cardioverter‐defibrillator for primary prevention is substantial and varies according to patient age and sex. These differences in outcome generally do not vary according to baseline heart failure characteristics.

A strategically designed sialyl-Tn building block was synthesized in a stereospecific manner for the rapid linear construction of a glycolipopeptide cancer vaccine.

AbstractBackgroundStudies point to a direct association between social support and better cancer outcomes. This study examined whether baseline social support is associated with better survival and fewer chemotherapy‐related adverse events in older, early‐stage breast cancer patients.MethodsThis study is a pre‐planned secondary analysis of CALGB 49907/Alliance A171301, a randomized trial that compared standard adjuvant chemotherapy versus capecitabine in breast cancer patients 65 years of age or older. A subset reported on the extent of their social support with questionnaires that were completed 6 times over 2 years.ResultsThe median age of this 331‐patient cohort was 72 years (range: 65, 90); 179 (55%) were married, and 210 (65%) lived with someone. One hundred forty‐five patients (46%) described a social network of 0–10 people; 110 (35%) of 11–25; and 58 (19%) of 26 or more. The Medical Outcomes Study (MOS) social support survey revealed that the median scores (range) for emotional/informational, tangible, positive social interaction, and affectionate social support were 94 (3, 100), 94 (0, 100), 96 (0, 100), and 100 (8, 100), respectively. Social support scores appeared stable over 2 years and higher (more support) than in other cancer settings. No statistically significant associations were observed between social support and survival and adverse events in multivariate analyses. However, married patients had smaller tumors, and those with arthritis reported less social support.ConclusionAlthough social support did not predict survival and adverse events, the exploratory but plausible inverse associations with larger tumors and arthritis suggest that social support merits further study. Copyright © 2015 John Wiley & Sons, Ltd.

A mouse model for ALS A G4C2 repeat expansion in C9ORF72 is known to be the major genetic cause of frontotemporal dementia and amyotrophic lateral sclerosis (c9FTD/ALS). However, a lack of animal models recapitulating key disease features has hindered efforts to understand and prevent c9FTD/ALS-related neurodegeneration. Until now. Chew et al. describe a mouse model that mimics both neuropathological and clinical phenotypes of c9FTD/ALS. Science , this issue p. 1151