The case for open science: rare diseases

The premise of Open Science is that research and medical management will progress faster if data and knowledge are openly shared. The value of Open Science is nowhere more important and appreciated than in the rare disease (RD) community. Research into RDs has been limited by insufficient patient data and resources, a paucity of trained disease experts, and lack of therapeutics, leading to long delays in diagnosis and treatment. These issues can be ameliorated by following the principles and practices of sharing that are intrinsic to Open Science. Here, we describe how the RD community has adopted the core pillars of Open Science, adding new initiatives to promote care and research for RD patients and, ultimately, for all of medicine. We also present recommendations that can advance Open Science more globally.

Consent Codes: Upholding Standard Data Use Conditions

A systematic way of recording data use conditions that are based on consent permissions as found in the datasets of the main public genome archives (NCBI dbGaP and EMBL-EBI/CRG EGA).

Point-of-Care Technologies for Precision Cardiovascular Care and Clinical Research: National Heart, Lung, and Blood Institute Working Group

Point-of-care technologies (POC or POCT) are enabling innovative cardiovascular diagnostics that promise to improve patient care across diverse clinical settings. The National Heart, Lung, and Blood Institute convened a working group to discuss POCT in cardiovascular medicine. The multidisciplinary working group, which included clinicians, scientists, engineers, device manufacturers, regulatory officials, and program staff, reviewed the state of the POCT field; discussed opportunities for POCT to improve cardiovascular care, realize the promise of precision medicine, and advance the clinical research enterprise; and identified barriers facing translation and integration of POCT with existing clinical systems. A POCT development roadmap emerged to guide multidisciplinary teams of biomarker scientists, technologists, health care providers, and clinical trialists as they: 1) formulate needs assessments; 2) define device design specifications; 3) develop component technologies and integrated systems; 4) perform iterative pilot testing; and 5) conduct rigorous prospective clinical testing to ensure that POCT solutions have substantial effects on cardiovascular care.

Data use under the NIH GWAS data sharing policy and future directions

Dina Paltoo, Laura Lyman Rodriguez, Michael Feolo and colleagues present their analysis of the usefulness and impact of the first seven years of data sharing via the dbGaP repository and announce the extension of data-sharing provisions to other types of research funded by the NIH.

In 2007, the US National Institutes of Health (NIH) introduced the Genome-Wide Association Studies (GWAS) Policy and the database of Genotypes and Phenotypes (dbGaP) to facilitate 'controlled' access to GWAS data based on participants' informed consent. dbGaP has provided 2,221 investigators access to 304 studies, resulting in 924 publications and significant scientific advances. Following on this success, the 2014 Genomic Data Sharing Policy will extend the GWAS Policy to additional data types.

Genetic simulation tools for post-genome wide association studies of complex diseases

Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled "Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases" at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to (1) identify opportunities, challenges, and resource needs for the development and application of genetic simulation models; (2) improve the integration of tools for modeling and analysis of simulated data; and (3) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting, the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation.

Genetics of coronary artery calcification among African Americans, a meta-analysis

Background

Coronary heart disease (CHD) is the major cause of death in the United States. Coronary artery calcification (CAC) scores are independent predictors of CHD. African Americans (AA) have higher rates of CHD but are less well-studied in genomic studies. We assembled the largest AA data resource currently available with measured CAC to identify associated genetic variants.

Methods

We analyzed log transformed CAC quantity (ln(CAC + 1)), for association with ~2.5 million single nucleotide polymorphisms (SNPs) and performed an inverse-variance weighted meta-analysis on results for 5,823 AA from 8 studies. Heritability was calculated using family studies. The most significant SNPs among AAs were evaluated in European Ancestry (EA) CAC data; conversely, the significance of published SNPs for CAC/CHD in EA was queried within our AA meta-analysis.

Results

Heritability of CAC was lower in AA (~30%) than previously reported for EA (~50%). No SNP reached genome wide significance (p < 5E-08). Of 67 SNPs with p < 1E-05 in AA there was no evidence of association in EA CAC data. Four SNPs in regions previously implicated in CAC/CHD (at 9p21 and PHACTR1) in EA reached nominal significance for CAC in AA, with concordant direction. Among AA, rs16905644 (p = 4.08E-05) had the strongest association in the 9p21 region.

Conclusions

While we observed substantial heritability for CAC in AA, we failed to identify loci for CAC at genome-wide significant levels despite having adequate power to detect alleles with moderate to large effects. Although suggestive signals in AA were apparent at 9p21 and additional CAC and CAD EA loci, overall the data suggest that even larger samples and an ethnic specific focus will be required for GWAS discoveries for CAC in AA populations.

Genome-wide association study of cardiac structure and systolic function in African Americans: the Candidate Gene Association Resource (CARe) study

BACKGROUND

Using data from 4 community-based cohorts of African Americans, we tested the association between genome-wide markers (single-nucleotide polymorphisms) and cardiac phenotypes in the Candidate-gene Association Resource study.

METHODS AND RESULTS

Among 6765 African Americans, we related age, sex, height, and weight-adjusted residuals for 9 cardiac phenotypes (assessed by echocardiogram or magnetic resonance imaging) to 2.5 million single-nucleotide polymorphisms genotyped using Genome-wide Affymetrix Human SNP Array 6.0 (Affy6.0) and the remainder imputed. Within the cohort, genome-wide association analysis was conducted, followed by meta-analysis across cohorts using inverse variance weights (genome-wide significance threshold=4.0 ×10(-7)). Supplementary pathway analysis was performed. We attempted replication in 3 smaller cohorts of African ancestry and tested lookups in 1 consortium of European ancestry (EchoGEN). Across the 9 phenotypes, variants in 4 genetic loci reached genome-wide significance: rs4552931 in UBE2V2 (P=1.43×10(-7)) for left ventricular mass, rs7213314 in WIPI1 (P=1.68×10(-7)) for left ventricular internal diastolic diameter, rs1571099 in PPAPDC1A (P=2.57×10(-8)) for interventricular septal wall thickness, and rs9530176 in KLF5 (P=4.02×10(-7)) for ejection fraction. Associated variants were enriched in 3 signaling pathways involved in cardiac remodeling. None of the 4 loci replicated in cohorts of African ancestry was confirmed in lookups in EchoGEN.

CONCLUSIONS

In the largest genome-wide association study of cardiac structure and function to date in African Americans, we identified 4 genetic loci related to left ventricular mass, interventricular septal wall thickness, left ventricular internal diastolic diameter, and ejection fraction, which reached genome-wide significance. Replication results suggest that these loci may be unique to individuals of African ancestry. Additional large-scale studies are warranted for these complex phenotypes.

Common genetic variation near the connexin-43 gene is associated with resting heart rate in African Americans: a genome-wide association study of 13,372 participants

BACKGROUND

Genome-wide association studies have identified several genetic loci associated with variation in resting heart rate in European and Asian populations. No study has evaluated genetic variants associated with heart rate in African Americans.

OBJECTIVE

To identify novel genetic variants associated with resting heart rate in African Americans.

METHODS

Ten cohort studies participating in the Candidate-gene Association Resource and Continental Origins and Genetic Epidemiology Network consortia performed genome-wide genotyping of single nucleotide polymorphisms (SNPs) and imputed 2,954,965 SNPs using HapMap YRI and CEU panels in 13,372 participants of African ancestry. Each study measured the RR interval (ms) from 10-second resting 12-lead electrocardiograms and estimated RR-SNP associations using covariate-adjusted linear regression. Random-effects meta-analysis was used to combine cohort-specific measures of association and identify genome-wide significant loci (P≤2.5×10(-8)).

RESULTS

Fourteen SNPs on chromosome 6q22 exceeded the genome-wide significance threshold. The most significant association was for rs9320841 (+13 ms per minor allele; P = 4.98×10(-15)). This SNP was approximately 350 kb downstream of GJA1, a locus previously identified as harboring SNPs associated with heart rate in Europeans. Adjustment for rs9320841 also attenuated the association between the remaining 13 SNPs in this region and heart rate. In addition, SNPs in MYH6, which have been identified in European genome-wide association study, were associated with similar changes in the resting heart rate as this population of African Americans.

CONCLUSIONS

An intergenic region downstream of GJA1 (the gene encoding connexin 43, the major protein of the human myocardial gap junction) and an intragenic region within MYH6 are associated with variation in resting heart rate in African Americans as well as in populations of European and Asian origin.

European ancestry as a risk factor for atrial fibrillation in African Americans

BACKGROUND

Despite a higher burden of standard atrial fibrillation (AF) risk factors, African Americans have a lower risk of AF than whites. It is unknown whether the higher risk is due to genetic or environmental factors. Because African Americans have varying degrees of European ancestry, we sought to test the hypothesis that European ancestry is an independent risk factor for AF.

METHODS AND RESULTS

We studied whites (n=4543) and African Americans (n=822) in the Cardiovascular Health Study (CHS) and whites (n=10 902) and African Americans (n=3517) in the Atherosclerosis Risk in Communities (ARIC) Study (n=3517). Percent European ancestry in African Americans was estimated with 1747 ancestry informative markers from the Illumina custom ITMAT-Broad-CARe array. Among African Americans without baseline AF, 120 of 804 CHS participants and 181 of 3517 ARIC participants developed incident AF. A meta-analysis from the 2 studies revealed that every 10% increase in European ancestry increased the risk of AF by 13% (hazard ratio, 1.13; 95% confidence interval, 1.03 to 1.23; P=0.007). After adjustment for potential confounders, European ancestry remained a predictor of incident AF in each cohort alone, with a combined estimated hazard ratio for each 10% increase in European ancestry of 1.17 (95% confidence interval, 1.07 to 1.29; P=0.001). A second analysis using 3192 ancestry informative markers from a genome-wide Affymetrix 6.0 array in ARIC African Americans yielded similar results.

CONCLUSIONS

European ancestry predicted risk of incident AF. Our study suggests that investigating genetic variants contributing to differential AF risk in individuals of African versus European ancestry will be informative.

Next generation analytic tools for large scale genetic epidemiology studies of complex diseases

Over the past several years, genome-wide association studies (GWAS) have succeeded in identifying hundreds of genetic markers associated with common diseases. However, most of these markers confer relatively small increments of risk and explain only a small proportion of familial clustering. To identify obstacles to future progress in genetic epidemiology research and provide recommendations to NIH for overcoming these barriers, the National Cancer Institute sponsored a workshop entitled "Next Generation Analytic Tools for Large-Scale Genetic Epidemiology Studies of Complex Diseases" on September 15-16, 2010. The goal of the workshop was to facilitate discussions on (1) statistical strategies and methods to efficiently identify genetic and environmental factors contributing to the risk of complex disease; and (2) how to develop, apply, and evaluate these strategies for the design, analysis, and interpretation of large-scale complex disease association studies in order to guide NIH in setting the future agenda in this area of research. The workshop was organized as a series of short presentations covering scientific (gene-gene and gene-environment interaction, complex phenotypes, and rare variants and next generation sequencing) and methodological (simulation modeling and computational resources and data management) topic areas. Specific needs to advance the field were identified during each session and are summarized.

Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project

Coronary heart disease (CHD) is the leading cause of mortality in African Americans. To identify common genetic polymorphisms associated with CHD and its risk factors (LDL- and HDL-cholesterol (LDL-C and HDL-C), hypertension, smoking, and type-2 diabetes) in individuals of African ancestry, we performed a genome-wide association study (GWAS) in 8,090 African Americans from five population-based cohorts. We replicated 17 loci previously associated with CHD or its risk factors in Caucasians. For five of these regions (CHD: CDKN2A/CDKN2B; HDL-C: FADS1-3, PLTP, LPL, and ABCA1), we could leverage the distinct linkage disequilibrium (LD) patterns in African Americans to identify DNA polymorphisms more strongly associated with the phenotypes than the previously reported index SNPs found in Caucasian populations. We also developed a new approach for association testing in admixed populations that uses allelic and local ancestry variation. Using this method, we discovered several loci that would have been missed using the basic allelic and global ancestry information only. Our conclusions suggest that no major loci uniquely explain the high prevalence of CHD in African Americans. Our project has developed resources and methods that address both admixture- and SNP-association to maximize power for genetic discovery in even larger African-American consortia.

Candidate gene association resource (CARe): design, methods, and proof of concept

BACKGROUND

The National Heart, Lung, and Blood Institute's Candidate Gene Association Resource (CARe), a planned cross-cohort analysis of genetic variation in cardiovascular, pulmonary, hematologic, and sleep-related traits, comprises >40,000 participants representing 4 ethnic groups in 9 community-based cohorts. The goals of CARe include the discovery of new variants associated with traits using a candidate gene approach and the discovery of new variants using the genome-wide association mapping approach specifically in African Americans.

METHODS AND RESULTS

CARe has assembled DNA samples for >40,000 individuals self-identified as European American, African American, Hispanic, or Chinese American, with accompanying data on hundreds of phenotypes that have been standardized and deposited in the CARe Phenotype Database. All participants were genotyped for 7 single-nucleotide polymorphisms (SNPs) selected based on prior association evidence. We performed association analyses relating each of these SNPs to lipid traits, stratified by sex and ethnicity, and adjusted for age and age squared. In at least 2 of the ethnic groups, SNPs near CETP, LIPC, and LPL strongly replicated for association with high-density lipoprotein cholesterol concentrations, PCSK9 with low-density lipoprotein cholesterol levels, and LPL and APOA5 with serum triglycerides. Notably, some SNPs showed varying effect sizes and significance of association in different ethnic groups.

CONCLUSIONS

The CARe Pilot Study validates the operational framework for phenotype collection, SNP genotyping, and analytic pipeline of the CARe project and validates the planned candidate gene study of approximately 2000 biological candidate loci in all participants and genome-wide association study in approximately 8000 African American participants. CARe will serve as a valuable resource for the scientific community.

Association of Vasectomy and Prostate Cancer Among Men in a Maryland Cohort

OBJECTIVES

To evaluate the association of vasectomy with prostate cancer.

METHODS

Participants were male members of the CLUE II cohort followed since 1989. On a questionnaire mailed in 1996, the men were asked if they had had a vasectomy and their age at vasectomy. Between 1996 and April 2004, 78 prostate cancer cases were confirmed among the 3373 men who were at least 35 years old at baseline and who completed the questions about vasectomy. Cox proportional hazards regression was used to estimate age-adjusted hazard ratios (HR) of prostate cancer.

RESULTS

The HR for prostate cancer for men who had had a vasectomy was 2.03 (95% CI: 1.24-3.32). Risk of low-grade disease (HR=2.87; 95% CI 1.49-5.54), but not high-grade disease (HR=0.99; 95% CI 0.36-2.76), was higher in men who had had a vasectomy. No statistically significant associations were observed for low- or high-stage disease. The association for vasectomy was more pronounced in men who were 40 years at the time of vasectomy (HR=2.63; 95% CI 1.40-4.94) than in men who were younger at vasectomy.

CONCLUSIONS

The results from this prospective study suggest a positive association between vasectomy and prostate cancer, especially low-grade disease.

Sequence variation within the 5' regulatory regions of the vitamin D binding protein and receptor genes and prostate cancer risk

BACKGROUND

The vitamin D receptor (VDR) and binding protein (DBP) mediate the cellular transport, activity, and anti-tumor action of 1,25-dihydroxyvitamin D3 [1,25-(OH)(2)D3]. The purpose of this investigation is to determine whether novel single nucleotide polymorphisms (SNPs) within the transcriptional regulatory regions of the VDR and DBP are associated with prostate cancer risk.

METHODS

Novel SNPs were identified in the VDR and DBP transcription regulatory gene regions and genotyped in a case-control study using male subjects with (n=258) or without (n=434) prostate cancer.

RESULTS

African-American men who possessed at least one variant VDR-5132 C allele had a increased risk of prostate cancer (OR=1.83; 95% CI: 1.02, 3.31). Further study revealed that the VDR-5132 T/C SNP eliminates a GATA-1 transcription factor-binding site.

CONCLUSION

The VDR-5132 T/C SNP, resulting in potential elimination of the GATA-1 transcription factor-binding site, may increase prostate cancer susceptibility in African-Americans. Confirmation of these findings is needed in larger observational studies.

Common Leptin Receptor Polymorphisms do not Modify the Effect of Alcohol Ingestion on Serum Leptin Levels in a Controlled Feeding and Alcohol Ingestion Study

We explored whether serum leptin response to alcohol ingestion was related to common leptin receptor gene polymorphisms, K109R (Lys109Arg), Q223R (Gln223Arg), S343S [Ser(T)343Ser(C)], and K656N (Lys656Asn), of reported physiologic significance during a controlled intervention. Fifty-three participants rotated through three 8-week treatment periods and consumed 0, 15 (equivalent to one drink), or 30 g (equivalent to two drinks) of alcohol (95% ethanol in 12 ounces of orange juice) per day, in random order. During the controlled feeding periods, all food and beverages including alcoholic beverages were prepared and supplied by the staff of the Beltsville Human Nutrition Research Center's Human Study Facility (Beltsville, MD), and energy intake was adjusted to maintain a constant weight. Blood was collected after an overnight fast on 3 separate days during the last week of each controlled feeding period and pooled for hormone analysis. Circulating serum leptin concentration was measured in duplicate by RIA and genotype analysis was done on DNA extracted from WBC using real-time PCR analysis amplification (TaqMan). Linear mixed models with a single random intercept reflecting a participant effect were used to estimate changes in serum leptin levels at 15 and 30 g of alcohol per day relative to 0 g of alcohol per day. No significant effects were found between common leptin receptor polymorphisms and serum leptin levels (P > or = 0.26).

Patterns in cancer incidence among American Indians/Alaska Natives, United States, 1992-1999

OBJECTIVE

Cancer is a major public health concern in American Indian and Alaska Native (AI/AN) communities. However, information on the incidence of cancer is lacking for this group. The purpose of this study is to report cancer incidence patterns for the U.S. AI/AN population.

METHODS

Age-adjusted annual cancer incidence rates for 1992 through 1999 were calculated for 12 Surveillance, Epidemiology and End Results (SEER) areas, representing a sample (42%) of the U.S. AI/AN population. Trends in cancer incidence rates for the AI/AN sample were determined using standard linear regression of log-transformed rates and were compared to those of the U.S. white population.

RESULTS

The top five incident cancers (from highest to lowest) among AI/AN males were prostate, lung and bronchus, colon and rectum, kidney and renal pelvis, and stomach cancers. Among AI/AN women, cancers of the breast, colon and rectum, lung and bronchus, endometrium, and ovary ranked highest. Four sites where cancer incidence rates are greater for AI/ANs than for whites include gallbladder (the AI/AN rate was 4.1 times the rate for white males and 2.6 times the rate for white females), liver and intrahepatic bile duct cancers (1.3 times for males and 2.3 times for females), stomach (1.2 times for males and 1.5 times for females), and kidney and renal pelvis (1.03 times for males and 1.07 times for females). The data show increasing trends for AI/AN males and females and declining trends for white males and females for colorectal, stomach, and pancreatic cancers and leukemia. Similar differences between AI/AN rates and white rates were found for urinary bladder cancers in males and gallbladder cancer in females.

CONCLUSIONS

Analysis of SEER data allowed for the determination of disparities in cancer incidence between a sample of the U.S. AI/AN population and the white population. The findings of this study provide baseline information necessary for developing cancer prevention and intervention strategies specific to the AI/AN population to address these cancer disparities.

Association between CBE, FOBT, and Pap smear adherence and mammography adherence among older low-income women

BACKGROUND

Adherence to regular and timely mammography screening, especially in older low-income women, continues to fall below objectives. The primary aim of this study was to examine whether engaging in other cancer screenings was associated with mammography adherence for older women.

METHODS

Women, ages 52 and over, without a self-reported history of breast cancer (N = 862) were selected from a larger sample of women residing in Washington, DC, census tracts with >/=30% of households below 200% of the federal poverty threshold. A computer-assisted telephone survey was used to collect data on health care system factors, demographics, cultural beliefs, clinical breast exam (CBE), Pap smear, fecal occult blood testing (FOBT), and mammography. Adherence was defined as receipt of the last two screening tests within recommended intervals for age.

RESULTS

After controlling for other variables, adherence to CBE (OR = 4.15; 95% CI, 2.55-6.73) and Pap smear (OR = 1.82; 95% CI, 1.07-3.12) were highly predictive of mammography adherence. Adherence to FOBT (OR = 1.66; 95% CI, 0.97-2.84) was marginally predictive.

CONCLUSIONS

Results of this study indicate that nonadherence to other cancer screenings can help identify women in need of additional interventions to improve mammography adherence.

Binding of terbium and cisplatin to C13* human ovarian cancer cells using time-resolved terbium luminescence

Terbium (Tb3+) has been shown to increase the cellular accumulation and cytotoxicity of cisplatin in cisplatin-resistant human breast and ovarian cancer cells. Time-resolved Tb3+ luminescence was used to describe the binding of cisplatin to cisplatin-resistant C13* cells. A high-affinity Tb3+ binding site was identified in the plasma membrane of the C13* cells (n=105+/-2 fmol/cell and Kd=36. 3+/-5.2 microM). The binding of Tb3+ is suggested to occur through a cation-pi interaction with tryptophan residues in the plasma membrane, resulting in an enhancement of the intensity and lifetime of Tb3+. Stern-Volmer quenching analysis revealed that the Tb3+ binding site is not readily accessible to the aqueous environment. The quenching of the Tb3+-C13* intensity by cisplatin occurred by static quenching processes, involving both a direct electron-exchange interaction as well as an indirect dipole-dipole resonant energy transfer mechanism. Formation of the Tb3+-C13*-cisplatin complex does not interfere with the high-affinity binding of Tb3+; cisplatin and Tb3+ bind within 5 to 10 A of each other. A specific terbium/cisplatin binding protein is suggested to play a role in the cellular accumulation and cytotoxicity of cisplatin. Therefore, the transport of cisplatin across the plasma membrane must also involve a facilitated diffusion process. Our results indicate that the binding of Tb3+ to the plasma membrane may be potentially useful in the reversal of cisplatin resistance.

Effects of terbium on the cytotoxicity of cisplatin in FaDu human head and neck squamous cell carcinoma

In this investigation, we report a relationship between the terbium (Tb3+) binding protein and the cytotoxicity of cisplatin in human head and neck cancer cells. In the FaDu cell line, the cytotoxic action of cisplatin was shown to be approximately six times more potent than the cytotoxicity of Tb3+. When cisplatin was combined with 80 microM Tb3+, the IC20 and IC50 values for cisplatin were reduced by 70% and 24%, respectively. The IC80 value, however, was increased by 124%. The results suggest that the cytotoxicity of cisplatin is enhanced by Tb3+ at low cisplatin concentrations. In agreement with previous studies, calcium and cisplatin were found to be mixed-type and noncompetitive inhibitors, respectively, of the Tb3+ -FaDu intensity. These findings imply that the receptor binding of Tb3+ can modulate the cytotoxic activity of cisplatin.