Advancing genomics to improve health equity.

Health equity is the state in which everyone has fair and just opportunities to attain their highest level of health. The field of human genomics has fallen short in increasing health equity, largely because the diversity of the human population has been inadequately reflected among participants of genomics research. This lack of diversity leads to disparities that can have scientific and clinical consequences. Achieving health equity related to genomics will require greater effort in addressing inequities within the field. As part of the commitment of the National Human Genome Research Institute (NHGRI) to advancing health equity, it convened experts in genomics and health equity research to make recommendations and performed a review of current literature to identify the landscape of gaps and opportunities at the interface between human genomics and health equity research. This Perspective describes these findings and examines health equity within the context of human genomics and genomic medicine.

Building blocks for better biorepositories in Africa.

BACKGROUND: Biorepositories archive and distribute well-characterized biospecimens for research to support the development of medical diagnostics and therapeutics. Knowledge of biobanking and associated practices is incomplete in low- and middle-income countries where disease burden is disproportionately high. In 2011, the African Society of Human Genetics (AfSHG), the National Institutes of Health (NIH), and the Wellcome Trust founded the Human Heredity and Health in Africa (H3Africa) consortium to promote genomic research in Africa and established a network of three biorepositories regionally located in East, West, and Southern Africa to support biomedical research. This manuscript describes the processes established by H3Africa biorepositories to prepare research sites to collect high-quality biospecimens for deposit at H3Africa biorepositories. METHODS: The biorepositories harmonized practices between the biorepositories and the research sites. The biorepositories developed guidelines to establish best practices and define biospecimen requirements; standard operating procedures (SOPs) for common processes such as biospecimen collection, processing, storage, transportation, and documentation as references; requirements for minimal associated datasets and formats; and a template material transfer agreements (MTA) to govern biospecimen exchange. The biorepositories also trained and mentored collection sites in relevant biobanking processes and procedures and verified biospecimen deposit processes. Throughout these procedures, the biorepositories followed ethical and legal requirements. RESULTS: The 20 research projects deposited 107,982 biospecimens (76% DNA, 81,067), in accordance with the ethical and legal requirements and established best practices. The biorepositories developed and customized resources and human capacity building to support the projects. [The biorepositories developed 34 guidelines, SOPs, and documents; trained 176 clinicians and scientists in over 30 topics; sensitized ethical bodies; established MTAs and reviewed consent forms for all projects; attained import permits; and evaluated pilot exercises and provided feedback. CONCLUSIONS: Biobanking in low- and middle-income countries by local skilled staff is critical to advance biobanking and genomic research and requires human capacity and resources for global partnerships. Biorepositories can help build human capacity and resources to support biobanking by partnering with researchers. Partnerships can be structured and customized to incorporate document development, ethics, training, mentorship, and pilots to prepare sites to collect, process, store, and transport biospecimens of high quality for future research.

Webinar report: stakeholder perspectives on informed consent for the use of genomic data by commercial entities.

In July 2020, the H3Africa Ethics and Community Engagement (E&CE) Working Group organised a webinar with ethics committee members and biomedical researchers from various African institutions throughout the Continent to discuss the issue of whether and how biological samples for scientific research may be accessed by commercial entities when broad consents obtained for the samples are silent. 128 people including Research Ethics Committee members (10), H3Africa researchers (46) including members of the E&CE working group, biomedical researchers not associated with H3Africa (27), representatives from the National Institutes of Health (16) and 10 other participants attended the webinar and shared their views. Several major themes emerged during the webinar, with the topics of broad versus explicit informed consent, defining commercial use, legacy samples and benefit sharing prevailing in the discussion. This report describes the consensus concerns and recommendations raised during the meeting and will be informative for future research on ethical considerations for genomic research in the African research context.

Alaska Native genomic research: perspectives from Alaska Native leaders, federal staff, and biomedical researchers.

Meaningful engagement of Alaska Native (AN) tribes and tribal health organizations is essential in the conduct of socially responsible and ethical research. As genomics becomes increasingly important to advancements in medicine, there is a risk that populations not meaningfully included in genomic research will not benefit from the outcomes of that research. AN people have historically been underrepresented in biomedical research; AN underrepresentation in genomics research is compounded by mistrust based on past abuses, concerns about privacy and data ownership, and cultural considerations specific to this type of research. Working together, the National Human Genome Research Institute and two Alaska Native health organizations, Southcentral Foundation and the Alaska Native Health Board, cosponsored a workshop in July 2018 to engage key stakeholders in discussion, strengthen relationships, and facilitate partnership and consideration of participation of AN people in community-driven biomedical and genomic research. AN priorities related to translation of genomics research to health and health care, return of genomic results, design of research studies, and data sharing were discussed. This report summarizes the perspectives that emerged from the dialogue and offers considerations for effective and socially responsible genomic research partnerships with AN communities.

Regional Patterns and Association Between Obesity and Hypertension in Africa: Evidence From the H3Africa CHAIR Study.

Hypertension and obesity are the most important modifiable risk factors for cardiovascular diseases, but their association is not well characterized in Africa. We investigated regional patterns and association of obesity with hypertension among 30 044 continental Africans. We harmonized data on hypertension (defined as previous diagnosis/use of antihypertensive drugs or blood pressure [BP]≥140/90 mmHg/BP≥130/80 mmHg) and obesity from 30 044 individuals in the Cardiovascular H3Africa Innovation Resource across 13 African countries. We analyzed data from population-based controls and the Entire Harmonized Dataset. Age-adjusted and crude proportions of hypertension were compared regionally, across sex, and between hypertension definitions. Logit generalized estimating equation was used to determine the independent association of obesity with hypertension (P value <5%). Participants were 56% women; with mean age 48.5±12.0 years. Crude proportions of hypertension (at BP≥140/90 mmHg) were 47.9% (95% CI, 47.4-48.5) for Entire Harmonized Dataset and 42.0% (41.1-42.7) for population-based controls and were significantly higher for the 130/80 mm Hg threshold at 59.3% (58.7-59.9) in population-based controls. The age-adjusted proportion of hypertension at BP≥140/90 mmHg was the highest among men (33.8% [32.1-35.6]), in western Africa (34.7% [33.3-36.2]), and in obese individuals (43.6%; 40.3-47.2). Obesity was independently associated with hypertension in population-based controls (adjusted odds ratio, 2.5 [2.3-2.7]) and odds of hypertension in obesity increased with increasing age from 2.0 (1.7-2.3) in younger age to 8.8 (7.4-10.3) in older age. Hypertension is common across multiple countries in Africa with 11.9% to 51.7% having BP≥140/90 mmHg and 39.5% to 69.4% with BP≥130/80 mmHg. Obese Africans were more than twice as likely to be hypertensive and the odds increased with increasing age.

The effect of North Carolina free clinics on hospitalizations for ambulatory care sensitive conditions among the uninsured.

BACKGROUND: Free clinics are volunteer based organizations that provide health care services to low-income individuals for free or minimal cost. Communities served by a free clinic can provide ambulatory care services for uninsured individuals, reducing reliance on costly hospital admissions for ambulatory care sensitive conditions. This study examines whether free clinics in North Carolina reduce hospitalizations for ambulatory care sensitive conditions for uninsured adults. METHODS: The study used North Carolina hospital discharge data from 2003 to 2007, restricted to uninsured adults residing in North Carolina (N = 270,325). Prevention Quality Indicators identified hospitalizations for ambulatory care sensitive conditions. The entry of new free clinics in some counties during this time period in conjunction with county-level and year fixed effects allows the logistic regression analysis to simulate a pre/post study design. RESULTS: Discharges for ambulatory care sensitive conditions constituted 12.6% of the sample. Despite the limited coverage provided by free clinics, which serve 5.5% of the uninsured in North Carolina, uninsured adults in counties served by a free clinic had an 8.0% reduced odds of a hospitalization being for an ambulatory care sensitive condition. When the model is limited to ambulatory care sensitive conditions related to chronic conditions, the odds of a hospitalization of an uninsured adult for an ambulatory care sensitive condition in counties served by a free clinic is reduced by 9.0%. CONCLUSION: Free clinics are effective providers of primary care services for uninsured individuals, particularly for those with chronic conditions. To enhance this impact by increasing free clinics' reach, state and local policy makers should support and encourage development of free clinics in high need areas.

Effect of a Digital Health Intervention on Receipt of Colorectal Cancer Screening in Vulnerable Patients: A Randomized Controlled Trial.

Background: Screening for colorectal cancer (CRC) reduces mortality, yet more than one third of age-eligible Americans are unscreened. Objective: To examine the effect of a digital health intervention, Mobile Patient Technology for Health-CRC (mPATH-CRC), on rates of CRC screening. Design: Randomized clinical trial. (ClinicalTrials.gov: NCT02088333). Setting: 6 community-based primary care practices. Participants: 450 patients (223 in the mPATH-CRC group and 227 in usual care) scheduled for a primary care visit and due for routine CRC screening. Intervention: An iPad application that displays a CRC screening decision aid, lets patients order their own screening tests, and sends automated follow-up electronic messages to support patients. Measurements: The primary outcome was chart-verified completion of CRC screening within 24 weeks. Secondary outcomes were ability to state a screening preference, intention to receive screening, screening discussions, and orders for screening tests. All outcome assessors were blinded to randomization. Results: Baseline characteristics were similar between groups; 37% of participants had limited health literacy, and 53% had annual incomes less than $20 000. Screening was completed by 30% of mPATH-CRC participants and 15% of those receiving usual care (logistic regression odds ratio, 2.5 [95% CI, 1.6 to 4.0]). Compared with usual care, more mPATH-CRC participants could state a screening preference, planned to be screened within 6 months, discussed screening with their provider, and had a screening test ordered. Half of mPATH-CRC participants (53%; 118 of 223) "self-ordered" a test via the program. Limitation: Participants were English speakers in a single health care system. Conclusion: A digital health intervention that allows patients to self-order tests can increase CRC screening. Future research should identify methods for implementing similar interventions in clinical care. Primary Funding Source: National Cancer Institute.

Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions.

Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. Here, we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype-specific transmission pathways in a social carnivore. We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIVPle ) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIVPle molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father- and/or mother-offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype-specific FIVPle co-occurrence networks and assessed what combination of social networks, spatial networks or co-infection best structured the FIVPle network. While social organization (i.e., pride) was an important component of FIVPle transmission pathways at all scales, we find that FIVPle subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIVPle transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype-specific. Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus subtypes, which can manifest into landscape-level effects.

Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array.

BACKGROUND: Our next generation sequencing (NGS)-based human papillomavirus (HPV) genotyping assay showed a high degree of concordance with the Roche Linear Array (LA) with as little as 1.25 ng formalin-fixed paraffin-embedded-derived genomic DNA in head and neck and cervical cancer samples. This sensitive genotyping assay uses barcoded HPV PCR broad-spectrum general primers 5+/6+ (BSGP)5+/6+ applicable to population studies, but it's diagnostic performance has not been tested in cases with multiple concurrent HPV infections. METHODS: We conducted a cross-sectional study to compare the positive and negative predictive value (PPV and NPV), sensitivity and specificity of the NGS assay to detect HPV genotype infections as compared to the LA. DNA was previously extracted from ten anal swab samples from men who have sex with men in Nigeria enrolled on the TRUST/RV368 cohort study. Two-sample tests of proportions were used to examine differences in the diagnostic performance of the NGS assay to detect high vs. low-risk HPV type-specific infections. RESULTS: In total there were 94 type-specific infections detected in 10 samples with a median of 9.5, range (9 to 10) per sample. Using the LA as the gold standard, 84.4% (95% CI: 75.2-91.2) of the same anal type-specific infections detected on the NGS assay had been detected by LA. The PPV and sensitivity differed significantly for high risk (PPV: 90%, 95% CI: 79.5-96.2; sensitivity: 93.1%, 95% CI: 83.3-98.1) as compared to low risk HPV (PPV: 73%, 95% CI: 54.1-87.7; sensitivity: 61.1, 95% CI: 43.5-76.9) (all p < 0.05). The NPV for all types was 92.5% (95% CI: 88.4-95.4). The NPV and specificity were similar for high and low risk HPVs (all p > 0.05). The NGS assay detected 10 HPV genotypes that were not among the 37 genotypes found on LA (30, 32, 43, 44, 74, 86, 87, 90, 91, 114). CONCLUSIONS: The NGS assay accurately detects multiple HPV infections in individual clinical specimens with limited sample volume and has extended coverage compared to LA.

Cost Analysis of Ceramic Heads in Primary Total Hip Arthroplasty.

BACKGROUND: The advent of adverse local tissue reactions seen in metal-on-metal bearings, and the recent recognition of trunnionosis, have led many surgeons to recommend ceramic-on-polyethylene articulations for primary total hip arthroplasty. However, to our knowledge, there has been little research that has considered whether the increased cost of ceramic provides enough benefit over cobalt-chromium to justify its use. The primary purpose of this study was to compare the cost-effectiveness of ceramic-on-polyethylene implants and metal-on-polyethylene implants in patients undergoing total hip arthroplasty. METHODS: Markov decision modeling was used to determine the ceramic-on-polyethylene implant revision rate necessary to be cost-effective compared with the revision rate of metal-on-polyethylene implants across a range of patient ages and implant costs. A different set of Markov models was used to estimate the national cost burden of choosing ceramic-on-polyethylene implants over metal-on-polyethylene implants for primary total hip arthroplasties. The Premier Research Database was used to identify 20,398 patients who in 2012 were ≥45 years of age and underwent a total hip arthroplasty with either a ceramic-on-polyethylene implant or a metal-on-polyethylene implant. RESULTS: The cost-effectiveness of ceramic heads is highly dependent on the cost differential between ceramic and metal femoral heads and the age of the patient. At a cost differential of $325, ceramic-on-polyethylene bearings are cost-effective for patients <85 years of age. At a cost differential of $600, it is cost-effective to utilize ceramic-on-polyethylene bearings in patients <65 years of age, and, at a differential of $1,003, ceramic-on-polyethylene bearings are not cost-effective at any age. CONCLUSIONS: The ability to recoup the initial increased expenditure of ceramic heads through a diminished lifetime revision cost is dependent on the price premium for ceramic and the age of the patient. A wholesale switch to ceramic bearings regardless of age or cost differential may result in an economic burden to the health system. LEVEL OF EVIDENCE: Economic and decision analysis, Level III. See Instructions for Authors for a complete description of levels of evidence.

Next-Generation Sequencing-Based HPV Genotyping Assay Validated in Formalin-Fixed, Paraffin-Embedded Oropharyngeal and Cervical Cancer Specimens.

Available clinical human papilloma virus (HPV) diagnostics for head and neck cancer have limited sensitivity and/or fail to define the HPV genotype. Common HPV genotyping assays are costly and labor intensive. We sought to develop a next-generation sequencing (NGS)-based HPV genotyping assay that was sensitive enough to work on formalin-fixed paraffin-embedded (FFPE) samples. We developed an ion torrent NGS HPV genotyping assay using barcoded HPV PCR broad-spectrum general primers 5(+)/6(+) (BSGP)5(+)/6(+). To validate genotype specificity and use in archived clinical FFPE tumor samples, we compared NGS HPV genotyping at 2 sequencing centers with typing by Roche Linear Array assay in 42 oropharyngeal and cervical cancer specimens representing 10 HPV genotypes, as well as HPV-negative cases. To demonstrate the detection of a broad range of HPV genotypes, we genotyped a cohort of 266 cervical cancers. A comparison of NGS genotyping of FFPE cancer specimens with genotyping by Linear Array showed concordant results in 34/37 samples (92%) at sequencing site 1 and 39/42 samples (93%) at sequencing site 2. Concordance between sites was 92%. Designed for use with 10 ng genomic DNA, the assay detected HPV using as little as 1.25 ng FFPE-derived genomic DNA. In 266 cervical cancer specimens, the NGS assay identified 20 different HPV genotypes, including all 13 carcinogenic genotypes. This novel NGS assay provides a sensitive and specific high-throughput method to detect and genotype HPV in a range of clinical specimens derived from FFPE with low per-sample cost.

Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level.

Development of HIV-1 drug resistance mutations (HDRMs) is one of the major reasons for the clinical failure of antiretroviral therapy. Treatment success rates can be improved by applying personalized anti-HIV regimens based on a patient's HDRM profile. However, the sensitivity and specificity of the HDRM profile is limited by the methods used for detection. Sanger-based sequencing technology has traditionally been used for determining HDRM profiles at the single nucleotide variant (SNV) level, but with a sensitivity of only ≥ 20% in the HIV population of a patient. Next Generation Sequencing (NGS) technologies offer greater detection sensitivity (~ 1%) and larger scope (hundreds of samples per run). However, NGS technologies produce reads that are too short to enable the detection of the physical linkages of individual SNVs across the haplotype of each HIV strain present. In this article, we demonstrate that the single-molecule long reads generated using the Third Generation Sequencer (TGS), PacBio RS II, along with the appropriate bioinformatics analysis method, can resolve the HDRM profile at a more advanced quasispecies level. The case studies on patients' HIV samples showed that the quasispecies view produced using the PacBio method offered greater detection sensitivity and was more comprehensive for understanding HDRM situations, which is complement to both Sanger and NGS technologies. In conclusion, the PacBio method, providing a promising new quasispecies level of HDRM profiling, may effect an important change in the field of HIV drug resistance research.

Does Increased Spending on Pharmaceutical Marketing Inhibit Pioneering Innovation?

The pharmaceutical industry has been criticized for developing and aggressively marketing drugs that do not provide significant health benefits relative to existing drugs but retain the benefits of patent protection. Critics argue that drug marketing increases health care expenditures and provides a disincentive for pioneering drug innovation. However, evidence that marketing expenditures have any relationship to new drug approvals has been anecdotal. We hypothesized that, at publicly traded pharmaceutical firms, increased marketing expenditures will result in a reduced volume of pioneering new drugs in comparison to less innovative new drugs. We also hypothesized that additional research and development spending will result in an increased volume of pioneering new drugs in comparison to less innovative drugs. Results confirm our hypotheses. Specific policy recommendations for altering firms' incentives for the development of pioneering drugs are provided.

Genome Analysis of Latin American Cervical Cancer: Frequent Activation of the PIK3CA Pathway.

PURPOSE: Cervical cancer is one of the most common causes of cancer mortality for women living in poverty, causing more than 28,000 deaths annually in Latin America and 266,000 worldwide. To better understand the molecular basis of the disease, we ascertained blood and tumor samples from Guatemala and Venezuela and performed genomic characterization. EXPERIMENTAL DESIGN: We performed human papillomavirus (HPV) typing and identified somatically mutated genes using exome and ultra-deep targeted sequencing with confirmation in samples from Mexico. Copy number changes were also assessed in the exome sequence. RESULTS: Cervical cancer cases in Guatemala and Venezuela have an average age of diagnosis of 50 years and 5.6 children. Analysis of 675 tumors revealed activation of PIK3CA and other PI3K/AKT pathway genes in 31% of squamous carcinomas and 24% of adeno- and adenosquamous tumors, predominantly at two sites (E542K, E545K) in the helical domain of the PIK3CA gene. This distribution of PIK3CA mutations is distinct from most other cancer types and does not result in the in vitro phosphorylation of AKT. Somatic mutations were more frequent in squamous carcinomas diagnosed after the age of 50 years. Frequent gain of chromosome 3q was found, and low PIK3CA mutation fractions in many tumors suggest that PI3K mutation can be a late event in tumor progression. CONCLUSIONS: PI3K pathway mutation is important to cervical carcinogenesis in Latin America. Therapeutic agents that directly target PI3K could play a role in the therapy of this common malignancy.

Cost-effectiveness of quantitative pretest probability intended to reduce unnecessary medical radiation exposure in emergency department patients with chest pain and dyspnea.

OBJECTIVES: Quantitative pretest probability (qPTP) incorporated into a decision support tool with advice can reduce unnecessary diagnostic testing among patients with symptoms suggestive of acute coronary syndrome (ACS) and pulmonary embolism (PE), reducing 30-day costs without an increase in 90-day adverse outcomes. This study estimates long-term (beyond 90-day) costs and outcomes associated with qPTP. The authors hypothesized that qPTP reduces lifetime costs and improves outcomes in low-risk patients with symptoms suggestive of ACS and PE. METHODS: This was a cost-effectiveness analysis of a multicenter, randomized controlled trial of adult emergency patients with dyspnea and chest pain, in which a clinician encountering a low-risk patient with symptoms suggestive of ACS or PE conducted either the intervention (qPTP for ACS and PE with advice) or the sham (no qPTP and no advice). Effect of the intervention over a patient's lifetime was assessed using a Markov microsimulation model. Short-term costs and outcomes were from the trial; long-term outcomes and costs were from the literature. Outcomes included lifetime transition to PE, ACS, and intracranial hemorrhage (ICH); mortality from cancer, ICH, PE, ACS, renal failure, and ischemic stroke; quality-adjusted life-years (QALYs); and total medical costs compared between simulated intervention and sham groups. RESULTS: Markov microsimulation for a 40-year-old patient receiving qPTP found lifetime cost savings of $497 for women and $528 for men, associated with small gains in QALYs (2 and 6 days, respectively) and lower rates of cancer mortality in both sexes, but a reduction in ICH only in males. Sensitivity analysis for patients aged 60 years predicted that qPTP would continue to save costs and also reduce mortality from both ICH and cancer. Use of qPTP significantly reduced the lifetime probability of PE diagnosis, with lower probability of death from PE in both sexes aged 40 to 60 years. However, use of qPTP reduced the rate of ACS diagnosis and death from ACS at age 40, but increased the death rate from ACS at age 60 for both sexes. CONCLUSIONS: Widespread use of a combined qPTP for both ACS and PE has the potential to decrease costs by reducing diagnostic testing, while improving most long-term outcomes in emergency patients with chest pain and dyspnea.

Community engagement strategies for genomic studies in Africa: a review of the literature.

BACKGROUND: Community engagement has been recognised as an important aspect of the ethical conduct of biomedical research, especially when research is focused on ethnically or culturally distinct populations. While this is a generally accepted tenet of biomedical research, it is unclear what components are necessary for effective community engagement, particularly in the context of genomic research in Africa. METHODS: We conducted a review of the published literature to identify the community engagement strategies that can support the successful implementation of genomic studies in Africa. Our search strategy involved using online databases, Pubmed (National Library of Medicine), Medline and Google scholar. Search terms included a combination of the following: community engagement, community advisory boards, community consultation, community participation, effectiveness, genetic and genomic research, Africa, developing countries. RESULTS: A total of 44 articles and 1 thesis were retrieved of which 38 met the selection criteria. Of these, 21 were primary studies on community engagement, while the rest were secondary reports on community engagement efforts in biomedical research studies. 34 related to biomedical research generally, while 4 were specific to genetic and genomic research in Africa. CONCLUSION: We concluded that there were several community engagement strategies that could support genomic studies in Africa. While many of the strategies could support the early stages of a research project such as the recruitment of research participants, further research is needed to identify effective strategies to engage research participants and their communities beyond the participant recruitment stage. Research is also needed to address how the views of local communities should be incorporated into future uses of human biological samples. Finally, studies evaluating the impact of CE on genetic research are lacking. Systematic evaluation of CE strategies is essential to determine the most effective models of CE for genetic and genomic research conducted in African settings.

GWATCH: a web platform for automated gene association discovery analysis.

BACKGROUND: As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations. FINDINGS: Here we present a dynamic web-based platform - GWATCH - that automates and facilitates four steps in genetic epidemiological discovery: 1) Rapid gene association search and discovery analysis of large genome-wide datasets; 2) Expanded visual display of gene associations for genome-wide variants (SNPs, indels, CNVs), including Manhattan plots, 2D and 3D snapshots of any gene region, and a dynamic genome browser illustrating gene association chromosomal regions; 3) Real-time validation/replication of candidate or putative genes suggested from other sources, limiting Bonferroni genome-wide association study (GWAS) penalties; 4) Open data release and sharing by eliminating privacy constraints (The National Human Genome Research Institute (NHGRI) Institutional Review Board (IRB), informed consent, The Health Insurance Portability and Accountability Act (HIPAA) of 1996 etc.) on unabridged results, which allows for open access comparative and meta-analysis. CONCLUSIONS: GWATCH is suitable for both GWAS and whole genome sequence association datasets. We illustrate the utility of GWATCH with three large genome-wide association studies for HIV-AIDS resistance genes screened in large multicenter cohorts; however, association datasets from any study can be uploaded and analyzed by GWATCH.

Evolution of puma lentivirus in bobcats (Lynx rufus) and mountain lions (Puma concolor) in North America.

Mountain lions (Puma concolor) throughout North and South America are infected with puma lentivirus clade B (PLVB). A second, highly divergent lentiviral clade, PLVA, infects mountain lions in southern California and Florida. Bobcats (Lynx rufus) in these two geographic regions are also infected with PLVA, and to date, this is the only strain of lentivirus identified in bobcats. We sequenced full-length PLV genomes in order to characterize the molecular evolution of PLV in bobcats and mountain lions. Low sequence homology (88% average pairwise identity) and frequent recombination (1 recombination breakpoint per 3 isolates analyzed) were observed in both clades. Viral proteins have markedly different patterns of evolution; sequence homology and negative selection were highest in Gag and Pol and lowest in Vif and Env. A total of 1.7% of sites across the PLV genome evolve under positive selection, indicating that host-imposed selection pressure is an important force shaping PLV evolution. PLVA strains are highly spatially structured, reflecting the population dynamics of their primary host, the bobcat. In contrast, the phylogeography of PLVB reflects the highly mobile mountain lion, with diverse PLVB isolates cocirculating in some areas and genetically related viruses being present in populations separated by thousands of kilometers. We conclude that PLVA and PLVB are two different viral species with distinct feline hosts and evolutionary histories. Importance: An understanding of viral evolution in natural host populations is a fundamental goal of virology, molecular biology, and disease ecology. Here we provide a detailed analysis of puma lentivirus (PLV) evolution in two natural carnivore hosts, the bobcat and mountain lion. Our results illustrate that PLV evolution is a dynamic process that results from high rates of viral mutation/recombination and host-imposed selection pressure.