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.

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.

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.

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.

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.

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.

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.

The principal genetic determinants for nasopharyngeal carcinoma in China involve the HLA class I antigen recognition groove.

Nasopharyngeal carcinoma (NPC) is an epithelial malignancy facilitated by Epstein-Barr Virus infection. Here we resolve the major genetic influences for NPC incidence using a genome-wide association study (GWAS), independent cohort replication, and high-resolution molecular HLA class I gene typing including 4,055 study participants from the Guangxi Zhuang Autonomous Region and Guangdong province of southern China. We detect and replicate strong association signals involving SNPs, HLA alleles, and amino acid (aa) variants across the major histocompatibility complex-HLA-A, HLA -B, and HLA -C class I genes (P(HLA-A-aa-site-62) = 7.4 × 10(-29); P (HLA-B-aa-site-116) = 6.5 × 10(-19); P (HLA-C-aa-site-156) = 6.8 × 10(-8) respectively). Over 250 NPC-HLA associated variants within HLA were analyzed in concert to resolve separate and largely independent HLA-A, -B, and -C gene influences. Multivariate logistical regression analysis collapsed significant associations in adjacent genes spanning 500 kb (OR2H1, GABBR1, HLA-F, and HCG9) as proxies for peptide binding motifs carried by HLA- A*11:01. A similar analysis resolved an independent association signal driven by HLA-B*13:01, B*38:02, and B*55:02 alleles together. NPC resistance alleles carrying the strongly associated amino acid variants implicate specific class I peptide recognition motifs in HLA-A and -B peptide binding groove as conferring strong genetic influence on the development of NPC in China.

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.

Outcomes and radiation exposure of emergency department patients with chest pain and shortness of breath and ultralow pretest probability: a multicenter study.

STUDY OBJECTIVE: Excessive radiation exposure remains a concern for patients with symptoms suggesting acute coronary syndrome and pulmonary embolism but must be judged in the perspective of pretest probability and outcomes. We quantify and qualify the pretest probability, outcomes, and radiation exposure of adults with both chest pain and dyspnea. METHODS: This was a prospective, 4-center, outcomes study. Patients were adults with dyspnea and chest pain, nondiagnostic ECGs, and no obvious diagnosis. Pretest probability for both acute coronary syndrome and pulmonary embolism was assessed with a validated method; ultralow risk was defined as pretest probability less than 2.5% for both acute coronary syndrome and pulmonary embolism. Patients were followed for diagnosis and total medical radiation exposure for 90 days. RESULTS: Eight hundred forty patients had complete data; 23 (3%) had acute coronary syndrome and 15 (2%) had pulmonary embolism. The cohort received an average of 4.9 mSv radiation to the chest, 48% from computed tomography pulmonary angiography. The pretest probability estimates for acute coronary syndrome and pulmonary embolism were less than 2.5% in 227 patients (27%), of whom 0 of 277 (0%; 95% confidence interval 0% to 1.7%) had acute coronary syndrome or pulmonary embolism and 7 of 227 (3%) had any significant cardiopulmonary diagnosis. The estimated chest radiation exposure per patient in this ultralow-risk group was 3.5 mSv, including 26 (3%) with greater than 5 mSv radiation to the chest and no significant cardiopulmonary diagnosis. CONCLUSION: One quarter of patients with chest pain and dyspnea had ultralow risk and no acute coronary syndrome or pulmonary embolism but were exposed to an average of 3.5 mSv radiation to the chest. These data can be used in a clinical guideline to reduce radiation exposure.

Role of exonic variation in chemokine receptor genes on AIDS: CCRL2 F167Y association with pneumocystis pneumonia.

Chromosome 3p21-22 harbors two clusters of chemokine receptor genes, several of which serve as major or minor coreceptors of HIV-1. Although the genetic association of CCR5 and CCR2 variants with HIV-1 pathogenesis is well known, the role of variation in other nearby chemokine receptor genes remain unresolved. We genotyped exonic single nucleotide polymorphisms (SNPs) in chemokine receptor genes: CCR3, CCRL2, and CXCR6 (at 3p21) and CCR8 and CX3CR1 (at 3p22), the majority of which were non-synonymous. The individual SNPs were tested for their effects on disease progression and outcomes in five treatment-naïve HIV-1/AIDS natural history cohorts. In addition to the known CCR5 and CCR2 associations, significant associations were identified for CCR3, CCR8, and CCRL2 on progression to AIDS. A multivariate survival analysis pointed to a previously undetected association of a non-conservative amino acid change F167Y in CCRL2 with AIDS progression: 167F is associated with accelerated progression to AIDS (RH = 1.90, P = 0.002, corrected). Further analysis indicated that CCRL2-167F was specifically associated with more rapid development of pneumocystis pneumonia (PCP) (RH = 2.84, 95% CI 1.28-6.31) among four major AIDS-defining conditions. Considering the newly defined role of CCRL2 in lung dendritic cell trafficking, this atypical chemokine receptor may affect PCP through immune regulation and inducing inflammation.

Effects of skilled nursing facility structure and process factors on medication errors during nursing home admission.

BACKGROUND: Older adults are at greatest risk of medication errors during the transition period of the first 7 days after admission and readmission to a skilled nursing facility (SNF). PURPOSE: The aim of this study was to evaluate structure- and process-related factors that contribute to medication errors and harm during transition periods at a SNF. METHODOLOGY/APPROACH: Data for medication errors and potential medication errors during the 7-day transition period for residents entering North Carolina SNFs were from the Medication Error Quality Initiative-Individual Error database from October 2006 to September 2007. The impact of SNF structure and process measures on the number of reported medication errors and harm from errors were examined using bivariate and multivariate model methods. FINDINGS: A total of 138 SNFs reported 581 transition period medication errors; 73 (12.6%) caused harm. Chain affiliation was associated with a reduction in the volume of errors during the transition period. One third of all reported transition errors occurred during the medication administration phase of the medication use process, where dose omissions were the most common type of error; however, dose omissions caused harm less often than wrong-dose errors did. Prescribing errors were much less common than administration errors but were much more likely to cause harm. PRACTICE IMPLICATIONS: Both structure and process measures of quality were related to the volume of medication errors.However, process quality measures may play a more important role in predicting harm from errors during the transition of a resident into an SNF. Medication errors during transition could be reduced by improving both prescribing processes and transcription and documentation of orders.

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.

Multicohort genomewide association study reveals a new signal of protection against HIV-1 acquisition.

BACKGROUND: To date, only mutations in CCR5 have been shown to confer resistance to human immunodeficiency virus type 1 (HIV-1) infection, and these explain only a small fraction of the observed variability in HIV susceptibility. METHODS: We performed a meta-analysis between 2 independent European genomewide association studies, each comparing HIV-1 seropositive cases with normal population controls known to be HIV uninfected, to identify single-nucleotide polymorphisms (SNPs) associated with the HIV-1 acquisition phenotype. SNPs exhibiting P < 10(-5) in this first stage underwent second-stage analysis in 2 independent US cohorts of European descent. RESULTS: After the first stage, a single highly significant association was revealed for the chromosome 8 rs6996198 with HIV-1 acquisition and was replicated in both second-stage cohorts. Across the 4 groups, the rs6996198-T allele was consistently associated with a significant reduced risk of HIV-1 infection, and the global meta-analysis reached genomewide significance: P(combined) = 7.76 × 10(-8). CONCLUSIONS: We provide strong evidence of association for a common variant with HIV-1 acquisition in populations of European ancestry. This protective signal against HIV-1 infection is the first identified outside the CCR5 nexus. First clues point to a potential functional role for a nearby candidate gene, CYP7B1, but this locus warrants further investigation.

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.

Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape.

Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches because of avoidance of intervening human development, which potentially leads to both reduced gene flow and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analysed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced gene flow between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenetic analyses indicates that pathogen genotypes are less spatially structured-exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured owing to low levels of effective bobcat migration resulting in gene flow. We illustrate the utility in using multiple molecular markers that differentially detect movement and gene flow between subpopulations when assessing connectivity.

Genome-wide association study implicates PARD3B-based AIDS restriction.

BACKGROUND: Host genetic variation influences human immunodeficiency virus (HIV) infection and progression to AIDS. Here we used clinically well-characterized subjects from 5 pretreatment HIV/AIDS cohorts for a genome-wide association study to identify gene associations with rate of AIDS progression. METHODS: European American HIV seroconverters (n = 755) were interrogated for single-nucleotide polymorphisms (SNPs) (n = 700,022) associated with progression to AIDS 1987 (Cox proportional hazards regression analysis, co-dominant model). RESULTS: Association with slower progression was observed for SNPs in the gene PARD3B. One of these, rs11884476, reached genome-wide significance (relative hazard = 0.3; P =3. 370 × 10(-9)) after statistical correction for 700,022 SNPs and contributes 4.52% of the overall variance in AIDS progression in this study. Nine of the top-ranked SNPs define a PARD3B haplotype that also displays significant association with progression to AIDS (hazard ratio, 0.3; P = 3.220 × 10(-8)). One of these SNPs, rs10185378, is a predicted exonic splicing enhancer; significant alteration in the expression profile of PARD3B splicing transcripts was observed in B cell lines with alternate rs10185378 genotypes. This SNP was typed in European cohorts of rapid progressors and was found to be protective for AIDS 1993 definition (odds ratio, 0.43, P = .025). CONCLUSIONS: These observations suggest a potential unsuspected pathway of host genetic influence on the dynamics of AIDS progression.

Isolation and characterization of the CYP2D6 gene in Felidae with comparison to other mammals.

The highly polymorphic CYP2D6 protein metabolizes about 25% of commonly used drugs and underlies a broad spectrum of drug responses among individuals. In contrast to extensive knowledge on the human CYP2D6 gene, little is known about the gene in non-human mammals. CYP2D6 mRNA from 23 cats (Felidae) spanning seven species were compared to available CYPD6 sequences in ten additional mammals and multiple allelic variants in humans. A relatively high mean dN/dS ratio (0.565) was observed, especially within Felidae. Pairwise dN/dS ratios were non-monotonically distributed with respect to evolutionary distance suggesting either positive selection or retention of slightly deleterious mutations. Positive selection on specific codons, most notably in regions involved in substrate recognition and membrane anchoring is supported and the possible influence of diet on specific amino acid changes in substrate binding sites is discussed.

Cost-effectiveness of an emergency department-based early sepsis resuscitation protocol.

OBJECTIVES: Guidelines recommend that sepsis be treated with an early resuscitation protocol such as early goal-directed therapy. Our objective was to assess the cost-effectiveness of implementing early goal-directed therapy as a routine protocol. DESIGN: Prospective before and after study. SETTING: Large urban hospital emergency department with >110,000 visits/yr. PATIENTS: The target population was patients with consensus criteria for septic shock. We excluded those with age <18 yrs, no aggressive care desired, or need for immediate surgery. INTERVENTIONS: Clinical and cost data were prospectively collected on two groups: 1) patients from 1 yr before; and 2) 2 yrs after implementing early goal-directed therapy as standard of care. Before phase patients received nonprotocolized care at attending discretion. The primary outcomes were 1-yr mortality, discounted life expectancy, and quality-adjusted life-years. Using costs and quality-adjusted life-years, we constructed an incremental cost-effectiveness ratio and performed a net monetary benefit analysis, producing the probability that the intervention was cost-effective given different values for the willingness to pay for a quality-adjusted life-year. RESULTS: Two hundred eighty-five subjects, 79 in the before and 206 in the after phases, were enrolled. Treatment with early goal-directed therapy was associated with an increased hospital cost of $7,028 and an increase in both discounted sepsis-adjusted life expectancy and quality-adjusted life years of 1.5 and 1.3 yrs, respectively. Early goal-directed therapy use was associated with a cost of $5,397 per quality-adjusted life-years gained and the net monetary benefit analysis indicates a 98% probability (p = .038) that early goal-directed therapy is cost-effective at a willingness to pay of $50,000 per quality-adjusted life-years. CONCLUSION: Implementation of early goal-directed therapy in the emergency department care of patients with severe sepsis is cost-effective.