How inclusive were UK-based randomised controlled trials of COVID-19 vaccines? A systematic review investigating enrolment of Black adults and adult ethnic minorities.

OBJECTIVES: To establish if Black adults and adult ethnic minorities, defined as any group except White British, were represented in UK-based COVID-19 vaccination randomised controlled trials (RCTs) when compared to corresponding UK population proportions, based on 2011 census data. DESIGN: Systematic review of COVID-19 Randomised Controlled Vaccine Trials SETTING: United Kingdom PARTICIPANTS: Randomised Controlled Trials of COVID-19 vaccines conducted in the UK were systematically reviewed following PRISMA guidelines. MeSH terms included "Covid-19 vaccine", "Ad26COVS1", and "BNT162 Vaccine" with keywords such as [covishield OR coronavac OR Vaxzevria OR NVX-CoV2373] also used. Studies that provided (A) participant demographics and (B) full eligibility criteria were included. The following key data was extracted for analysis: number of participants analysed, number of Black adults and number of adult minority ethnicity participants. PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcome is the mean percentage of Black adults randomised to COVID-19 vaccine trials deemed eligible within this review. The secondary outcome is the mean percentage of adult ethnic minorities randomised. RESULTS: The final review included 7 papers and a total of 87 sets of data collated from trial sites across the UK. The standard mean percentage of Black adults included in the trials (0.59%, 95% CI: 0.13% - 1.05%) was significantly lower compared to the recorded Black adult population (2.67%) indicating that they were under-served in UK based COVID-19 vaccine RCTs (p < 0.001). Adult ethnic minority presence (8.94%, 95% CI: 2.07% - 15.80%) was also lower than census data (16.30%), indicating they were also under-served (p = 0.039). CONCLUSION: The findings show that COVID-19 vaccine trials failed to adequately randomise proportionate numbers of Black adults and adult minority ethnicities. More inclusive practices must be developed and implemented in the recruitment of underserved groups to understand the true impact of COVID-19.

The Effect of Bimatoprost Implant on Glaucoma Patients: An Observational Study.

PRCIS: In this retrospective study of glaucoma patients receiving the bimatoprost implant at Duke Eye Center, the number of topical intraocular pressure-lowering medications was significantly reduced through 12 months after the implant. PURPOSE: To study the effects of the bimatoprost implant on intraocular pressure (IOP) and the need for topical IOP-lowering medications in glaucoma patients in the clinical practice setting. PATIENTS AND METHODS: Patients who received the bimatoprost implant at Duke Eye Center from November 2020 to October 2021 were identified. Exclusion criteria included addition of other IOP-lowering medications concurrent with the implant and less than 1 month of follow-up. The change in IOP and number of topical IOP-lowering medications from baseline to months 1, 3, 6, 9, and 12 after the implant was calculated. Subgroup analysis was performed for different glaucoma severities. RESULTS: A total of 63 patients and 92 eyes were included (mean age 77.8 ± 10.1 years). Glaucoma severity ranged from mild (11%), moderate (30%), to severe (54%). There was a nonsignificant decrease in IOP at all timepoints. The mean number of topical IOP-lowering medications significantly decreased by 0.81, 0.75, 0.63, 0.70, and 0.67 at month 1, 3, 6, 9, and 12, respectively (all P < 0.001). There was no significant change in the total number of medications including the bimatoprost implant. When divided by glaucoma severity, the reduction in the number of topical medications was significant at 1, 3, and 6 months for mild/moderate disease, and at 1 month for severe disease. During the follow-up period, 19 eyes underwent additional laser or surgical procedures, 68% of which had a history of prior incisional glaucoma surgery. CONCLUSIONS: The bimatoprost implant may reduce the need for topical IOP-lowering agents over a 1-year period, especially in mild-to-moderate stage glaucoma. The efficacy of the implant may be more limited in severe glaucoma, and further work is needed to characterize its long-term effects.

An Economic Evaluation of a Streamlined Day-Case Atrial Fibrillation Ablation Protocol and Conventional Cryoballoon Ablation versus Antiarrhythmic Drugs in a UK Paroxysmal Atrial Fibrillation Population.

BACKGROUND AND AIMS: Symptom control for atrial fibrillation can be achieved by catheter ablation or drug therapy. We assessed the cost effectiveness of a novel streamlined atrial fibrillation cryoballoon ablation protocol (AVATAR) compared with optimised antiarrhythmic drug (AAD) therapy and a conventional catheter ablation protocol, from a UK National Health Service (NHS) perspective. METHODS: Data from the AVATAR study were assessed to determine the cost effectiveness of the three protocols in a two-step process. In the first stage, statistical analysis of clinical efficacy outcomes was conducted considering either a three-way comparison (AVATAR vs. conventional ablation vs. optimised AAD therapies) or a two-way comparison (pooled ablation protocol data vs. optimised AAD therapies). In the second stage, models assessed the cost effectiveness of the protocols. Costs and some of the clinical inputs in the models were derived from within-trial cost analysis and published literature. The remaining inputs were derived from clinical experts. RESULTS: No significant differences between the ablation protocols were found for any of the clinical outcomes used in the model. Results of a within-trial cost analysis show that AVATAR is cost-saving (£1279 per patient) compared with the conventional ablation protocol. When compared with optimised AAD therapies, AVATAR (pooled conventional and AVATAR ablation protocols efficacy) was found to be more costly while offering improved clinical benefits. Over a lifetime time horizon, the incremental cost-effectiveness ratio of AVATAR was estimated as £21,046 per quality-adjusted life-year gained (95% credible interval £7086-£71,718). CONCLUSIONS: The AVATAR streamlined protocol is likely to be a cost-effective option versus both conventional ablation and optimised AAD therapy in the UK NHS healthcare setting.

Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica.

Genomic structural variation (SV) has profound effects on organismal evolution; often serving as a source of novel genetic variation. Gene copy number variation (CNV), one type of SV, has repeatedly been associated with adaptive evolution in eukaryotes, especially with environmental stress. Resistance to the widely used herbicide, glyphosate, has evolved through target-site CNV in many weedy plant species, including the economically important grass, Eleusine indica (goosegrass); however, the origin and mechanism of these CNVs remain elusive in many weed species due to limited genetic and genomic resources. To study this CNV in goosegrass, we present high-quality reference genomes for glyphosate-susceptible and -resistant goosegrass lines and fine-assembles of the duplication of glyphosate's target site gene 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). We reveal a unique rearrangement of EPSPS involving chromosome subtelomeres. This discovery adds to the limited knowledge of the importance of subtelomeres as genetic variation generators and provides another unique example for herbicide resistance evolution.

ROptimus: a parallel general-purpose adaptive optimization engine.

MOTIVATION: Various computational biology calculations require a probabilistic optimization protocol to determine the parameters that capture the system at a desired state in the configurational space. Many existing methods excel at certain scenarios, but fail in others due, in part, to an inefficient exploration of the parameter space and easy trapping into local minima. Here, we developed a general-purpose optimization engine in R that can be plugged to any, simple or complex, modelling initiative through a few lucid interfacing functions, to perform a seamless optimization with rigorous parameter sampling. RESULTS: ROptimus features simulated annealing and replica exchange implementations equipped with adaptive thermoregulation to drive Monte Carlo optimization process in a flexible manner, through constrained acceptance frequency but unconstrained adaptive pseudo temperature regimens. We exemplify the applicability of our R optimizer to a diverse set of problems spanning data analyses and computational biology tasks. AVAILABILITY AND IMPLEMENTATION: ROptimus is written and implemented in R, and is freely available from CRAN (http://cran.r-project.org/web/packages/ROptimus/index.html) and GitHub (http://github.com/SahakyanLab/ROptimus).

The Use of Optical Coherence Tomography for Early Glaucoma Screening in a Population of Patients with Diabetes.

PURPOSE: The utility of screening for early diagnosis of glaucoma remains a widely debated topic in the care of ophthalmic patients. There are currently no population-based guidelines regarding screening for glaucoma. The purpose of this study is to determine the utility of optical coherence tomography (OCT) for early glaucoma screening in a population of diabetic patients. The results of this study may inform future screening practices. METHODS: The current study is a post hoc analysis of OCT data collected from diabetic patients screened for eye disease over 6 months. Glaucoma suspects (GS) were identified based on abnormal retinal nerve fiber layer (RNFL) thickness on OCT. Fundus photographs of GS were graded by two independent raters for vertical cup-to-disc ratio (CDR) and other signs of glaucomatous changes. RESULTS: Of the 807 subjects screened, 50 patients (6.2%) were identified as GS. The mean RNFL thickness for GS was significantly lower than the mean RNFL in the total screening population (p < .001). Median CDR for GS was 0.44. Twenty-eight eyes of 17 GS were marked as having optic disc notching or rim thinning by at least one grader. Cohen's kappa statistic for inter-rater reliability was 0.85. Racial differences showed that mean CDR was significantly higher in non-whites (p < .001). Older age was associated with thinner RNFL (r = -0.29, p = .004). CONCLUSIONS: Results of this study suggest that in a sample of diabetic patients, a small but clinically significant minority may be flagged as GS based on OCT. Nearly one-third of GS eyes were found to have glaucomatous changes on fundus photography by at least one grader. These results suggest screening with OCT may be useful in detecting early glaucomatous changes in high-risk populations, particularly older, non-white patients with diabetes.

Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) copy number variation confers glyphosate resistance in Eleusine indica.

Genomic structural variation (SV) can have profound effects on an organism’s evolution, often serving as a novel source of genetic variation. Gene copy number variation (CNV), a specific form of SV, has repeatedly been associated with adaptive evolution in eukaryotes, especially to biotic and abiotic stresses. Resistance to the most widely used herbicide, glyphosate, has evolved through target-site CNV in many weedy plant species, including the economically important cosmopolitan grass, Eleusine indica (goosegrass); however, the origin and mechanisms of these resistance CNVs remain elusive in many weed species due to limited genetic and genomics resources. In order to study the target site CNV in goosegrass, we generated high-quality reference genomes for both glyphosate-susceptible and -resistant individuals, fine assembled the duplication of glyphosate's target site gene enolpyruvylshikimate-3-phosphate synthase (EPSPS), and revealed a novel rearrangement of EPSPS into the subtelomeric region of the chromosomes, ultimately leading to herbicide resistance evolution. This discovery adds to the limited knowledge of the importance of subtelomeres as rearrangement hotspots and novel variation generators as well as provides an example of yet another unique pathway for the formation of CNVs in plants.

Factors Associated with Ophthalmology Referral and Adherence in a Teleretinal Screening Program: Insights from a Federally Qualified Health Center.

Background: Early detection of ophthalmic conditions such as diabetic retinopathy (DR) and glaucoma is crucial to preventing vision loss. Previous studies have evaluated teleretinal screening programs for DR in well-insured populations. The purpose of this retrospective study was to evaluate a teleretinal screening program in a population of uninsured and underinsured patients seen in a Federally Qualified Health Center (FQHC). Methods: We conducted a retrospective chart review of patients (age ≥18) who underwent teleretinal imaging (TRI) at a FQHC between January 2015 and September 2019. TRI gradings and patient demographic and clinical information were abstracted. Factors associated with referral for a dilated eye exam by an ophthalmologist, adherence to recommended follow-up dilated eye exam, and ophthalmology visit attendance were examined. Results: 3130 TRIs were graded in 2216 eyes (1107 patients). 65.2% (N = 722) self-identified as Hispanic and 56.3% (N = 623) required interpreter services. Follow-up dilated fundus examination (DFE) was recommended for 388 TRIs, 49% (N = 190) of which were completed within 1 year. Adherence to the recommended ophthalmology exam was not associated with any baseline clinical or demographic characteristics (p > 0.05). Older age, male sex, hypertension, proteinuria, and higher A1c were significantly associated with greater odds of ophthalmology referral based on TRI (all p < 0.05), after adjusting for covariates. Less severe diabetic retinopathy, no insurance coverage, and Hispanic ethnicity were associated with lower odds of attending an ophthalmology visit, regardless of follow-up recommendations based on TRI (all p < 0.05). Conclusion: In an FQHC serving predominantly uninsured and underinsured patients, only 49% of recommended DFE were completed within one year. Less severe diabetic retinopathy, lack of insurance coverage, and Hispanic ethnicity were associated with a lower likelihood of having a DFE regardless of recommendation. These results suggest that greater system-level efforts are needed to increase adherence to follow-up eye exams after TRI to ensure sight-saving care for underserved populations.

Does Bypass of the Proximal Small Intestine Impact Food Intake, Preference, and Taste Function in Humans? An Experimental Medicine Study Using the Duodenal-Jejunal Bypass Liner.

The duodenal-jejunal bypass liner (Endobarrier) is an endoscopic treatment for obesity and type 2 diabetes mellitus (T2DM). It creates exclusion of the proximal small intestine similar to that after Roux-en-Y Gastric Bypass (RYGB) surgery. The objective of this study was to employ a reductionist approach to determine whether bypass of the proximal intestine is the component conferring the effects of RYGB on food intake and sweet taste preference using the Endobarrier as a research tool. A nested mechanistic study within a large randomised controlled trial compared the impact of lifestyle modification with vs. without Endobarrier insertion in patients with obesity and T2DM. Forty-seven participants were randomised and assessed at several timepoints using direct and indirect assessments of food intake, food preference and taste function. Patients within the Endobarrier group lost numerically more weight compared to the control group. Using food diaries, our results demonstrated similar reductions of food intake in both groups. There were no significant differences in food preference and sensory, appetitive reward, or consummatory reward domain of sweet taste function between groups or changes within groups. In conclusion, the superior weight loss seen in patients with obesity and T2DM who underwent the Endobarrier insertion was not due to a reduction in energy intake or change in food preferences.

Effect of Diabetes Control on Rates of Structural and Functional Loss in Patients with Glaucoma.

PURPOSE: To investigate the association between levels of diabetes mellitus (DM) control and rates of visual field and retinal nerve fiber layer (RNFL) loss over time in glaucoma. DESIGN: Retrospective cohort study. PARTICIPANTS: A total of 351 eyes of 222 patients with type 2 DM with concomitant primary open-angle glaucoma (POAG) or suspected glaucoma extracted from the Duke Glaucoma Registry. METHODS: All patients had at least 2 reliable standard automated perimetry (SAP) tests, 2 spectral domain OCT (SD-OCT) tests, and 2 glycated hemoglobin (HbA1c) measures over time with a minimum follow-up of 6 months. Values of HbA1c were summarized for each patient as mean, peak, and fluctuation across time. Multivariable linear mixed models were used to estimate the effect of HbA1c on rates of change in SAP mean deviation (MD) and OCT RNFL thickness loss over time while adjusting for various confounding factors. MAIN OUTCOME MEASURES: Rates of change in MD and RNFL thickness over time. RESULTS: Subjects had a mean baseline age of 62.5 ± 10.2 years and follow-up time of 6.9 ± 5.1 years. Subjects had an average of 4.8 SAP tests (range, 2-28), 3.6 SD-OCT tests (range, 2-10), and 8.3 HbA1c tests (range, 2-21). Average HbA1c mean was 7.1% ± 1.1% (range, 5.4-11.7), peak HbA1c over time was 8.1% ± 2% (range, 5.5-15.6), and HbA1c fluctuation was 0.6% ± 0.6% (range, 0-4.4). Mean rate of SAP MD change was -0.09 ± 0.20 decibel/year (median -0.06 decibel/year; interquartile range -0.15 to 0.01 decibel/year), and mean rate of RNFL change was -0.83 ± 0.51 µm/year (median -0.76 µm/year; interquartile range -1.06 to 0.56 µm/year). After adjustment for confounding factors, mean, peak, and fluctuation in HbA1c levels were not significantly associated with rates of MD change over time (P = 0.994, P = 0.689, P = 0.920, respectively), nor were rates of change in RNFL loss over time (P = 0.805, P = 0.575, P = 0.770). CONCLUSIONS: We did not find a significant association between diabetes control, as measured by levels of HbA1c, and rates of visual field or RNFL loss over time in individuals with glaucoma or suspected glaucoma.

Synthesis, characterization, in vitro SAR study, and preliminary in vivo toxicity evaluation of naphthylmethyl substituted bis-imidazolium salts.

A series of novel bis-imidazolium salts was synthesized, characterized, and evaluated in vitro against a panel of non-small cell lung cancer (NSCLC) cells. Two imidazolium cores were connected with alkyl chains of varying lengths to develop a structure activity relationship (SAR). Increasing the length of the connecting alkyl chain was shown to correlate to an increase in the anti-proliferative activity. The National Cancer Institute's NCI-60 human tumor cell line screen confirmed this trend. The compound containing a decyl linker chain, 10, was chosen for further in vivo toxicity studies with C578BL/6 mice. The compound was well tolerated by the mice and all of the animals survived and gained weight over the course of the study.

Evidence of unexplained discrepancies between planned and conducted statistical analyses: a review of randomised trials.

BACKGROUND: Choosing or altering the planned statistical analysis approach after examination of trial data (often referred to as 'p-hacking') can bias the results of randomised trials. However, the extent of this issue in practice is currently unclear. We conducted a review of published randomised trials to evaluate how often a pre-specified analysis approach is publicly available, and how often the planned analysis is changed. METHODS: A review of randomised trials published between January and April 2018 in six leading general medical journals. For each trial, we established whether a pre-specified analysis approach was publicly available in a protocol or statistical analysis plan and compared this to the trial publication. RESULTS: Overall, 89 of 101 eligible trials (88%) had a publicly available pre-specified analysis approach. Only 22/89 trials (25%) had no unexplained discrepancies between the pre-specified and conducted analysis. Fifty-four trials (61%) had one or more unexplained discrepancies, and in 13 trials (15%), it was impossible to ascertain whether any unexplained discrepancies occurred due to incomplete reporting of the statistical methods. Unexplained discrepancies were most common for the analysis model (n = 31, 35%) and analysis population (n = 28, 31%), followed by the use of covariates (n = 23, 26%) and the approach for handling missing data (n = 16, 18%). Many protocols or statistical analysis plans were dated after the trial had begun, so earlier discrepancies may have been missed. CONCLUSIONS: Unexplained discrepancies in the statistical methods of randomised trials are common. Increased transparency is required for proper evaluation of results.

Recent Developments in the Medicinal Applications of Silver-NHC Complexes and Imidazolium Salts.

Because of their great structural diversity and multitude of chemical properties, N-heterocyclic carbenes (NHCs) have been utilized in a variety of capacities. Most recently, NHCs have been utilized as carrier molecules for many transition metals in medicinal chemistry. Specifically, Ag(I)-NHCs have been investigated as potent antibacterial agents and chemotherapeutics and have shown great efficacy in both in vitro and in vivo studies. Ag(I)-NHC compounds have been shown to be effective against a wide range of both Gram-positive and Gram-negative bacterial strains. Many compounds have also shown great efficacy as antitumor agents demonstrating comparable or better antitumor activity than standard chemotherapeutics such as cisplatin and 5-fluorouracil. While these compounds have shown great promise, clinical use has remained an unattained goal. Current research has been focused upon synthesis of novel Ag(I)-NHC compounds and further investigations of their antibacterial and antitumor activity. This review will focus on recent advances of Ag(I)-NHCs in medicinal applications.

Group 13 Superacid Adducts of [PCl2N]3.

Irrespective of the order of the addition of reagents, the reactions of [PCl2N]3 with MX3 (MX3 = AlCl3, AlBr3, GaCl3) in the presence of water or gaseous HX give the air- and light-sensitive superacid adducts [PCl2N]3·HMX4. The reactions are quantitative when HX is used. These reactions illustrate a Lewis acid/Brønsted acid dichotomy in which Lewis acid chemistry can become Brønsted acid chemistry in the presence of adventitious water or HX. The crystal structures of all three [PCl2N]3·HMX4 adducts show that protonation weakens the two P-N bonds that flank the protonated nitrogen atom. Variable-temperature NMR studies indicate that exchange in solution occurs in [PCl2N]3·HMX4, even at lower temperatures than those for [PCl2N]3·MX3. The fragility of [PCl2N]3·HMX4 at or near room temperature and in the presence of light suggests that such adducts are not involved directly as intermediates in the high-temperature ring-opening polymerization (ROP) of [PCl2N]3 to give [PCl2N]n. Attempts to catalyze or initiate the ROP of [PCl2N]3 with the addition of [PCl2N]3·HMX4 at room temperature or at 70 °C were not successful.

Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations.

Blood lipid concentrations are heritable risk factors associated with atherosclerosis and cardiovascular diseases. Lipid traits exhibit considerable variation among populations of distinct ancestral origin as well as between individuals within a population. We performed association analyses to identify genetic loci influencing lipid concentrations in African American and Hispanic American women in the Women's Health Initiative SNP Health Association Resource. We validated one African-specific high-density lipoprotein cholesterol locus at CD36 as well as 14 known lipid loci that have been previously implicated in studies of European populations. Moreover, we demonstrate striking similarities in genetic architecture (loci influencing the trait, direction and magnitude of genetic effects, and proportions of phenotypic variation explained) of lipid traits across populations. In particular, we found that a disproportionate fraction of lipid variation in African Americans and Hispanic Americans can be attributed to genomic loci exhibiting statistical evidence of association in Europeans, even though the precise genes and variants remain unknown. At the same time, we found substantial allelic heterogeneity within shared loci, characterized both by population-specific rare variants and variants shared among multiple populations that occur at disparate frequencies. The allelic heterogeneity emphasizes the importance of including diverse populations in future genetic association studies of complex traits such as lipids; furthermore, the overlap in lipid loci across populations of diverse ancestral origin argues that additional knowledge can be gleaned from multiple populations.

Genetic architecture of skin and eye color in an African-European admixed population.

Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3 × 10(-62), SLC24A5 P = 9.6 × 10(-9)) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4 × 10(-27), TYR P = 1.1 × 10(-9), APBA2[OCA2] P = 1.5 × 10(-8), SLC45A2 P = 6 × 10(-9)) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (~44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ~70% of the estimated heritability.

Association of DXA-derived bone mineral density and fat mass with African ancestry.

CONTEXT: Both genes and environment have been implicated in determining the complex body composition phenotypes in individuals of European ancestry; however, few studies have been conducted in other race/ethnic groups. OBJECTIVE: We conducted a genome-wide admixture mapping study in an attempt to localize novel genomic regions associated with genetic ancestry. SETTING/PARTICIPANTS: We selected a sample of 842 African-American women from the Women's Health Initiative single nucleotide polymorphism (SNP) Health Association Resource for whom several dual-energy X-ray absorptiometry (DXA)-derived bone mineral density (BMD) and fat mass phenotypes were available. METHODS: We derived both global and local ancestry estimates for each individual from Affymetrix 6.0 data and analyzed the correlation of DXA phenotypes with global African ancestry. For each phenotype, we examined the association of local genetic ancestry (number of African ancestral alleles at each marker) and each DXA phenotype at 570 282 markers across the genome in additive models with adjustment for important covariates. RESULTS: We identified statistically significant correlations of whole-body fat mass, trunk fat mass, and all 6 measures of BMD with a proportion of African ancestry. Genome-wide (admixture) significance for femoral neck BMD was achieved across 2 regions ∼3.7 MB and 0.3 MB on chromosome 19q13; similarly, total hip and intertrochanter BMD were associated with local ancestry in these regions. Trunk fat was the most significant fat mass phenotype showing strong, but not genomewide significant associations on chromosome Xp22. CONCLUSIONS: Our results suggest that genomic regions in postmenopausal African-American women contribute to variance in BMD and fat mass existence and warrant further study.

ACCURATE CONSTRUCTION OF LONG RANGE HAPLOTYPE IN UNRELATED INDIVIDUALS.

Haplotype, or the sequence of alleles along a single chromosome, has important applications in phenotype-genotype association studies, as well as in population genetics analyses. Because haplotype cannot be experimentally assayed in diploid organisms in a high-throughput fashion, numerous statistical methods have been developed to reconstruct probable haplotype from genotype data. These methods focus primarily on accurate phasing of a short genomic region with a small number of markers, and the error rate increases rapidly for longer regions. Here we introduce a new phasing algorithm, emphases, which aims to improve long-range phasing accuracy. Using datasets from multiple populations, we found that emphases reduces long-range phasing errors by up to 50% compared to the current state-of-the-art methods. In addition to inferring the most likely haplotypes, emphases produces confidence measures, allowing downstream analyses to account for the uncertainties associated with some haplotypes. We anticipate that emphases offers a powerful tool for analyzing large-scale data generated in the genome-wide association studies (GWAS).

Genetic markers of ovarian follicle number and menopause in women of multiple ethnicities.

Oocyte loss has a significant impact on fertility and somatic health. Yet, we know little about factors that impact this process. We sought to identify genetic variants associated with ovarian reserve (oocyte number as measured by antral follicle count, AFC). Based on recently published genome-wide scans that identified loci associated with age of menopause, we also sought to test our hypothesis that follicle number and menopausal age share underlying genetic associations. We analyzed menopause-related variants for association with follicle number in an independent population of approximately 450 reproductive-aged women of European and African ancestry; these women were assessed for AFC, anthropometric, clinical, and lifestyle factors. One SNP strongly associated with later menopausal age in Caucasian women (+1.07 ± 0.11 years) in previous work was also associated with higher follicle counts in Caucasians (+2.79 ± 1.67 follicles) in our study. This variant is within the Minichromosome Maintenance Complex Component 8 (MCM8) gene, which we found was expressed within oocytes in follicles of the human ovary. In genome-wide scans of AFC, we also identified one marginally genome-wide and several nominally significant SNPs within several other genes associated with follicle number in both ethnic groups. Further, there were overlapping variants associated with multiple ovarian reserve markers (AFC, serum hormone levels, menopausal age). This study provides the first evidence for direct genetic associations underlying both follicle number and menopause and identifies novel candidate genes. Genetic variants associated with ovarian reserve may facilitate discovery of genetic markers to predict reproductive health and lifespan in women.

Genetic variants and environmental factors associated with hormonal markers of ovarian reserve in Caucasian and African American women.

BACKGROUND: The ovarian reserve (number and quality of oocytes) is correlated with reproductive potential as well as somatic health, and is likely to have multiple genetic and environmental determinants. Several reproductive hormones are closely linked with the oocyte pool and thus can serve as surrogate markers of ovarian reserve. However, we know little about the underlying genes or genetic variants. METHODS: We analyzed genetic variants across the genome associated with two hormonal markers of ovarian reserve, FSH and anti-Mullerian hormone, in a reproductively normal population of Caucasian (n = 232) and African American (n = 200) women, aged 25-45 years. We also examined the effects of environmental or lifestyle factors on ovarian reserve phenotypes. RESULTS: We identified one variant approaching genome-wide significance (rs6543833; P= 8.07 × 10⁻8) and several nominal variants nearby and within the myeloid-associated differentiation marker-like (MYADML) gene, that were associated with FSH levels in African American women; these were validated in Caucasian women. We also discovered effects of smoking and oral contraceptive use on ovarian reserve phenotypes, with alterations in several reproductive hormones. CONCLUSIONS: This work is the largest study on ovarian reserve in women of reproductive age and is the only genome-wide study on ovarian reserve markers. The genes containing or near the identified variants have no known roles in ovarian biology and represent interesting candidate genes for future investigations. The discovery of genetic markers may lead to better long-range predictions of declining ovarian function, with implications for reproductive and somatic health.