Assessing ascertainment bias in atrial fibrillation across US minority groups
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ABSTRACT:
SUBMITTER: Hulstaert L
PROVIDER: S-EPMC11020362 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:AimsThe Catheter Ablation vs. Antiarrhythmic Drug Therapy for Atrial Fibrillation (CABANA) trial aimed to assess the impact of ablation on morbidity and mortality. This observational study was conducted in parallel to CABANA to assess trial generalizability.Methods and resultsUsing a large US administrative database, we identified 183 760 patients with atrial fibrillation (AF) treated with ablation or medical therapy (antiarrhythmic or rate control drugs) between 1 August 2009 and 30 April 2016 (CABANA enrolment period). Propensity score weighting was used to balance patients treated with ablation (N = 12 032) or medical therapy alone (N = 171 728) on 90 dimensions. Ablation was associated with a reduction in the composite endpoint of all-cause mortality, stroke, major bleeding, and cardiac arrest [hazard ratio (HR) 0.75, 95% confidence interval (CI) 0.70-0.81; P < 0.001]. The majority of patients (73.8%) were potentially trial eligible; among whom the risk reduction associated with ablation was greatest (HR 0.70, 95% CI 0.63-0.77; P < 0.001). Among the 3.8% of patients who failed to meet the inclusion criterion, i.e. patients under 65 years without stroke risk factors, the event rates were low and there was no significant relationship with ablation (HR 0.67, 95% CI 0.29-1.56; P = 0.35). Among the 22.4% patients who met at least one of the trial exclusion criteria, there was a lesser but statistically significant reduction associated with ablation (HR 0.85, 95% CI 0.75-0.95; P = 0.01).ConclusionIn routine clinical care, ablation was associated with a reduction in the primary CABANA composite endpoint of all-cause mortality, stroke, major bleeding, and cardiac arrest, particularly in patients who were eligible for the trial.
| S-EPMC6475520 | biostudies-literature
Project description:Single nucleotide polymorphisms (SNPs), genotyped with arrays, have become a widely used marker type in population genetic analyses over the last 10 years. However, compared to whole genome re-sequencing data, arrays are known to lack a substantial proportion of globally rare variants and tend to be biased towards variants present in populations involved in the development process of the respective array. This affects population genetic estimators and is known as SNP ascertainment bias. We investigated factors contributing to ascertainment bias in array development by redesigning the Axiom™ Genome-Wide Chicken Array in silico and evaluating changes in allele frequency spectra and heterozygosity estimates in a stepwise manner. A sequential reduction of rare alleles during the development process was shown. This was mainly caused by the identification of SNPs in a limited set of populations and a within-population selection of common SNPs when aiming for equidistant spacing. These effects were shown to be less severe with a larger discovery panel. Additionally, a generally massive overestimation of expected heterozygosity for the ascertained SNP sets was shown. This overestimation was 24% higher for populations involved in the discovery process than not involved populations in case of the original array. The same was observed after the SNP discovery step in the redesign. However, an unequal contribution of populations during the SNP selection can mask this effect but also adds uncertainty. Finally, we make suggestions for the design of specialized arrays for large scale projects where whole genome re-sequencing techniques are still too expensive.
| S-EPMC8009414 | biostudies-literature
Project description:BackgroundPopulation genetic studies based on genotyped single nucleotide polymorphisms (SNPs) are influenced by a non-random selection of the SNPs included in the used genotyping arrays. The resulting bias in the estimation of allele frequency spectra and population genetics parameters like heterozygosity and genetic distances relative to whole genome sequencing (WGS) data is known as SNP ascertainment bias. Full correction for this bias requires detailed knowledge of the array design process, which is often not available in practice. This study suggests an alternative approach to mitigate ascertainment bias of a large set of genotyped individuals by using information of a small set of sequenced individuals via imputation without the need for prior knowledge on the array design.ResultsThe strategy was first tested by simulating additional ascertainment bias with a set of 1566 chickens from 74 populations that were genotyped for the positions of the Affymetrix Axiom™ 580 k Genome-Wide Chicken Array. Imputation accuracy was shown to be consistently higher for populations used for SNP discovery during the simulated array design process. Reference sets of at least one individual per population in the study set led to a strong correction of ascertainment bias for estimates of expected and observed heterozygosity, Wright's Fixation Index and Nei's Standard Genetic Distance. In contrast, unbalanced reference sets (overrepresentation of populations compared to the study set) introduced a new bias towards the reference populations. Finally, the array genotypes were imputed to WGS by utilization of reference sets of 74 individuals (one per population) to 98 individuals (additional commercial chickens) and compared with a mixture of individually and pooled sequenced populations. The imputation reduced the slope between heterozygosity estimates of array data and WGS data from 1.94 to 1.26 when using the smaller balanced reference panel and to 1.44 when using the larger but unbalanced reference panel. This generally supported the results from simulation but was less favorable, advocating for a larger reference panel when imputing to WGS.ConclusionsThe results highlight the potential of using imputation for mitigation of SNP ascertainment bias but also underline the need for unbiased reference sets.
| S-EPMC8114708 | biostudies-literature
Project description:The risks of major bleeding and intracranial hemorrhage (ICH) are higher in Asian patients with atrial fibrillation (AF) compared to non-Asians. We aimed to investigate risk factors for bleeding, and validate the predictive value of available bleeding risk scores (mOBRI, HEMORR2HAGES, Shireman, HAS-BLED, ATRIA and ORBIT) in a large cohort of Chinese inpatients with AF. Using hospital electronic medical databases, we identified 4824 AF patients (mean age 67 years; 34.9% female) from January 1, 1995 to May 30, 2015, with median (interquartile) in-hospital days of 10 (7-16) days. On multivariate analysis, prior bleeds, vascular disease, anemia, prior stroke, and liver dysfunction were independent risk factors of major bleeding (all p < 0.05). C-statistics (95%CI) of the HAS-BLED score were 0.72 (0.65-0.79) for major bleeding events and 0.83 (0.75-0.91) for ICH (all p < 0.001). Compared to other risk scores, the HAS-BLED score was significantly better in predicting major bleeding events (Delong test, all P < 0.05, apart from mOBRI, HEMORR2HAGES) and ICH (all p < 0.05), and additionally, resulted in a net reclassification improvement (NRI) of 17.1-65.5% in predicting major bleeding events and 29.5-67.3% in predicting ICH (all p < 0.05). We conclude that the HAS-BLED score had the best predictive and discriminatory ability for major bleeding and ICH in an Asian/Chinese AF population.
| S-EPMC4997334 | biostudies-literature
Project description:The aim of this study is to perform transcriptome analysis on mouse left atrium tissue after long-term ibrutinib treatment or cardiac CSK knockout, in order to compared the enriched gene clusters.
2020-04-01 | GSE139427 | GEO
Project description:Reconstructing phylogeny from retrotransposon insertions is often limited by access to only a single reference genome, whereby support for clades that do not include the reference taxon cannot be directly observed. Here we have developed a new statistical framework that accounts for this ascertainment bias, allowing us to employ phylogenetically powerful retrotransposon markers to explore the radiation of the largest living marsupials, the kangaroos and wallabies of the genera Macropus and Wallabia. An exhaustive in silico screening of the tammar wallaby (Macropus eugenii) reference genome followed by experimental screening revealed 29 phylogenetically informative retrotransposon markers belonging to a family of endogenous retroviruses. We identified robust support for the enigmatic swamp wallaby (Wallabia bicolor) falling within a paraphyletic genus, Macropus. Our statistical approach provides a means to test for incomplete lineage sorting and introgression/hybridization in the presence of the ascertainment bias. Using retrotransposons as "molecular fossils", we reveal one of the most complex patterns of hemiplasy yet identified, during the rapid diversification of kangaroos and wallabies. Ancestral state reconstruction incorporating the new retrotransposon phylogenetic information reveals multiple independent ecological shifts among kangaroos into more open habitats, coinciding with the Pliocene onset of increased aridification in Australia from ~3.6 million years ago.
| S-EPMC5711953 | biostudies-literature
Project description:This study will report the incidence of atrial fibrillation after elective colorectal cancer resection in the over 65 age group. This will be used to validate a risk model for the development of post-operative atrial fibrillation.
Eligible patients will undergo electrocardiogram based screening for atrial fibrillation, as well as brain natriuretic peptide tests prior to surgery. They will undergo 24 hour holter monitor prior to surgery, and at 30 and 90 days following surgery.
The primary outcome will be occurrence of atrial fibrillation within 90 days of surgery. Secondary outcomes include quality of life change, use of hospital services for atrial fibrillation, and complications of atrial fibrillation. This will be used to validate the pre-existing model for prediction of atrial fibrillation.
| 2312263 | ecrin-mdr-crc
Project description:ImportanceAlthough rare variants in cardiac ion channels, transcription factors, and myocardial structural proteins are associated with early-onset atrial fibrillation (AF) in White individuals of European descent, it remains unclear whether genetic variation also contributes to the cause of AF in those of minority ethnicity.ObjectivesTo assess the prevalence of rare and novel pathogenic variants in candidate genes in ethnic minority probands with early-onset AF and determine genotype-phenotype associations.Design, setting, and participantsIn this cohort, family-based study, probands of African and Hispanic descent with early-onset AF (defined as AF occurring in individuals aged ≤66 years) prospectively enrolled in a clinical and genetic biorepository underwent sequencing of 60 candidate genes. Recruitment took place from July 1, 2015, to June 30, 2019. Data were analyzed from February 1 to February 28, 2020.ExposuresRare and novel variants categorized as pathogenic or likely pathogenic.Main outcomes and measuresThe prevalence of rare and novel pathogenic variants in African American and Hispanic/Latinx probands with early-onset AF and genotype-phenotype associations.ResultsAmong 227 probands with early-onset AF, mean (SD) age at onset of AF was 51.0 (9.9) years, 132 probands (58.1%) were men, 148 (65.2%) were African American, and 79 (34.8%) were Hispanic/Latinx. A family history of AF was verified in 24 probands with early-onset AF (10.6%). Sequencing 60 candidate genes identified 53 (23 rare and 30 novel) variants with 16 of the 227 (7.0%) probands harboring likely pathogenic (43.8%) or pathogenic (56.2%) variants, with most loss-of-function variants in TTN, the gene encoding the sarcomeric protein titin (46.7%). In 6 families with more than 2 affected members, variants of unknown significance in sodium channel (SCN10A), potassium channel (KCNE5), sarcomeric proteins (MYH6 and TTN), and atrial natriuretic peptide (NPPA) cosegregated with AF.Conclusions and relevanceIn this study, likely pathogenic and pathogenic variants were identified, with most loss-of-function variants in TTN, that increase susceptibility to early-onset AF in African American and Hispanic/Latinx individuals. These findings provide further understanding toward molecular phenotyping of AF and suggest novel mechanism-based therapeutic approaches for this common arrhythmia in ethnic minority groups.
| S-EPMC8100900 | biostudies-literature
Project description:How Array Design creates SNP Ascertainment Bias
| PRJEB41928 | ENA
Project description: Not available
| S-EPMC5837825 | biostudies-literature