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Efficient variance components analysis across millions of genomes.

ABSTRACT: While variance components analysis has emerged as a powerful tool in complex trait genetics, existing methods for fitting variance components do not scale well to large-scale datasets of genetic variation. Here, we present a method for variance components analysis that is accurate and efficient: capable of estimating one hundred variance components on a million individuals genotyped at a million SNPs in a few hours. We illustrate the utility of our method in estimating and partitioning variation in a trait explained by genotyped SNPs (SNP-heritability). Analyzing 22 traits with genotypes from 300,000 individuals across about 8 million common and low frequency SNPs, we observe that per-allele squared effect size increases with decreasing minor allele frequency (MAF) and linkage disequilibrium (LD) consistent with the action of negative selection. Partitioning heritability across 28 functional annotations, we observe enrichment of heritability in FANTOM5 enhancers in asthma, eczema, thyroid and autoimmune disorders.

SUBMITTER: Pazokitoroudi A

PROVIDER: S-EPMC7419517 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Efficient variance components analysis across millions of genomes.

Pazokitoroudi Ali A Wu Yue Y Burch Kathryn S KS Hou Kangcheng K Zhou Aaron A Pasaniuc Bogdan B Sankararaman Sriram S

Nature communications 20200811 1

While variance components analysis has emerged as a powerful tool in complex trait genetics, existing methods for fitting variance components do not scale well to large-scale datasets of genetic variation. Here, we present a method for variance components analysis that is accurate and efficient: capable of estimating one hundred variance components on a million individuals genotyped at a million SNPs in a few hours. We illustrate the utility of our method in estimating and partitioning variation ...[more]

PMID: 32782262

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Project description:BackgroundThe ratings of physician-patient communication are an important indicator of the quality of health care delivery and provide guidance for many important decisions in the health care setting and in health research. But there is no gold standard to assess physician-patient communication. Thus, depending on the specific measurement condition, multiple sources of variance may contribute to the total score variance of ratings of physician-patient communication. This may systematically impair the validity of conclusions drawn from rating data.ObjectiveTo examine the extent to which different measurement conditions and rater perspectives, respectively contribute to the variance of physician-patient communication ratings.MethodsVariance components of ratings of physician-patient communication gained from 32 general practitioners and 252 patients from 25 family practices in Germany were analyzed using generalizability theory. The communication dimensions "shared decision making", "effective and open communication" and "satisfaction" were considered.ResultsPhysician-patient communication ratings most substantially reflect unique rater-perspective and communication dimension combinations (32.7% interaction effect). The ratings also represented unique physician and rater-perspective combinations (16.3% interaction effect). However, physicians' communication behavior and the observed communication dimensions revealed only a low extent of score variance (1% physician effect; 3.7% communication dimension effect). Approximately half of the variance remained unexplained (46.2% three-way interaction, confounded with error).ConclusionThe ratings of physician-patient communication minimally reflect physician communication skills in general. Instead, these ratings exhibit primarily differences among physicians and patients in their tendency to perceive shared decision making and effective and open communication and to be satisfied with communication, regardless of the communication behavior of physicians. Rater training and assessing low inferential ratings of physician-patient communication dimensions should be considered when subjective aspects of rater perspectives are not of interest.

Dataset Information

Efficient variance components analysis across millions of genomes.

Publications

Efficient variance components analysis across millions of genomes.

Similar Datasets

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