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SumHer better estimates the SNP heritability of complex traits from summary statistics

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SumHer better estimates the SNP heritability of complex traits from summary statistics. / Speed, Doug; Balding, David J.

In: Nature Genetics, Vol. 51, No. 2, 2019, p. 277-284.

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Speed, Doug ; Balding, David J. / SumHer better estimates the SNP heritability of complex traits from summary statistics. In: Nature Genetics. 2019 ; Vol. 51, No. 2. pp. 277-284.

Bibtex

@article{0afd650cbdef4557a78f2199f59aee14,
title = "SumHer better estimates the SNP heritability of complex traits from summary statistics",
abstract = "We present SumHer, software for estimating confounding bias, SNP heritability, enrichments of heritability and genetic correlations using summary statistics from genome-wide association studies. The key difference between SumHer and the existing software LD Score Regression (LDSC) is that SumHer allows the user to specify the heritability model. We apply SumHer to results from 24 large-scale association studies (average sample size 121,000) using our recommended heritability model. We show that these studies tended to substantially over-correct for confounding, and as a result the number of genome-wide significant loci was under-reported by about a quarter. We also estimate enrichments for 24 categories of SNPs defined by functional annotations. A previous study using LDSC reported that conserved regions were 13-fold enriched, and found a further six categories with above threefold enrichment. By contrast, our analysis using SumHer finds that none of the categories have enrichment above twofold. SumHer provides an improved understanding of the genetic architecture of complex traits, which enables more efficient analysis of future genetic data.",
author = "Doug Speed and Balding, {David J.}",
year = "2019",
doi = "10.1038/s41588-018-0279-5",
language = "English",
volume = "51",
pages = "277--284",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Publishing Group",
number = "2",

}

RIS

TY - JOUR

T1 - SumHer better estimates the SNP heritability of complex traits from summary statistics

AU - Speed, Doug

AU - Balding, David J.

PY - 2019

Y1 - 2019

N2 - We present SumHer, software for estimating confounding bias, SNP heritability, enrichments of heritability and genetic correlations using summary statistics from genome-wide association studies. The key difference between SumHer and the existing software LD Score Regression (LDSC) is that SumHer allows the user to specify the heritability model. We apply SumHer to results from 24 large-scale association studies (average sample size 121,000) using our recommended heritability model. We show that these studies tended to substantially over-correct for confounding, and as a result the number of genome-wide significant loci was under-reported by about a quarter. We also estimate enrichments for 24 categories of SNPs defined by functional annotations. A previous study using LDSC reported that conserved regions were 13-fold enriched, and found a further six categories with above threefold enrichment. By contrast, our analysis using SumHer finds that none of the categories have enrichment above twofold. SumHer provides an improved understanding of the genetic architecture of complex traits, which enables more efficient analysis of future genetic data.

AB - We present SumHer, software for estimating confounding bias, SNP heritability, enrichments of heritability and genetic correlations using summary statistics from genome-wide association studies. The key difference between SumHer and the existing software LD Score Regression (LDSC) is that SumHer allows the user to specify the heritability model. We apply SumHer to results from 24 large-scale association studies (average sample size 121,000) using our recommended heritability model. We show that these studies tended to substantially over-correct for confounding, and as a result the number of genome-wide significant loci was under-reported by about a quarter. We also estimate enrichments for 24 categories of SNPs defined by functional annotations. A previous study using LDSC reported that conserved regions were 13-fold enriched, and found a further six categories with above threefold enrichment. By contrast, our analysis using SumHer finds that none of the categories have enrichment above twofold. SumHer provides an improved understanding of the genetic architecture of complex traits, which enables more efficient analysis of future genetic data.

UR - http://www.scopus.com/inward/record.url?scp=85058009681&partnerID=8YFLogxK

U2 - 10.1038/s41588-018-0279-5

DO - 10.1038/s41588-018-0279-5

M3 - Journal article

C2 - 30510236

AN - SCOPUS:85058009681

VL - 51

SP - 277

EP - 284

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

IS - 2

ER -