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Reconciling S-LDSC and LDAK functional enrichment estimates

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Fig. 1: Likelihood comparison of different models of per-SNP heritability.
Fig. 2: Comparison of functional enrichment estimates in analyses of UK Biobank traits.

Data availability

Baseline-LD model version 1.1 can be found at https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_baselineLD_v1.1_ldscores.tgz. UK Biobank association statistics, computed with BOLT-LMM v2.3, are available at http://data.broadinstitute.org/alkesgroup/UKBB/.

Code availability

LDSC software is available at https://github.com/bulik/ldsc. LDAK version 5 is available at http://dougspeed.com/downloads/.

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Acknowledgements

We are grateful to P.-R. Loh for assistance with UK Biobank data and to L. O’Connor, D. Speed and D. Balding for helpful discussions. This research was conducted by using the UK Biobank Resource under Application 16549. A.L.P. is funded by NIH grants U01 HG009379, R01 MH101244 and R01 MH107649. S.G. is funded by NIH K99 HG010160-01. H.K.F. is funded by Eric and Wendy Schmidt and NIH DP5-OD024582. Computational analyses were performed on the Orchestra High-Performance Compute Cluster at Harvard Medical School.

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Author notes

  1. These authors jointly supervised this work: Hilary K. Finucane, Alkes L. Price.

Authors and Affiliations

  1. Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA

    Steven Gazal & Alkes L. Price

  2. Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Steven Gazal, Carla Marquez-Luna, Hilary K. Finucane & Alkes L. Price

  3. Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA

    Carla Marquez-Luna & Alkes L. Price

Authors
  1. Steven Gazal
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  2. Carla Marquez-Luna
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  3. Hilary K. Finucane
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  4. Alkes L. Price
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Contributions

S.G., H.K.F. and A.L.P. designed experiments. S.G. performed experiments. S.G., C.M.L. and H.K.F. analyzed data. S.G., H.K.F. and A.L.P., with assistance from C.M.L., wrote the manuscript.

Corresponding authors

Correspondence to Steven Gazal, Hilary K. Finucane or Alkes L. Price.

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Competing interests

The authors declare no competing interests.

Supplementary information

Supplementary Information

Supplementary Notes, Supplementary Figs. 1–23 and Supplementary Tables 1 and 5

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Supplementary Tables

Supplementary Tables 2–4 and 6–10

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Gazal, S., Marquez-Luna, C., Finucane, H.K. et al. Reconciling S-LDSC and LDAK functional enrichment estimates. Nat Genet 51, 1202–1204 (2019). https://doi.org/10.1038/s41588-019-0464-1

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