A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data

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Abstract

High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present pedigree-VAAST (pVAAST), a disease-gene identification tool designed for high-throughput sequence data in pedigrees. pVAAST uses a sequence-based model to perform variant and gene-based linkage analysis. Linkage information is then combined with functional prediction and rare variant case-control association information in a unified statistical framework. pVAAST outperformed linkage and rare-variant association tests in simulations and identified disease-causing genes from whole-genome sequence data in three human pedigrees with dominant, recessive and de novo inheritance patterns. The approach is robust to incomplete penetrance and locus heterogeneity and is applicable to a wide variety of genetic traits. pVAAST maintains high power across studies of monogenic, high-penetrance phenotypes in a single pedigree to highly polygenic, common phenotypes involving hundreds of pedigrees.

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Figure 1: A schematic illustration of pVAAST.
Figure 2: Rare Mendelian and common complex disease simulations.
Figure 3: pVAAST results on the enteropathy pedigree.
Figure 4: pVAAST identifies the dominant causal gene GATA4 in cardiac septal defect pedigree.
Figure 5: pVAAST identifies the recessive causal genes for Miller's syndrome (DHODH) and primary ciliary dyskinesia (DNAH5) with a two-generation pedigree.
Figure 6: The genome-wide ranking and lod score of GATA4 in challenging situations of pedigree studies.

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Acknowledgements

An allocation of computer time on the University of Texas MD Anderson Research Computing High Performance Computing (HPC) facility is gratefully acknowledged. This work was supported by US National Institutes of Health grants R01 GM104390 (M.Y., L.B.J., C.D.H. and H.H.), R01 DK091374 (S.L.G., C.D.H. and L.B.J.), R01 CA164138 (S.V.T. and C.D.H.), R44HG006579 (M.G.R. and M.Y.) and R01 GM59290 (L.B.J.) as well as the University of Luxembourg—Institute for Systems Biology Program. D.S. was supported by grants from the NHLBI (UO1 HL100406 and U01 HL098179) related to this project. H.C. was supported by NIH grants R01 MH094400 and R01 MH099134. H.H. was supported by the MD Anderson Cancer Center Odyssey Program. J.X. was supported by NIH grant R00HG005846.

Author information

C.D.H. conceived of the project. C.D.H. oversaw and coordinated the research. C.D.H. and H.H. designed the algorithms. H.H. and B.M. wrote the software. C.D.H., H.H. and P.S. contributed to the statistical development. C.D.H., H.H., J.C.R., M.Y., S.V.T., D.S., K.V.V., L.H., L.B.J., M.G.R. and S.L.G. designed the experiments. H.H., H.C., W.W., R.L.M., J.D.D., S.W., H.L., J.X., Shankaracharya, R.H., B.M., J.C. and G.G. performed the experiments. H.H., C.D.H., M.Y., S.V.T., S.L.G. and L.B.J. analyzed and interpreted the data. H.H. generated the figures. H.H., C.D.H., L.B.J., M.Y., S.L.G., P.S., and S.V.T. wrote the paper. S.L.G., D.S., V.G., D.J.G., L.H., H.L., R.H., K.V.V., R.L.M., J.D.D., G.G. participated in pedigree identification, recruitment and validation.

Correspondence to Mark Yandell or Chad D Huff.

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Competing interests

M.G.R. is a founder and officer of Omicia, Inc.

Supplementary information

Supplementary Text and Figures

Supplementary Notes 1–4, Supplementary Figures 1–10 and Supplementary Table 1 (PDF 10164 kb)

Supplementary Code

pVAAST source code (ZIP 97 kb)

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Hu, H., Roach, J., Coon, H. et al. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nat Biotechnol 32, 663–669 (2014) doi:10.1038/nbt.2895

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