Hum Hered 2012;73:84–94

ARIEL and AMELIA: Testing for an Accumulation of Rare Variants Using Next-Generation Sequencing Data

Asimit J.L.a · Day-Williams A.G.a · Morris A.P.b · Zeggini E.a
aWellcome Trust Sanger Institute, Hinxton, and bWellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
email Corresponding Author

 goto top of outline Key Words

  • Whole-genome sequencing
  • Exome sequencing
  • Association analysis
  • Accounting for uncertainty
  • Complex trait

 goto top of outline Abstract

Objectives: There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. Here, we propose two locus-based methods that incorporate variant quality scores: a regression-based collapsing approach and an allele-matching method. Methods: Using simulated sequencing data we compare 4 locus-based tests of trait association under different scenarios of data quality. We test two collapsing-based approaches and two allele-matching-based approaches, taking into account variant quality scores and ignoring variant quality scores. We implement the collapsing and allele-matching approaches accounting for variant quality in the freely available ARIEL and AMELIA software. Results: The incorporation of variant quality scores in locus-based association tests has power advantages over weighting each variant equally. The allele-matching methods are robust to the presence of both protective and risk variants in a locus, while collapsing methods exhibit a dramatic loss of power in this scenario. Conclusions: The incorporation of variant quality scores should be a standard protocol when performing locus-based association analysis on sequencing data. The ARIEL and AMELIA software implement collapsing and allele-matching locus association analysis methods, respectively, that allow the incorporation of variant quality scores.

Copyright © 2012 S. Karger AG, Basel

 goto top of outline References
  1. Cohen J, et al: Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 2004;305:869–872.
  2. Ji W, et al: Rare independent mutations in renal salt handling genes contribute to blood pressure variation. Nat Genet 2008;40:592–599.
  3. Nejentsev S, Walker N, Riches D, Egholm M, Todd J: Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 2009;324:387–389.
  4. Li B, Leal S: Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 2008;83:311–321.
  5. Bodmer W, Bonillna C: Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 2008;40:695–701.
  6. Madsen B, Browning S: A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 2009;5:e1000384. DOI: 10.1371/journal.pgen.1000384.
  7. Morris A, Zeggini E: An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 2010;34:188–193.
  8. Han F, Pan W: A data-adaptive sum test for disease association with multiple common or rare variants. Hum Hered 2010;70:42–54.
  9. Zawistowski M, et al: Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. Am J Hum Genet 2010;87:604–617.
  10. Price A, et al: Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 2010;86:832–838.
  11. Bhatia G, et al: A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol 2010;6:e1000954. DOI: 10.1371/journal.pcbi.1000954.

    External Resources

  12. Shriner D, Vaughan L: A unified framework for multi-locus association analysis of both common and rare variants. BMC Genomics 2011;12:89.

    External Resources

  13. Ionita-Laza I, Buxbaum J, Laird N, Lange C: A new testing strategy to identify rare variants with either risk or protective effect on disease. PLoS Genet 2011;7:e1001289. DOI: 10.1371/journal.pgen.1001289.
  14. Neale B, et al: Testing for an unusual distribution of rare variants. PLoS Genet 2011;7:e1001322. DOI: 10.1371/journal.pgen. 1001322.
  15. Mukhopadhyay I, Feingold E, Weeks D, Thalamuthu A: Association tests using kernel-based measures of multi-locus genotype similarity between individuals. Genet Epidemiol 2010;34:213–221.
  16. Lawrence R, Day-Williams AG, Elliot KS, Morris AP, Zeggini E: CCRaVAT and QuTie-enabling analysis of rare variants in large-scale case control and quantitative trait association studies. BMC Bioinformatics 2010;11:527.

    External Resources

  17. Durbin R, et al: A map of human genome variation from population-scale sequencing. Nature 2010;467:1061–1073.
  18. Montana G: HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients. Bioinformatics 2005;21:4309–4311.

 goto top of outline Author Contacts

Eleftheria Zeggini
Wellcome Trust Sanger Institute
The Morgan Building, Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1HH (UK)
Tel. +44 122 349 6868, E-Mail

 goto top of outline Article Information

Received: July 14, 2011
Accepted after revision: January 24, 2012
Published online: March 22, 2012
Number of Print Pages : 11
Number of Figures : 4, Number of Tables : 2, Number of References : 18
Additional supplementary material is available online - Number of Parts : 1

 goto top of outline Publication Details

Human Heredity (International Journal of Human and Medical Genetics)

Vol. 73, No. 2, Year 2012 (Cover Date: May 2012)

Journal Editor: Devoto M. (Philadelphia, Pa./Rome)
ISSN: 0001-5652 (Print), eISSN: 1423-0062 (Online)

For additional information:

Open Access License / Drug Dosage / Disclaimer

Open Access License: This is an Open Access article licensed under the terms of the Creative Commons Attribution 3.0 Unported license (CC BY 3.0) (, applicable to the online version of the article only.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in goverment regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.