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Nieuwoudt C, Jones SJ, Brooks-Wilson A, et al. Simulating pedigrees ascertained for multiple disease-affected relatives. Source Code Biol Med. 2018;13:2doi: 10.1186/s13029-018-0069-6.
Nieuwoudt, C., Jones, S. J., Brooks-Wilson, A., & Graham, J. (2018). Simulating pedigrees ascertained for multiple disease-affected relatives. Source code for biology and medicine, 132. https://doi.org/10.1186/s13029-018-0069-6
Nieuwoudt, Christina, et al. "Simulating pedigrees ascertained for multiple disease-affected relatives." Source code for biology and medicine vol. 13 (2018): 2. doi: https://doi.org/10.1186/s13029-018-0069-6
Nieuwoudt C, Jones SJ, Brooks-Wilson A, Graham J. Simulating pedigrees ascertained for multiple disease-affected relatives. Source Code Biol Med. 2018 Oct 15;13:2. doi: 10.1186/s13029-018-0069-6. eCollection 2018. PMID: 30356812; PMCID: PMC6190569.
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Source Code Biol Med. 2018 Oct 15;13:2. doi: 10.1186/s13029-018-0069-6. eCollection 2018.

Simulating pedigrees ascertained for multiple disease-affected relatives.

Source code for biology and medicine

Christina Nieuwoudt, Samantha J Jones, Angela Brooks-Wilson, Jinko Graham

Affiliations

  1. 1Department of Statistics and Actuarial Science, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, Canada.
  2. 2Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 675 W 10th Ave, V5Z 1L3, Vancouver, Canada.
  3. 3Department of Medical Genetics, University of British Columbia, Vancouver, Canada.
  4. 4Department of Biomedical Physiology and Kinesiology, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, Canada.

PMID: 30356812 PMCID: PMC6190569 DOI: 10.1186/s13029-018-0069-6

Abstract

BACKGROUND: Studies that ascertain families containing multiple relatives affected by disease can be useful for identification of causal, rare variants from next-generation sequencing data.

RESULTS: We present the R package SimRVPedigree, which allows researchers to simulate pedigrees ascertained on the basis of multiple, affected relatives. By incorporating the ascertainment process in the simulation, SimRVPedigree allows researchers to better understand the within-family patterns of relationship amongst affected individuals and ages of disease onset.

CONCLUSIONS: Through simulation, we show that affected members of a family segregating a rare disease variant tend to be more numerous and cluster in relationships more closely than those for sporadic disease. We also show that the family ascertainment process can lead to apparent anticipation in the age of onset. Finally, we use simulation to gain insight into the limit on the proportion of ascertained families segregating a causal variant. SimRVPedigree should be useful to investigators seeking insight into the family-based study design through simulation.

Keywords: Anticipation; Ascertainment bias; Family-based study; Pedigree simulation; Rare variant

Conflict of interest statement

Not applicable.Not applicable.The authors declare they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations

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