Familial Cancer

, Volume 17, Issue 2, pp 295–302 | Cite as

A comparison of cosegregation analysis methods for the clinical setting

  • John Michael O. Rañola
  • Quanhui Liu
  • Elisabeth A. Rosenthal
  • Brian H. Shirts
Original Article
  • 162 Downloads

Abstract

Quantitative cosegregation analysis can help evaluate the pathogenicity of genetic variants. However, genetics professionals without statistical training often use simple methods, reporting only qualitative findings. We evaluate the potential utility of quantitative cosegregation in the clinical setting by comparing three methods. One thousand pedigrees each were simulated for benign and pathogenic variants in BRCA1 and MLH1 using United States historical demographic data to produce pedigrees similar to those seen in the clinic. These pedigrees were analyzed using two robust methods, full likelihood Bayes factors (FLB) and cosegregation likelihood ratios (CSLR), and a simpler method, counting meioses. Both FLB and CSLR outperform counting meioses when dealing with pathogenic variants, though counting meioses is not far behind. For benign variants, FLB and CSLR greatly outperform as counting meioses is unable to generate evidence for benign variants. Comparing FLB and CSLR, we find that the two methods perform similarly, indicating that quantitative results from either of these methods could be combined in multifactorial calculations. Combining quantitative information will be important as isolated use of cosegregation in single families will yield classification for less than 1% of variants. To encourage wider use of robust cosegregation analysis, we present a website (http://www.analyze.myvariant.org) which implements the CSLR, FLB, and Counting Meioses methods for ATM, BRCA1, BRCA2, CHEK2, MEN1, MLH1, MSH2, MSH6, and PMS2. We also present an R package, CoSeg, which performs the CSLR analysis on any gene with user supplied parameters. Future variant classification guidelines should allow nuanced inclusion of cosegregation evidence against pathogenicity.

Keywords

Bayes factor Counting meioses Likelihood ratio Linkage analysis Variants of uncertain significance 

Notes

Aknowledgements

This study was supported by the Damon Runyon Cancer Research Foundation (DRR-33-15), the National Human Genome Research Institute (R21HG008513), and the Fred Hutch/University of Washington Cancer Consortium (NCI 5P30 CA015704-39).

Supplementary material

10689_2017_17_MOESM1_ESM.docx (1.2 mb)
Supplementary material 1 (DOCX 1219 KB)

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Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  • John Michael O. Rañola
    • 1
  • Quanhui Liu
    • 2
  • Elisabeth A. Rosenthal
    • 3
  • Brian H. Shirts
    • 1
  1. 1.Department of Laboratory MedicineUniversity of WashingtonSeattleUSA
  2. 2.Department of BioengineeringUniversity of WashingtonSeattleUSA
  3. 3.Department of Medicine, Division of Medical GeneticsUniversity of WashingtonSeattleUSA

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