A variable age of onset segregation model for linkage analysis, with correction for ascertainment, applied to glioma

Xiangqing Sun, Jaime Vengoechea, Robert Elston, Yanwen Chen, Christopher I. Amos, Georgina Armstrong, Jonine L. Bernstein, Elizabeth Claus, Faith Davis, Richard S. Houlston, Dora Il'yasova, Robert Brian Jenkins, Christoffer Johansen, Rose Lai, Ching C. Lau, Yanhong Liu, Bridget J. McCarthy, Sara H. Olson, Siegal Sadetzki, Joellen SchildkrautSanjay Shete, Robert Yu, Nicholas A. Vick, Ryan Merrell, Margaret Wrensch, Ping Yang, Beatrice Melin, Melissa L. Bondy, Jill S. Barnholtz-Sloan

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Background: We propose a 2-step model-based approach, with correction for ascertainment, to linkage analysis of a binary trait with variable age of onset and apply it to a set of multiplex pedigrees segregating for adult glioma. Methods: First, we fit segregation models by formulating the likelihood for a person to have a bivariate phenotype, affection status and age of onset, along with other covariates, and from these we estimate population trait allele frequencies and penetrance parameters as a function of age (N = 281 multiplex glioma pedigrees). Second, the best fitting models are used as trait models in multipoint linkage analysis (N = 74 informative multiplex glioma pedigrees). To correct for ascertainment, a prevalence constraint is used in the likelihood of the segregation models for all 281 pedigrees. Then the trait allele frequencies are reestimated for the pedigree founders of the subset of 74 pedigrees chosen for linkage analysis. Results: Using the best-fitting segregation models in model-based multipoint linkage analysis, we identified 2 separate peaks on chromosome 17; the first agreed with a region identified by Shete and colleagues who used model-free affected-only linkage analysis, but with a narrowed peak: and the second agreed with a second region they found but had a larger maximum log of the odds (LOD). Conclusions: Our approach was able to narrow the linkage peak previously published for glioma. Impact: We provide a practical solution to model-based linkage analysis for disease affection status with variable age of onset for the kinds of pedigree data often collected for linkage analysis.

Original languageEnglish (US)
Pages (from-to)2242-2251
Number of pages10
JournalCancer Epidemiology Biomarkers and Prevention
Volume21
Issue number12
DOIs
StatePublished - Dec 2012

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Pedigree
Age of Onset
Glioma
Gene Frequency
Chromosomes, Human, Pair 17
Penetrance
Phenotype
Population

ASJC Scopus subject areas

  • Epidemiology
  • Oncology

Cite this

A variable age of onset segregation model for linkage analysis, with correction for ascertainment, applied to glioma. / Sun, Xiangqing; Vengoechea, Jaime; Elston, Robert; Chen, Yanwen; Amos, Christopher I.; Armstrong, Georgina; Bernstein, Jonine L.; Claus, Elizabeth; Davis, Faith; Houlston, Richard S.; Il'yasova, Dora; Jenkins, Robert Brian; Johansen, Christoffer; Lai, Rose; Lau, Ching C.; Liu, Yanhong; McCarthy, Bridget J.; Olson, Sara H.; Sadetzki, Siegal; Schildkraut, Joellen; Shete, Sanjay; Yu, Robert; Vick, Nicholas A.; Merrell, Ryan; Wrensch, Margaret; Yang, Ping; Melin, Beatrice; Bondy, Melissa L.; Barnholtz-Sloan, Jill S.

In: Cancer Epidemiology Biomarkers and Prevention, Vol. 21, No. 12, 12.2012, p. 2242-2251.

Research output: Contribution to journalArticle

Sun, X, Vengoechea, J, Elston, R, Chen, Y, Amos, CI, Armstrong, G, Bernstein, JL, Claus, E, Davis, F, Houlston, RS, Il'yasova, D, Jenkins, RB, Johansen, C, Lai, R, Lau, CC, Liu, Y, McCarthy, BJ, Olson, SH, Sadetzki, S, Schildkraut, J, Shete, S, Yu, R, Vick, NA, Merrell, R, Wrensch, M, Yang, P, Melin, B, Bondy, ML & Barnholtz-Sloan, JS 2012, 'A variable age of onset segregation model for linkage analysis, with correction for ascertainment, applied to glioma', Cancer Epidemiology Biomarkers and Prevention, vol. 21, no. 12, pp. 2242-2251. https://doi.org/10.1158/1055-9965.EPI-12-0703
Sun, Xiangqing ; Vengoechea, Jaime ; Elston, Robert ; Chen, Yanwen ; Amos, Christopher I. ; Armstrong, Georgina ; Bernstein, Jonine L. ; Claus, Elizabeth ; Davis, Faith ; Houlston, Richard S. ; Il'yasova, Dora ; Jenkins, Robert Brian ; Johansen, Christoffer ; Lai, Rose ; Lau, Ching C. ; Liu, Yanhong ; McCarthy, Bridget J. ; Olson, Sara H. ; Sadetzki, Siegal ; Schildkraut, Joellen ; Shete, Sanjay ; Yu, Robert ; Vick, Nicholas A. ; Merrell, Ryan ; Wrensch, Margaret ; Yang, Ping ; Melin, Beatrice ; Bondy, Melissa L. ; Barnholtz-Sloan, Jill S. / A variable age of onset segregation model for linkage analysis, with correction for ascertainment, applied to glioma. In: Cancer Epidemiology Biomarkers and Prevention. 2012 ; Vol. 21, No. 12. pp. 2242-2251.
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T1 - A variable age of onset segregation model for linkage analysis, with correction for ascertainment, applied to glioma

AU - Sun, Xiangqing

AU - Vengoechea, Jaime

AU - Elston, Robert

AU - Chen, Yanwen

AU - Amos, Christopher I.

AU - Armstrong, Georgina

AU - Bernstein, Jonine L.

AU - Claus, Elizabeth

AU - Davis, Faith

AU - Houlston, Richard S.

AU - Il'yasova, Dora

AU - Jenkins, Robert Brian

AU - Johansen, Christoffer

AU - Lai, Rose

AU - Lau, Ching C.

AU - Liu, Yanhong

AU - McCarthy, Bridget J.

AU - Olson, Sara H.

AU - Sadetzki, Siegal

AU - Schildkraut, Joellen

AU - Shete, Sanjay

AU - Yu, Robert

AU - Vick, Nicholas A.

AU - Merrell, Ryan

AU - Wrensch, Margaret

AU - Yang, Ping

AU - Melin, Beatrice

AU - Bondy, Melissa L.

AU - Barnholtz-Sloan, Jill S.

PY - 2012/12

Y1 - 2012/12

N2 - Background: We propose a 2-step model-based approach, with correction for ascertainment, to linkage analysis of a binary trait with variable age of onset and apply it to a set of multiplex pedigrees segregating for adult glioma. Methods: First, we fit segregation models by formulating the likelihood for a person to have a bivariate phenotype, affection status and age of onset, along with other covariates, and from these we estimate population trait allele frequencies and penetrance parameters as a function of age (N = 281 multiplex glioma pedigrees). Second, the best fitting models are used as trait models in multipoint linkage analysis (N = 74 informative multiplex glioma pedigrees). To correct for ascertainment, a prevalence constraint is used in the likelihood of the segregation models for all 281 pedigrees. Then the trait allele frequencies are reestimated for the pedigree founders of the subset of 74 pedigrees chosen for linkage analysis. Results: Using the best-fitting segregation models in model-based multipoint linkage analysis, we identified 2 separate peaks on chromosome 17; the first agreed with a region identified by Shete and colleagues who used model-free affected-only linkage analysis, but with a narrowed peak: and the second agreed with a second region they found but had a larger maximum log of the odds (LOD). Conclusions: Our approach was able to narrow the linkage peak previously published for glioma. Impact: We provide a practical solution to model-based linkage analysis for disease affection status with variable age of onset for the kinds of pedigree data often collected for linkage analysis.

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