The Annals of Applied Statistics

Capturing heterogeneity of covariate effects in hidden subpopulations in the presence of censoring and large number of covariates

Farhad Shokoohi, Abbas Khalili, Masoud Asgharian, and Shili Lin

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Abstract

The advent of modern technology has led to a surge of high-dimensional data in biology and health sciences such as genomics, epigenomics and medicine. The high-grade serous ovarian cancer (HGS-OvCa) data reported by The Cancer Genome Atlas (TCGA) Research Network is one example. The TCGA and other research groups have analyzed several aspects of these data. Here we study the relationship between Disease Free Time (DFT) after surgery among ovarian cancer patients and their DNA methylation profiles of genomic features. Such studies pose additional challenges beyond the typical big data problem due to population substructure and censoring. Despite the availability of several methods for analyzing time-to-event data with a large number of covariates but a small sample size, there is no method available to date that accommodates the additional feature of heterogeneity. To this end, we propose a regularized framework based on the finite mixture of accelerated failure time model to capture intangible heterogeneity due to population substructure and to account for censoring simultaneously. We study the properties of the proposed framework both theoretically and numerically. Our data analysis indicates the existence of heterogeneity in the HGS-OvCa data, with one component of the mixture capturing a more aggressive form of the disease, and the second component capturing a less aggressive form. In particular, the second component portrays a significant positive relationship between methylation and DFT for BRCA1. By further unearthing the negative relationship between expression and methylation for this gene, one may provide a biologically reasonable explanation that sheds light on the relationship between DNA methylation, gene expression and mutation.

Article information

Source
Ann. Appl. Stat., Volume 13, Number 1 (2019), 444-465.

Dates
Received: May 2017
Revised: March 2018
First available in Project Euclid: 10 April 2019

Permanent link to this document
https://projecteuclid.org/euclid.aoas/1554861656

Digital Object Identifier
doi:10.1214/18-AOAS1198

Mathematical Reviews number (MathSciNet)
MR3937436

Zentralblatt MATH identifier
07057435

Keywords
DNA methylation ovarian cancer finite mixture of AFT model penalized regression right censoring

Citation

Shokoohi, Farhad; Khalili, Abbas; Asgharian, Masoud; Lin, Shili. Capturing heterogeneity of covariate effects in hidden subpopulations in the presence of censoring and large number of covariates. Ann. Appl. Stat. 13 (2019), no. 1, 444--465. doi:10.1214/18-AOAS1198. https://projecteuclid.org/euclid.aoas/1554861656


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Supplemental materials

  • Supplement to “Capturing heterogeneity of covariate effects in hidden subpopulations in the presence of censoring and large number of covariates”. Supplementary Materials referenced in Section 2–4, including regularity conditions, proofs, numerical approaches, supplementary tables and figures, and the fmrs output are available with this paper at the Annals of Applied Statistics website.