Detecting genetic risk factors for Alzheimer's disease in whole genome sequence data via Lasso screening

Tao Yang, Jie Wang, Qian Sun, Derrek P. Hibar, Neda Jahanshad, Li Liu, Yalin Wang, Liang Zhan, Paul M. Thompson, Jieping Ye

Research output: Chapter in Book/Report/Conference proceedingConference contribution

22 Scopus citations

Abstract

Genetic factors play a key role in Alzheimer's disease (AD). The Alzheimer's Disease Neuroimaging Initiative (ADNI) whole genome sequence (WGS) data offers new power to investigate mechanisms of AD by combining entire genome sequences with neuroimaging and clinical data. Here we explore the ADNI WGS SNP (single nucleotide polymorphism) data in depth and extract approximately six million valid SNP features. We investigate imaging genetics associations using Lasso regression - a widely used sparse learning technique. To solve the large-scale Lasso problem more efficiently, we employ a highly efficient screening rule for Lasso - called dual polytope projections (DPP) - to remove irrelevant features from the optimization problem. Experiments demonstrate that the DPP can effectively identify irrelevant features and leads to a 400× speedup. This allows us for the first time to run the compute-intensive model selection procedure called stability selection to rank SNPs that may affect the brain and AD risk.

Original languageEnglish (US)
Title of host publicationProceedings - International Symposium on Biomedical Imaging
PublisherIEEE Computer Society
Pages985-989
Number of pages5
Volume2015-July
ISBN (Print)9781479923748
DOIs
StatePublished - Jul 21 2015
Event12th IEEE International Symposium on Biomedical Imaging, ISBI 2015 - Brooklyn, United States
Duration: Apr 16 2015Apr 19 2015

Other

Other12th IEEE International Symposium on Biomedical Imaging, ISBI 2015
CountryUnited States
CityBrooklyn
Period4/16/154/19/15

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Keywords

  • Alzheimer's Disease
  • Lasso
  • Lasso Screening
  • Whole Genome Sequence

ASJC Scopus subject areas

  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging

Cite this

Yang, T., Wang, J., Sun, Q., Hibar, D. P., Jahanshad, N., Liu, L., Wang, Y., Zhan, L., Thompson, P. M., & Ye, J. (2015). Detecting genetic risk factors for Alzheimer's disease in whole genome sequence data via Lasso screening. In Proceedings - International Symposium on Biomedical Imaging (Vol. 2015-July, pp. 985-989). [7164036] IEEE Computer Society. https://doi.org/10.1109/ISBI.2015.7164036