Statistical advances and challenges for analyzing correlated high dimensional SNP data in genomic study for complex diseases

DOI10.1214/07-SS026zbMATH Open1196.62144arXiv0803.4065OpenAlexW2076593601MaRDI QIDQ975561FDOQ975561

Yulan Liang, Arpad Kelemen

Publication date: 9 June 2010

Published in: Statistics Surveys (Search for Journal in Brave)

Abstract: Recent advances of information technology in biomedical sciences and other applied areas have created numerous large diverse data sets with a high dimensional feature space, which provide us a tremendous amount of information and new opportunities for improving the quality of human life. Meanwhile, great challenges are also created driven by the continuous arrival of new data that requires researchers to convert these raw data into scientific knowledge in order to benefit from it. Association studies of complex diseases using SNP data have become more and more popular in biomedical research in recent years. In this paper, we present a review of recent statistical advances and challenges for analyzing correlated high dimensional SNP data in genomic association studies for complex diseases. The review includes both general feature reduction approaches for high dimensional correlated data and more specific approaches for SNPs data, which include unsupervised haplotype mapping, tag SNP selection, and supervised SNPs selection using statistical testing/scoring, statistical modeling and machine learning methods with an emphasis on how to identify interacting loci.

Full work available at URL: https://arxiv.org/abs/0803.4065

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zbMATH Keywords

high dimensional datasingle nucleotide polymorphismcomplex disease

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Medical applications (general) (92C50)

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Cited In (6)

• Sequential support vector regression with embedded entropy for SNP selection and disease classification
• Sequential Markov coalescent algorithms for population models with demographic structure
• Aspects of the design and analysis of high-dimensional SNP studies for disease risk estimation
• Methods for analysis and visualization of SNP genotype data for complex diseases
• Sparse logistic principal components analysis for binary data
• Multiple Imputation and Random Forests (MIRF) for Unobservable, High-Dimensional Data

Uses Software

• CLUSTAG
• HaploBlockFinder

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