The efficiency of single SNP and SNP-set analysisin genome-wide association studies

Sookkhee, Sirikanlaya; Kirdwichai, Pianpool; Baksh, M. Fazil

doi:10.14456/sjst-psu.2021.32

Cited by 1 publication

(2 citation statements)

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“…Conducting numerous tests poses challenges in meeting the required significance threshold. In high-dimensional GWAS with hundreds of thousands of SNPs, each test is conducted at some nominal significance level, potentially leading to a high number of false positives (FPs) [5][6][7]. This limitation arises from the difficulty of detecting SNPs with minor effects genuinely associated with the disease.…”

Section: Introductionmentioning

confidence: 99%

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Statistical Study Design for Analyzing Multiple Gene Loci Correlation in DNA Sequences

Kamoljitprapa,

Baksh,

De Gaetano

et al. 2023

Mathematics

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This study presents a novel statistical and computational approach using nonparametric regression, which capitalizes on correlation structure to deal with the high-dimensional data often found in pharmacogenomics, for instance, in Crohn’s inflammatory bowel disease. The empirical correlation between the test statistics, investigated via simulation, can be used as an estimate of noise. The theoretical distribution of −log10(p-value) is used to support the estimation of that optimal bandwidth for the model, which adequately controls type I error rates while maintaining reasonable power. Two proposed approaches, involving normal and Laplace-LD kernels, were evaluated by conducting a case-control study using real data from a genome-wide association study on Crohn’s disease. The study successfully identified single nucleotide polymorphisms on the NOD2 gene associated with the disease. The proposed method reduces the computational burden by approximately 33% with reasonable power, allowing for a more efficient and accurate analysis of genetic variants influencing drug responses. The study contributes to the advancement of statistical methodology for analyzing complex genetic data and is of practical advantage for the development of personalized medicine.

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Section: Introductionmentioning

confidence: 99%

“…It is, therefore, highly desirable to have available test procedures that result in a low number of FPs in GWAS. Many methods have been proposed to deal with this challenge [7][8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%