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Methods for SNP Regression Analysis in Clinical Studies
Published in John Crowley, Antje Hoering, Handbook of Statisticsin Clinical Oncology, 2012
Michael LeBlanc, Bryan Goldman, Charles Kooperberg
We have not addressed sensible ways to combine SNPs that may be close together; for instance, some sets of SNPs may be thought to correspond to a haplotype block. In that setting, prior to doing some of the modeling proposals we have made in this chapter, one may first want to use a haplotype reconstruction method (e.g., Li et al. 2006). After appropriately acknowledging the haplotype uncertainty, one can use regression methods to predict the outcome. An adaptive technique that does SNP selection and haplotype regression, “SNP and HAplotype REgression” was developed by Dai et al. (2009).An alternative approach is to group using regularized methods on SNPs localized in a region; see, for instance, Chen et al. (2010).
The Genetics of Diabetes and Its Complications in Older Adults
Published in Medha N. Munshi, Lewis A. Lipsitz, Geriatric Diabetes, 2007
Jeremy D. Walston, Kristi D. Silver
In a study of Ashkenazi Jews, Love-Gregory et al. identified a SNP in the P2 promoter (rsl884614) that was significantly associated with T2DM (26.9% cases vs. 20.3% controls, P = 0.00078, OR = 1.45) (dm 4/04 pll34). Through further studies, this group identified a >10 kb haplotype block that is associated with T2DM and accounted for a linkage signal on chromosome 20q. In an independent association analysis of T2DM in the Finland–United States Investigation of NIDDM (FUSION) Genetics cohort, Silander et al. identified a SNP (rs2144908) which was located 1.3 kb downstream of the P2 promoter that was also associated with T2DM (OR = 1.33,95% CI = 1.06–1.65, P = 0.011) (59). Each of these SNPs was tested in the other population and the associations confirmed. Similar associations with either individual SNPs or haplotypes have been found in the Japanese (60), Pima Indians (61), and Caucasian (62,63) populations though not in all populations (64,65).
ALSgeneScanner: a pipeline for the analysis and interpretation of DNA sequencing data of ALS patients
Published in Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration, 2019
Alfredo Iacoangeli, Ahmad Al Khleifat, William Sproviero, Aleksey Shatunov, Ashley R. Jones, Sarah Opie-Martin, Ersilia Naselli, Simon D. Topp, Isabella Fogh, Angela Hodges, Richard J. Dobson, Stephen J. Newhouse, Ammar Al-Chalabi
The literature review was performed using several databases, including PubMed, MEDLINE, and EMBASE, to identify all articles reporting the contribution of genetic variations to the development of the disease or the modification of the phenotype in ALS from 1993, when SOD1 was the first gene discovered to cause ALS (41), until the date of the last manuscript revision. Review articles were discarded. The resulting list of genes and loci was filtered by keeping only the ones for which the link with ALS was shown in at least two independent studies (e.g. SOD1, FUS, C9orf72, etc.) or cohorts (e.g. KIF5A), or whose variants passed the genome-wide significance threshold in GWAS studies (e.g. CAMTA1). In the latter case, if a replication study was not yet available, to avoid spurious associations, we also required that these variants were surrounded by proxies in tight linkage disequilibrium (LD) that clearly indicated the presence of an associated haplotype block. The resulting list of ALS genes and loci is kept up to date by reviewing new articles as they become available. This list, as well as the complete list of reviewed articles, is available on GitHub (https://github.com/KHP-Informatics/ALSgeneScanner).
Association of catalase polymorphisms with primary open-angle glaucoma in a Chinese population
Published in Ophthalmic Genetics, 2018
Bo Gong, Yi Shi, Chao Qu, Zimeng Ye, Yilin Yin, Chang Tan, Ping Shuai, Jing Li, Xiaoxin Guo, Yilian Cheng, Zhenglin Yang, Ying Lin, Xiaoqi Liu
Pairwise LD analysis showed high LD between rs769217 and rs7943316 (D’ = 0.857, r2 = 0.252, confidence bounds 0.71–0.93), but SNPs rs769217 and rs1001179 (D’= 0.237, r2 = 0.003, confidence bounds 0.02–0.65), and rs7943316 and rs1001179 were not in the same LD (D’ = 0.298, r2 = 0.013, confidence bounds 0.04–0.62, Figure 1). However, after the association analysis for haplotype block structure generated from SNPs rs769217 with rs7943316, the haplotypes showed no significant association between the cases and controls (Table 4).
VEGF single nucleotide polymorphisms predict improved outcome in advanced non-small cell lung cancer patients treated with platinum-based chemotherapy
Published in Journal of Chemotherapy, 2023
Huijie Qi, Wenxin Zhang, Yan Wang, Mengxi Ge, Tianxiao Wang, Liudi Zhang, Mingkang Zhong, Xiaojin Shi, Xiaohua Liang, Qiong Zhan, Qunyi Li
Ten SNPs were chosen for genotyping. The details of the genetic variants, minor allele frequency (MAF) and primer sequences are summarized in Table 2. As shown in Figure 1, with a stringent threshold, D′>0.8, rs699947, rs833061, rs1005230 were in complete linkage disequilibrium and formed a haplotype block. The three SNPs had exactly the same genotype distribution. Hence, rs699947 and rs1005230 were omitted in the next analysis. Results for rs833061 T/T, T/C, and C/C are representative of rs699947 C/C, C/A, and A/A, rs1005230 C/C, T/C and T/T respectively. In addition, rs3024998 and rs2010963 were in high linkage disequilibrium.