Genetic Association Studies and Next Generation Sequencing in Stroke: Methods

2017 ◽  
pp. 21-52
Author(s):  
Jane M. Maguire ◽  
Elizabeth G. Holliday ◽  
Christopher J. Oldmeadow ◽  
John Attia ◽  
Matthew P. A. Henderson ◽  
...  
Author(s):  
Zeynep Baskurt ◽  
Scott Mastromatteo ◽  
Jiafen Gong ◽  
Richard F Wintle ◽  
Stephen W Scherer ◽  
...  

Abstract Integration of next generation sequencing data (NGS) across different research studies can improve the power of genetic association testing by increasing sample size and can obviate the need for sequencing controls. If differential genotype uncertainty across studies is not accounted for, combining data sets can produce spurious association results. We developed the Variant Integration Kit for NGS (VikNGS), a fast cross-platform software package, to enable aggregation of several data sets for rare and common variant genetic association analysis of quantitative and binary traits with covariate adjustment. VikNGS also includes a graphical user interface, power simulation functionality and data visualization tools. Availability The VikNGS package can be downloaded at http://www.tcag.ca/tools/index.html. Supplementary information Supplementary data are available at Bioinformatics online.


2011 ◽  
Vol 21 (7) ◽  
pp. 1099-1108 ◽  
Author(s):  
L. Luo ◽  
E. Boerwinkle ◽  
M. Xiong

Author(s):  
Jean Louis Gueant ◽  
A Romano ◽  
Abderrahim OUSSALAH ◽  
Celine Chery ◽  
Rosa Maria Rodriguez-Gueant ◽  
...  

Background: Nonimmediate (delayed) allergic reactions to penicillins are common and some of them can be life-threatening. The genetic factors influencing these reactions are unknown/poorly known/poorly understood. We assessed the genetic predictors of a delayed penicillin allergy that cover the HLA loci. Methods: Using next-generation sequencing (NGS), we genotyped the MHC region in 24 patients with delayed hypersensitivity compared with 20 patients with documented immediate hypersensitivity to penicillins recruited in Italy. Subsequently, we analyzed in silico Illumina Immunochip genotyping data that covered the HLA loci in 98 Spanish patients with delayed hypersensitivity and 315 with immediate hypersensitivity compared to 1,308 controls. Results: The two alleles DRB3*02:02:01:02 and DRB3*02:02:01:01 were reported in twenty cases with delayed reactions (83%) and ten cases with immediate reactions (50%), but not in the Allele Frequency Net Database. Bearing at least one of the two alleles increased the risk of delayed reactions compared to immediate reactions, with an OR of 8.88 (95% CI, 3.37–23.32; P <0.0001). The haplotype (ACAA) from rs9268835, rs6923504, rs6903608, and rs9268838 genetic variants of the HLA-DRB3 genomic region was significantly associated with an increased risk of delayed hypersensitivity to penicillins (OR, 1.7; 95% CI: 1.06–1.92; P=0.001), but not immediate hypersensitivity. Conclusion: We showed that the HLA-DRB3 locus is strongly associated with an increased risk of delayed penicillin hypersensitivity, at least in Southwestern Europe. The determination of HLA-DRB3*02:02 alleles in the risk management of severe delayed hypersensitivity to penicillins should be evaluated further in larger population samples of different origins.


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