A hybrid qPCR/SNP array approach allows cost efficient assessment of KIR gene copy numbers in large samples.

Related Articles

A hybrid qPCR/SNP array approach allows cost efficient assessment of KIR gene copy numbers in large samples.

BMC Genomics. 2014 Apr 11;15(1):274

Authors: Pontikos N, Smyth DJ, Schuilenburg H, Howson JM, Walker NM, Burren OS, Guo H, Onengut-Gumuscu S, Chen WM, Concannon P, Rich SS, Jayaraman J, Jiang W, Traherne JA, Trowsdale J, Todd JA, Wallace C

Abstract
BACKGROUND: Killer Immunoglobulin-like Receptors (KIRs) are surface receptors of natural killer cells that bind to their corresponding Human Leukocyte Antigen (HLA) class I ligands, making them interesting candidate genes for HLA-associated autoimmune diseases, including type 1 diabetes (T1D). However, allelic and copy number variation in the KIR region effectively mask it from standard genome-wide association studies: single nucleotide polymorphism (SNP) probes targeting the region are often discarded by standard genotype callers since they exhibit variable cluster numbers. Quantitative Polymerase Chain Reaction (qPCR) assays address this issue. However, their cost is prohibitive at the sample sizes required for detecting effects typically observed in complex genetic diseases.
RESULTS: We propose a more powerful and cost-effective alternative, which combines signals from SNPs with more than three clusters found in existing datasets, with qPCR on a subset of samples. First, we showed that noise and batch effects in multiplexed qPCR assays are addressed through normalisation and simultaneous copy number calling of multiple genes. Then, we used supervised classification to impute copy numbers of specific KIR genes from SNP signals. We applied this method to assess copy number variation in two KIR genes, \textit{KIR3DL1} and \textit{KIR3DS1}, which are suitable candidates for T1D susceptibility since they encode the only KIR molecules known to bind with HLA-Bw4 epitopes. We find no association between \textit{KIR3DL1/3DS1} copy number and T1D in 6744 cases and 5362 controls; a sample size twenty-fold larger than in any previous KIR association study. Due to our sample size, we can exclude odds ratios larger than 1.1 for the common \textit{KIR3DL1/3DS1} copy number groups at the 5% significance level.
CONCLUSION: We found no evidence of association of \textit{KIR3DL1/3DS1} copy number with T1D, either overall or dependent on HLA-Bw4 epitope. Five other KIR genes, \textit{KIR2DS4}, \textit{KIR2DL3}, \textit{KIR2DL5}, \textit{KIR2DS5} and \textit{KIR2DS1}, in high linkage disequilibrium with \textit{KIR3DL1} and \textit{KIR3DS1}, are also unlikely to be significantly associated. Our approach could potentially be applied to other KIR genes to allow cost effective assaying of gene copy number in large samples.

PMID: 24720548 [PubMed - as supplied by publisher]

Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering.

Related Articles

Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering.

BMC Bioinformatics. 2014 Apr 10;15(1):102

Authors: Guo X, Meng Y, Yu N, Pan Y

Abstract
Backgroud: Taking the advantage of high-throughput single nucleotide polymorphism (SNP) genotyping technology, large genome-wide association studies (GWASs) have been considered to hold promise for unravelling complex relationships between genotype and phenotype. At present, traditional single-locus-based methods are insufficient to detect interactions consisting of multiple-locus, which are broadly existing in complex traits. In addition, statistic tests for high order epistatic interactions with more than 2 SNPs propose computational and analytical challenges because the computation increases exponentially as the cardinality of SNPs combinations gets larger.
RESULTS: In this paper, we provide a simple, fast and powerful method using dynamic clustering and cloud computing to detect genome-wide multi-locus epistatic interactions. We have constructed systematic experiments to compare powers performance against some recently proposed algorithms, including TEAM, SNPRuler, EDCF and BOOST. Furthermore, we have applied our method on two real GWAS datasets, Age-related macular degeneration (AMD) and Rheumatoid arthritis (RA) datasets, where we find some novel potential disease-related genetic factors which are not shown up in detections of 2-loci epistatic interactions.
CONCLUSIONS: Experimental results on simulated data demonstrate that our method is more powerful than some recently proposed methods on both two- and three-locus disease models. Our method has discovered many novel high-order associations that are significantly enriched in cases from two real GWAS datasets. Moreover, the running time of the cloud implementation for our method on AMD dataset and RA dataset are roughly 2 hours and 50 hours on a cluster with forty small virtual machines for detecting two-locus interactions, respectively. Therefore, we believe that our method is suitable and effective for the full-scale analysis of multiple-locus epistatic interactions in GWAS.

PMID: 24717145 [PubMed - as supplied by publisher]

High-dose methotrexate in Egyptian pediatric acute lymphoblastic leukemia: the impact of ABCG2 C421A genetic polymorphism on plasma levels, what is next?

Related Articles

High-dose methotrexate in Egyptian pediatric acute lymphoblastic leukemia: the impact of ABCG2 C421A genetic polymorphism on plasma levels, what is next?

J Cancer Res Clin Oncol. 2014 Apr 10;

Authors: El Mesallamy HO, Rashed WM, Hamdy NM, Hamdy N

Abstract
PURPOSE: High-dose methotrexate (HD-MTX) is a cornerstone antineoplastic drug in most treatment protocols of pediatric acute lymphoblastic leukemia (ALL). Among the membrane efflux transporters of MTX, the human breast cancer resistant protein is the second member of the G subfamily of ATP-binding cassette (ABC) efflux pump (ABCG2). A single-nucleotide polymorphism (SNP) in ABCG2, the exchange of C to A at position 421, represents 13 % in the Middle Eastern population. We studied the effect of this SNP on the plasma levels of HD-MTX in Egyptian pediatric ALL.
METHODS: Two hundred ALL patients were recruited from Children's Cancer Hospital Egypt-57357, and all were treated according to the St Jude Total XV protocol. Determination of plasma MTX levels was done at 23, 42 and 68 h. Genotyping of C421A of ABCG2 was done by polymerase chain reaction-restriction fragment length polymorphism.
RESULTS: We found 14.5 % of the variant allele of the ABCG2 C421A SNP. The statistical association between ABCG2 421C>A SNP and the cutoff toxic plasma level of 24 h HD-MTX infusion at different time points tested was not statistically significant. There was no statistical significance between steady-state plasma concentration in patients with and without with this SNP.
CONCLUSION: To date, this is the largest study on Egyptian ALL patients for this SNP. This study shows that there is no effect of ABCG2 421C>A on plasma concentrations of HD-MTX. Replacing candidate gene association studies with genome-wide studies of HD-MTX is now mandatory and is part of our research blueprint.

PMID: 24718721 [PubMed - as supplied by publisher]

Prenatal diagnosis of congenital heart defect by genome-wide high resolution SNP array.

Related Articles

Prenatal diagnosis of congenital heart defect by genome-wide high resolution SNP array.

Prenat Diagn. 2014 Apr 9;

Authors: Can L, Li R, Fu F, Xie G, Zhang Y, Pan M, Li J, Li D

Abstract
OBJECTIVE: To detect genomic imbalances in fetuses with congenital heart defect (CHD) by high resolution SNP array.
METHODS: A total of 99 fetuses with CHDs with or without other ultrasound anomalies (including structural anomalies and soft markers) but normal karyotypes were investigated using Affymetrix CytoScan HD array.
RESULTS: Clinical significant copy number variations (CNVs) were detected in 19 fetuses (19.2%). The proportion for variants of unknown significance was 3% after parental analysis. Five known microdeletion/microduplication syndromes were identified. The detection rate in CHD plus structural anomaly (27.8%) or soft marker (25%) group was higher than but not statistically different from isolated CHD group (15.9%). There was no significant difference between the detection rates in simple and complex CHD groups (20.7% vs 16.7%). The detection rate in fetuses with CHD and neurologic defect was significantly higher than those with other types of structural anomaly (75% vs 14.3%, P < 0.05).
CONCLUSIONS: Our results demonstrated the value of high resolution SNP arrays in prenatal diagnosis of CHD, it should become an integral aspect in clinically molecular diagnosis and genetic counseling. The complexity of the cardiac defect was not related to the frequency of clinical significant CNV, but the presence of neurologic defect was related. This article is protected by copyright. All rights reserved.

PMID: 24718970 [PubMed - as supplied by publisher]

Page 3 of 371«12345»102030...Last »

RSS Genotyping industry news