Microfluidic Linear Hydrogel Array for Multiplexed Single Nucleotide Polymorphism (SNP) Detection.

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Microfluidic Linear Hydrogel Array for Multiplexed Single Nucleotide Polymorphism (SNP) Detection.

Anal Chem. 2015 Feb 12;

Authors: Jung YK, Kim J, Mathies RA

Abstract
A PDMS-based microfluidic linear hydrogel array is developed for multiplexed single nucleotide polymorphism (SNP) detection. A sequence of three-dimensional (3D) hydrogel plugs containing the desired DNA probes is prepared by UV polymerization within a PDMS microchannel system. The fluorescently labeled target DNA is then electrophoresed through the sequence of hydrogel plugs for hybridization. Continued electrophoresis provides an electrophoretic wash that removes nonspecific binders. The capture gel array is imaged after washing at various temperatures (temperature gradient electrophoresis) to further distinguish perfect matches from mismatches. The ability of this microdevice to perform multiplex SNP genotyping is demonstrated by analyzing a mixture of model E. coli bacterial targets. This microfluidic hydrogel array is ~1000 times more sensitive than planar microarrays due to the 3D gel capture, the hybridization time is much shorter due to electrophoretic control of the transport properties, and the stringent wash with the temperature gradient electrophoresis enables analysis of single nucleotide mismatchs with high specificity.

PMID: 25673175 [PubMed - as supplied by publisher]

Genome-wide copy number profiling using high-density SNP array in chickens.

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Genome-wide copy number profiling using high-density SNP array in chickens.

Anim Genet. 2015 Feb 6;

Authors: Yi G, Qu L, Chen S, Xu G, Yang N

Abstract
Phenotypic diversity is a direct consequence resulting mainly from the impact of underlying genetic variation, and recent studies have shown that copy number variation (CNV) is emerging as an important contributor to both phenotypic variability and disease susceptibility. Herein, we performed a genome-wide CNV scan in 96 chickens from 12 diversified breeds, benefiting from the high-density Affymetrix 600 K SNP arrays. We identified a total of 231 autosomal CNV regions (CNVRs) encompassing 5.41 Mb of the chicken genome and corresponding to 0.59% of the autosomal sequence. The length of these CNVRs ranged from 2.6 to 586.2 kb with an average of 23.4 kb, including 130 gain, 93 loss and eight both gain and loss events. These CNVRs, especially deletions, had lower GC content and were located particularly in gene deserts. In particular, 102 CNVRs harbored 128 chicken genes, most of which were enriched in immune responses. We obtained 221 autosomal CNVRs after converting probe coordinates to Galgal3, and comparative analysis with previous studies illustrated that 153 of these CNVRs were regarded as novel events. Furthermore, qPCR assays were designed for 11 novel CNVRs, and eight (72.73%) were validated successfully. In this study, we demonstrated that the high-density 600 K SNP array can capture CNVs with higher efficiency and accuracy and highlighted the necessity of integrating multiple technologies and algorithms. Our findings provide a pioneering exploration of chicken CNVs based on a high-density SNP array, which contributes to a more comprehensive understanding of genetic variation in the chicken genome and is beneficial to unearthing potential CNVs underlying important traits of chickens.

PMID: 25662183 [PubMed - as supplied by publisher]

High-density SNP arrays improve detection of HER2 amplification and polyploidy in breast tumors.

High-density SNP arrays improve detection of HER2 amplification and polyploidy in breast tumors.

BMC Cancer. 2015 Feb 6;15(1):35

Authors: Hansen TV, Vikesaa J, Buhl SS, Rossing HH, Timmermans-Wielenga V, Nielsen FC

Abstract
BackgroundHuman epidermal growth factor receptor-2 (HER2) overexpression and gene amplification are currently established by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), respectively. This study investigates whether high-density single nucleotide polymorphism (SNP) arrays can provide additional diagnostic power to assess HER2 gene status.MethodsDNA from 65 breast tumor samples previously diagnosed by HER2 IHC and FISH analysis were blinded and examined for HER2 copy number variation employing SNP array analysis.ResultsSNP array analysis identified 24 (37%) samples with selective amplification or imbalance of the HER2 region in the q-arm of chromosome 17. In contrast, only 15 (23%) tumors were found to have HER2 amplification by IHC and FISH analysis. In total, there was a discrepancy in 19 (29%) samples between SNP array and IHC/FISH analysis. In 12 of these cases, the discrepancy towards FISH could be attributed to concomitant amplification or deletion of the centromeric region, which harbors the FISH reference probe sequence. In 3 tumors, repeated IHC/FISH analysis revealed that the original IHC/FISH analysis had failed to indicate the correct HER2 expression level. Finally, the SNP array analysis revealed that more than two thirds of the samples exhibited polyploidy that was unrecognized by conventional FISH.ConclusionsCollectively, the data show that determination of HER2 copy number variations by SNP array-based genomic segmentation analysis is an effective supplement to IHC/FISH HER2 analysis that, by providing additional diagnostic sensitivity and accuracy, may elect more women for targeted treatment with HER2 inhibitors.

PMID: 25655188 [PubMed - as supplied by publisher]

Development, validation, and genetic analysis of a large soybean SNP genotyping array.

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Development, validation, and genetic analysis of a large soybean SNP genotyping array.

Plant J. 2014 Dec 30;

Authors: Lee YG, Jeong N, Kim JH, Lee K, Kim KH, Pirani A, Ha BK, Kang ST, Park BS, Moon JK, Kim N, Jeong SC

Abstract
Soybean has suffered from a narrow cultivated (Glycine max) germplasm relative to other crop species probably because of underuse of wild (G. soja) soybean as a breeding resource. A single nucleotide polymorphism (SNP) genotyping array is a promising tool for dissecting cultivated and wild germplasms to find important adaptive genes by high-density genetic mapping and genome-wide association studies (GWAS). Here, we describe a large soybean SNP array that will be useful for diversity, linkage mapping, and genome-wide association analyses. More than 4 million high-quality SNPs identified from 16 high-depth and 31 low-depth soybean genome resequencing data were used to select 180,961 SNPs for the Axiom(®) SoyaSNP array. Our validation analysis for a set of 222 diverse soybean lines showed that 170,223 markers were of good quality for genotyping. Phylogenetic and allele frequency analyses of the validation set data indicated that intermediates in morphology between cultivated and wild soybeans collected in Korea were natural hybrids. We showed that >90 unanchored scaffolds in the current soybean reference sequence could be assigned to chromosomes using this array. Finally, dense average spacing and preferential distribution of the SNPs in gene-rich chromosomal regions will likely enable this array to be suitable for GWAS of soybean germplasm. Taken together, these results indicate that this SoyaSNP array will be a powerful tool for soybean genetics and many aspects of soybean breeding. This article is protected by copyright. All rights reserved.

PMID: 25641104 [PubMed - as supplied by publisher]

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