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Allele-specific expression analysis methods for high-density SNP microarray data

Ruijie Liu, Ana-Teresa Maia, Roslin Russell, Carlos Caldas, Bruce A. Ponder, Matthew E. Ritchie
2012 Bioinformatics  
Results: We analyze data from two experiments that make use of high-density Illumina Infinium II genotyping arrays to measure ASE.  ...  Motivation: In the past decade, a number of technologies to quantify allele-specific expression (ASE) in a genome-wide manner have become available to researchers.  ...  Genome-wide assessment of allele-specific expression has recently become feasible with the availability of high-density SNP chips and second-generation sequencing.  ... 
doi:10.1093/bioinformatics/bts089 pmid:22355082 fatcat:pnyzpoohmvghplvnuvb7cogc4u

Toward genome-wide SNP genotyping

Ann-Christine Syvänen
2005 Nature Genetics  
The development of microarray-based methods for SNP genotyping on this scale remains a demanding task, despite many recent advances in technology for the production of high-density microarrays.  ...  Highly multiplexed microarray systems for SNP genotyping have recently been developed by combining well-known reaction principles for DNA amplification and SNP genotyping in clever ways.  ...  Enzyme-assisted SNP genotyping methods provide highly specific distinction between SNP alleles 34 .  ... 
doi:10.1038/ng1558 pmid:15920530 fatcat:3qdudyccxbffnhpn4tkektn5jy

Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression

Hang He, Huiyong Zhang, Xiangfeng Wang, Nicholas Wu, Xiaozeng Yang, Runsheng Chen, Yi Li, Xing Wang Deng, Lei Li
2010 Genomics  
Together, our work demonstrates the utility and advantages of the tiling array method in interrogating large numbers of SNPs for quantifying allele-specific gene expression.  ...  for each SNP.  ...  Acknowledgments We thank Farah Steele for her technical assistance. This work was  ... 
doi:10.1016/j.ygeno.2010.07.008 pmid:20688151 fatcat:7xehar46cvhuxjso55numqyxoa

Genome-Wide Mapping Of Copy Number Variations using SNP Arrays

Daniel Nowak, Wolf-Karsten Hofmann, H. Phillip Koeffler
2009 Transfusion Medicine and Hemotherapy  
Acknowledgment We thank the Parker Hughes Fund and National Institutes of Health grants for supporting our work. D. Disclosure The authors declared no conflict of interest.  ...  Summary The availability of high-density single nucleotide polymorphism (SNP) microarrays in recent years has proven to be a great step forward in the context of global analysis of genomic abnormalities  ...  Apart from copy number data, the method also yields a genotype data set generated by the SNP calls of either AA, AB or BB standing for the alleles of the SNPs.  ... 
doi:10.1159/000225372 pmid:21049075 pmcid:PMC2941829 fatcat:bt6ffhypczc3fc53hn3tfblcgq

The Application of Single Nucleotide Polymorphism Microarrays in Cancer Research

Xueying Mao, Bryan D. Young, Yong-Jie Lu
2007 Current Genomics  
This review will focus on the wide range of applications of SNP microarray analysis to cancer research.  ...  Our laboratory has applied SNP microarray analysis to uncover frequent uniparental disomies and sub-microscopic genomic copy number gains and losses in different cancers.  ...  Although SNP arrays can be used for allelic specific gene expression analysis, they are principally designed for genomic study.  ... 
doi:10.2174/138920207781386924 pmid:18645599 pmcid:PMC2430687 fatcat:vw5rlctgjrdghgzifopns3y7mi

Progress in concurrent analysis of loss of heterozygosity and comparative genomic hybridization utilizing high density single nucleotide polymorphism arrays

Xiaofeng Zhou, Nagesh P. Rao, Steven W. Cole, Samuel C. Mok, Zugen Chen, David T. Wong
2005 Cancer Genetics and Cytogenetics  
The recent introduction of high-density oligonucleotide arrays for measuring single nucleotide polymorphisms (SNP) has sparked a new wave of highresolution genetic mapping studies, including LOH and CGH  ...  This review highlights recent progress on concurrent LOH and CGH analyses utilizing high density SNP arrays and their application in cancer research. Ć  ...  The Affymetrix 10K SNP mapping array hybridization and scanning were done in the UCLA DNA microarray facility.  ... 
doi:10.1016/j.cancergencyto.2004.09.014 pmid:15860358 fatcat:k4pihvuy2zhevk54ctmbf74pce

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

Andreas Massouras, Sebastian M. Waszak, Monica Albarca-Aguilera, Korneel Hens, Wiebke Holcombe, Julien F. Ayroles, Emmanouil T. Dermitzakis, Eric A. Stone, Jeffrey D. Jensen, Trudy F. C. Mackay, Bart Deplancke, Brian Oliver
2012 PLoS Genetics  
Rather, our data suggest that the elevated SNP density around variants is mainly due to population-level processes.  ...  While the SNP density is higher near other variants, we find that variants themselves are not mutagenic, nor are regions with high variant density particularly mutation-prone.  ...  Acknowledgments The authors wish to thank Maria Gutierrez-Arcelus, Zoltan Kutalik, Frédéric Schütz, and Daniel Wegmann for their assistance and very helpful discussions, and Vital-IT High Performance Computing  ... 
doi:10.1371/journal.pgen.1003055 pmid:23189034 pmcid:PMC3499359 fatcat:u7cvezvn5vcubebknwdjlffssm

A novel multifunctional oligonucleotide microarray for Toxoplasma gondii

Amit Bahl, Paul H Davis, Michael Behnke, Florence Dzierszinski, Manjunatha Jagalur, Feng Chen, Dhanasekaran Shanmugam, Michael W White, David Kulp, David S Roos
2010 BMC Genomics  
Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications.  ...  Additional applications facilitating SNP and transcript discovery, alternative statistical methods for quantifying gene expression, etc. are also pursued at pilot scale to inform future array designs.  ...  For example, the type I RH strain correctly exhibits high relative minor allele strength (minor allele/(major allele + minor allele)) for most type I SNPs, but not for type II or type II.  ... 
doi:10.1186/1471-2164-11-603 pmid:20974003 pmcid:PMC3017859 fatcat:57qzai2dpjd7jenrrxckj7ogf4

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation

Tomas Babak, Philip Garrett-Engele, Christopher D Armour, Christopher K Raymond, Mark P Keller, Ronghua Chen, Carol A Rohl, Jason M Johnson, Alan D Attie, Hunter B Fraser, Eric E Schadt
2010 BMC Genomics  
Results: Here we demonstrate that genomic regions with allele-specific expression (ASE) detected by sequencing cDNA are highly enriched for cis-acting expression quantitative trait loci (cis-eQTL) identified  ...  We also observed widespread noncoding and antisense ASE and identified several allele-specific alternative splicing variants.  ...  Acknowledgements We would like to thank Brian DeVeale and Derek van der Kooy at the University of Toronto for donating all mouse embryos used in this study. Author details  ... 
doi:10.1186/1471-2164-11-473 pmid:20707912 pmcid:PMC3091669 fatcat:o2gsqeb2avdibdxk6hw3zo2sc4

Statistical Comparison Framework and Visualization Scheme for Ranking-Based Algorithms in High-Throughput Genome-Wide Studies

Waibhav D. Tembe, John V. Pearson, Nils Homer, James Lowey, Edward Suh, David W. Craig
2009 Journal of Computational Biology  
As a first step in analyzing high-throughput data in genome-wide studies, several algorithms are available to identify and prioritize candidates lists for downstream fine-mapping.  ...  The results provide a theoretical basis to compare the accuracy of various methods and to identify redundant methods, thus providing guidance for selecting the most suitable analysis method in genome-wide  ...  ACKNOWLEDGMENTS We thank the High-Performance Bio-Computing Center of TGen for providing the high-performance cluster computing resources for this study.  ... 
doi:10.1089/cmb.2008.0151 pmid:19361328 pmcid:PMC3148127 fatcat:oo3ty2jxszckdktzjwmkr2ju7m

Detecting imbalanced expression of SNP alleles by minisequencing on microarrays

Ulrika Liljedahl, Mona Fredriksson, Andreas Dahlgren, Ann-Christine Syvänen
2004 BMC Biotechnology  
Methods with high accuracy to be used in a high throughput setting are needed for systematic surveys of expressed sequence variation.  ...  In this study we evaluated two formats of multiplexed, microarray based minisequencing for quantitative detection of imbalanced expression of SNP alleles.  ...  Acknowledgements We acknowledge Raul Figueroa for array production, Ann-Christin Wiman for assistance with the SNPstream assays and David Fange for programming Microsoft ® Excel macros.  ... 
doi:10.1186/1472-6750-4-24 pmid:15500681 pmcid:PMC529269 fatcat:dlxeu7w3kzdp3d5mpqdq6jxubi

Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays

Marko Laakso, Sari Tuupanen, Auli Karhu, Rainer Lehtonen, Lauri A. Aaltonen, Sampsa Hautaniemi
2007 Computer applications in the biosciences : CABIOS  
Recently, several platforms for high-throughput SNP analysis have become available, capable of measuring thousands of SNPs across the genome.  ...  This hinders effective use of the SNP-array data in research on complex diseases, such as cancer.  ...  We thank Finnish Genome Center and Dr Janna Saarela for technical help to get the data, and Scientific Computing Ltd. (CSC) for computing resources.  ... 
doi:10.1093/bioinformatics/btm263 pmid:17510170 fatcat:4x2xni2c3bcsdkx47fechdeqva

Data analysis issues for allele-specific expression using Illumina's GoldenGate assay

Matthew E Ritchie, Matthew S Forrest, Antigone S Dimas, Caroline Daelemans, Emmanouil T Dermitzakis, Panagiotis Deloukas, Simon Tavaré
2010 BMC Bioinformatics  
High-throughput measurement of allele-specific expression (ASE) is a relatively new and exciting application area for array-based technologies.  ...  This platform exploits coding SNPs to obtain relative expression measurements for alleles at approximately 1500 positions in the genome.  ...  With microarrays, SNPs that fall within the coding regions of transcripts are used to quantify allelic imbalances in expression.  ... 
doi:10.1186/1471-2105-11-280 pmid:20504309 pmcid:PMC2887809 fatcat:oo6w5fjkajdcpcsz4ksdyxdmaa

Microarray Based Genotyping: A Review

2014 Journal of Cancer Sciences  
, this technique is an ideal candidate for performing multiplex high-throughput genetic analysis at a relatively low cost.  ...  DNA microarrays are widely used for genotyping and gene expression thus aiding molecular diagnosis.  ...  Electronic microarrays Similar to high-density bead arrays, electronic microarrays are a unique platform for genomic and proteomic expression assays.  ... 
doi:10.13188/2377-9292.1000001 fatcat:z6dmfdxxczfwbdk3jqvmgqikuq

Getting it right: designing microarray (and not 'microawry') comparative genomic hybridization studies for cancer research

David S P Tan, Maryou B K Lambros, Rachael Natrajan, Jorge S Reis-Filho
2007 Laboratory Investigation  
and against the various microarray platforms that are currently available, and methods for data validation and integration.  ...  for translational research by facilitating detailed analysis of entire cancer genomes in a single experiment.  ...  ACKNOWLEDGEMENTS We thank Dr C Westbury, Mrs M Iravani, and the other members of the Molecular Pathology Laboratory at The Breakthrough Breast Cancer Research Centre for their insightful comments in the  ... 
doi:10.1038/labinvest.3700593 pmid:17558419 fatcat:44vjwn2odrg3bpk2r53jeesmby
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