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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  
In this paper, we explore several data sets which make use of Illumina's GoldenGate BeadArray technology to measure ASE.  ...  High-throughput measurement of allele-specific expression (ASE) is a relatively new and exciting application area for array-based technologies.  ...  The default preprocessing steps used in this analysis have been shown to offer good performance on spike-in data sets for Illumina's single-channel expression data [14] .  ... 
doi:10.1186/1471-2105-11-280 pmid:20504309 pmcid:PMC2887809 fatcat:oo6w5fjkajdcpcsz4ksdyxdmaa

Evolving Molecular Marker Technologies in Plants: From RFLPs to GBS [chapter]

Reyazul Rouf Mir, Pavana J. Hiremath, Oscar Riera-Lizarazu, Rajeev K. Varshney
2013 Diagnostics in Plant Breeding  
Acknowledgements Authors are thankful to Theme Leader Discretionary Grant of CGIAR-Generation Challenge Programme (GCP) and Centre of Excellence (CoE) grant from Department of Biotechnology (DBT) for funding  ...  GoldenGate Assays Illumina's GoldenGate assay provides SNP genotyping for genome-wide marker profiling.  ...  of genotyping assays (e.g., Illumina) can readily be used for primer design (one common and two allele-specific primers) for KASPar assays (for review see McCouch et al. 2010) .  ... 
doi:10.1007/978-94-007-5687-8_11 fatcat:paabylzzxffzbockexjr3il2p4

Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed, paraffin-embedded paired tumor and normal tissue

Farzana Jasmine, Ronald Rahaman, Shantanu Roy, Maruf Raza, Rupash Paul, Muhammad Rakibuz-Zaman, Rachelle Paul-Brutus, Charlotte Dodsworth, Mohammed Kamal, Habibul Ahsan, Muhammad G Kibriya
2012 BMC Research Notes  
Recently, Thirlwell et al. (2010) have reported a modified ligation-based DNA repair protocol to prepare FFPE DNA for the Infinium methylation assay.  ...  Formalin-fixed, paraffin-embedded (FFPE) samples are a highly desirable resource for epigenetic studies, but there is no suitable platform to assay genome-wide methylation in these widely available resources  ...  In a previous study we compared genome-wide gene expression (using Illumina's DASL assay, based on GoldenGate chemistry) in paired FF and FFPE breast tumor tissues and surrounding healthy tissues [31]  ... 
doi:10.1186/1756-0500-5-117 pmid:22357164 pmcid:PMC3309956 fatcat:rv5yamvtpreyjfcwmy7ghwnf4u

High, clustered, nucleotide diversity in the genome of Anopheles gambiae revealed through pooled-template sequencing: implications for high-throughput genotyping protocols

Craig S Wilding, David Weetman, Keith Steen, Martin J Donnelly
2009 BMC Genomics  
We illustrate these issues in the context of the design of Illumina GoldenGate assays.  ...  Conclusion: The high frequency and clustering of SNPs has important ramifications for the design of high-throughput genotyping assays based on allele specific primer extension or probe hybridisation.  ...  We are also grateful to three anonymous reviewers for their constructive criticism of the manuscript. This work was supported by the Innovative Vector Control Consortium (IVCC).  ... 
doi:10.1186/1471-2164-10-320 pmid:19607710 pmcid:PMC2723138 fatcat:mnnoeork6nhntizh3x6odjp5by

Statistical approaches for the analysis of DNA methylation microarray data

Kimberly D. Siegmund
2011 Human Genetics  
I finish with a section describing down-stream analyses of the data, focusing on methods that model percentage DNA methylation as the outcome, and methods for integrating DNA methylation with gene expression  ...  I then describe the microarray technologies most commonly in use, along with the methods used for pre-processing and obtaining a summary measure.  ...  I would also like to thank Tim Triche Jr. for his work on Beta Regression and the preprocessing of DNA methylation data from Illumina's Infinium platform, and Dr. Peter W.  ... 
doi:10.1007/s00439-011-0993-x pmid:21519831 pmcid:PMC3166559 fatcat:mktqc3l5kfbkdoqik35iu2rusm

Detection, breakpoint identification and detailed characterisation of a CNV at the FRA16D site using SNP assays

L. Winchester, D.F. Newbury, A.P. Monaco, J. Ragoussis
2008 Cytogenetic and Genome Research  
Genotyping using the GoldenGate Illumina system The GoldenGate assay is based on a PCR reaction using a template of two allele specific primers and a bead specific primer.  ...  During analysis of data for an SNP association study for Specific Language Impairment (SLI) a deletion was identified.  ... 
doi:10.1159/000184724 pmid:19287171 fatcat:s4rau2drj5fkrav6q52hnlcu4q

Novel Genomic Tools and Modern Genetic and Breeding Approaches for Crop Improvement

Rajeev K. Varshney, Anuja Dubey
2009 Journal of Plant Biochemistry and Biotechnology  
In recent past, genomic tools especially molecular markers have been extensively used for understanding genome dynamics as well for applied aspects in crop breeding.  ...  These technologies promise to provide an insight into the way gene(s) are expressed and regulated in cell and to unveil metabolic pathways involved in trait(s) of interest for breeders not only in model  ...  useful discussions on different technologies and approaches.  ... 
doi:10.1007/bf03263311 fatcat:43slup4755d73i5zgd5o45vgl4

Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce

Nathalie Pavy, Betty Pelgas, Stéphanie Beauseigle, Sylvie Blais, France Gagnon, Isabelle Gosselin, Manuel Lamothe, Nathalie Isabel, Jean Bousquet
2008 BMC Genomics  
To explore the potential value of high-throughput genotyping assays in the analysis of large and complex genomes, we designed two highly multiplexed Illumina bead arrays using the GoldenGate SNP assay  ...  For white spruce and black spruce, respectively, 69.2% and 77.1% of genotyped SNPs had valid GoldenGate assay scores and segregated in the mapping populations.  ...  Acknowledgements We thank Alexandre Montpetit and his team at the Genome Québec Innovation Centre (Montréal, Québec) for assistance with the acquisition of SNP data on the Illumina platform.  ... 
doi:10.1186/1471-2164-9-21 pmid:18205909 pmcid:PMC2246113 fatcat:4eajvejvtnfwfcafonayophrmu

Copy number variation has little impact on bead-array-based measures of DNA methylation

E. Andrés Houseman, Brock C. Christensen, Margaret R. Karagas, Margaret R. Wrensch, Heather H. Nelson, Joseph L. Wiemels, Shichun Zheng, John K. Wiencke, Karl T. Kelsey, Carmen J. Marsit
2009 Computer applications in the biosciences : CABIOS  
Therefore, we present a detailed analysis of the statistical properties of the GoldenGate methylation assay.  ...  In parallel, analyses of epigenetic alterations, and specifically promoter CpG island DNA methylation can be performed using BeadArray technologies for both cancer related genes (Goldengate Methylation  ... 
doi:10.1093/bioinformatics/btp364 pmid:19542153 pmcid:PMC2723008 fatcat:wkfzj3sj3jhtvjbrv5exzkepmi

In Vitro vs In Silico Detected SNPs for the Development of a Genotyping Array: What Can We Learn from a Non-Model Species?

Camille Lepoittevin, Jean-Marc Frigerio, Pauline Garnier-Géré, Franck Salin, María-Teresa Cervera, Barbara Vornam, Luc Harvengt, Christophe Plomion, Pär K. Ingvarsson
2010 PLoS ONE  
used for SNP detection, the SNP minor allele frequency and the quality of SNP flanking sequences.  ...  Conclusions/Significance: This study demonstrates that ESTs provide a resource for SNP identification in non-model species, which do not require any additional bench work and little bio-informatics analysis  ...  Alazard from FCBA for collecting the samples, and E. Eveno (Treesnips EU project nu836501), F. Bedon, L. Cancino and F. Hubert for sequence data production.  ... 
doi:10.1371/journal.pone.0011034 pmid:20543950 pmcid:PMC2882948 fatcat:lvd4fubk3nf6jed6vx23se32ym

Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes

Pavana J. Hiremath, Ashish Kumar, Ramachandra Varma Penmetsa, Andrew Farmer, Jessica A. Schlueter, Siva K. Chamarthi, Adam M. Whaley, Noelia Carrasquilla-Garcia, Pooran M. Gaur, Hari D. Upadhyaya, Polavarapu B. Kavi Kishor, Trushar M. Shah (+2 others)
2012 Plant Biotechnology Journal  
sharing plant material/DNA/RNA of some genotypes used for validation of KASPar assays in this study.  ...  Thanks are also due to Neha Gujaria, Thudi of ICRISAT for useful discussions received from them during the course of this study. We also thank Hari C.  ...  High-throughput SNP genotyping platforms such as Illumina's GoldenGate or Infinium assays are being used for large-scale SNP genotyping.  ... 
doi:10.1111/j.1467-7652.2012.00710.x pmid:22703242 pmcid:PMC3465799 fatcat:i6rx2gmsovdf7o6jprkgmccabu

Plant growth-promoting traits of biocontrol potential bacteria isolated from rice rhizosphere

Subramaniam Gopalakrishnan, HD Upadhyaya, Srinivas Vadlamudi, Pagidi Humayun, Meesala Sree Vidya, Gottumukkala Alekhya, Amit Singh, Rajendran Vijayabharathi, Ratna Kumari Bhimineni, Murali Seema, Abhishek Rathore, Om Rupela
2012 SpringerPlus  
sharing plant material/DNA/RNA of some genotypes used for validation of KASPar assays in this study.  ...  Thanks are also due to Neha Gujaria, Thudi of ICRISAT for useful discussions received from them during the course of this study. We also thank Hari C.  ...  High-throughput SNP genotyping platforms such as Illumina's GoldenGate or Infinium assays are being used for large-scale SNP genotyping.  ... 
doi:10.1186/2193-1801-1-71 pmid:23397013 pmcid:PMC3565085 fatcat:ffhh4ydzjfabrftyq3lzhf453y

The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don

Yoshinari Moriguchi, Tokuko Ujino-Ihara, Kentaro Uchiyama, Norihiro Futamura, Maki Saito, Saneyoshi Ueno, Asako Matsumoto, Naoki Tani, Hideaki Taira, Kenji Shinohara, Yoshihiko Tsumura
2012 BMC Genomics  
using the GoldenGate genotyping assay.  ...  Results: We constructed a high-density saturated genetic linkage map for C. japonica using expressed sequencederived co-dominant single nucleotide polymorphism (SNP) markers, most of which were genotyped  ...  Shibaya of the QTL Genomics Research Center at the National Institute of Agrobiological Sciences for their technical advice regarding GoldenGate SNP genotyping and for giving us permission to use their  ... 
doi:10.1186/1471-2164-13-95 pmid:22424262 pmcid:PMC3386010 fatcat:fyyhn5o4wnc3pj7vq2x5svqkdi

A Genome-Wide Gene Expression Signature of Environmental Geography in Leukocytes of Moroccan Amazighs

Youssef Idaghdour, John D. Storey, Sami J. Jadallah, Greg Gibson, Greg Barsh
2008 PLoS Genetics  
Genetic network analysis further implies that specific aspects of immune function are strongly affected by regional factors and may influence susceptibility to respiratory and inflammatory disease.  ...  Genome-wide polymorphism analysis indicates that genetic differentiation in the total sample is limited and is unlikely to explain the expression divergence.  ...  Analyzed the data: YI JS GG. Wrote the paper: YI GG. Provided logistical support: SJ.  ... 
doi:10.1371/journal.pgen.1000052 pmid:18404217 pmcid:PMC2290968 fatcat:caa2dwssdfeitou56nnfnhv6gu

High-throughput SNP-genotyping analysis of the relationships among Ponto-Caspian sturgeon species

Sergey M. Rastorguev, Artem V. Nedoluzhko, Alexander M. Mazur, Natalia M. Gruzdeva, Alexander A. Volkov, Anna E. Barmintseva, Nikolai S. Mugue, Egor B. Prokhortchouk
2013 Ecology and Evolution  
We performed high-throughput single-nucleotide polymorphism (SNP)-genotyping analysis on different populations of Russian (Acipenser gueldenstaedtii), Persian (A. persicus), and Siberian (A. baerii) sturgeon  ...  However, the available genetic data are insufficient to distinguish between different sturgeon populations, and are even unable to distinguish between some species.  ...  Acknowledgments We thank Anthon Teslyuk for useful discussions and for technical support with the computer cluster of the NRC Kurchatov Institute, Maria Tolochkova for help in obtaining samples from the  ... 
doi:10.1002/ece3.659 pmid:24567827 pmcid:PMC3930046 fatcat:snwqfpowuvgctfxbgxrgaahjdu
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