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Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays

Publication ,  Journal Article
Ronald, J; Akey, JM; Whittle, J; Smith, EN; Yvert, G; Kruglyak, L
Published in: Genome Research
February 2005

Oligonucleotide microarrays provide a high-throughput method for exploring genomes. In addition to their utility for gene-expression analysis, oligonucleotide-expression arrays have also been used to perform genotyping on genomic DNA. Here, we show that in segregants from a cross between two unrelated strains of , high-quality genotype data can also be obtained when mRNA is hybridized to an oligonucleotide-expression array. We were able to identify and genotype nearly 1000 polymorphisms at an error rate close to 3% in segregants and at an error rate of 7% in diploid strains, a performance comparable to methods using genomic DNA. In addition, we demonstrate how simultaneous genotyping and gene-expression profiling can reveal -regulatory variation by screening hundreds of genes for allele-specific expression. With this method, we discovered 70 ORFs with evidence for preferential expression of one allele in a diploid hybrid of two strains.

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Published In

Genome Research

DOI

ISSN

1088-9051

Publication Date

February 2005

Volume

15

Issue

2

Start / End Page

284 / 291

Publisher

Cold Spring Harbor Laboratory

Related Subject Headings

  • Bioinformatics
  • 11 Medical and Health Sciences
  • 06 Biological Sciences
 

Citation

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Ronald, J., Akey, J. M., Whittle, J., Smith, E. N., Yvert, G., & Kruglyak, L. (2005). Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Research, 15(2), 284–291. https://doi.org/10.1101/gr.2850605
Ronald, James, Joshua M. Akey, Jacqueline Whittle, Erin N. Smith, Gael Yvert, and Leonid Kruglyak. “Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays.” Genome Research 15, no. 2 (February 2005): 284–91. https://doi.org/10.1101/gr.2850605.
Ronald J, Akey JM, Whittle J, Smith EN, Yvert G, Kruglyak L. Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Research. 2005 Feb;15(2):284–91.
Ronald, James, et al. “Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays.” Genome Research, vol. 15, no. 2, Cold Spring Harbor Laboratory, Feb. 2005, pp. 284–91. Crossref, doi:10.1101/gr.2850605.
Ronald J, Akey JM, Whittle J, Smith EN, Yvert G, Kruglyak L. Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Research. Cold Spring Harbor Laboratory; 2005 Feb;15(2):284–291.

Published In

Genome Research

DOI

ISSN

1088-9051

Publication Date

February 2005

Volume

15

Issue

2

Start / End Page

284 / 291

Publisher

Cold Spring Harbor Laboratory

Related Subject Headings

  • Bioinformatics
  • 11 Medical and Health Sciences
  • 06 Biological Sciences