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Pastinen T, Sladek R, Gurd S, et al. A survey of genetic and epigenetic variation affecting human gene expression. Physiol Genomics. 2004;16(2):184-93doi: 10.1152/physiolgenomics.00163.2003.
Pastinen, T., Sladek, R., Gurd, S., Sammak, A., Ge, B., Lepage, P., Lavergne, K., Villeneuve, A., Gaudin, T., Brändström, H., Beck, A., Verner, A., Kingsley, J., Harmsen, E., Labuda, D., Morgan, K., Vohl, M. C., Naumova, A. K., Sinnett, D., & Hudson, T. J. (2004). A survey of genetic and epigenetic variation affecting human gene expression. Physiological genomics, 16(2), 184-93. https://doi.org/10.1152/physiolgenomics.00163.2003
Pastinen, Tomi, et al. "A survey of genetic and epigenetic variation affecting human gene expression." Physiological genomics vol. 16,2 (2004): 184-93. doi: https://doi.org/10.1152/physiolgenomics.00163.2003
Pastinen T, Sladek R, Gurd S, Sammak A, Ge B, Lepage P, Lavergne K, Villeneuve A, Gaudin T, Brändström H, Beck A, Verner A, Kingsley J, Harmsen E, Labuda D, Morgan K, Vohl MC, Naumova AK, Sinnett D, Hudson TJ. A survey of genetic and epigenetic variation affecting human gene expression. Physiol Genomics. 2004 Jan 15;16(2):184-93. doi: 10.1152/physiolgenomics.00163.2003. PMID: 14583597.
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Physiol Genomics. 2004 Jan 15;16(2):184-93. doi: 10.1152/physiolgenomics.00163.2003.

A survey of genetic and epigenetic variation affecting human gene expression.

Physiological genomics

Tomi Pastinen, Robert Sladek, Scott Gurd, Alya'a Sammak, Bing Ge, Pierre Lepage, Karine Lavergne, Amelie Villeneuve, Tiffany Gaudin, Helena Brändström, Allon Beck, Andrei Verner, Jade Kingsley, Eef Harmsen, Damian Labuda, Kenneth Morgan, Marie-Claude Vohl, Anna K Naumova, Daniel Sinnett, Thomas J Hudson

Affiliations

  1. McGill University and Genome Quebec Innovation Centre H3A 1A4, Canada.

PMID: 14583597 DOI: 10.1152/physiolgenomics.00163.2003

Abstract

The identification of human sequence polymorphisms that regulate gene expression is key to understanding human genetic diseases. We report a survey of human genes that demonstrate allelic differences in gene expression, reflecting the presence of putative allele-specific cis-acting factors of either genetic or epigenetic nature. The expression of allelic transcripts in heterozygous samples is assessed directly by relative quantitation of intragenic marker alleles in messenger or heteronuclear RNA derived from cells or tissues. This survey used 193 single-nucleotide polymorphisms (SNPs) from 129 genes expressed in lymphoblastoid cell lines, to identify 23 genes (18%) with common allele-specific transcripts whose expression deviated from the expected equimolar ratio. A subset of these deviations, or "allelic imbalances," can be observed in multiple samples derived from reference CEPH ("Centre d'Etude du Polymorphisme Humain") pedigrees and demonstrate a spectrum of patterns of transmission, including cosegregation of allelic skewing across generations compatible with Mendelian inheritance as well as random monoallelic expression for three genes (IL1A, HTR2A, and FGB). Additional studies for BTN3A2 provide evidence of SNPs and haplotypes in complete linkage disequilibrium with high- and low-expressing transcripts. The pipeline described herein offers tools for efficient identification and characterization of allelic expression allowing identification of regulatory sequence variants as well as epigenetic variation affecting human gene expression.

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