Open Access Highly Accessed Research article

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

Caroline Daelemans123, Matthew E Ritchie45, Guillaume Smits1, Sayeda Abu-Amero2, Ian M Sudbery1, Matthew S Forrest1, Susana Campino1, Taane G Clark1, Philip Stanier2, Dominic Kwiatkowski1, Panos Deloukas1, Emmanouil T Dermitzakis16, Simon Tavaré4, Gudrun E Moore2* and Ian Dunham17*

Author Affiliations

1 Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1 SA, UK

2 Molecular and Clinical Genetics Unit, Institute of Child Health, London, WC1 1EH, UK

3 Department of Obstetrics and Gynecology, Institute for Women's Health, University College London, London, WC1E 6HX, UK

4 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK

5 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia

6 Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland

7 European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK

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BMC Genetics 2010, 11:25  doi:10.1186/1471-2156-11-25

Published: 19 April 2010

Additional files

Additional file 1:

Supplemental Table S1: List of SNPs and genes tested on Sequenom platform. Supplemental Table S2: List of SNPs and genes tested on Illumina platform. Supplemental Table S3: SNPs with an average intensity > 11.25 units

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Additional file 2:

Figure showing preferential allelic expression of ACSS2 on the Sequenom platform. Averaged allelic ratios for heterozygous gDNA and cDNA were plotted. The higher C/T ratio in cDNA shows preferential C allele expression (t-test p value = 0.0075).

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Additional file 3:

Figure confirming imprinting of ZNF331 in human term placenta by Sanger Sequencing. Sequences (top for rs8100247 (exon 1, 5'UTR) and bottom for rs8109631 (exon 7, CDS)) of informative term placenta samples in gDNA and cDNA with corresponding genotyping data for the father and the mother. Complete imprinting is visible for the exon 1 SNP, while partial imprinting is present for the exon 7 SNP suggesting an isoform specific imprinting. It is the maternal allele that is (more) expressed.

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Additional file 4:

Figure showing statistically significant genes exhibiting preferential ASE on the Illumina array. ASE for SQSTM1, UBE2V1 and XRRA1 is evident while the effect for CAST and MAN2C1 is more subtle.

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