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Am J Hum Genet. 2017 Mar 2;100(3):444-453. doi: 10.1016/j.ajhg.2017.01.028. Epub 2017 Feb 9.

Detection of Imprinted Genes by Single-Cell Allele-Specific Gene Expression.

Author information

1
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland; University Hospitals of Geneva, Geneva 1211, Switzerland. Electronic address: federico.santoni@unige.ch.
2
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland.
3
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland; University Hospitals of Geneva, Geneva 1211, Switzerland; Institute of Genetics and Genomics of Geneva, Geneva 1211, Switzerland. Electronic address: stylianos.antonarakis@unige.ch.

Abstract

Genomic imprinting results in parental-specific gene expression. Imprinted genes are involved in the etiology of rare syndromes and have been associated with common diseases such as diabetes and cancer. Standard RNA bulk cell sequencing applied to whole-tissue samples has been used to detect imprinted genes in human and mouse models. However, lowly expressed genes cannot be detected by using RNA bulk approaches. Here, we report an original and robust method that combines single-cell RNA-seq and whole-genome sequencing into an optimized statistical framework to analyze genomic imprinting in specific cell types and in different individuals. Using samples from the probands of 2 family trios and 3 unrelated individuals, 1,084 individual primary fibroblasts were RNA sequenced and more than 700,000 informative heterozygous single-nucleotide variations (SNVs) were genotyped. The allele-specific coverage per gene of each SNV in each single cell was used to fit a beta-binomial distribution to model the likelihood of a gene being expressed from one and the same allele. Genes presenting a significant aggregate allelic ratio (between 0.9 and 1) were retained to identify of the allelic parent of origin. Our approach allowed us to validate the imprinting status of all of the known imprinted genes expressed in fibroblasts and the discovery of nine putative imprinted genes, thereby demonstrating the advantages of single-cell over bulk RNA-seq to identify imprinted genes. The proposed single-cell methodology is a powerful tool for establishing a cell type-specific map of genomic imprinting.

KEYWORDS:

allele-specific expression; imprinting; single cell

PMID:
28190458
PMCID:
PMC5339288
DOI:
10.1016/j.ajhg.2017.01.028
[Indexed for MEDLINE]
Free PMC Article

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