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Allele-Specific Expression 1

ABSTRACT: Physiologic allele-specific expression (ASE) in germline tissues occurs during random X-chromosome inactivation and in genomic imprinting, wherein the two alleles of a gene in a heterozygous individual are not expressed equally. Recent studies have confirmed the existence of ASE in apparently non-imprinted autosomal genes; however, the extent of ASE in the human genome is unknown. We explored ASE in lymphoblastoid cell lines of 145 individuals using an oligonucleotide array based assay. ASE of autosomal genes was found to be a very common phenomenon in ~20% of heterozygotes at 78% of SNPs at 84% of the genes examined. Comparison of 100 affected individuals from familial pancreatic cancer kindreds and 45 controls revealed three types of changes in the germline: (a) loss of ASE, (b) gain of ASE, and, (c) rare instances of "extreme" (near monoallelic) ASE. The latter changes identified heterozygous deleterious mutations in a subset of these genes. Consequently, an ASE assay efficiently identifies candidate disease genes with altered germline expression properties as compared to controls, and provides insights into mechanisms that confer disease risk as for pancreatic cancer. Keywords: allele-specific expression

ORGANISM(S): Homo sapiens

PROVIDER: GSE8054 | GEO | 2008/01/05

SECONDARY ACCESSION(S): PRJNA123767

REPOSITORIES: GEO

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Allele-Specific Expression 2

Project description:Physiologic allele-specific expression (ASE) in germline tissues occurs during random X-chromosome inactivation and in genomic imprinting, wherein the two alleles of a gene in a heterozygous individual are not expressed equally. Recent studies have confirmed the existence of ASE in apparently non-imprinted autosomal genes; however, the extent of ASE in the human genome is unknown. We explored ASE in lymphoblastoid cell lines of 145 individuals using an oligonucleotide array based assay. ASE of autosomal genes was found to be a very common phenomenon in ~20% of heterozygotes at 78% of SNPs at 84% of the genes examined. Comparison of 100 affected individuals from familial pancreatic cancer kindreds and 45 controls revealed three types of changes in the germline: (a) loss of ASE, (b) gain of ASE, and, (c) rare instances of "extreme" (near monoallelic) ASE. The latter changes identified heterozygous deleterious mutations in a subset of these genes. Consequently, an ASE assay efficiently identifies candidate disease genes with altered germline expression properties as compared to controls, and provides insights into mechanisms that confer disease risk as for pancreatic cancer. Keywords: allele specific expression

2008-01-05 | GSE8055 | GEO

Germline Aberrations of PAX5 Cause Susceptibility to pre-B cell Acute Lymphoblastic Leukemia

Project description:A novel heterozygous germline variant, c.547G>A (p.Gly183Ser), in the paired box protein encoding gene, PAX5, was found to segregate with disease in two unrelated kindreds with autosomal dominant pre-B cell acute lymphoblastic leukemia (ALL). Leukemic cells from both families exhibited 9p deletion, with loss-of-heterozygosity and retention of the mutant PAX5 allele at 9p13. Two additional sporadic ALL cases with 9p loss demonstrated PAX5 Gly183 substitution in the leukemic cells. Functional and gene expression analysis of the PAX5 germline variants demonstrated reduced transcriptional activity. These data extend the role of PAX5 alterations in the pathogenesis of pre-B ALL, and implicate PAX5 in a novel syndrome of germline susceptibility to pre-B cell neoplasia. We analyzed 40 samples comprising sevenfold replicates of transductions with empty vector, wild type PAX5 and 4 mutant PAX5 constructs

2013-08-01 | E-GEOD-45260 | biostudies-arrayexpress

Germline Aberrations of PAX5 Cause Susceptibility to pre-B cell Acute Lymphoblastic Leukemia

2013-08-01 | GSE45260 | GEO

Germline Aberrations of PAX5 Cause Susceptibility to pre-B cell Acute Lymphoblastic Leukemia

2014-04-06 | GSE45834 | GEO

Germline Aberrations of PAX5 Cause Susceptibility to pre-B cell Acute Lymphoblastic Leukemia

Project description:A novel heterozygous germline variant, c.547G>A (p.Gly183Ser), in the paired box protein encoding gene, PAX5, was found to segregate with disease in two unrelated kindreds with autosomal dominant pre-B cell acute lymphoblastic leukemia (ALL). Leukemic cells from both families exhibited 9p deletion, with loss-of-heterozygosity and retention of the mutant PAX5 allele at 9p13. Two additional sporadic ALL cases with 9p loss demonstrated PAX5 Gly183 substitution in the leukemic cells. Functional and gene expression analysis of the PAX5 germline variants demonstrated reduced transcriptional activity. These data extend the role of PAX5 alterations in the pathogenesis of pre-B ALL, and implicate PAX5 in a novel syndrome of germline susceptibility to pre-B cell neoplasia. We analyzed 10 samples of J558 murine myeloma cells infected with MSCV-Puro-IRES-GFP (PIG) empty vector (EV; three independent replicates), MSCV-PIG Pax5 WT (WT; three independent replicates), and MSCV-PIG Pax5 G183S (Mut; four independent replicates). Cells were selected with puromycin after infection for 5-7 days, subsequently cells were sorted for GFP and IgM expression by FACS.

2014-04-06 | E-GEOD-45834 | biostudies-arrayexpress

ASEP: gene-based detection of allele-specific expression cross individuals in a population by RNA sequencing

Project description:Allele-specific expression (ASE) quantifies the relative expression of two alleles in a diploid individual, and such expression imbalance potentially contributes to phenotypic variation and disease pathophysiology among individuals. We developed ASEP, a method that is able to detect gene-level ASE under one condition, as well as, ASE difference between two conditions (e.g., pre- vs post-treatment) across individuals. Application of ASEP to human macrophage RNA-seq dataset has illustrated its ability to uncover ASE / differential ASE genes related to cardiometabolic traits.

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Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

Project description:Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE).We generated sixteen million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias towards higher mapping rates of the allele in the reference sequence, compared to the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did not lead to more reliable results overall. We find that even after masking, $\sim$5-10\% of SNPs still have an inherent bias towards more effective mapping of one allele. Filtering out inherently biased SNPs removes 40\% of the top signals of ASE. The remaining SNPs showing ASE are enriched in genes previously known to harbor cis-regulatory variation or known to show uniparental imprinting. Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data. Scripts, written in Perl and R, for simulating short reads, masking SNP variation in a reference genome, and analyzing the simulation output are available upon request from JFD. RNA-Seq on two YRI Hapmap cell lines. Each individual sequenced on two lanes of the Illumina Genome Analyzer

2009-10-22 | E-GEOD-18156 | biostudies-arrayexpress

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

2009-10-22 | GSE18156 | GEO

Placental Transcriptome and Stunting

Project description:<p>Therian mammals and angiosperms evolved genomic imprinting in nutritive tissues, the placenta and endosperm, where maternal and paternal genomes are in conflict with respect to resource allocation. In imprinted genes, transcription is repressed from either the paternal or the maternal allele, resulting in allele specific expression (ASE). We studied variation in ASE of imprinted genes in human placentas to detect loss of imprinting (LOI), which refers to departures from mono-allelic expression. The placental tissue was collected in connection with a multigenerational, prospective cohort study in Mali, West Africa, in which individuals were followed from infancy and early childhood to adulthood (age 18+ years). When young women for whom we had longitudinal growth data gave birth, we collected placental tissue and umbilical cord tissue. We genotyped the umbilical cord tissue and saliva samples from parents using targeted DNAseq to identify SNPs in 96 genes known from the literature to be imprinted in human placentas. We used RNAseq to analyze allele specific expression of the heterozygous SNPs. Our results provide the first systematic analysis of variation in LOI across genes and individuals and make it possible to test the hypothesis that modulation of imprinting is an epigenetic mechanism that contributes to the regulation of offspring growth. </p>

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Differential pancreatic islet global gene expression in young heterozygous Men1 mice and wildtype littermates

Project description:Multiple Endocrine Neoplasia Tumor Syndrome type 1 (MEN 1) is an autosomal dominant tumor syndrome affecting individuals with a heterozygous germline mutaion of the MEN1 gene. MEN 1 carriers commonly develop parathyroid, anterior pituitary, duodenal and pancreatic endocrine tumors. The phenotype of existing mouse models for the MEN 1 syndrome, with a germline heterozygous (hz) Men1 gene inactivation, show close resemblance to the human MEN 1 syndrome. Menin, the protein encoded for by the MEN1/Men1 gene, lacks homology with known proteins, and evidence of its involvement in different cellular processes is steadily growing. Several interaction partners have been identified, involving different interaction sites on the menin protein. Accumulating evidence suggests a role for menin in transcriptional regulation, cell cycle control, apoptosis, chromatin modification and DNA damage response and repair. Loss of heterozygosity (LOH) of the MEN1 gene precedes tumor formation in the MEN 1 heterozygous pancreas. We set out to determine if there is a change in gene expression early on in the hz islet, as compared with islets in wildtype (wt) littermates, long before the LOH events occur. We performed a global mRNA expression microarray on islets from young, five-week-old, hz Men1 mice and their wt littermates, and we have subsequently corroborated a subset of the findings on the qPCR and protein level. Islets were isolated and RNA prepared from five five-week-old female mice heterozygous for the Men1 gene and five female wildtype littermates, and then a global gene expression microarray was performed.

2011-06-02 | E-GEOD-29674 | biostudies-arrayexpress

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