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Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15

ABSTRACT: Methylation profiles of chr12-16 were generated by meDIP and array hybridisation in 3 cases with maternal uniparental disomy of chromosome 15, and three cases of paternal uniparental disomy of chromosome 15. Comparison of these profiles reveals differentially methylated (imprinted) regions on chromosome 15.

ORGANISM(S): Homo sapiens

PROVIDER: GSE22188 | GEO | 2010/06/12

SECONDARY ACCESSION(S): PRJNA127549

REPOSITORIES: GEO

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Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15

Project description:Methylation profiles of chr12-16 were generated by meDIP and array hybridisation in 3 cases with maternal uniparental disomy of chromosome 15, and three cases of paternal uniparental disomy of chromosome 15. Comparison of these profiles reveals differentially methylated (imprinted) regions on chromosome 15. Methylated DNA was enriched by immunoprecipitation using antibodies against 5-methylcytosine. meDIP and input DNA was labeled with cy5 and cy3 respectively and hybridized to Nimblegen arrays comprising 2.1 million 50-85mers covering human chromosomes 12-16 at a mean density of ~1 probe per 100bp. Resulting log2 fluorescence ratios correspond to methylation levels. Six samples were analyzed, with technical replicates for each DNA.

2010-06-12 | E-GEOD-22188 | biostudies-arrayexpress

Uniparental disomy: expanding the clinical and molecular phenotypes of whole chromosomes

Project description:Uniparental disomy (UPD) refers to as both homologous chromosomes inherited from only one parent without identical copies from the other parent. Current knowledge of the phenotypes is associated with imprinting disorders or autosomal recessive mutations. Recent studies had reported that UPD for chromosomes 6, 7, 11, 14, 15, and 20 accompanied with definite imprinted disorders. However, the phenotypes and outcomes of UPD with other chromosomes have not been completely identified. Herein, we combined three remarkable UPD patients involving different chromosomes and presented their phenotypes. The chromosomal microarray (CMA) demonstrated a whole homozygous region on chromosome 2 in patient A, on chromosome 9 in patient B, accompanied by a gain mosaic region (ratio:22%) of 19.18Mb in 9p22.2p13.2, and a LOH region on 14q23.2q32.12 and several genes with compound heterozygous mutation were detected in patient C

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Detection of uniparental disomy from genome sequencing of family trio

Project description:We created a bioinformatics pipeline to detect uniparental disomy from whole genome sequence data of family trios. We use inheritance patterns of single nucleotide polymorphisms to identify uniparental disomy events.

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PRR14L mutations are associated with chromosome 22 acquired uniparental disomy, age related clonal hematopoiesis and myeloid neoplasia

Project description:Whole exome sequencing of 5 MDS/MPN patients to identify the target of chromosome 22 acquired uniparental disomy (22aUPD). For samples E4051 and E6523, peripheral blood leucocytes (tumour) and cultured T-cells (germline) were prepared for exome sequencing using the Agilent SureSelect kit (Agilent Technologies, Palo Alto, CA, USA) (Human All Exon 50 Mb) and then sequenced on an Illumina HiSeq 2000 (Illumina, Great Abington, UK) at the Wellcome Trust Centre for Human Genetics, Oxford, UK. For samples ULSAM1182, ULSAM1242 and ULSAM1356, peripheral blood leukocyte DNA only were exome sequenced by SciLifeLab (Stockholm, Sweden).

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Untimely expression of gametogenic genes in vegetative cells causes uniparental disomy

Project description:Untimely expression of gametogenic genes in vegetative cells causes uniparental disomy

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Uniparental disomy: expanding the clinical and molecular phenotypes of whole chromosomes

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Novel regions of acquired uniparental disomy discovered in acute myeloid leukemia

Project description:The acquisition of uniparental disomy (aUPD) in acute myeloid leukemia (AML) results in homozygosity for known gene mutations. Uncovering novel regions of aUPD has the potential to identify previously unknown mutational targets, therefore, we aimed to develop a comprehensive map of the regions of aUPD in AML. Here, we have analyzed a large set of diagnostic AML samples (n=455) using genotype arrays. Acquired UPD was found in 17% of the samples with a non-random distribution particularly affecting chromosomes 13q, 11p and 11q. Novel recurrent regions of aUPD were uncovered at 2p, 17p, 2q, 17q, 1p and Xq. Overall, aUPDs were observed across all cytogenetic risk groups, although samples with aUPD13q (5.4% of samples) belonged exclusively to the intermediate-risk group. All cases with a high FLT3-ITD level, measured previously, had aUPD13q covering the FLT3 gene. Of the 120 aUPDs observed, the majority (87%) were due to mitotic recombination while only 13% were due to non-disjunction. This study demonstrates aUPD is a frequent and significant finding in AML and pinpoints regions that may contain novel mutational targets. Keywords: Genomic analysis of AML samples

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Affymetrix Cytogenetics array data for a study of D45-deficiency resulting from uniparental disomy: a novel cause of SCID

Project description:Analysis of the molecular etiologies of severe combined immunodeficiency (SCID) has led to important insights into the control of immune cell development. Most cases of SCID result from either X-linked or autosomal recessive inheritance of mutations in a known causative gene. However, in some cases, the molecular etiology remains unclear. To identify the cause of SCID in a patient known to lack the protein tyrosine phosphatase CD45, we utilized single nucleotide polymorphisms (SNP) Cytogenetics arrays; The patient’s mother was heterozygous for an inactivating mutation in CD45, while the paternal alleles exhibited no detectable mutations. The patient exhibited a single CD45 mutation identical to the maternal allele. Patient SNP array analysis revealed no change in copy number but loss of heterozygosity for the entire length of chromosome 1 (Chr1), indicating that disease was caused by uniparental disomy (UPD) with isodisomy of the entire maternal Chr1 bearing the mutant CD45 allele. Non-lymphoid blood cells and other mesoderm and ectoderm-derived tissues retained UPD of the entire maternal Chr1 in this patient who had undergone successful bone marrow transplantation. These findings represent the first reported case of SCID caused by UPD and suggest UPD should be considered in SCID and other recessive disorders, especially when the patient appears homozygous for an abnormal gene found in only one parent. Evaluation for alterations in other genes affected by UPD should also be considered in such cases.

2012-02-10 | GSE35674 | GEO

Affymetrix Cytogenetics array data for a study of D45-deficiency resulting from uniparental disomy: a novel cause of SCID

2012-02-10 | E-GEOD-35674 | biostudies-arrayexpress

Identification of Acquired Copy Number Alterations and Uniparental Disomies in Cytogenetically Normal AML

Project description:Identification of Acquired Copy Number Alterations and Uniparental Disomies in Cytogenetically Normal Acute Myeloid Leukemia Using High-Resolution Single Nucleotide Polymorphism Analysis Recent advances in genome-wide single nucleotide polymorphism (SNP) analyses have revealed previously unrecognized microdeletions and uniparental disomy (UPD) in a broad spectrum of human cancers. As acute myeloid leukemia (AML) represents a genetically heterogeneous disease, this technology might prove helpful especially for cytogenetically normal AML (CN-AML) cases. Thus, we performed high-resolution SNP analyses in 157 adult cases of CN-AML. Regions of acquired UPD were identified in 12% of cases and most frequently affected chromosomes 6p, 11p, and 13q. Notably, acquired UPD was invariably associated with mutations in NPM1 or CEBPA that impair hematopoietic differentiation (P=0.008), suggesting that UPDs may preferentially target genes that are essential for proliferation and survival of hematopoietic progenitors. Acquired copy number alterations (CNAs) were detected in 49% of cases with losses found in two or more cases affecting e.g. chromosome bands 3p13-p14.1 and 12p13. Furthermore, we identified two cases with a cryptic t(6;11) as well as several non-recurrent aberrations pointing to leukemia relevant regions. With regard to clinical outcome, there appeared to be an association between UPD 11p and UPD 13q cases with overall survival. These data demonstrate the potential of high-resolution SNP analysis for identifying genomic regions of potential pathogenic and clinical relevance in AML.

2009-12-01 | GSE19101 | GEO

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