Copy number (SNP) analysis from leukemic patients with complex structural variants
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ABSTRACT:
PROVIDER: PRJNA511662 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Structural variants can lead to an alteration of gene expression which may be associated with disease worsening. In our study we attempted to describe expression changes associated with the presence of extensive genomic rearrangements in chronic lymphocytic leukemia.
2019-05-13 | GSE124330 | GEO
Project description:Expression data from leukemic patients with complex structural variants
| PRJNA511661 | ENA
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2010-12-16 | GSE26075 | GEO
Project description:Ongoing studies using genomic microarrays and next-generation sequencing have demonstrated that the genetic contributions to cardiovascular diseases have been significantly ignored in the past. The aim of this study was to identify rare copy number variants in individuals with congenital pulmonary atresia (PA). Based on the hypothesis that rare structural variants encompassing key genes play an important role in heart development in PA patients, we performed high-resolution genome-wide microarrays for copy number variations (CNVs) in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform. CNVs were identified in 17/82 patients (20.7%), and eight of these CNVs (9.8%) are considered potentially pathogenic. Five de novo CNVs occurred at two known congenital heart disease (CHD) loci (16p13.1 and 22q11.2). Two de novo CNVs that may affect folate and vitamin B12 metabolism were identified for the first time. A de novo 1-Mb deletion at 17p13.2 may represent a rare genomic disorder that involves mild intellectual disability and associated facial features. high-resolution genome-wide microarrays for copy number variations (CNVs) in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform. Only 21 samples with potentially pathogenic CNVs are included in this records
2014-04-02 | E-GEOD-56422 | biostudies-arrayexpress
Project description:Ovarian cancer is characterized by multiple structural aberrations; most are passenger alterations which do not confer tumor growth. Like many cancers, it is a heterogeneous disease and till date, the histotype-specific copy number landscape has been difficult to elucidate. To dissect the heterogeneity of ovarian cancer and understand the pathogenesis of its various histotypes, we developed an in silico hypothesis-driven workflow to identify histotype-specific copy number aberrations across multiple datasets of epithelial ovarian cancer. In concordance with previous studies on global copy number changes, our study showed similar alterations. However, when the landscape was de-convoluted into histotypes, distinct alterations were observed. We report here a comprehensive histotype-specific copy number landscape of ovarian cancer and showed that there is genomic diversity between the histotypes; some involving well known cancer genes and some novel potential driver genes. Besides preferential occurrence of alterations in some histotypes, opposite trends of alteration were observed; such as ERBB2 amplification in mucinous but deletion in serous tumors. The landscape highlights the need for identifying histotype-specific aberrations in ovarian cancer and present potential to tailor management of ovarian cancer based on molecular signature of histotypes.
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Project description:Structural changes of chromosomes play important roles in the carcinogenesis of colorectal carcinoma (CRC). Here, by using SNP-typing arrays, we have tried to screen for recurrent chromosome copy number changes and loss-of-heterozygosity in the genome of colorectal carcinoma. Genomic DNA was isolated from tumor and paired normal tissues of CRC (n=94), and was hybridized to Affymetrix Mapping 50K Xba 240 arrays. Chromosome copy number and LOH likelihood score was inferred at every SNP locus with CNAG2.0 software (http://www.genome.umin.jp). Keywords: Comparative genomic hybridization
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Project description:Ongoing studies using genomic microarrays and next-generation sequencing have demonstrated that the genetic contributions to cardiovascular diseases have been significantly ignored in the past. The aim of this study was to identify rare copy number variants in individuals with congenital pulmonary atresia (PA). Based on the hypothesis that rare structural variants encompassing key genes play an important role in heart development in PA patients, we performed high-resolution genome-wide microarrays for copy number variations (CNVs) in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform. CNVs were identified in 17/82 patients (20.7%), and eight of these CNVs (9.8%) are considered potentially pathogenic. Five de novo CNVs occurred at two known congenital heart disease (CHD) loci (16p13.1 and 22q11.2). Two de novo CNVs that may affect folate and vitamin B12 metabolism were identified for the first time. A de novo 1-Mb deletion at 17p13.2 may represent a rare genomic disorder that involves mild intellectual disability and associated facial features.
2014-04-02 | GSE56422 | GEO
Project description:Human pluripotent stem cell (hPSC) lines exhibit repeated patterns of genetic variation, which can alter in vitro properties as well as suitability for clinical use. We examined associations between copy number variations (CNVs) on chromosome 17 and hPSC mesodiencephalic dopaminergic (mDA) differentiation. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved stem cell samples. Copy number analysis of Affymetrix Genome-Wide Human SNP Array 6.0 was performed for 17 stem cell samples.
2014-12-17 | E-GEOD-64241 | biostudies-arrayexpress
Project description:The genomic loci with copy number alterations are known to harbor cancer genes. We investigated a comprehensive panel of gastric cancer cell lines for their genome-wide copy number alterations. Eighteen gastric cancer cell lines were profiled using Affymetrix 500K SNP arrays. For copy number calculation, seven independent normal blood samples were profiled together. The copy numbers were calculated genome-wide, in these cell lines with high resolution and reveal the cell line specific amplification and copy number changes.
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Project description:T-cell acute lymphoblastic leukemia (T-ALL) is a genetically highly heterogeneous disease, and numerous genetic aberrations in the leukemic genome are responsible for the biological and clinical differences among particular ALL subtypes. However, there is limited knowledge about the association of whole genome copy number abnormalities (CNAs) in childhood T-cell ALL with the course of leukemia and outcome. The aim of study was identification the pattern of whole genome CNAs in 86 newly diagnosed childhood T-ALL using a high-density single-nucleotide polymorphism (SNP) array.A series of bone marrow aspirates from 86 children with newly diagnosed T-ALL were analysed prior to any oncological treatment.
2020-03-24 | GSE147381 | GEO