Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE81402 | GEO | 2016/07/04
SECONDARY ACCESSION(S): PRJNA321469
REPOSITORIES: GEO
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Project description:Genomic instability has profound effects on cellular phenotypes. Studies have shown that pluripotent cells with abnormal karyotypes may grow faster, differentiate less and become more resistance to apoptosis. Previously, we showed that microarray gene expression profiles can be utilized for the analysis of chromosomal aberrations by comparing gene expression levels between normal and aneuploid samples. Here we adopted this method for RNA-Seq data and present eSNP-Karyotyping for the detection of chromosomal aberrations, based on measuring the ratio of expression between the two alleles. We demonstrate its ability to detect chromosomal gains and losses in pluripotent cells and their derivatives, as well as meiotic recombination patterns. This method is advantageous since it does not require matched diploid samples for comparison, is less sensitive to global expression changes caused by the aberration, and utilizes already available gene expression profiles to determine chromosomal aberrations. RNA was extracted from different cell lines and analyzed for chromosomal stability using eSNP-Karyotyping
2016-07-04 | E-GEOD-81402 | biostudies-arrayexpress
Project description:<p>As part of an effort to correlate molecular copy number variation determinations with state of the art karyotype analyses, 716 samples derived from 697 individuals from the Chromosomal Aberrations and Inherited Disorders collections of the NIGMS Human Genetic Cell Repository were genotyped and analyzed for CNV determination by the Microarray Center at the Coriell Institute for Medical Research. Karyotyping is performed on all cell cultures in the Repository with reported chromosome abnormalities. The samples chosen for genotyping in this study are intended to represent a diverse set of copy number variants, but the selection was also weighted to over-sample commonly manifested types of aberrations. When available, the ISCN description of the sample based on G-banding and FISH analysis is included in the phenotypic data. Karyotypes for these cells can be viewed in the online Repository catalog (<a href="http://ccr.coriell.org/Sections/Collections/NIGMS/?SsId=8" target="_blank">http://ccr.coriell.org/Sections/Collections/NIGMS/?SsId=8</a>).</p>
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Project description:Extensive genome analysis of pregnancy loss products by genome haplarithmisis. Pregnancy loss (PL) is the primary pregnancy complication, mostly caused by chromosomal abnormalities of the conceptus. However, the nature and prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental compartments during intrauterine development remains elusive. We analyzed 1,745 spontaneous PLs and found that ~50% were karyotypically normal. We applied genome haplarithmisis to 91 PL families with normal karyotypes, following whole-genome genotypes of the parents as well as of the extraembryonic mesoderm (EM) and chorionic villi (CV), representing embryonic and placental cells, of the product of conception (POC), which allowed characterizing genomic landscape of both lineages. 36.4% of these PLs have chromosomal aberrations not previously detected by karyotyping. In contrast to viable pregnancies where mosaic chromosomal abnormalities are often restricted to the CV, we find that in spontaneous abortions, the situation is reversed with a higher degree of mosaic chromosomal imbalances in EM rather than CV.
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Project description:Extensive genome analysis of pregnancy loss products by genome haplarithmisis. Pregnancy loss (PL) is the primary pregnancy complication, mostly caused by chromosomal abnormalities of the conceptus. However, the nature and prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental compartments during intrauterine development remains elusive. We analyzed 1,745 spontaneous PLs and found that ~50% were karyotypically normal. We applied genome haplarithmisis to 91 PL families with normal karyotypes, following whole-genome genotypes of the parents as well as of the extraembryonic mesoderm (EM) and chorionic villi (CV), representing embryonic and placental cells, of the product of conception (POC), which allowed characterizing genomic landscape of both lineages. 36.4% of these PLs have chromosomal aberrations not previously detected by karyotyping. In contrast to viable pregnancies where mosaic chromosomal abnormalities are often restricted to the CV, we find that in spontaneous abortions, the situation is reversed with a higher degree of mosaic chromosomal imbalances in EM rather than CV.
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Project description:Chromosomal aberrations were studied both in a lung cancer cell line and colorectal cancer tumor samples. Results were verified by SKY karyotypes and by DNA ploidy analysis. The sensitivity of detecting chromosomal aberrations in tumor samples was evaluated by analyzing data from simulated mixtures of the lung cancer cell line H1395 and the normal cell line 1395BL from the same patient.
2011-09-09 | GSE26302 | GEO
Project description:The pathogenesis of paediatric central nervous system tumours is still poorly understood. In an attempt to increase the knowledge of the genetic mechanisms underlying these tumours, we performed genome-wide screening of 17 paediatric gliomas and embryonal tumours using a combination of G-band karyotyping and array comparative genomic hybridisation (aCGH). G-banding revealed abnormal karyotypes in 56% of tumour samples (9 of 16; one failed in culture), whereas aCGH analysis found copy number aberrations in all 13 tumours that could be examined. Pilocytic astrocytomas (n=3) showed normal karyotypes or simple non-recurrent translocations by karyotyping, but revealed the now well-established recurrent gain of 7q34 by aCGH. Our series included one anaplastic oligoastrocytoma, tumours that have not previously been characterised genomically in children, and an anaplastic neuroepithelial tumour (probably an oligoastrocytoma); both tumours showed losses of chromosomes 14 by G-banding as well as structural aberrations of the long arm of chromosome 6, and loss of 14q, 17p, and 22q by aCGH. Three supratentorial primitive neuroectodermal tumours (n=5) showed aberrant karyotypes; two near-diploid with mainly structural changes and one near-triploid with several trisomies including gains of one copy of chromosomes 1, 2, and 7. aCGH confirmed these findings and revealed additional recurrent gains of 1q21-44, 3p21, and 3q29. We also describe cytogenetically for the first time a cribriform neuroepithelial tumour, a recently identified variant of atypical teratoid/rhabdoid tumour with a favourable prognosis, which showed loss of 1p33, 4q13.2, 10p12.31, 10q11.22, and 22q by aCGH. Tumour sample analysed with control DNA (supplied by Agilent)
2011-07-01 | E-GEOD-27671 | biostudies-arrayexpress
Project description:Pregnancy loss is often caused by chromosomal abnormalities of the conceptus. The prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental lineages during intrauterine development remain elusive. We analyzed 1,745 spontaneous pregnancy losses and found that roughly half (50.4%) of the products of conception (POC) were karyotypically abnormal, with maternal and paternal age independently contributing to the increased genomic aberration rate in pregnancy loss. We applied genome haplarithmisis to a subset of 94 pregnancy losses with normal parental and POC karyotypes. Genotyping of parental DNA as well as POC extraembryonic mesoderm and chorionic villi DNA, representing embryonic and trophoblastic tissues, enabled characterization of the genomic landscape of both lineages. Of these pregnancy losses, 35.1% had chromosomal aberrations not previously detected by karyotyping, increasing the rate of aberrations of pregnancy losses to 67.8% by extrapolation. In contrast to viable pregnancies where mosaic chromosomal abnormalities are often restricted to chorionic villi, such as confined placental mosaicism, we found a higher degree of mosaic chromosomal imbalances in extraembryonic mesoderm rather than chorionic villi in pregnancy losses. Our results stress the importance of scrutinizing the full allelic architecture of genomic abnormalities in pregnancy loss to improve clinical management and basic research of this devastating condition.
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Project description:Purpose: Genomic aberrations are of dominant importance to the biology and clinical outcome of patients with acute myelogenous leukemia (AML), and conventional karyotyping-based risk classifications are routinely used in clinical decision making in AML. One of the known limitations of karyotyping is the low sensitivity of this method to detect genomic abnormalities in the sub-megabase (Mb) to ~5 Mb range, and it is currently unclear whether overcoming this limitation with array-based high-resolution karyotyping could be clinically relevant. Furthermore, given the heterogeneity of molecular mechanisms/aberrations that underlie the risks inherent in conventional karyotyping-based risk classifications, it is likely that further refinements in genomic risk prognostication can be achieved. Here, we have analyzed FACS-sorted AML blast-derived and paired buccal DNA from 114 previously untreated prospectively enrolled AML patients for acquired genomic copy number changes and LOH using Affymetrix SNP 6.0 arrays, and we have correlated genomic lesion load and specific chromosomal abnormalities with patient survival. Conclusions: Using multivariate analyses, we found that having ≥2 genomic lesions detected through SNP 6.0 array profiling approximately doubles the risk of death when controlling for age and karyotype-based risk. Finally, we identified an independent negative prognostic impact of p53 mutations, 17p-LOH or both on survival in AML.
2010-11-30 | GSE23452 | GEO
Project description:The pathogenesis of paediatric central nervous system tumours is still poorly understood. In an attempt to increase the knowledge of the genetic mechanisms underlying these tumours, we performed genome-wide screening of 17 paediatric gliomas and embryonal tumours using a combination of G-band karyotyping and array comparative genomic hybridisation (aCGH). G-banding revealed abnormal karyotypes in 56% of tumour samples (9 of 16; one failed in culture), whereas aCGH analysis found copy number aberrations in all 13 tumours that could be examined. Pilocytic astrocytomas (n=3) showed normal karyotypes or simple non-recurrent translocations by karyotyping, but revealed the now well-established recurrent gain of 7q34 by aCGH. Our series included one anaplastic oligoastrocytoma, tumours that have not previously been characterised genomically in children, and an anaplastic neuroepithelial tumour (probably an oligoastrocytoma); both tumours showed losses of chromosomes 14 by G-banding as well as structural aberrations of the long arm of chromosome 6, and loss of 14q, 17p, and 22q by aCGH. Three supratentorial primitive neuroectodermal tumours (n=5) showed aberrant karyotypes; two near-diploid with mainly structural changes and one near-triploid with several trisomies including gains of one copy of chromosomes 1, 2, and 7. aCGH confirmed these findings and revealed additional recurrent gains of 1q21-44, 3p21, and 3q29. We also describe cytogenetically for the first time a cribriform neuroepithelial tumour, a recently identified variant of atypical teratoid/rhabdoid tumour with a favourable prognosis, which showed loss of 1p33, 4q13.2, 10p12.31, 10q11.22, and 22q by aCGH.
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