Genetics of non-syndromic idiopathic autism spectrum disorders in India
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PROVIDER: EGAS00001006060 | EGA |
REPOSITORIES: EGA
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Project description:Giant cell ependymoma (GCE), a rare ependymoma subtype, was only recently recognised as a separate diagnostic entity with variations both in malignant potential and in course of disease. The pathogenetic mechanisms behind ependymomas remain unknown. Only one karyotyped GCE has so far been reported. We present the first genomic characterisation of a supratentorial GCE using G-band karyotyping, DNA ploidy analysis and array comparative genomic hybridisation (aCGH). The G-banded karyotype was hypodiploid with multiple monosomies, a feature present also in the previously published case and, hence, probably characteristic of these tumours. We could also analyse cytogenetically a subsequent recurrent tumour, phenotypically an anaplastic ependymoma, but exhibiting a pattern of monosomies largely similar to that found in the primary tumour, allowing a first insight into the genetic events involved also in disease progression.
2010-08-30 | GSE23065 | GEO
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:Giant cell ependymoma (GCE), a rare ependymoma subtype, was only recently recognised as a separate diagnostic entity with variations both in malignant potential and in course of disease. The pathogenetic mechanisms behind ependymomas remain unknown. Only one karyotyped GCE has so far been reported. We present the first genomic characterisation of a supratentorial GCE using G-band karyotyping, DNA ploidy analysis and array comparative genomic hybridisation (aCGH). The G-banded karyotype was hypodiploid with multiple monosomies, a feature present also in the previously published case and, hence, probably characteristic of these tumours. We could also analyse cytogenetically a subsequent recurrent tumour, phenotypically an anaplastic ependymoma, but exhibiting a pattern of monosomies largely similar to that found in the primary tumour, allowing a first insight into the genetic events involved also in disease progression. 2 tumour samples analysed with the control DNA (supplied by Agilent)
2010-08-30 | E-GEOD-23065 | biostudies-arrayexpress
Project description:Genomic DNA from IDH1 mutant and WT tumors were used to detect genome wide methylation using Agilent SureSelect XT Mouse Methyl-Seq Enrichment System capture kit following manufacturer’s recommendations.
2018-12-01 | GSE107614 | GEO
Project description:The identification of target antigens recognized by monoclonal antibodies that have been derived from oligoclonal band IgG of CSF samples from multiple sclerosis patients.
2016-06-06 | GSE72789 | GEO
Project description:Identify biomarkers to predict response to therapy in polyarticular juvenile idiopathic arthritis (JIA) using gene expression microarrays. 42 samples from 13 controls, 14 active patients, 9 patients in clinical remission with medication (CRM), and 6 patients in clinical remission without medication (CR). All patients had polyarticular JIA.
2009-04-13 | E-GEOD-15645 | biostudies-arrayexpress
Project description:Whole genome microarray expression profiling was employed to identify differential gene expression profiles characteristic of tuberculosis patients in the South-Indian cohort. Whole blood samples were extracted from tuberculosis patients at the time of diagnosis and from healthy controls. The experiment served to validate computational predictions from a meta-analysis study of host transcriptional profiles in tuberculosis.
2016-05-24 | GSE81746 | 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:The study included 15 patients (7 males, 8 females) with JMML. Peripheral blood and/or bone marrow aspirates were collected on EDTA at diagnosis. Non-hematopoietic tissues (fibroblasts) was derived from skin biopsy for each patient. Exome sequencing was performed in several distinct series between 2012 and 2017, which explains the differences in capture kit versions and reference genome version.Targeted enrichment and massive parallel sequencing were performed on paired genomic DNA from leukocytes and fibroblasts. Exome capture was carried out using the SureSelect Human All Exon V4+UTRs or V5 or V5+UTRs or SureSelect Clinical Research (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer’s instruction and protocols by IntegraGen (Evry, France). Paired-end 75 bases sequencing was performed on a HiSeq2000 or HiSeq4000 instrument (Illumina, San Diego, CA, USA). Image analysis and base calling were performed using the Real Time Analysis (RTA) pipeline v. 1.14 (Illumina) with default parameters. The alignment of paired-end reads to the reference human genome (UCSC GRCh37/hg19 or UCSC GRCh38), variant calling and generation of Quality variants scores were carried out using the CASAVA v.1.8 pipeline (Illumina).
2018-03-14 | E-MTAB-6461 | biostudies-arrayexpress
Project description:Binding of transcription factors (TFs) to regulatory sequences is a pivotal step in the control of gene expression. Despite many advances in the characterization of sequence motifs recognized by TFs, our ability to quantitatively predict TF binding to different regulatory sequences is still limited. Here, we present a novel experimental assay termed BunDLE-seq that provides quantitative measurements of TF binding to thousands of fully designed sequences of 200 bp in length within a single experiment. Applying this binding assay to two yeast TFs we demonstrate that sequences outside the core TF binding site profoundly affect TF binding. We show that TF-specific models based on the sequence or DNA shape of the regions flanking the core binding site are highly predictive of the measured differential TF binding. We further characterize the dependence of TF binding, accounting for measurements of single and co-occurring binding events, on the number and location of binding sites and on the TF concentration. Finally, by coupling our in vitro TF binding measurements, and another application of our method probing nucleosome formation, to in vivo expression measurements carried out with the same template sequences now serving and promoters, we offer insights into mechanisms that may determine the different expression outcomes observed. Our assay thus paves the way to a more comprehensive understanding of TF binding to regulatory sequences, and allows the characterization of TF binding determinants within and outside of core binding sites. Binding experiments were carried out with one of two input libraries; Lib1 (also referred to as “main lib”) includes designed sequence variants of length 150bp, and Lib2 (also referred to as “constant flanks lib”) includes designed sequence variants of length 200bp. The sequences of the variants of interest can be found in the second column of the processed data file (BunDLE-seq_data, see 3 excel sheets). EXP1, EXP2 and EXP3 were carried out using Lib1, and EXP4 was carried out using Lib2. Binding experiments were carried out with different proteins (in different concentrations) – DNA was extracted from bound bands that were formed on the gel and amplified with a primer with a unique 5bp upstream tail specifying the identity of the originating band (also referred to as “band barcode”). Data from the following bands was used in the analysis: EXP1_band1, no-protein band – with band barcode “AACGA”, EXP1_band2, single Gcn4 (conc 1:8) bound band* – with band barcode “TCGTA” , EXP1_band3, histones bound band – with band barcode “AGATA”, EXP2_band1, no-protein band – with band barcode “AACGA”, EXP2_band2, single Gcn4 (conc 1:8) bound band* – with band barcode “AGATA”, EXP2_band2, single Gcn4 (conc 1:7) bound band – with band barcode “CACTT”, EXP2_band2, single Gcn4 (conc 1:6) bound band – with band barcode “TCGTA”, EXP2_band2, single Gcn4 (conc 1:5) bound band – with band barcode “CATCA”, EXP2_band2, single Gcn4 (conc 1:4) bound band – with band barcode “TATTA”, EXP2_band2, single Gcn4 (conc 1:3) bound band – with band barcode “AGTCA”, EXP2_band2, single Gcn4 (conc 1:2) bound band – with band barcode “ACGAA”, EXP2_band2, single Gcn4 (conc 1:1) bound band – with band barcode “ACAGA”, EXP2_band2, two Gcn4 (conc 1:1) bound band – barcoded with “GTAGA”, EXP3_band1, no-protein band – with band barcode “GCATA”, EXP3_band2, single Gal4 (conc 1:1) bound band – with band barcode “GATGT”, EXP3_band3, single Gal4 (conc 3:1) bound band – with band barcode “GTTCA”, EXP3_band4, two Gal4 (conc 3:1) bound band – with band barcode “CTCAA”, EXP4_band1, no-protein band – with band barcode “GAGTA”, EXP4_band2, single Gcn4 (conc 1:3) bound band – “TACCA”, EXP4_band3, no-protein band – with band barcode “TCGTT”, EXP4_band3, single Gal4 (conc 3:1) bound band – with band barcode “ACATC”, *biological replicates
2015-03-04 | E-GEOD-66143 | biostudies-arrayexpress