Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25619057_1.fastq.gz | Fastqsanger.gz | |||
| SRR25619057_2.fastq.gz | Fastqsanger.gz | |||
| SRR25619058_1.fastq.gz | Fastqsanger.gz | |||
| SRR25619058_2.fastq.gz | Fastqsanger.gz | |||
| SRR25619059_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Routine karyotyping combined with CMA testing should be provided for fetuses with omphalocele. WES is an option if karyotype and CMA tests are normal. In addition, if conventional karyotype, CMA detection and WES detection are normal, then further molecular biology methods can be used to rule out disease phenotypes like BWS syndrome. We analyzed the ultrasonographic features, genetic characteristics, and maternal and fetal outcomes of fetuses with omphalocele and provide a reference for perinatal management of such cases.
2023-09-27 | GSE235430 | GEO
Project description:Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality. Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality. Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality. DNA copy number profiles generated with a new tool, ENCODER, were compared to DNA copy number profiles from SNP6, NimbleGen and low-coverage Whole Genome Sequencing.
2014-08-12 | GSE60254 | GEO
Project description:Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality. Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality. Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality. DNA copy number profiles generated with a new tool, ENCODER, were compared to DNA copy number profiles from SNP6, NimbleGen and low-coverage Whole Genome Sequencing.
2014-08-12 | GSE60168 | GEO
Project description:Whole exome sequencing (WES) files of a patient suffering from a combined immunodeficiency, and his parents.
2014-10-31 | E-MTAB-2962 | biostudies-arrayexpress
Project description:To understand the genetic mechanisms by which IGFBP5 regulates aggressive progression and squamous traits, we performed whole-exome sequencing (WES) on three distinct cell lines: CTR-MGH-U3-LT, UCSD-MGH-U3-LT, and MP-MGH-U3-LT. WES revealed no mutations in IGFBP5, suggesting that its regulatory role may involve epigenetic mechanisms. We next sought to perform single-cell ATAC-seq to investigate a potential epigenetic mechanism underlying IGFBP5 regulated squamous traits and aggressiveness.
2026-04-07 | GSE326929 | GEO
Project description:To explore the genetic cause of a Chinese woman with fetal hydrocephalus X-linked hydrocephalus (XLH), a genetic disorder, has an incidence of 1/30,000 male births. The great proportion of XLH is ascribed to loss of function mutations of L1 cell adhesion molecule gene (L1CAM), but silent mutations in L1CAM with pathogenic potential were rare, and were usually ignored especially in WES detection. In the present study, we describe a novel silent L1CAM mutation in a Chinese pregnant woman reporting continuous five times pregnancies with fetal hydrocephalus. After fetal blood sampling, we found c.453G>T (p.Gly151=) in L1CAM gene of the fetus by whole exome sequencing (WES), RT-PCR of the mRNA from cord blood mononuclear cells and subsequent sequence analysis identified the mutation created a potential 5' splice site consensus sequence, which would result in an in-frame deletion of 72 bp from exon 5 and 24 amino acids of the L1CAM protein. Heterozygous mutations were confirmed in analyzing DNA and mRNA from peripheral blood mononuclear cells of the woman, and, a severe L1 syndrome was confirmed by fetal ultrasound scan and MRI. Our study first indicated c.453G>T (p.Gly151=) in L1CAM could be disease causing for hydrocephalus, which would aid in genetic counseling for the prenatal diagnosis of hydrocephalus. Meanwhile, it suggested some silent mutations detected in WES should not be ignored, splicing predictions of these mutations were necessary.
2019-07-16 | GSE133063 | GEO
Project description:Single Gland Whole-exome sequencing: building on our prior description of multi-region WES of colorectal tumors and targeted single gland sequencing (E-MTAB-2247), we performed WES of multiple single glands from different sides (right: A and left: B) of two tumors in this study (tumor O and U) on the illumina platform using the Agilent SureSelect 2.0 or illumina Nextera Rapid Capture Exome kit (SureSelect or NRCE, as indicated in the naming of fastq files). Colorectal Cancer Xenograft Whole-exome sequencing: The HCT116 and LoVo Mismatch-Repair-deficient colorectal adenocarcinoma cell lines were obtained from the ATCC and cultured under standard conditions. For both cell lines, a single âfoundingâ cell was cloned and expanded in vitro to ~6M cells. Two aliquots of ~1M cells were subcutaneously injected into opposite flanks (right and left) of a nude mouse and tumors allowed to reach a size of ~1B cells (1cm3) before the animal was sacrificed. Tumor tissue was collected separately from the right and left lesions and DNA was extracted for WES using the illumina TruSeq Exome kit or Nextera Rapid Capture Exome expanded Kits (Truseq or NRCEe), as was DNA from the first passage population (a polyclonal tissue culture for HCT116 and a polyclonal xenograft sample for LoVo), which were employed as a control to study mutation accumulation in culture and post xenotransplantation.
2017-05-01 | E-MTAB-5547 | biostudies-arrayexpress
Project description:Mutations in isocitrate dehydrogenase 2 (IDH2) occur in many cancers including Acute Myeloid Leukemia (AML). In preclinical models mutant IDH2 causes partial hemopoietic differentiation arrest. Recently, we showed that single agent Enasidenib, a first-in-class, selective mutant IDH2 inhibitor, produces a 40% response in relapsed/refractory AML patients by promoting differentiation. Yet, the rate, extend and duration of the clinical benefits of Enasidenib vary from one patient to another. To investigate how the genetic mutational landscape, at baseline or at relapse, contributes in modulating response to Enasidenib, WES analyses on FACS-sorted blasts from baseline, best response and/or relapse samples from 16 Enasidenib-treated patients were performed. WES analyses were also performed on the CD3+ cells from the same patients, which may be used as germinal control samples.
2018-08-13 | E-MTAB-6299 | biostudies-arrayexpress
Project description:Blood samples from patients with myeloid malignancies were analyzed using whole exome sequencing (WES). Data set from genotyping by microarray of the same samples has been deposited in ArrayExpress under accession number E-MTAB-1845 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1845/).
2013-11-01 | E-MTAB-1850 | biostudies-arrayexpress