Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32501500_1.fastq.gz | Fastqsanger.gz | |||
| SRR32501500_2.fastq.gz | Fastqsanger.gz | |||
| SRR32501501_1.fastq.gz | Fastqsanger.gz | |||
| SRR32501501_2.fastq.gz | Fastqsanger.gz | |||
| SRR32501495_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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 define clonal evolution of somatic copy number alterations (CNAs) in chronic lymphocytic leukemia (CLL), sequential samples of 103 individuals were investigated by SNP-array analysis for appearance of novel CNAs. Patients were enrolled on the CLL8 trial and uniformly received fludarabine, cyclophosphamide +/- rituximab (FC/FCR). Comparing two sequential samples prior to therapy (N=27, a median of 2.9 years apart), CNA evolution occurred in 19% of cases. In contrast, when comparing treatment‑initiation and relapse genomic profiles (a median of 3.6 years apart), CNA evolution was seen in 40% of cases. This suggested association of FC(R) treatment with higher rate of CNA evolution. The only clinical feature significantly associated with CNA evolution was FCR therapy compared with FC (OR=2.806, p=0.024). As this might be related to narrower evolutionary bottlenecks imposed by the more effective FCR therapy, which could execute more selection pressure, we examined matched minimal residual disease data. We found CNA evolution more frequently in cases with CLL cell numbers rapidly receding in early phases of treatment. Finally, we observed frequent rises of TP53 mutant/deficient clones with therapy (N=19, 22%) that were associated with decreased overall survival (p=0.016). These results demonstrated that re-examination of TP53 status upon relapse provides important information.
2017-08-25 | GSE83566 | GEO
Project description:Slow-growing Korat chicken (KR) is an alternative to broiler chickens that has been used as a national tool to support smallholder farmers due to a higher selling price of KR meat. However, the individual variability of feed efficiency (FE) within a KR stockbreeding results in a lack of competitiveness. Therefore, improvement of FE of KR is of major importance to improve the profitability of livestock production enterprises. Here, we selected two groups of KR with divergent feed conversion ratios (FCR). We performed RNA-sequencing in order to profile KR jejunal transcriptome and to identify the transcriptional variations and biological pathways implied in response to divergent FCR. The biological pathways involved were revealed by enrichment of the Gene Ontology (GO) terms, and the Kyoto Encyclopedia of Gene and Genome (KEGG) pathways. The results showed that main pathways involved in KR FCR divergence were related to immune response, glutathione metabolism, vitamin transport and metabolism, lipid metabolism, and maturation, development and growth. This is the first study to investigate the molecular genetic mechanisms affecting the FCR values in jejunum of slow-growing chicken. This study will be useful in the line-breeding programs for slow growing chickens to improve FE in the stockbreeding and its profitability.
2021-09-29 | GSE178916 | GEO
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: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