Exome analysis MD
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB44188 | ENA |
REPOSITORIES: ENA
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Project description:Background: Whole exome sequencing (WES) has been proven to serve as a valuable basis for various applications such as variant calling and copy number variation (CNV) analyses. For those analyses the read coverage should be optimally balanced throughout protein coding regions at sufficient read depth. Unfortunately, WES is known for its uneven coverage within coding regions due to GC-rich regions or off-target enrichment. Results: In order to examine the irregularities of WES within genes, we applied Agilent SureSelectXT exome capture on human samples and sequenced these via Illumina in 2x101 paired-end mode. As we suspected the sequenced insert length to be crucial in the uneven coverage of exome captured samples, we sheared 12 genomic DNA samples to two different DNA insert size lengths, namely 130 and 170 bp. Interestingly, although mean coverages of target regions were clearly higher in samples of 130 bp insert length, the level of evenness was more pronounced in 170 bp samples. Moreover, merging overlapping paired-end reads revealed a positive effect on evenness indicating overlapping reads as another reason for the unevenness. In addition, mutation analysis on a subset of the samples was performed. In these isogenic subclones almost twofold mutations were failed in the 130 bp samples when compared to the 170 bp samples. Visual inspection of the discarded mutation sites exposed low coverages at the sites embedded in high amplitudes of coverage depth in the affected region. Conclusions: Producing longer insert reads could be a good strategy to achieve better uniform read coverage in coding regions and hereby enhancing the effective sequencing yield to provide an improved basis for further variant calling and CNV analyses.
2016-07-28 | E-MTAB-4527 | biostudies-arrayexpress
Project description:Copy number variation analysis of human Barrett's esophagus stem cells
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Project description:To evaluate the effects of mitotic degradation of SMARCE1 upon gene expression, we performed RNA-sequencing (RNA-seq) of cultures of four independent subclones each of Smarce1-MD and control Smarce1-MD (R42A) mESCs. We found that transcription of the core pluripotency regulatory network was not disrupted. In contrast, GO analysis showed that neural differentiation-associated terms were enriched among genes upregulated in Smarce1-MD mESCs. To better understand the difference in neural fates in the neural induction experiments, we performed differential gene expression analysis and gene set enrichment analysis (GSEA) studies. Mitotic degradation of SMARCE1 resulted in higher expression of GABA receptors and hyper-activation of synaptic signaling on neural induction, indicating the aberrant neural cell fate commitment compared to SMARCE1-MD (R42A) cultures. And then we add back BMP4 to partically rescue the phenotype and very small amount of BMP4 will rescue the phenotype.
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Project description:Primary uveal melanomas show multiple chromosomal aberrations. To identify genome variation in six human primary uveal melanomas, genome wide copy number variation (CNV) analyses were carried out in human primary uveal melanoma samples using array comparative genome hybridization.
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Project description:Interventions: Gold Standard:Fluorescence PCR Analysis;Index test:Human BRAF Gene V600E Mutation Diagnostic kit (Fluorescence PCR Analysis)
Primary outcome(s): colorectal cancer;cancerous goiter
Study Design: Diagnostic test for accuracy
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Project description:With the whole genome SNPs array information, we could evaluate the sensitivity and specificity of the point mutation we conclude from the next-generation sequencing data. Furthermore, we could use the true positive mutation as our guidance to exclude the most unreliable single nucleotide variation detected from sequence. After the process, we could promise a very high specificity under minimum loss of sensitivity.
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Project description:Integrative variation analysis reveals that complex genotype may specify phenotype in syndromic autism spectrum disorder siblings
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Project description:Allelic variation in gene expression is common in human genome. To understand genetic and epigenetic basis of allelic gene expression variation, we conducted allele specific RNA polymerase occupancy and allele specific gene expression analysis in CEPH lymphoblastoid cell lines.
2014-12-31 | GSE35099 | GEO
Project description:Comparative genomic hybridization analysis for detection of recurring gene copy number variation (CNV) among a set of lung cancer mestastatic brain tumors DNA was isolated and analyzed in a two-color experiment using Cancer CGH+SNP 180Kx4 arrays from Agilent and Agilent SureScan system: Cy5-labeled specimen DNA and Cy3-labeled Agilent characterized normal human reference DNA
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