Project description:CytoScan 750K array was performed for the detection of CNV associated with the patient's phenotype CytoScan 750K array was performed according to the manufacturer's directions on DNA extracted from peripheral blood sample.
Project description:BACs-on-Beads (BoBs) assay and Copy Number Variation Sequencing (CNV-Seq) are two frequently used methods in today’s prenatal diagnosis. Several researches studies were conducted to investigate the performance of each approach, but they were never compared side by side. This dataset is intended to be used as the 'gold standard dataset' for the validation of BoBs/CNV-seq test reasults on 10 amniotic fluid samples with pathogenic fetal CNVs.
Project description:A diploid 46(XX) human embryonic stem cell (HESC) line affected by Spinal muscular atrophy type 1 (SMA) due to homozygosity for a common deletion in the SMN1 gene was derived. By characterizing the methylation status of three different imprinted loci (MEST, SNRPN and H19) and carrying out genome-wide SNP analysis, we provide evidence that this cell line was established from the activation of a mutant haploid oocyte through parthenogenesis, resulting in homozygote diploidization of the entire genome. Affymetrix CytoScan 750K array analysis was performed according to the manufacturer's directions on DNA extracted from tissue culture. Copy number and LOH analysis of the Affymetrix CytoScan 750K array was performed for the SMA HESC line.
Project description:Genome variation profiling of BRAFi resistant melanoma cell lines comapered to the original ones by Affymetrix CytoScan 750K microarray
Project description:BackgroundThe well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveries using SNP data. Even so, they were not able to explain the full heritability of complex diseases. Now, other structural variants like copy number variants or DNA inversions, either germ-line or in mosaicism events, are being studies. We present the R package affy2sv to pre-process Affymetrix CytoScan HD/750k array (also for Genome-Wide SNP 5.0/6.0 and Axiom) in structural variant studies.ResultsWe illustrate the capabilities of affy2sv using two different complete pipelines on real data. The first one performing a GWAS and a mosaic alterations detection study, and the other detecting CNVs and performing an inversion calling.ConclusionBoth examples presented in the article show up how affy2sv can be used as part of more complex pipelines aimed to analyze Affymetrix SNP arrays data in genetic association studies, where different types of structural variants are considered.
Project description:Autism spectrum disorder (ASD) is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number variants (CNV). The aim of the study was to identify new candidate genes for ASD in the studied cohort of ASD-diagnosed patients. We used chromosomal microarray analysis (CMA) - a Cytoscan HD (Affymetrix, Santa Clara, CA, USA) to detect CNV in 87 ASD patients and their relatives and evaluated their clinical significance. Pathogenic and likely pathogenic mutations were identified by CMA in 8 and 9 ASD patients, respectively. CMA revealed 89 rare CNV: 8 pathogenic, 12 designated VOUS - likely pathogenic, 12 VOUS - uncertain, and 57 VOUS - likely benign or benign. CNV (pathogenic/VOUS-likely pathogenic/VOUS - uncertain) overlapping the same gene in more than one patient were observed in DOCK8 gene and PARK2 gene. This work presents new evidence about the possible roles of PARK2 and DOCK8 in the etiology of ASD, and suggests CTNNA2 as a candidate gene for ASD risk.
Project description:The Affymetrix CytoScan 750K Array chip contains 200000 SNP markers and 550000 CNV markers, distributed across the entire human genome at an average density of approximately 1 marker/4kb (not covering all loci of the entire chromosome genome). It is used to detect clinically significant chromosomal microdeletions/microduplications, chromosomal subtelomer deletion syndrome, and other abnormal chromosomal copy number variations (CNVs) as well as loss of heterozygosity (LOH). In a case study of Zhangzhou Municipal Hospital of Fujian Province, copy number variation detection was performed on a fetus with Silver-Russell syndrome using CytoScan 750K Array chip, and variations in the corresponding region were identified.