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:Human pluripotent cell lines were derived from blastocyst-stage embryos and propagated in self-renewal conditions that maintain features of naive pluripotency characteristic of mouse embryonic stem cells. Genomic integrity of the HNES1 cell line was assessed with the Affymetrix CytoScan 750K array.
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: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.
Project description:Genome variation profiling of BRAFi resistant melanoma cell lines comapered to the original ones by Affymetrix CytoScan 750K microarray
Project description:The progressive mechanism of myelodysplastic syndrome (MDS) remains unknown. We report that ROBO1 and ROBO2 are identified as novel progression-related somatic mutations using whole-exome and targeted sequencing in six of 16 (37.5%) paired MDS patients undergoing disease progression. To investigated the effect of ROBO1 or ROBO2 on ROBO1/2 CN number and LOH, we employed a Cytosan 750K chip to analyze the copy-number variations (CNVs) and loss of heterogeneity (LOH) in MDS patients with ROBO1&2 mutations. Copy number and LOH analysis of Affymetrix CytoScan 750K array was performed for 14 MDS patients with ROBO1 or ROBO2 mutations
