Project description:Illumina human Omni5Exome arrays were used to investigate CNVs in Sѐzary syndrome tumours as part of a larger study involving whole exome sequencing of the same samples and targeted resequencing of a further cohort.
2016-07-22 | GSE80650 | GEO
Project description:Whole Exome Sequencing in patient with Incomplete Alagille Syndrome
Project description:Illumina human Omni5Exome arrays were used to investigate CNVs in SÑzary syndrome tumours as part of a larger study involving whole exome sequencing of the same samples and targeted resequencing of a further cohort. 16 Samples underwent SNP array including 10 tumour/gDNA matched samples that also underwent whole exome sequencing, public databases were used as further control data for calling CNVs.
Project description:The whole exome sequencing experiment is part of the study: “Analysis of 5-azacytidine resistance models reveals a set of targetable pathways”. In the study we generated myelodysplastic syndrome/acute myeloid leukemia (MDS/AML) OCI-M2 cell lines as well as patient-derived bone marrow cell lines that are resistant to hypomethylating therapy by 5-azacytidine (AZA). By integrated analysis of expression and mutation data obtained from these samples we have identified multiple signaling pathways whose modulation by specific small molecule inhibitors significantly block proliferation of AZA-resistant cell lines without increasing their sensitivity to AZA. The understanding of the molecular mechanisms which characterize the AZA-R phenotype can be used for broadening therapeutic options at progressing states during AZA therapy.
Project description:HLA Class I immunopeptides were affinity purified by W6/32 antibody and analyzed by Orbitrap Fusion Lumos with FAIMS. Personalized database which includes patient-specific somatic mutations obtained from whole exome sequencing (WES) data was used for database search. Identification results were filtered at 1% FDR thresholds by searching against a randomized decoy database using Proteome Discoverer 2.4 (Sequest HT).
