Project description:Interventions: Genomic test CANCERPLEX-JP OncoGuide NCC oncopanel system FndationONe CDx genome profile GUARDANT360 MSI Analysis System BRACAnalysis
Primary outcome(s): Development of genome database
Study Design: Single arm Non-randomized
Project description:The study is intended to collect specimens to support the application of genome analysis technologies, including large-scale genome sequencing. This study will ultimately provide cancer researchers with specimens that they can use to develop comprehensive catalogs of genomic information on at least 50 types of human cancer. The study will create a resource available to the worldwide research community that could be used to identify and accelerate the development of new diagnostic and prognostic markers, new targets for pharmaceutical interventions, and new cancer prevention and treatment strategies. This study will be a competitive enrollment study conducted at multiple institutions.
Project description:Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome we investigated 130 regions which we hypothesized as candidates for novel genomic disorders 1. We tested 290 patients with mental retardation by BAC array CGH, identifying sixteen pathogenic rearrangements, including four patients with de novo microdeletions of 17q21.31. Using oligonucleotide arrays we refined the breakpoints of this microdeletion, defining a 478 kb critical region containing six genes that were deleted in all four cases. The breakpoints of this deletion, and of four other pathogenic rearrangements in 1q21.1, 15q13, 15q24 and 17q12 were mapped to flanking segmental duplications, suggesting that these are also sites of recurrent rearrangement. In common with the 17q21.31 deletion, these breakpoint regions are also sites of copy number polymorphism in controls, indicating that these may be inherently unstable genomic regions. Keywords: BAC comparative genomic hybridization of individuals with mental retardation and congenital anomalies
Project description:Discovering useful genetic resources based on multi-omics of useful microorganisms for agriculture and food and developing technology to enhance value (KAP220309)
Project description:The contribution to genetic diversity of genomic segmental copy number variations (CNVs) is less well understood than that of single-nucleotide polymorphisms (SNPs). While less frequent than SNPs, CNVs have greater potential to affect phenotype. In this study, we have performed the most comprehensive survey to date of CNVs in mice, analyzing the genomes of 42 Mouse Phenome Consortium priority strains. This microarray comparative genomic hybridization (CGH)-based analysis has identified 2094 putative CNVs, with an average of 10 Mb of DNA in 51 CNVs when individual mouse strains were compared to the reference strain C57BL/6J. This amount of variation results in gene content that can differ by hundreds of genes between strains. These genes include members of large families such as the major histocompatibility and pheromone receptor genes, but there are also many singleton genes including genes with expected phenotypic consequences from their deletion or amplification. Using a whole-genome association analysis, we demonstrate that complex multigenic phenotypes, such as food intake, can be associated with specific copy number changes. Keywords: comparative genomic hybridization
Project description:Comparative genomic hybridization (CGH) analysis of CiPSCs (clone CiPS-57 and CiPS-58) and OSKM-iPSCs. C57BL/6 mouse embryonic fibroblasts (MEFs) genome DNA as a reference. No consistent copy number variations (CNVs) among CiPSCs and OSKM-iPSCs.