- GENOMICS AND COMPUTATIONAL ANALYSIS FACILITY The Genomics and Computational Analysis Facility (GCAF) brings together two previously-separate AECC Genomics and Bioinformatics shared resources into one seamless service, in order to make these elements more accessible to researchers and to promote operational efficiencies. This restructuring reflects the traditional close interactions between these facilities, along with the High Performance Computing Core (HPC) and the Biostatistics shared resources. The GCAF provides genomics and epigenomics technologies with bioinformatics support to AECC researchers, achieved in part by means of an Integrated Assay Portal, allowing for a simplified interaction with a growing and complex list of services, many of which are performed in-house. These encompass massively parallel sequencing (MPS) technologies, including whole exome sequencing (WES), RNA-seq, ChIP-seq, ATAC-seq, miRNA-Seq, and Mito-seq. Additionally, when needed, the New York Genome Center (NYGC) in Manhattan, of which Einstein is a founding member, provides Illumina HiSeq X and NovaSeq technologies for whole genome sequencing approaches. The GCAF also develops novel technologies to the AECC community. These include a sequencing-based HELP-tagging assay, the BGT- tagging assay for hydroxymethylation of DNA, the MAD-seq assay and an associated analytical approach for mosaic aneuploidy detection using sequencing, whole genome bisulphite sequencing using the Illumina HiSeq X system (X-WGBS), and the SeqCap Epi assay for targeted bisulphite sequencing, co-developed with Roche- NimbleGen. The facility has recently implemented single cell RNA-seq and single cell western blotting as new technologies. Once data are generated, they are managed in the GCAF's Wiki-based Automated Sequence Processor (WASP) system, which hosts automated analytical pipelines for many of the more commonly-used assays. Access to the data is controlled, allowing their complete security, with the flexibility to add collaborators to projects rather than requiring transfer of the data elsewhere. For more customized analytical services, the GCAF offers fee-for-service bioinformatics consultation, from the time of project design through to data uploads to public servers at the time of publication. Specialized analytical services are also available through the NYGC on a fee-for-service basis. What had been separate genomics and epigenetics/sequencing facilities are now being co-located to facilitate cross-training and load sharing. The new GCAF represents the maturation of services that have been offered separately over the last decade, and is capable of offering the most powerful assays and analyses currently available in cancer research.
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