Project Workflow

Project Initiation
PI receives letter of approval to initiate study from Executive Director, CIDR Board of Governors
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CIDR Project Manager sends Project Initiation Documents & Instructions to PI
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Signed CIDR Service Agreement received from PI
Completed CIDR Contact Authorization Form received from PI
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Project Manager sends plating supplies and instructions to sites
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Prior to sending samples to CIDR, Institutional Certification (IC) Letter(s) for data sharing must be approved by the NIH funding institute
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Project Manager receives completed files from sites
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Completed files are reviewed by Project Manager. Any issues flagged are reported back to the site(s) for resolution; new submission of files may be required.
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Project Manager approves finalized files for sample shipment
Sample Evaluation & Processing
Samples shipped to CIDR, after approval has been received from NIH funding institute
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Upon receipt of sample shipment, CIDR Project Manager will complete validation checks to ensure there are no discrepancies between the shipment and the completed files received.
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2D barcodes imprinted on each physical tube will be associated with sample information in our LIMS upon receipt.
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Sample QC evaluation is completed
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Problematic samples flagged during sample QC are reported back to site for resolution. Replacement aliquots or new subjects can be sent.
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Once all problem samples have been resolved and/ or replacements received, sample tubes are rearrayed for production processing. The plate map design is determined after consultation with the PI group in order to reduce batch effects.
Data Generation & QC
Sample and plate level QC checks performed daily on all data generated
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Samples are repeated one time if data fails quality threshold
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Final dataset undergoes thorough sample and variant level QC review and documentation
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CIDR must have approval from the NIH funding institute to release data to the PI. In most instances, the IC will require that phenotypic data and supporting documents be submitted to dbGaP prior to data release
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The final data release and documentation are made available through a secure Aspera server.
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For GWAS studies, data cleaning and imputation are completed by CIDR Genetic Analysts in consultation with the PI group.
For sequencing studies, raw data files (CRAM), genotype files ( VCF) and metadata are uploaded to dbGaP by CIDR.
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Raw data files (i.e. .idat), genotype files (i.e. PLINK or VCF), data cleaning files, QC reports and the imputed dataset are all uploaded to dbGaP