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Genotyping Laboratory Certification Procedure

Introduction

The Genotyping Laboratory Certification procedure involves a series of steps that applying genotyping labs are required to perform to demonstrate their capability of providing standard, accurate data to CDCB in the required formats.
During the certification process, genotyping laboratories are required to pay a certification fee, produce a series of legal and administrative documentation and prepare and submit files similarly to already approved labs. However, each step of the procedure is run manually for the first time.
As described in the Genotyping Laboratory Quality Certification Guidelines, the CDCB Genotyping Laboratory Certification fee entitles Genotyping Laboratories up to five file submission review processes. The inability of a Genotyping Laboratory to fully comply with CDCB requirements within this number of reviews, will result in the termination of the process. In such an event, the Genotyping Lab will be required to start the process again (including the payment of the CDCB Genotyping Laboratory Certification fee).
A general scheme of the data flow between certified genotyping laboratories and CDCB is available here, in the Genomic flow for genotyping labs

Certification Process

  1. All applying genotyping labs are required to read all the materials available under GENOMIC NOMINATOR APPLICATION AND CERTIFICATION INFORMATION. In this section you'll find all the required forms, documents and contracts, together with highly useful information about the CDCB standard requirements for genotyping laboratories. If you have questions regarding any of these documents, please contact the CDCB genomics team via email.
  2. Download, complete, sign (where applicable) and submit via email to the CDCB genomics team all the required documents listed below:
    • CDCB Genotyping Laboratories - Application Form, fully compiled and signed. Note this file is provided in Microsoft Word for your convenience. The Application form will be evaluated by the CDCB Staff and an approval (or not) to continue the process will be communicated to the proponent.
      Once the Application form is approved, the proponent is required to produce:
      • Copy of ISO-17025 certification of the genotyping technique. Please note the certification MUST indicate the genotyping technology and (at minimum) be referred to animal data (e.g. not necessarily dairy cattle).
      • Appointment of personnel who will access the CDCB IT services. In case the Application Form does not cover all the people in the company that will access the CDCB IT infrastructure, the people entitled to gain access to it should be described separately.
      • Complete Standard Operating Procedures (SOP). The CDCB Genotyping Laboratories - SOP template format should be followed.
      • Signed Material License Agreement (MLA). The document is available here: CDCB Genotyping Laboratories - MLA.
      • Payment of the certification processing fee ($1000) - Note instructions and details about this payment will be received by the applicant once the Application Form is approved.
  3. Once all documentation is produced and verified, CDCB staff will generate and share detailed information about the new account and connection details (username, password, protocols, folder structure).
  4. The proponent will indicate the/a collaborating nominator to nominate the samples being tested in the certification process. CDCB requires real data to be submitted for this purpose. Genotypes must be generated using chips used in CDCB Evaluation. However, if the proponent lab intends to use a genotyping array (SNP chip) not currently accepted by CDCB, the array must undergo a SNP array validation process, detailed in the policy SNP array validation and SNP information. The lab certification process will be interrupted at this stage, until the array is successfully validated.

Requirement

  • The genotype file should contain at least 50 samples
  • At least one of the parents's genotypes are stored at CDCB
  1. Provide CDCB genomic files (Sample Sheet and Final Report files) in specified SFTP directory (all details are given in step 4).
    • CDCB staff will perform up to five file submission reviews within 3 months from the application date. The impossibility of successfully completing the submission process in accordance with these rules will lead to the termination of the process and the laboratory will have to reapply.
    • The CDCB staff will verify file formats and quality of the data provided.
  2. After the verification process is complete, report files will be placed in your "out" directory of the CDCB SFTP. The files below are some of the files you may receive in a zipped file.
  3. The proponent should check the file named DataQC_lab10-byte-date_*.csv, to quickly verify what are the QC criteria the submission passed/failed.
    • If the submission failed any criteria, the applicant should fix the problem and re-submit a new Sample Sheet (and Final Report, where applicable) file in "check" directory.
      • If you have reasons to believe that CDCB should still accept the submission as is, a comment explaining why CDCB should accept the submission should be placed at the bottom of the "DataQC_lab10-byte-date_*.csv" file before placing it in "in" directory.
    • If all QC criteria are passed, then the "DataQC_lab10-byte-date_*.csv" should be placed in the "in" directory without comments for the data to be loaded in the database.
  4. CDCB will start the automation process once the certification process is complete. This will allow all files from the genotyping laboratory to be the automatically processed.
  5. Once the certification process is complete, the CDCB staff will guide the applicant in the use of online queries.

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