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Analytes/procedures in bold type are regulated for proficiency testing by the Centers for Medicare & Medicaid Services (CMS).

Analyte/Procedure Challenges per Shipment Number of Activities
Somatic in silico mutagenized sequencing file 1 Two online activities per year

Additional Information/Minimum Requirements

  • This in silico program is designed to optimize bioinformatics pipelines, augment validations, and assist with pipeline verification after changes to NGS/ bioinformatics processes. This is not traditional proficiency testing and no results will be returned to the CAP; information regarding the variants introduced will be sent along with the mutagenized file.
  • Laboratories must provide a gene panel or exome sequencing data file that has been generated using one of the following sources: a specimen from the NGS-Germline Survey program or from one of the following NIST Reference Material cell lines: RM 8398 (NA12878), RM 8391, RM 8392, or RM 8393. Specimens from the NGSST and NGSHM Surveys cannot be used for this program.
  • FASTQs or unaligned BAMs must be submitted along with a BED file describing the regions targeted and interrogated by your laboratory.
  • The mutagenized sequencing file will contain up to 75 somatic variants (depending on the size of the panel/exome provided) at allele fractions from 3% to 99% (higher allele fraction to mimic loss of heterozygosity or homozygosity) and will include:
    • Single nucleotide variants
    • Insertions, deletions, delins, and/or duplications ranging from 1-100bp (1-15bp, 15-50bp, 51-100bp)
    • Copy number variants of single exons, partial or whole genes, and/or partial or whole chromosomes
    • DNA fusions (if a laboratory indicates that they detect such structural rearrangements, if the rearrangements are specified and submitted in the BED file, and there is appropriate intronic coverage)
    • Microsatellite instability at mono nucleotide tracts included in the submitted capture design
    • Simulated artifactual sequence
    All variants will be modeled based on actual somatic mutations from the COSMIC and/or cBIOPORTAL databases
  • Laboratories can transfer and download files from most modern browsers/ operating systems. For the most up-to-date information on system requirements, go to and click System Requirements, located at the bottom of the home page.
  • Due to the extremely large file sizes, a minimum allowable transfer speed of 40 Mbps or higher is needed to ensure successful transfer of your laboratory’s sequencing files to the CAP. Contact your IT department for allowable transfer speeds to determine estimated transfer time and browser/operating system access.
  • Laboratories must comply with all of the above requirements to participate in this program. Additional information and steps to provide your laboratory’s sequencing file will be included in the kit materials.

Program Information

  • One panel or exome sequencing data file, originating from your laboratory and provided to the CAP, for in silico mutagenesis
  • The mutagenized panel or exome sequencing data file is to be downloaded and analyzed by your laboratory bioinformatics pipeline and compared with the variant information provided by CAP
  • Your CAP shipping contact will be notified via email when the activity is available

Shipping Schedule

  • Shipment A: June 7
  • Shipment B: November 22

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