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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 Shipments
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 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:
    • Internet Explorer (IE) 11
    • Safari - The two latest, released versions on Mac OS X and iOS
    • Firefox - The two latest, released versions
    • Chrome - The two latest, released versions
    • Windows - 7 (32-bit and 64-bit), 8 (64-bit), and 10 (32-bit and 64-bit)
  • Due to the extremely large file sizes, a minimum allowable transfer speed of 20Mbps will be needed to ensure the successful transfer of sequencing files between laboratories and CAP; however, 40 Mbps and higher is strongly recommended. Note: Laboratories should check with their technology 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 regarding how and where to provide your laboratory’s sequencing file will be sent closer to the ship date.

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 10
  • Shipment B: November 25

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