Analytes/procedures in bold type are regulated for proficiency testing by the Centers for Medicare & Medicaid Services (CMS).
Challenges per Shipment
Number of Activities
In silico mutagenized sequencing file(s) containing somatic variants of relevance in hematologic malignancies - platform agnostic
Two online activities per year
This is a platform agnostic hybrid in silico proficiency testing and validated materials program for laboratories performing targeted NGS of cancer genes or mutational hotspots in solid tumors. This program requires the submission of the laboratory's sequencing file, which undergoes mutagenesis and is returned to the laboratory for bioinformatics analysis. The proficiency testing portion of this program is designed to complement and augment NGS somatic variant wet bench proficiency testing programs by testing for a greater diversity of variants with a wide range of variant allele fractions (VAF) while the validated materials portion is designed to optimize bioinformatics pipelines, augment validations, and assist with pipeline verification after changes to NGS/bioinformatics processes.
Laboratories must provide a gene panel sequencing data file (FASTQ or unaligned BAM) that has been generated using their current clinical sequencing protocols from one of the following sources: A specimen from the NGS - Germline program or from one of the following NIST Reference Material cell lines: RM 8398 (NA12878), RM 8391, RM 8392, or RM 8393. FASTQs or unaligned BAMs must be submitted along with a BED file describing the regions targeted and interrogated by your laboratory. Specimens from the NGSST and NGSHM programs or additional Coriell/NIST Reference Material cell lines cannot be used for this program.
Laboratories can transfer and download files from most modern browsers/ operating systems. For the most up-to-date information on system requirements, go to cap.org and click Browser and Operating System Requirements, located at the bottom of the homepage.
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.
Laboratories will be asked to identify somatic single nucleotide variants and small (1-15bp) insertions, deletions, duplications, and deletions-insertions (delins) in a subset of hematologic malignancies mutational hotspots/genes with VAF potentially as low as 5%. Laboratories will be required to submit results of the variants identified.
The sequencing file will contain up to 75 custom somatic variants that are tailored to the specific assay submitted (depending on the size of the panel provided) at VAF from 3% to 99% (higher allele fractions 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,16-50bp, 51-100bp)
All variants will be modeled based on actual somatic mutations from the COSMIC and/or cBioPortal databases. This portion of the program 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.
For panel-specific hematologic malignancies bioinformatic proficiency testing challenges, refer to the NGSB3 program
One panel sequencing data file (FASTQ or unaligned BAM), originating from your laboratory and provided to the CAP, for in silico mutagenesis
Sequencing files containing somatic variants to be downloaded and analyzed by your laboratory bioinformatics pipeline
Two online activities per year; your CAP shipping contact will be notified via email when the activity is available