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NGS UNDIAGNOSED DISORDER - TRIO ANALYSIS - NGSET
Analytes/procedures in bold type are regulated for proficiency testing by the Centers for Medicare & Medicaid Services (CMS).
Challenges per Shipment
Number of Activities
Trio (parents and proband) exome analysis for germline undiagnosed disorders
Two online activities per year
Additional Information/Minimum Requirements
This in silico based program will assess the ability of the laboratory to identify germline variants responsible for a provided clinical phenotype as is encountered in an undiagnosed disease scenario. In addition to analyzing the in silico mutagenized file to identify a genetic diagnosis for the provided clinical scenario, pathogenic or likely pathogenic ACMG secondary findings may also be reported.
Laboratories must provide an exome 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 NIST Reference Material cell lines: RM 8398 (NA12878), RM 8391, RM 8392, or RM 8393. Specimens from the NGSST and NGSHM programs or additional Coriell/NIST Reference Material cell lines 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. Additionally, >90% of exons targeted and interrogated by your laboratory must have a minimum read coverage of 10X.
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 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 exome file will be included in the kit materials.
Three exome sequencing data file (1 from each parent plus the proband), originating from your laboratory and provided to the CAP, for in silico mutagenesis. The mutagenized exome sequencing data file is to be downloaded and analyzed by your bioinformatics pipeline
The mutagenized exome sequencing file will be accompanied by a clinical history, relevant laboratory data, and results of ancillary studies, where appropriate
Your CAP shipping contact will be notified via email when the activity is available