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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 in a proband as is encountered in an undiagnosed disease scenario using a tri approach (ie, laboratories will analyze the proband and parents in an effort to determine the diagnosis in the proband). In addition to analyzing the in silico mutagenized file to identify a genetic diagnosis for the provided clinical scenario,inheritance patterns as well as pathogenic or likely pathogenic ACMG secondary findings may also be reported.
Laboratories must provide exome sequencing data files (FASTQs or unaligned BAMs) that have been generated using their current clinical sequencing protocols from one of the following Genome in a Bottle Consortium trio sources: the Ashkenazi Jewish trio (Coriell IDs GM24385, GM24149, and GM24143 or NIST RM8392) or the Han Chinese trio (Coriell IDs GM24631, GM 24694, and GM24695).All exome files must be from the same trio (Ashkenazi Jewish or Han Chinese). Specimens from the NGS, NGSST and NGSHM programs or additional Coriell/Genome in a Bottle Consortium sources 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 extremely large file sizes, a minimum allowable transfer speed 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 files will be included in the kit materials.
Three exome sequencing data file (one from each parent plus the proband), originating from your laboratory and provided to the CAP, for in silico mutagenesis. The mutagenized exome sequencing data files are to be downloaded and analyzed by your bioinformatics pipeline
The mutagenized exome sequencing files 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