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NGS UNDIAGNOSED DISORDERS-EXOME - NGSE
Analytes/procedures in bold type are regulated for proficiency testing by the Centers for Medicare & Medicaid Services (CMS).
Challenges per Shipment
Number of Shipments
Exome analysis for germline undiagnosed disorders
Two online activities per year
Additional Information/Minimum Requirements
This in silico based Survey 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 that has been generated using one of the following sources: a specimen from the NGS Survey 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 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. 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:
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 exome file will be sent closer to the ship date
One exome sequencing data file, 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