CPT Knowledgebase - Oct 12, 2016

What is the appropriate CPT code to report the next generation sequencing (NGS) and analysis of data described in the following scenario? A patient sample has been extracted and prepared for exome sequencing through a next-generation sequencer that will produce genetic data for over 3,000 targeted clinical genes. The output is analyzed for NGS artifacts (false positives), coverage (accuracy), and sensitivity (false negatives). A clinical test is ordered for a subset of 300 genes within the total of 3,000 genes, in which the Guanidinoacetate N-Methyltransferase (GAMT) gene, a gene not listed in the Molecular Pathology Table, with 5 exons (NM_001258332) is included. Each of the variants found in the GAMT gene, as well as in the other 299 genes, is analyzed in a curation procedure to call each variants pathogenicity.

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