A: CNVs are detected using an in-house-developed and validated tool (VisCap) that will range from single exon to whole gene deletions or duplications. All CNVs will be confirmed, using a secondary assay (droplet digital PCR), ensuring maximum accuracy. Please note that this service will only be included for samples whose NGS results meet quality requirements for copy number calling. About 50% of samples will not meet these criteria and for those, only single nucleotide variants and small insertions and deletions will be returned. Reports will note when CNV analysis was not possible.

A: CNV analysis is currently included as part of all targeted next-generation (NGS) sequencing gene panels at no additional cost. These currently include the Pan Cardiomyopathy Panel and all sub-panels, the Expanded RASopathy Panel, the OtoGenome Test for Hearing Loss, as well as the PulmoGene Panel.

A: Approximately 50% of samples will not meet the quality criteria and for those, only single nucleotide variants and small insertions and deletions will be returned.

A: Unfortunately, because this service utilizes the next-generation sequencing data, this testing is not available as a stand-alone test.

A: ....the NGS targeted panel was previously tested and specimen is eligible per dates? - No additional specimen maybe required. A written request should be forwarded to the LMM to initiate CNV assessment.
    ....the NGS targeted panel was ordered on or after May 28, 2013? – No specimen or additional documentation required as this will now be part of our routine NGS service.
    ....patient testing was completed prior to eligibility dates? - A new specimen maybe required, and will be assessed on a case by case basis. Sample requirements are the same as for other NGS test requests. Contact the laboratory for more instructions.

A: Please contact the Laboratory for Molecular Medicine at (617) 768-8500 or email us at LMM@partners.org.