POMC/PCSK1/LEPR Companion Diagnostic (CDx) Panel

For questions about ordering, please call PreventionGenetics at 1-844-513-3994

The POMC/PCSK1/LEPR CDx Panel is a next generation sequencing (NGS)-based in vitro diagnostic test that analyzes genomic DNA isolated from blood or saliva. Specimens used with the test are K2EDTA blood collected using certain indicated K2EDTA blood collection devices and saliva collected using ORAcollect-Dx™ OCD 100 devices. The test detects germline nucleotide substitutions, short insertions and deletions, and copy number variants (CNVs) within the following 3 genes:

• Pro-opiomelanocortin (POMC)
• Proprotein Convertase Subtilisin/Kexin type 1 (PCSK1)
• Leptin Receptor (LEPR)

The test is a companion diagnostic device intended to select adult and pediatric patients 6 years of age and older who have obesity and certain variants in POMC, PCSK1, or LEPR genes for treatment with IMCIVREE® (setmelanotide) in accordance with the approved therapeutic product labeling. The POMC/PCSK1/LEPR CDx Panel is a single-site assay performed at PreventionGenetics, LLC (Marshfield, WI).

Contraindications

There are no known contraindications.

Warnings and Precautions

Therapeutic decisions must be based on the independent medical judgement of the treating physician, taking into consideration the test results and all applicable information concerning the patient’s condition, clinical history, and other findings.

• For in vitro diagnostic use.
• For prescription use only. This test must be ordered by a qualified medical professional in accordance with clinical laboratory regulations. The classification and interpretation of all variants identified reflects the current state of scientific understanding at the time the result report is issued.
• When NGS does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles. Occasionally, a patient may carry an allele, which does not capture or amplify, due for example to a large deletion or insertion.
• Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.
• The POMC/PCSK1/LEPR CDx Panel is not intended to detect mosaic variants.
• We cannot be certain that the reference sequences are correct. Genome build hg19, GRCh37 (Feb2009) is used as reference for this assay.
• Insertions and deletions larger than 18 base pairs in the variable number tandem repeat (VNTR) region in exon 3 (NM_000939.3) of the POMC gene with coordinates chr2:25,384,457-25,384,474 (GRCh37/hg19) containing repeated sequence “AGCAGCGGC” were not validated with this device and will not be reported.
• Two runs of intronic mononucleotide repeats (e.g., (A)n or (T)n) are excluded from the analysis. The excluded regions reside in LEPR (NM_002303.5) intron 4 (chr1:66,037,998-66,038,001) and post-coding (chr1:66,096,092-66,096,098) (GRCh37/hg19).
• Balanced translocations or inversions within a targeted gene, or large unbalanced translocations or inversions that extend beyond the genomic location of a targeted gene are not detected.
• In nearly all cases, our ability to determine the exact copy number change within a targeted gene is limited. In particular, when we find copy excess within a targeted gene, we cannot be certain that the region is duplicated, triplicated, etc. In many duplication cases, we are unable to determine the genomic location or the orientation of the duplicated segment with respect to the gene. In particular, we often cannot determine if the duplicated segment is inserted in tandem within the gene or inserted elsewhere in the genome. Similarly, we may not be able to determine the orientation of the duplicated segment (direct or inverted), and whether it will disrupt the open reading frame of the given gene.
• The performance of the POMC/PCSK1/LEPR CDx Panel was assessed for single nucleotide variants (SNVs), insertions and deletions <50 base pairs, and a single copy number variant (CNV; a homozygous deletion in exons 6, 7, and 8 in the LEPR gene). Due to limitations in the POMC/PCSK1/LEPR CDx Panel for CNV detection, any CNV duplication or deletion > 50 base pairs reported by the device may not be accurate other than the homozygous deletion in exons 6, 7, and 8 in the LEPR gene.
• The accuracy of the POMC/PCSK1/LEPR CDx Panel was not assessed for PCSK1 exon 2 and LEPR exon 7.
• The POMC/PCSK1/LEPR CDx Panel is for use only with whole blood collected in K2EDTA blood collection tubes or saliva specimens collected in DNA Genotek ORAcollect Dx™ OCD-100 saliva collection devices.
• The assay has been validated with the Illumina NovaSeq6000.
• By definition, there is not sufficient scientific information available to make a pathogenicity assignment to variants of uncertain significance (VUS/VOUS). All variants and these variants in particular could change classification as new scientific information becomes available, which may impact patient eligibility for IMCIVREE (setmelanotide) injection.
• The pathogenicity assignments determined with the POMC/PCSK1/LEPR CDx Panel are intended to predict response to therapy with setmelanotide and are not intended for diagnostic purposes.

The POMC/PCSK1/LEPR CDx Panel is a NGS assay for the detection of germline variants in 3 genes (POMC/PCSK1, and LEPR) developed and implemented under Clinical Laboratory Improvement Amendments (CLIA) regulations and standards at PreventionGenetics, an ISO 15189 certified and CLIA/CAP (College of American Pathologists) accredited laboratory. This assay has been utilized by Rhythm Pharmaceuticals for the genetic confirmation of POMC/PCSK1/LEPR deficiency obesity in clinical studies.

Whole blood and ORAcollect-Dx™ OCD-100 assisted saliva samples are collected and shipped to the PreventionGenetics laboratory (Marshfield, WI). The laboratory utilizes NGS technologies to cover the full coding regions of the genes plus ~10 bases of noncoding DNA flanking each exon. DNA is captured using an optimized set of DNA hybridization capture probes and then sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA). Capture probes are custom designed by PreventionGenetics and cover all coding exons in all transcripts of each gene plus any deep intronic or intergenic regions that have been reported to harbor pathogenic variants. Variant interpretations are based on the 2015 American College of Medical Genetics and Genomics (ACMG)/Association of Molecular Pathology (AMP) guidelines (Richards 2015). Variants interpreted as pathogenic (P), likely pathogenic (LP), or VUS (or VOUS) are reported.

• Whole blood specimens are collected via standard venipuncture into an FDA-cleared K2EDTA collection tube and shipped to the laboratory ambient or frozen in the original container. A refrigerated gel pack must be included with blood specimens shipped at ambient temperature. Note that blood specimens previously frozen but which arrive thawed at the laboratory are unacceptable.
• ORAcollect-Dx™ OCD-100 assisted saliva kit (Genotek) and shipped to the laboratory under ambient conditions. We are currently unable to supply OCD-100 Sample Kits for this testing.

Testing Strategy

The test is a companion diagnostic device intended to select adult and pediatric patients 6 years of age and older who have obesity and certain variants in POMC, PCSK1, or LEPR genes for treatment with IMCIVREE® (setmelanotide) in accordance with the approved therapeutic product labeling.