PGLNext


Related Gene(s): EGLN1, FH, KIF1B, MAX, MEN1, NF1, RET, SDHA, SDHAF2, SDHB, SDHC, SDHD, TMEM127, VHL

PGLNext is a next generation sequencing panel that simultaneously analyzes 14 genes associated with an increased risk of developing paragangliomas (PGLs) and/or pheochromocytomas (PCCs).

PGLNext analyzes 14 genes (listed above). All genes are evaluated by next generation sequencing (NGS) or Sanger sequencing of all coding domains, and well into the flanking 5’ and 3’ ends of all the introns and untranslated regions. For EGLN1, only missense variants in the catalytic domain (codons 188-418) are routinely reported. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Additional Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection. Potentially homozygous variants, variants in regions complicated by pseudogene interference, and variant calls not satisfying depth of coverage and variant allele frequency quality thresholds are verified by Sanger sequencing.

Gross deletion/duplication analysis is performed for the covered exons and untranslated regions of all sequenced genes (excluding EGLN1) using read-depth from NGS data with confirmatory multiplex ligation-dependent probe amplification (MLPA) and/or targeted chromosomal microarray.

Single gene testing and genetic testing for a known familial mutation can also be ordered. If there is a previously identified mutation in a family member, please include a copy of the test report with the requisition form.


Specimen Requirements

  • Whole blood: Two 4.5 mL EDTA tubes (lavender top)
  • For transfusion patients, please wait at least 2 weeks after a packed cell/platelet transfusion, and at least 4 weeks after a whole blood transfusion prior to blood draw for testing
  • For chemotherapy patients, the DNA quality may be affected if patient has received chemotherapy within the last 120 days. Sema4 may request an additional specimen if DNA quality is insufficient

  • Saliva: 2 mL of freshly-collected saliva in an Oragene container per kit’s specific instructions
  • Fill up to black line with 2 mL of saliva and close the lid. Once the lid is closed, it automatically adds 2 mL of buffer, for a total volume of 4 mL
  • Please note that 2 containers are required for all pediatric saliva testing kits

Saliva and blood are the most common specimen types we receive. For questions regarding other specimen types and requirements for patients with a significant medical history (including allogenic transplant and hematological diseases), please call us at 203-483-3459 to discuss before sample submission.


Ordering Information

Shipping

  • Ship at room temperature

Turnaround Time

  • 14-21 days from receipt of specimen
  • If required by insurance, benefits investigation and pretest genetic counseling may delay test results

Related Tests


Resources

Hereditary Cancer Requisition
Hereditary Cancer Genetic Testing Consent