Related Gene(s): AIP, ALK, APC, CDKN1B, CDKN2A, DICER1, EPCAM, LZTR1, MEN1, MLH1, MSH2, MSH6, NBN, NF1, NF2, PHOX2B, PMS2, POT1, PRKAR1A, PTCH1, PTEN, SMARCA4, SMARCB1, SMARCE1, SUFU, TP53, TSC1, TSC2, VHL
BrainTumorNext is a next generation sequencing panel that simultaneously analyzes 29 genes associated with increased risk for brain tumors and other cancers/tumors.
BrainTumorNext analyzes 29 genes (listed above). All genes (excluding EPCAM) 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. The inversion of coding exons 1-7 of the MSH2 gene is detected by NGS and confirmed by PCR and agarose gel electrophoresis. For ALK, only variants located within the kinase domain (c.3286-c.4149) are routinely reported. For PHOX2B, the polyalanine repeat region is excluded from analysis. 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 using read-depth from NGS data with confirmatory multiplex ligation-dependent probe amplification (MLPA) and/or targeted chromosomal microarray. For EPCAM, only gross deletions encompassing the 3’ end of the gene are reported. For APC, all promoter 1B gross deletions as well as single nucleotide substitutions within the promoter 1B YY1 binding motif (NM_001127511 c.-196_c.-186) are analyzed and reported. Gross deletion/duplication analysis of PMS2 is performed using MLPA. If a deletion is detected in exons 13, 14, or 15 of PMS2, double stranded sequencing of the appropriate exon(s) of the pseudogene, PMS2CL, will be performed to determine if the deletion is located in the PMS2 gene or pseudogene.
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.
- 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.
- Ship at room temperature
- 14-21 days from receipt of specimen