What sequencing options are available for understanding and identifying cancer hotspots?*
Whole Genome Sequencing
One can look at the entire human genome as a way to ascertain the total number of mutations, expressed as Tumor Mutational Burdon, or the number of mutations per million bases (MB). This has predictive value for treatments like immunotherapy. This same therapy was used successfully to cure former president Jimmy Carter’s stage 4 melanoma, which in August of 2015 had metastasized to his brain and liver. Three years later he is still cancer free.
However, there is no currently defined best practices for measuring tumor mutational burden, such as what sequencing depth is required, nor is there much understanding about how to group different levels of burdens, or how important burden is for different types of cancer. As a crude measure, a relatively low burden (10-100 mutations/MB) is likely to have a poor response to immunotherapy, medium burden (100-500) a mixed response and a high burden (500+) is likely to respond well. This field of research is still developing.
As an alternative to WGS, which can be prohibitively expensive, we also offer the Ampliseq Cancer Hotspot panel. This looks at 2500 specific mutations known to be linked to cancer in 50 different Oncogenes and tumor suppressing genes:
ABL1 EGFR GNAS KRAS PTPN11
AKT1 ERBB2 GNAQ MET RB1
ALK ERBB4 HNF1A MLH1 RET
APC EZH2 HRAS MPL SMAD4
ATM FBXW7 IDH1 NOTCH1 SMARCB1
BRAF FGFR1 JAK2 NPM1 SMO
CDH1 FGFR2 JAK3 NRAS SRC
CDKN2A FGFR3 IDH2 PDGFRA STK11
CSF1R FLT3 KDR PIK3CA TP53
CTNNB1 GNA11 KIT PTEN VHL
This includes genes like EGFR, known to be important in lung cancer as well as many others**. Please contact us at email@example.com or call (404) 665-2166 to learn more about our cancer hotspot screening service.
*Omega Bioservices’ offerings are for research purposes only, not diagnostics.
**Some well known oncogenes are not included however, such as BRCA1 and BRCA2 cuz patents.