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Cancer Personalized Genomics

Genetic analysis of tumors to offer targeted therapies to patients with presence of certain gene markers is within the realm of personalized genomics for Cancer. Starting with the use of Herceptin for breast cancers positive for mutations in the HER2 gene, genetic analysis of tumors has resulted in the development and application of many drugs for specific cancers with other biomarkers. A summary of a few of the cancers with approved targeted drugs is tabulated below. This table is adapted from information captured from NCI (NCI Cancer site). However, it does not capture data on the stage (early onset, metastasis).

Solutions from

  • Cancer Biomarker
  • Next Generation Sequencing (NGS)

Evaluation of the markers which are “Actionable” or “Druggable”, namely, those for which a therapy option exists, can be carried out using Sanger sequencing or Real-Time PCR where one or few genes mutation need to be studied.

Cancer is a heterogeneous disease and while initial therapy may reduce the tumor load or result in short term remission, newer foci of metastasis due to other gene mutations are known to arise and drive new tumor formation. Hence, it is not uncommon for patients to undergo normal regimens of chemotherapy followed by other targeted therapies for recurrences.

Solutions for Biomarker analysis looking at protein, epigenetic, real-time PCR and Sanger sequencing methodologies can be found here: Read more

Other information: NCI info on targeted therapy

Type of Cancer Approved Drug (Generic name) Genetic Markers
Adenocarcinoma of the stomach or gastroesophageal junction Trastuzumab (Herceptin®)
 Ramucirumab (Cyramza®) 
Her2 positive cancers
EGFR+, ALK mutations
Bladder cancer Atezolizumab (Tecentriq™)
nivolumab (Opdivo®)  
 pembrolizumab (Keytruda®)
EGFR+, ALK mutations
MSI-H (metastatic instability high), dMMR (mismatch repair) and BRAF+/- mutation
PDL-1 protein, MSI-H, dMMR & PDL+ (EGFR-/ALK-)
Breast cancer
(Visit NCI for additional drug info for this category)
Everolimus (Afinitor®)
toremifene (Fareston®)
Trastuzumab (Herceptin®)
fulvestrant (Faslodex®)
anastrozole (Arimidex®)
exemestane (Aromasin®)
lapatinib (Tykerb®)
letrozole (Femara®)
pertuzumab (Perjeta®)
ado-trastuzumab emtansine (Kadcyla®)
Her2-
Estrogen Receptor+ or unknown ER status
(Human epidermal growth factor receptor)HER-2+
HR (estrogen or progesterone receptor)+/HER-
HR+ or HR status unknown
Estrogen Receptor ER+
HER2+, HER2&HR+
HR+, HER2+&HR+, HR+ or unknown HR
HER2+
HER2+

Next Generation Sequencing (NGS) is a more powerful tool for such analysis and using the targeted approach (such as Ion Torrent Ampliseq Cancer Panels) to navigate commonly known tumor-causing genetic mutations works with limited biopsy (Formalin fixed paraffin embedded (FFPE) or frozen fixed-FF) samples:  (Reference: Lolkema M.P et al)

The benefits of using the Ion Torrent chemistry as summarized by the study by Lokema et al are:

  1. Ability to use 10ng or less DNA to detect low frequency variants (50-200 ngs for other technologies)
  2. Faster turnaround time
  3. Multiple chip options to select various sample throughput for analysis
  4. 500-1000x coverage (for example needed for KRAS and NRAS) for cancers such as colorectal
  5. Reliable recovery of data at Variant allelic frequencies (VAF) of 2% (typically 5-15% for other technologies) 
  6. Manageable and actionable data reported using the Ion torrent browser without having to handle too much data as in whole genome methods

The typical NGS workflow can be deployed with dedicated Oncomine Cancer panels on FFPE or FF samples from biopsied tumors. Read More on: Reagents for isolation of DNA from FFPE.

Ion AmpliSeq™ Comprehensive Cancer Panel Provides coverage of half (409 genes) from
Cancer gene census by Wellcome Trust Sanger Institute
 
Ion AmpliSeq™ RNA Cancer Panel
Serves as the RNA complement to the Ion Amliseq Cancer Hotspot Panel v2 with 50 oncogenes and tumor suppressor genes from COSMIC database
Oncomine™ Comprehensive Assay v3C Consists of 161 genes for drug discovery research and clinical trial research program
Ion AmpliSeq™ Cancer Hotspot Panel v2 Designed with 207 amplicons from 2800 COSMIC mutations from 50 oncogenes and tumor suppressor genes

Newer methods that use Cell free DNA from liquid biopsies and plasma can be adapted for patients unable to undergo tumor biopsies or for non-solid tumors. Read more and below.

Oncomine™ Pan-Cancer Cell-Free Assay (Cat no: A37664) is a 52 gene panel for use with plasma samples to study common cancer hotspot and insertions-deletions (indels) in ALK, BRAF etc., Gene fusions of ALK, BRAF and others, Copy number variations (CNV) in CCND1, EGFR and tumor suppressor genes like TP53, APC, PTEN and others for various cancers (Bladder, brain, colorectal, cervical, thyroid, prostate, melanoma, lung, liver, kidney, esophageal, gastric, Head and neck).

Additional citation:  Hormone Receptor & HER2 in breast cancer

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