sing both immunomagnetic enrichment/fluorescence-activated cell sorting (IE/FACS) and long fragment read (LFR) technologies, researchers detected potentially targetable mutations from just five circulating tumor cells (CTCs) in a patient with metastatic breast cancer, showing the potential of advanced whole genome sequencing (WGS) to guide precision medicine (Cancer Res 2017; doi: 10.1158/0008-5472.CAN-17-0688). “On the basis of our whole genome data of mutations found in all CTCs, we identified driver mutations and the tissue of origin of these cells, suggesting personalized combination therapies beyond the scope of most gene panels,” the investigators wrote.
The researchers performed the analysis on two blood samples taken at two time points from a 61-year old woman with estrogen receptor-positive/human epidermal growth factor receptor 2-negative metastatic breast cancer. IE/FACS enabled the investigators to isolate 34 CTCs from “an overwhelming background (106-fold excess) of leukocytes” in the samples by sorting them into groups of about 5 cells each. Using LFR the researchers were able to divide genomic DNA from the CTCs into 3,072 individual compartments of long DNA, each containing about 5% of the cancer’s genome. They barcoded and combined these compartments, creating eight LFR libraries. WGS then achieved 23x coverage per cell, and the researchers were able to determine that mutations were present in as few as 12% of CTCs.
The investigators found 2,766 somatic single nucleotide variants, as well as 543 indels and multi-base substitutions. They confirmed 77 of these somatic mutations in both CTCs and tissue from the primary tumor and lymph node metastasis using two methods. The researchers found in all CTCs, the primary tumor, and metastasis a frameshift mutation in the tumor suppressor gene CDH1, and identified it as well as the loss of one copy of 16q, which contains CDH1, as the likely driver events for the patient’s disease.
The investigators speculated that within the next few years the analysis they performed will cost about $3,000.