DNA in Blood Tracks Cancer Development and Response

Circulating tumor DNA analysis can be used to track tumor burden and analyze cancer genomes noninvasively, but the extent to which it represents metastatic heterogeneity is unknown.

Analysis of circulating tumor DNA in plasma (ctDNA) is a less-invasive approach than repeated metastatic tumor biopsies and could provide a summary of somatic alterations contributed by distinct metastases potentially circumventing the problem of spatial heterogeneity.

Scientists at the Cancer Research UK Cambridge Institute (University of Cambridge; UK) and their colleagues carried out an extensive analysis of eight tumor biopsies and nine plasma samples collected from a patient with estrogen receptor-positive (ER+) human epidermal growth factor receptor 2-positive (HER2+) metastatic breast cancer treated with sequential targeted therapies (tamoxifen and trastuzumab, followed by lapatinib) over a three year clinical course. They performed whole-exome followed by deep amplicon sequencing to validate and quantify several hundred somatic mutations.

Exome sequencing of tumor samples and additional sequencing of germline DNA (N1) was performed using commercially available kits. Genomic libraries were quantified using quantitative polymerase chain reaction (qPCR) and pooled for exome enrichment by hybridization using the TruSeq Exome Enrichment Kit and enriched libraries were quantified using qPCR and pooled for sequencing on the HiSeq 2500 (Illumina; San Diego, CA, USA). Targeted sequencing libraries were prepared using droplet-based PCR amplification for ThunderBolts Cancer Panel with specific modifications (RainDance Technologies; Billerica, MA, USA).

The team carefully studied small fragments of DNA from dying tumor cells that are shed into the blood, comparing them with DNA from the biopsy that was taken at the same point in time. The results show that the DNA in the blood samples matched up with that from the biopsies, reflecting the same pattern and timing of genetic changes appearing as the cancer developed and responded to treatment. The results provide the first proof-of-principle that analyzing tumor DNA in the blood can accurately monitor cancer within the body.

Carlos Caldas, MD, a professor of oncology and senior author of the study, said, “This definitively shows that we can use blood-based DNA tests to track the progress of cancer in real time. The findings could change the way we monitor patients, and may be especially important for people with cancers that are difficult to reach, as taking a biopsy can sometimes be quite an invasive procedure. We were able to use the blood tests to map out the disease as it progressed. We now need to see if this works in more patients and other cancer types, but this is an exciting first step.” The study was published on November 4, 2015, in the journal Nature Communications.

Related Links:
Cancer Research UK Cambridge Institute 
Illumina 
RainDance Technologies