Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies

Abstract

The development of noninvasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital polymerase chain reaction–based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. We found that ctDNA was detectable in >75% of patients with advanced pancreatic, ovarian, colorectal, bladder, gastroesophageal, breast, melanoma, hepatocellular, and head and neck cancers, but in less than 50% of primary brain, renal, prostate, or thyroid cancers. In patients with localized tumors, ctDNA was detected in 73, 57, 48, and 50% of patients with colorectal cancer, gastroesophageal cancer, pancreatic cancer, and breast adenocarcinoma, respectively. ctDNA was often present in patients without detectable circulating tumor cells, suggesting that these two biomarkers are distinct entities. In a separate panel of 206 patients with metastatic colorectal cancers, we showed that the sensitivity of ctDNA for detection of clinically relevant KRAS gene mutations was 87.2% and its specificity was 99.2%. Finally, we assessed whether ctDNA could provide clues into the mechanisms underlying resistance to epidermal growth factor receptor blockade in 24 patients who objectively responded to therapy but subsequently relapsed. Twenty-three (96%) of these patients developed one or more mutations in genes involved in the mitogen-activated protein kinase pathway. Together, these data suggest that ctDNA is a broadly applicable, sensitive, and specific biomarker that can be used for a variety of clinical and research purposes in patients with multiple different types of cancer.

Detection of KRAS Mutations in Plasma DNA Using a fully Automated Rapid Detection System in Colorectal Cancer Patients

“…These data indicate that the anti-cancer effect of chemotherapy containing anti-EGFR antibody is correlated with the mutant load. The detection rate using MBP-QP was relatively low compared to other detection systems previously reported [21,23,24]. It seems to be related to the fact that patients in our study included non-metastatic cancer patients, and sample collection was conducted during chemotherapy in 2/3 of those patients.…”

“…KRAS mutations were frequently detected in systemic metastatic cancers, and these were newly detected after acquired resistance to anti-EGFR antibody. Recently, mutation analysis using peripheral blood-socalled liquid biopsy-has been applied to colorectal cancer [9,10,[23][24][25]. In most published reports, quantitative PCR and BEAMing were used for detection with plasma DNA.…”

“…White and black arrows in BKRAS mutation in plasma DNA^indicate the peaks for KRAS wild type and mutant type, respectively plasma DNA in from 76% to 98% of cases using these detection methods [21,23,24]. According to results using digital PCR, tumor derived DNA was detected in more than 75% of colorectal cancer patients, and the detection rate was equivalent to advanced pancreas, ovarian, breast, and gastroesophageal cancers [24]. KRAS mutations with plasma DNA are sometimes detected even if KRAS mutations were not found in cancer tissues [21].…”

The next step: mechanisms driving adrenocortical carcinoma metastasis

“…The exact mechanism by which the tumor releases DNA into the bloodstream is still obscure, although necrosis and apoptosis, often occurring in the tumoral mass, might be involved. The circulating levels of ctDNA largely depend on the tumor type, diameter, disease stage and therapeutic response (Bettegowda et al 2014). Being essentially a waste product, the quality of this DNA is very poor and together with its extremely low levels makes the analysis of genomic profile and methylation state quite difficult (Perdigones & Murtaza 2017).…”

Nanopore sequencing detects structural variants in cancer

“…CDKN2A/p16 and SMAD4/DPC4 are 2 of the most commonly deleted TSGs in human cancer, and complex SVs have been found to underlie approximately half of these deletions in pancreatic ductal adenocarcinoma (PDAC). [4][5][6] The sensitive detection of tumor-specific mutations, including both small alterations such as single base substitutions and large alterations such as SVs, of circulating tumor DNA is critical for applications such as molecular relapse, 7 early detection, 8 and possibly therapeutic monitoring of cancer patients. 9 The arrival of 2nd generation sequencing has provided ample opportunity to investigate small alterations, but the large SV alterations remain under-studied because of the difficulty detecting them with the short reads (<300 bp) of 2nd generation sequencing.…”