Serial monitoring of ctDNA to highlight mutation profiles in colorectal cancer.

641 Background: Circulating tumor DNA (ctDNA) represents an ideal platform to obtain the most current genomic profile of a patient’s tumor. We aimed to investigate how stable these profiles remain during serial ctDNA assays in metastatic colorectal cancer (mCRC). Methods: In 77 patients (pts) with mCRC and serial Guardant360 assays with a detectable mutation (mt), we compared mt stability by assessing whether variants were gained/lost between serial assays and changes in relative mutant allele frequency (rMAF). rMAF of a mt was defined as (mt allele frequency / mt present at the maximum allele frequency in that assay). rMAF results were normalized to detected ctDNA concentration changes between assays to ensure changes in rMAF were not due to changes in ctDNA concentration. MAPK pathway mutations were defined as RAS, BRAF, EGFR, KIT, or MET mutations. Results: Of 77 pts, 64 (83%) had 2 serial assays and 13 (16.9%) had 3 or 4 assays performed. Serial assays occurred an average of 138 days apart (+/- SD of 111 days). Only 13/77 (17%) pts had no change in the number of mts detected between assays. A new mt was detected in 42/77 (55%) pts, while 43/77 (56%) lost a previously detected mt. Of 52 mts detected in patients with > 2 assays, 16 (31%) were gained and subsequently lost. After controlling for ctDNA concentration, mts were equally likely to have an increasing (129/308 – 42%) or decreasing (150/308 – 49%) allele frequency. Potentially clinically relevant MAPK variants were gained/lost in 29% of patients; though MAPK mts developed in a large number of pts (16/77 – 21%), many pts also lost MAPK mts (9/77 – 12%), showing ongoing subclonal dynamics. Median time between assays did not differ between pts with gain/lost mts or stable mt profiles (P = 0.73), however mt rMAF shift of > 25% was more common if assays were > 90 days apart (OR 4.3, P < 0.0001). Conclusions: Serial ctDNA assays demonstrate ongoing mutational changes in mCRC, with emergence/disappearance of MAPK variants being more common than expansion of a pre-existing clone. Our results suggest repeated sampling may be important to optimize selection of targeted therapies at each regimen alteration.

Download Full-text

Impact of circulating tumor DNA mutant allele fraction on prognosis in RAS ‐mutant metastatic colorectal cancer

Molecular Oncology ◽

10.1002/1878-0261.12547 ◽

2019 ◽

Vol 13 (9) ◽

pp. 1827-1835 ◽

Cited By ~ 8

Author(s):

Elena Elez ◽

Chiara Chianese ◽

Enrique Sanz‐García ◽

Erica Martinelli ◽

Alba Noguerido ◽

...

Keyword(s):

Colorectal Cancer ◽

Metastatic Colorectal Cancer ◽

Mutant Allele ◽

Circulating Tumor Dna ◽

Tumor Dna ◽

Dna Mutant ◽

Allele Fraction

Download Full-text

Mutational profiles and amplifications on circulating tumor DNA testing in patients with young-onset colorectal cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.e15067 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. e15067-e15067

Author(s):

Saivaishnavi Kamatham ◽

Dorin Colibaseanu ◽

Amit Merchea ◽

Faisal Shahjehan ◽

Pashtoon Murtaza Kasi

Keyword(s):

Colorectal Cancer ◽

Age Distribution ◽

Circulating Tumor Dna ◽

Rectal Tumors ◽

Dna Testing ◽

Wild Type ◽

Young Onset ◽

Rectal Cancers ◽

Tumor Dna ◽

Selection Of

e15067 Background: There has been a concerning rise of colorectal cancer (CRC) in young individuals (<50 years). There appears to be a preponderance of left-sided tumors and rectal cancers, however, the etiology and biology is not entirely known. Our aim was to describe the results of circulating tumor DNA based (ctDNA) testing in young-onset CRC. Methods: We studied the results of 186 patients with CRC who had ctDNA testing, of whom 41 (22%) had young-onset CRC from January 2017 to January 2019 at Mayo Clinic, Florida. They were categorized based on their age at diagnosis. Results: The age distribution and the aberrations seen are summarized in the table. 25 (61%) were left sided, 9 (22%) were right sided, 7 (17%) were rectal tumors. ctDNA testing was able to identify mutations in 4 (9.8%) patients with BRAFV600E, 8 (19.5%) with RAS and categorized 29 (70.7%) as RAS/RAF wild-type. Furthermore, amplifications were detected in MYC 6 (14.6%) , MET 3 (7.3%) and ERBB2 1 (2.4%). 3(7.3%) were MSI-High and there were 4 individuals with BRCA1/2 noted on ctDNA testing. Conclusions: ctDNA testing for young onset CRC is feasible and identifies a spectrum of clinically meaningful and actionable aberrations. These can further be of use to evaluate treatment response, progression or help in selection of clinical trials. [Table: see text]

Download Full-text

OA 07.03 Circulating Tumor DNA Mutant Allele Frequency and Tumor Burden as Biomarkers for Response to Immune Checkpoint Blockade

Journal of Thoracic Oncology ◽

10.1016/j.jtho.2017.09.363 ◽

2017 ◽

Vol 12 (11) ◽

pp. S1762 ◽

Cited By ~ 1

Author(s):

Y.K. Chae ◽

A. Davis ◽

S. Agte ◽

A. Pan ◽

N. Mohindra ◽

...

Keyword(s):

Allele Frequency ◽

Immune Checkpoint ◽

Mutant Allele ◽

Circulating Tumor Dna ◽

Immune Checkpoint Blockade ◽

Tumor Burden ◽

Checkpoint Blockade ◽

Mutant Allele Frequency ◽

Tumor Dna ◽

Dna Mutant

Download Full-text

Impact in prognosis of circulating tumor DNA mutant allele fraction (MAF) in RAS mutant metastatic colorectal cancer (mCRC)

Annals of Oncology ◽

10.1093/annonc/mdx262.009 ◽

2017 ◽

Vol 28 ◽

pp. iii140 ◽

Cited By ~ 1

Author(s):

Sanz-García Enrique ◽

Elena Elez ◽

Ginevra Caratu ◽

Judit Matito ◽

Ariadna Garcia ◽

...

Keyword(s):

Colorectal Cancer ◽

Metastatic Colorectal Cancer ◽

Mutant Allele ◽

Circulating Tumor Dna ◽

Tumor Dna ◽

Dna Mutant ◽

Allele Fraction

Download Full-text

Circulating Tumor DNA Analysis to Optimize the Operative and Postoperative Treatment for Patients With Colorectal Cancer - Intervention Trial 2

Case Medical Research ◽

10.31525/ct1-nct04084249 ◽

2019 ◽

Author(s):

Keyword(s):

Colorectal Cancer ◽

Dna Analysis ◽

Circulating Tumor Dna ◽

Postoperative Treatment ◽

Intervention Trial ◽

Cancer Intervention ◽

Tumor Dna

Download Full-text

Faculty Opinions recommendation of Clinical Utility of Analyzing Circulating Tumor DNA in Patients with Metastatic Colorectal Cancer.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.733118524.793553325 ◽

2018 ◽

Author(s):

Kellie Mathis

Keyword(s):

Colorectal Cancer ◽

Metastatic Colorectal Cancer ◽

Clinical Utility ◽

Circulating Tumor Dna ◽

Tumor Dna

Download Full-text

INVESTIGATION KRAS MUTATION IN CIRCULATION TUMOR DNA IN DIFFERENT STAGES OF COLORECTAL CANCER

Problems in oncology ◽

10.37469/0507-3758-2019-65-5-701-707 ◽

2019 ◽

Vol 65 (5) ◽

pp. 701-707

Author(s):

Vitaliy Shubin ◽

Yuriy Shelygin ◽

Sergey Achkasov ◽

Yevgeniy Rybakov ◽

Aleksey Ponomarenko ◽

...

Keyword(s):

Colorectal Cancer ◽

Plasma Volume ◽

Kras Mutation ◽

Stage Iv ◽

Circulating Tumor Dna ◽

Stage Ii ◽

Kras Gene ◽

Kras Mutations ◽

Droplet Pcr ◽

Tumor Dna

To determine mutations in the plasma KRAS gene in patients with colorectal cancer was the aim of this study. The material was obtained from 44 patients with colorectal cancer of different stages (T1-4N0-2bM0-1c). Plasma for the presence of KRAS gene mutation in circulating tumor DNA was investigated using digital droplet polymerase chain reaction (PCR). KRAS mutations in circulating tumor DNA isolated from 1 ml of plasma were detected in 13 (30%) patients with cancer of different stages. Of these, with stage II, there were 3 patients, with III - 5 and with IV - 5. Patients who did not have mutations in 1 ml of plasma were analyzed for mutations of KRAS in circulating tumor DNA isolated from 3 ml of plasma. Five more patients with KRAS mutations were found with II and III stages. The highest concentrations of circulating tumor DNA with KRAS mutation were found in patients with stage IV. The increase in plasma volume to 3 ml did not lead to the identification of mutations in I stage. This study showed that digital droplet PCR allows identification of circulating tumor DNA with the KRAS mutations in patients with stage II-IV of colon cancer. The results can be used to determine the degree of aggressiveness of the tumor at different stages of the disease, but not the 1st, and it is recommended to use a plasma volume of at least 3 ml.

Download Full-text

18 New method of assessing tumor heterogeneity utilizing both circulating tumor DNA and tissue DNA to predict the response to immunotherapy

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2020-sitc2020.0018 ◽

2020 ◽

Vol 8 (Suppl 3) ◽

pp. A18-A18

Author(s):

Jaeyoun Choi ◽

Myungwoo Nam ◽

Stanislav Fridland ◽

Jinyoung Hwang ◽

Chan Mi Jung ◽

...

Keyword(s):

Lung Cancer ◽

Immune Response ◽

Allele Frequency ◽

Scoring System ◽

Tumor Heterogeneity ◽

Metastatic Breast ◽

Circulating Tumor Dna ◽

List Type ◽

Multiple Biopsies ◽

Tumor Dna

BackgroundTumor heterogeneity assessment may help predict response to immunotherapy. In melanoma mouse models, tumor heterogeneity impaired immune response.1 In addition, among lung cancer patients receiving immunotherapy, the high clonal neoantigen group had favorable survival and outcomes.2 Ideal methods of quantifying tumor heterogeneity are multiple biopsies or autopsy. However, these are not feasible in routine clinical practice. Circulating tumor DNA (ctDNA) is emerging as an alternative. Here, we reviewed the current state of tumor heterogeneity quantification from ctDNA. Furthermore, we propose a new tumor heterogeneity index(THI) based on our own scoring system, utilizing both ctDNA and tissue DNA.MethodsSystematic literature search on Pubmed was conducted up to August 18, 2020. A scoring system and THI were theoretically derived.ResultsTwo studies suggested their own methods of assessing tumor heterogeneity. One suggested clustering mutations with Pyclone,3 and the other suggested using the ratio of allele frequency (AF) to the maximum somatic allele frequency (MSAF).4 According to the former, the mutations in the highest cellular prevalence cluster can be defined as clonal mutations. According to the latter, the mutations with AF/MSAF<10% can be defined as subclonal mutations. To date, there have been no studies on utilizing both ctDNA and tissue DNA simultaneously to quantify tumor heterogeneity. We hypothesize that a mutation found in only one of either ctDNA or tissue DNA has a higher chance of being subclonal.We suggest a scoring system based on the previously mentioned methods to estimate the probability for a mutant allele to be subclonal. Adding up the points that correspond to the conditions results in a subclonality score (table 1). In a given ctDNA, the number of alleles with a subclonality score greater than or equal to 2 divided by the total number of alleles is defined as blood THI (bTHI) (figure 1). We can repeat the same calculation in a given tissue DNA for tissue THI (tTHI) (figure 2). Finally, we define composite THI (cTHI) as the mean of bTHI and tTHI.Abstract 18 Table 1Subclonality scoreAbstract 18 Figure 1Hypothetical distribution of all alleles found in ctDNA bTHI = the number of alleles with a subclonality score greater than or equal to 2/the total number of alleles found in ctDNA = 10/20 =50%Abstract 18 Figure 2Hypothetical distribution of all alleles found in tissue DNA tTHI= the number of alleles with a subclonality score greater than or equal to 2/the total number of alleles found in tissue DNA = 16/40 = 40% cTHI= (bTHI + tTHI)/2 = 45%ConclusionsTumor heterogeneity is becoming an important biomarker for predicting response to immunotherapy. Because autopsy and multiple biopsies are not feasible, utilizing both ctDNA and tissue DNA is the most comprehensive and practical approach. Therefore, we propose cTHI, for the first time, as a quantification measure of tumor heterogeneity.ReferencesWolf Y, Bartok O. UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma. Cell 2019;179:219–235.McGranahan N, Swanton C. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science 2016;351:1463–1469.Ma F, Guan Y. Assessing tumor heterogeneity using ctDNA to predict and monitor therapeutic response in metastatic breast cancer. Int J Cancer 2020;146:1359–1368.Liu Z, Xie Z. Presence of allele frequency heterogeneity defined by ctDNA profiling predicts unfavorable overall survival of NSCLC. Transl Lung Cancer Res 2019;8:1045–1050.

Download Full-text

Small EVs-Associated DNA as Complementary Biomarker to Circulating Tumor DNA in Plasma of Metastatic Colorectal Cancer Patients

Pharmaceuticals ◽

10.3390/ph14020128 ◽

2021 ◽

Vol 14 (2) ◽

pp. 128

Author(s):

Silvia Galbiati ◽

Francesco Damin ◽

Dario Brambilla ◽

Lucia Ferraro ◽

Nadia Soriani ◽

...

Keyword(s):

Colorectal Cancer ◽

Metastatic Colorectal Cancer ◽

Cancer Patients ◽

Digital Pcr ◽

Extracellular Vesicle ◽

Circulating Tumor Dna ◽

Mutation Status ◽

Promising Practice ◽

Colorectal Cancer Patients ◽

Tumor Dna

It is widely accepted that assessing circular tumor DNA (ctDNA) in the plasma of cancer patients is a promising practice to evaluate somatic mutations from solid tumors noninvasively. Recently, it was reported that isolation of extracellular vesicles improves the detection of mutant DNA from plasma in metastatic patients; however, no consensus on the presence of dsDNA in exosomes has been reached yet. We analyzed small extracellular vesicle (sEV)-associated DNA of eleven metastatic colorectal cancer (mCRC) patients and compared the results obtained by microarray and droplet digital PCR (ddPCR) to those reported on the ctDNA fraction. We detected the same mutations found in tissue biopsies and ctDNA in all samples but, unexpectedly, in one sample, we found a KRAS mutation that was not identified either in ctDNA or tissue biopsy. Furthermore, to assess the exact location of sEV-associated DNA (outside or inside the vesicle), we treated with DNase I sEVs isolated with three different methodologies. We found that the DNA inside the vesicles is only a small fraction of that surrounding the vesicles. Its amount seems to correlate with the total amount of circulating tumor DNA. The results obtained in our experimental setting suggest that integrating ctDNA and sEV-associated DNA in mCRC patient management could provide a complete real-time assessment of the cancer mutation status.

Download Full-text