Genomic profiling of circulating tumor DNA (ctDNA) from patients (pts) with advanced non-small cell lung cancer (NSCLC).

9025 Background: Tissue biopsy is the gold standard for detection of genomic alterations (GA) and selection of matched targeted therapies in NSCLC, but ctDNA assay provides a possible complementary approach for some pts. Methods: Hybrid-capture based genomic profiling of 62 genes using a ctDNA assay (FoundationACT™) was performed on blood samples from 1,019 consecutive NSCLC pts. The fraction of ctDNA in the blood was estimated using the maximum somatic allele frequency (MSAF) for each sample. Results: Pt characteristics: Median age 69 years (range 8-94); 54% were female. Histologies included adenocarcinoma (n = 720), NSCLC not otherwise specified (NSCLC NOS; n = 179), squamous cell (n = 57), LC NOS (n = 51), large cell (n = 6), and sarcomatoid (n = 6). ≥1 reportable GA was detected in 71% of all cases and in 83% of cases with evidence of ctDNA in the blood (MSAF > 0). For 22 pts with paired blood and tissue samples collected within 30 days and MSAF > 0, 33/64 (52%) GA detected in tissue were also detected in ctDNA. In 55 pts for whom tissue was insufficient for analysis, ≥1 GA was detected in ctDNA in 43 (78%) cases. For 856 cases with MSAF > 0, an average of 1.8 GA/sample were reported. GA were most frequently detected in TP53 (57%), EGFR (23%) and KRAS (17%). Comparative analysis with the tissue-based FoundationCORE™ database (n = 19,264) showed similar frequencies of GA per gene, although KRAS mutation was more frequent in tissue than ctDNA (27% vs 17%, P < 0.0001), and EGFR T790M was more frequent in ctDNA than tissue (7% vs 2%, P < 0.0001), likely reflecting use of liquid versus tissue biopsy after relapse on targeted therapy .Kinase fusions ( ALK, ROS1, RET, FGFR3, PDGFRA) were identified in 5% (39/856) of cases. Diverse and novel mechanisms of acquired resistance (AR) were detected in ctDNA including MET Y1230C and EGFR amplification post-crizotinib, FGFR3-TACC3 fusion post-EGFR inhibitor, and multiple EGFRAR mutations post-osimertinib. Conclusions: In this series, use of a rigorously validated capture-based assay revealed evidence of ctDNA in the blood in 84% of cases. Our results provide clinical support for use of this assay as a complementary technology to tissue-based genomic testing in a subset of pts with NSCLC.

Download Full-text

Genomic profiling of circulating tumor DNA (ctDNA) from patients (pts) with pancreatic ductal adenocarcinoma (PDA).

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.15_suppl.4128 ◽

2017 ◽

Vol 35 (15_suppl) ◽

pp. 4128-4128

Author(s):

Nathan Bahary ◽

Jie He ◽

Mark Bailey ◽

Shan Zhong ◽

Gerald Li ◽

...

Keyword(s):

Cancer Biology ◽

Clinical Care ◽

Circulating Tumor Dna ◽

The Cancer Genome Atlas ◽

Ductal Adenocarcinoma ◽

Genomic Profiling ◽

Tissue Samples ◽

Comprehensive Genomic Profiling ◽

Cancer Genome Atlas ◽

Genomic Characterization

4128 Background: PDA is a lethal and increasingly common malignancy and tissue samples for genomic characterization may be limited. As PDA has a high and consistent frequency of KRAS, p53 and CDKN2A mutations it serves as a robust indication to test the utility of ctDNA in accurately characterizing genomic alterations (GA). A prior study suggested significant differences between ctDNA and tissue base profiling but assays were not conducted on the same platform (PMID27833075). We undertook this study to see whether ctDNA could recapitulate the known genomic hallmarks of tumor based profiling. Methods: Hybrid-capture based genomic profiling of 62 genes (FoundationACT) was performed on ctDNA from 78 pts with advanced PDA with samples received in the course of clinical care. The fraction of ctDNA in the blood was estimated using the maximum somatic allele frequency (MSAF) for each sample. Frequencies of alterations in these common drivers were then compared to those seen in tumors of pts who underwent comprehensive genomic profiling (CGP) tissue testing performed on the same core platform, FoundationOne, and The Cancer Genome Atlas (TCGA). Results: Pt characteristics: Median age 65 (range, 47-88); Female (33) /Male (45). FoundationACT results show that 53/78 (68%) cases had MSAF >0 (56%-78%%, 95% CI). ≥1 GA was reported in 81% of the cases with evidence of ctDNA in the blood. The most common GA detected by FoundationACT (based on cases with evidence of ctDNA in blood) vs FoundationOne were in KRAS (59% vs 89%, p< 0.0001), TP53 (69% vs.74%, p=0.19), and CDKN2A (14% vs.45%). Other detected clinically relevant GA detected by FoundationACT included: BRCA1, ERBB2, NF1, PIK3CA. Conclusions: This study demonstrates significant differences between the established driver oncogenic alterations for PDA, as assessed by ct DNA and tissue based genomic profiling which are unlikely to be explained by differences in assay, but rather novel cancer biology. At present use of ctDNA genomic profiling in PDA should not routinely replace tissue based genomic characterization. [Table: see text]

Download Full-text

Genomic profiling of circulating tumor DNA (ctDNA) from patients (pts) with advanced cancers of the GI tract and anus.

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.4_suppl.618 ◽

2017 ◽

Vol 35 (4_suppl) ◽

pp. 618-618 ◽

Cited By ~ 1

Author(s):

Alexa Betzig Schrock ◽

Lauren Young ◽

Samuel Jacob Klempner ◽

Rodolfo Bordoni ◽

Jeffrey S. Ross ◽

...

Keyword(s):

Molecular Profiling ◽

Circulating Tumor Dna ◽

Genomic Profiling ◽

Tissue Sampling ◽

Gi Tract ◽

Hybrid Capture ◽

Non Invasive ◽

Clinical Support ◽

Average Maximum ◽

Tumor Dna

618 Background: The treatment of GI carcinomas (CA) is influenced by the presence or absence of prognostic and predictive genomic alterations (GA). Tissue sampling is the historical platform for genomic biomarker assessment, but non-invasive ctDNA assay provides an alternative when tissue is unavailable or cannot be safely obtained. Methods: Hybrid-capture based genomic profiling using a ctDNA assay (FoundationACT) was performed on blood samples from 82 consecutive pts with lower alimentary canal CA. Results: Median age was 62 (range 28-92) and 61% were male. Anatomic breakdown included CRC (n = 51), esophageal (n = 9), gastric (n = 8), gastroesophageal (n = 3) and small bowel adenoCA (SBA, n = 2), anus squamous cell CA (n = 5), and other GI CA (n = 4). At least one GA was reported in 72% of cases. In 23 cases with no GA reported, the average maximum somatic allele frequency was 0.17% (95% CI: 0-0.6%) vs. 16.7% (95% CI: 0-54.4%) for the 59 cases with GAs (P < 0.0001). For the 3 of 18 patients with both blood and tissue testing performed and samples collected within a 30-day interval, 8/9 (89%) GA detected in tissue were also detected in ctDNA. An average of 1.7 GA/sample were detected in ctDNA. The most commonly altered genes were TP53 (61%), KRAS (24%), BRAF (10%) and PIK3CA (10%). Comparative analysis using the tissue-based Foundation Core database showed a similar trend with overall slightly higher frequencies of GAs in individual genes . RAF and RAS short variants (SV) were exclusive to lower GI and anal CA. KRAS and RAF1 amplification (amp) occurred only in esophageal CA (4/11, 36%). FGFR SV or amp was identified in 3 cases across the cohort. Of CRC, 4 (8%) had ≥ 1 ERBB2 activating SV or amp, 2 (4%) had IDH1/2 hotspot SV, and 2 (4%) had BRCA2 inactivating alterations. ERBB2 activating SV and EGFR amp were found in a SBA and an esophagus CA, respectively. A kinase fusion was identified as the sole driver in 1 CRC ( STRN-ALK) and 1 SBA ( GOPC-ROS1). Outcomes to targeted therapies will be presented for the available subset of patients. Conclusions: Our results provide early clinical support and confirm that hybrid-capture based ctDNA testing can reliably detect all 4 classes of GA and provide a molecular profiling option for patients with GI CA.

Download Full-text

Illustration of temporal evolution in patients with metastatic renal cell carcinoma (mRCC) using both circulating tumor DNA (ctDNA) and tissue-based genomic data.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.6_suppl.347 ◽

2021 ◽

Vol 39 (6_suppl) ◽

pp. 347-347

Author(s):

Zeynep Busra Zengin ◽

Caroline Weipert ◽

Joann Hsu ◽

Nicholas Salgia ◽

Chuck Hensel ◽

...

Keyword(s):

Circulating Tumor Dna ◽

Genomic Profiling ◽

Temporal Separation ◽

Tissue Samples ◽

Sequencing Platform ◽

Targeted Next Generation Sequencing ◽

Paired Samples ◽

Significant Difference ◽

The Difference ◽

Ctdna Analysis

347 Background: We have previously demonstrated the feasibility of ctDNA assessment in mRCC and preliminarily showed agreement between ctDNA and tissue-based genomic findings (Zengin et al ESMO 2020). Our data suggested that the degree of agreement is dependent upon the temporal separation of blood and tissue samples. We sought to further explore this temporal impact in a separate validation cohort. Methods: Patients (pts) with mRCC who underwent ctDNA genomic profiling were identified. ctDNA analysis was performed using a CLIA-certified 73-74 gene panel (Guardant360). From this cohort we identified a subset of pts who also underwent tissue-based genomic profiling using either a whole exome sequencing platform (GemExtra [TGen, Phoenix, AZ]) or a targeted next generation sequencing platform (Foundation Medicine [Cambridge, MA] or Tempus [Chicago, IL]). Only alterations covered by both assays were included for the current analysis. The difference in the proportion of alterations detected on tissue and ctDNA was compared between these cohorts and at a 6-mo landmark using the χ2 test. Results: In total, ctDNA and tissue based genomic profiling was assessed in 112 pts (M:F, 81:31); with most common histology was clear cell (85.7%). Median time between ctDNA and tissue assessments was 9.8 months (IQR 1.15-23.7). When examining paired samples in which >1 ctDNA alteration was detected, 32% (43/133) of alterations detected on tissue were also detected in ctDNA. This proportion increased to 43% (29/67) when samples collected within 6 months of each other, and was 51% (28/55) in samples collected within 3 months of each other. There was no significant difference in the frequency of shared mutations between the cohorts (P=0.09; Table). Conclusions: Our study confirms that ctDNA and tissue-based genomic profiling continue to provide consistently high levels of agreement. Notably, the percentage of samples with ≥1 ctDNA alteration detected was significantly lower in both cohorts compared to previous studies in RCC. More shared alterations were found on ctDNA when both ctDNA and tissue-based assessment were obtained at closer intervals. [Table: see text]

Download Full-text

Hybrid capture-based genomic profiling of circulating tumor DNA from patients with advanced hepatocellular carcinoma.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.e15606 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. e15606-e15606

Author(s):

Mao Li ◽

Ailin Wei ◽

Wenzhuan Xie ◽

Jing Zhao ◽

Zhengyi Zhao ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Circulating Tumor Dna ◽

Chinese Patients ◽

Advanced Hepatocellular Carcinoma ◽

Genomic Profiling ◽

Promising Alternative ◽

Hybrid Capture ◽

Advanced Hcc ◽

Tissue Biopsy ◽

Tumor Dna

e15606 Background: Hepatocellular carcinoma (HCC) is one of the most common malignancies with a particularly high prevalence in China. The genomic profiling in HCC had been widely explored with tissue biopsy, however, given the intrinsic risks of invasive approach, blood-based circulating tumor DNA (ctDNA) has been proposed as a promising alternative. In this study, we aim to investigate whether the ctDNA may serve as a reliable tool to provide a more accurate molecular snapshot of HCC in Chinese patients. Methods: Plasma samples from 385 Chinese patients with advanced HCC were assayed for somatic genomic alternations by hybrid capture-based next-generation sequencing (NGS) with 150 genes and a mean sequencing depth of more than 3000×. The results were compared with our internal tissue genomic database of Chinese HCC patients (N = 873) tested by NGS and TCGA database (N = 373) tested by whole exome sequencing. Genomic alterations including single nucleotide variation (SNV), insertions/deletions, copy number variations, gene rearrangement and fusions were assessed. Results: Among 385 patients with ctDNA testing, somatic genomic alternations were detected in 97% of the patients (median = 5 alterations/patient). The most prevalent SNV mutations from ctDNA sequencing were TP53 (45.7%), TERT (19.5%), CTNNB1 (12.5%), and LRP1B (8.3%) compared to our tissue database (TP53 (61.2%), CTNNB1 (15.6%), TERT (13.3%), and LRP1B (11.0%)). While in TCGA database, the most common SNV mutations were found in TP53 (30.1%), CTNNB1 (26.0%), LRP1B (8.8%), ARID1A (8.6%), and SPTA1 (7.5%). Moreover, the level of MSAF was associated with detectable variant types, evidenced by a significant higher MSAF level observed when amplifications (P < 0.0001) or fusions (P = 0.008) were detected in the samples. Conclusions: Molecular analysis of patients with advanced HCC through ctDNA can serve as a reliable alternative to tissue biopsy. Chinese HCC patients may have different mutational landscapes to Western population. The utility of ctDNA analysis can provide therapeutically exploitable genomic profiles to identify potentially actionable gene alterations for targeted therapies.

Download Full-text

Comprehensive landscape of gene amplifications (amps) in tissue and circulating tumor DNA (ctDNA) in metastatic colorectal cancer (mCRC).

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.4_suppl.604 ◽

2019 ◽

Vol 37 (4_suppl) ◽

pp. 604-604

Author(s):

Kanwal Pratap Singh Raghav ◽

Rona Yaeger ◽

Jonathan M. Loree ◽

Arvind Dasari ◽

Van K. Morris ◽

...

Keyword(s):

Copy Number ◽

Acquired Resistance ◽

High Sensitivity ◽

Circulating Tumor Dna ◽

Tissue Samples ◽

Individual Gene ◽

Therapeutic Implications ◽

Oncogenic Pathways ◽

Number Variation ◽

Tumor Dna

604 Background: Amps, as oncogenic and resistance drivers, have therapeutic implications, but unlike mutations, have been sparsely described in mCRC. Functional account is piecemeal due to vague definitions, limited data on co-occurring alterations and use of primary tissue samples nonrepresentative of tumor heterogeneity. Our aim was to define the amp landscape in mCRC using tissue and ctDNA sequencing. Methods: We performed systematic analyses of copy-number variation in 2 cohorts of mCRC patients (pts) [tissue (TC) (N = 1,134) and ctDNA (BC) (N = 3,218)] who had high sensitivity targeted sequencing with MSK-IMPACT (341-468 genes) or Guardant Health (70-73 genes) panel, respectively. For BC, plasma copy number was adjusted (ApCN) to account for variable tumor DNA shedding using max allele frequency and high amp (HAmp) was defined as > 4 copies (similar to predefined tissue cutoff). Results: 166 (15%) and 405 (13%) pts in TC and BC harbored amp in at least one of 18 genes assessed by both panels (Table). Amp prevalence for individual gene was similar in both cohorts ( r = 0.9; P < .01) with RTK amps ( EGFR, ERBB2, MET, FGFR1/2, PDGFRA) seen in 8% pts. Key RTK amps were enriched in RAS/BRAF wild type (RB WT) compared to mutant (RB MUT) (OR 3.5; P < .01) pts in both cohorts, in contrast to low prevalence RTK and non-RTK amps. Median ApCN was higher for RTKs in RB WT vs MUT cases ( ERBB2: 12 vs 5; P = .02). Using validated EGFRab exposure (EGFRi) ctDNA signature, we found that EGFRi pts had higher prevalence of EGFR, MET, BRAF, KRAS, PIK3CA and FGFR1 amps compared to EGFRab naïve pts. Conclusions: While individually uncommon, amps occur across key oncogenic pathways in mCRC and after adjusting for ctDNA shedding, are seen at similar prevalence in tissue and plasma. Amps in RTKs are seen in 10-12% of RB WT tumors, suggesting clinically relevant roles as oncogenic effectors and targets. After EGFRi, a number of amps emerge, including PIK3CA and FGFR1 amps, not previously implicated in acquired resistance. [Table: see text]

Download Full-text

Hybrid Capture-based Genomic Profiling of Circulating Tumor DNA From Patients With Advanced Ovarian Cancer

Pathology & Oncology Research ◽

10.3389/pore.2021.581534 ◽

2021 ◽

Vol 27 ◽

Author(s):

Wenbin Shen ◽

Boer Shan ◽

Shanhui Liang ◽

Junling Zhang ◽

Yangyang Yu ◽

...

Keyword(s):

Ovarian Cancer ◽

Mutation Frequency ◽

Advanced Ovarian Cancer ◽

Circulating Tumor Dna ◽

Cancer Tissue ◽

Genomic Profiling ◽

Tissue Samples ◽

Hybrid Capture ◽

Ovarian Cancer Tissue ◽

Tumor Dna

Objective: We conducted this study to characterize somatic genomic alterations in circulating tumor DNA (ctDNA) from patients with ovarian cancer and compare GAs detected in ctDNA with tissue databases.Methods: Hybrid capture-next generation sequencing genomic profiling of 150 genes was performed on ctDNA from 138 patients with ovarian cancer with 1,500× sequencing depth. The GAs detected in ctDNA were compared with those in our ovarian cancer tissue database (N = 488) and the Cancer Genome Atlas (TCGA) database (N = 489).Results: 115 patients (83%) had at least 1 GA detected in ctDNA. The most frequently altered genes detected in ctDNA were TP53 (72%), KRAS (11%), LRP1B (10%), ZNF703 (9%) and NF1 (8%). Comparative analysis with our tissue database showed similar frequencies of GAs per gene, although PIK3CA and KRAS mutations were more frequent in tissue and ctDNA, respectively (p < 0.05). Gene amplification and rearrangement were more frequent in ctDNA samples. The mutation frequency of homologous recombination repair associated-genes, VEGF signal/angiogenesis pathways, RAS pathways, NOTCH pathways and MSI-H ratio was not statistically different either in ctDNA or in tissue database. However, the mutation frequency of AKT, PIK3CA, PTEN and STK11 in PI3K/AKT/mTOR pathway was significantly lower than that in tissue samples (p < 0.05).Conclusions: Our results suggest that genomic profiling of ctDNA could detect somatic GAs in a significant subset of patients with ovarian cancer. Hybrid capture-NGS based on liquid biopsy has the potential capability to serve as a substitute to tissue biopsy and further studies are warranted.

Download Full-text

Genomic profiling of circulating tumor DNA (ctDNA) from patients (pts) with metastatic breast cancer (mBC).

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.15_suppl.1016 ◽

2017 ◽

Vol 35 (15_suppl) ◽

pp. 1016-1016 ◽

Cited By ~ 1

Author(s):

Lajos Pusztai ◽

Jon Chung ◽

Lauren Young ◽

Alexa Betzig Schrock ◽

Ryan Hartmaier ◽

...

Keyword(s):

Clinical Decision Making ◽

Clonal Evolution ◽

Clinical Care ◽

Metastatic Breast ◽

Clinical Decision ◽

Circulating Tumor Dna ◽

Genomic Profiling ◽

Treatment Information ◽

Complementary Approach ◽

In Cis

1016 Background: Clonal evolution during progression to and treatment of mBC highlights the importance of genomic profiling of recent samples to guide clinical decision making. We undertook this study to characterize genomic alterations (GA) in ctDNA from pts with mBC during the course of clinical care. Methods: Hybrid-capture based genomic profiling of 62 genes (FoundationACT) was performed on ctDNA from 255 BC pts. The fraction of ctDNA in the blood was estimated using the maximum somatic allele frequency (MSAF) for each sample. Results: 168 pts were ER+ [16 HER2+, 134 HER2(-), 18 HER2 unknown (unk)]; 51 were ER(-) [7 HER2+, 38 triple negative (TNBC), 6 HER2 unk]; 36 were ER unk; 95% were stage 4. For pts with treatment information, 90% had prior chemotherapy and 90% ER+ pts had prior aromatase inhibitor therapy (AI). ≥1 GA was reported in 78% of all cases and in 88% of cases with evidence of ctDNA in the blood (MSAF >0). For 226 cases with MSAF >0, an average of 2.7 GA/case were reported. The most common GA for ER+ pts were in TP53 (44%), PIK3CA (39%), ESR1 (36%), CDH1 (11%), KRAS (10%) and ERBB2 ( HER2, 9%). 101 ESR1 GA were identified in 61 pts [54 ER+, 7 ER unk], including 4 HER2+ pts. For ER+ pts with treatment information: 37% (22/60) with prior AI had ESR1 GA; all pts with ESR1 GA had prior AI. 24 pts had >1 ESR1 GA, with instances of GA in cis. Frequent ESR1 GA were Y537S/N (n=47), D538G (n=29) and E380Q (n=7); rearrangement (n=3) and amplification (n=1) were also detected. Concurrent GA with ESR1 were found in PIK3CA (41%), FGFR1 (13%), BRCA1/2 (5%), HER2 (5%) and AKT1 (3%). In ER(-) pts, the most common GA were in TP53 (74%), PIK3CA (17%), NF1 (11%), BRCA1 (9%) and EGFR (9%). HER2 activating mutation occurred in 3% of cases that were HER2(-) by prior testing. Kinase fusions in FGFR2/3 (3 ER+) and EGFR (1 TNBC) were observed. Conclusions: In this study, evidence of ctDNA in the blood was observed in 89% of cases. PIK3CA and ESR1 GA frequencies were similar to those reported in previous studies of ctDNA from ER+ pts after AI. Diverse ESR1 GA and co-occurring GA suggest therapeutic approaches for AI refractory ER+ mBC. Our results demonstrate that genomic profiling of ctDNA may be a complementary approach to tissue-based genomic testing for pts with mBC.

Download Full-text

Combining tissue and circulating tumor DNA increases the detection rate of a CTNNB1 mutation in hepatocellular carcinoma

BMC Cancer ◽

10.1186/s12885-021-08103-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Stine Karlsen Oversoe ◽

Michelle Simone Clement ◽

Britta Weber ◽

Henning Grønbæk ◽

Stephen Jacques Hamilton-Dutoit ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Mutation Rate ◽

Detection Rate ◽

Tumor Tissue ◽

Circulating Tumor Dna ◽

Treatment Modalities ◽

Advanced Hepatocellular Carcinoma ◽

Tissue Samples ◽

The Impact ◽

Tumor Dna

Abstract Background and aims Studies suggest that mutations in the CTNNB1 gene are predictive of response to immunotherapy, an emerging therapy for advanced hepatocellular carcinoma (HCC). Analysis of circulating tumor DNA (ctDNA) offers the possibility of serial non-invasive mutational profiling of tumors. Combining tumor tissue and ctDNA analysis may increase the detection rate of mutations. This study aimed to evaluate the frequency of the CTNNB1 p.T41A mutation in ctDNA and tumor samples from HCC patients and to evaluate the concordance rates between plasma and tissue. We further evaluated changes in ctDNA after various HCC treatment modalities and the impact of the CTNNB1 p.T41A mutation on the clinical course of HCC. Methods We used droplet digital PCR to analyze plasma from 95 patients and the corresponding tumor samples from 37 patients during 3 years follow up. Results In tumor tissue samples, the mutation rate was 8.1% (3/37). In ctDNA from HCC patients, the CTNNB1 mutation rate was 9.5% (9/95) in the pre-treatment samples. Adding results from plasma analysis to the subgroup of patients with available tissue samples, the mutation detection rate increased to 13.5% (5/37). There was no difference in overall survival according to CTNNB1 mutational status. Serial testing of ctDNA suggested a possible clonal evolution of HCC or arising multicentric tumors with separate genetic profiles in individual patients. Conclusion Combining analysis of ctDNA and tumor tissue increased the detection rate of CTNNB1 mutation in HCC patients. A liquid biopsy approach may be useful in a tailored therapy of HCC.

Download Full-text