Tumor-informed or tumor-agnostic circulating tumor DNA as a biomarker for risk of recurrence in resected colorectal cancer patients

Introduction

Circulating tumor DNA (ctDNA) has been increasingly recognized as a promising minimally-invasive biomarker that could identify patients with minimal residual disease and a high risk of recurrence after definitive treatment. In this study, we've compared the clinical utility and sensitivity of 2 different approaches to ctDNA analyses: tumor-informed and tumor-agnostic in the management of colorectal (CRC) patients. The clinical benefits of a single timepoint ctDNA analysis compared to serial ctDNA monitoring after definitive treatment were also evaluated to uncover the ideal surveillance protocol.

Methods

Patient-paired resected tumor tissues, peripheral blood cells, and a total of 127 pre-operative and serial plasma cell-free DNA (cfDNA) samples after definitive treatment from 38 CRC patients that had undergone curative intent surgery were analyzed using a commercial NGS cfDNA panel.

Results

Up to 84% (32/38) of the recruited patients were detected with at least 1 genomic alteration from the tumor tissues that could be monitored using the tumor-informed ctDNA approach and none of the detected alterations were clonal hematopoiesis (CH) related. In contrast, 37% (14/38) of patients were detected with at least 1 monitoring alteration after exclusion of CH mutations using the tumor-agnostic approach. Serial plasma samples after definitive therapy were available for 31 patients. In the landmark ctDNA analysis, 24% (7/29) of patients had detectable ctDNA and were more likely to relapse than ctDNA-negative patients (p < 0.05). The landmark analysis sensitivity and specificity for recurrence were 67% and 87%, respectively. The incorporation of longitudinal ctDNA analysis at 6-months intervals improved the sensitivity to 100%. The median variant allele frequency (VAF) of the ctDNA mutations detected during surveillance was 0.028% (range: 0.018-0.783), where up to 80% (8/10) of the mutations were detected at VAF lower than the tumor-agnostic detection limit of 0.1%. Utilizing the tumor-agnostic approach reduced the recurrence detection sensitivity to 67% (4/6). Serial ctDNA analyses predicted disease recurrence at a median of 5 months ahead of radiological imaging.

Conclusion

Longitudinal monitoring using tumor-informed ctDNA testing shows high analytical sensitivity, low probability of false-positive results due to CH mutations, and improved sensitivity in detecting recurrence which may modify the clinical management of CRC.

Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges

Genomic profiling using tumor biopsies remains the standard approach for the selection of approved molecular targeted therapies. However, this is often limited by its invasiveness, feasibility, and poor sample quality. Liquid biopsies provide a less invasive approach while capturing a contemporaneous and comprehensive tumor genomic profile. Recent advancements in the detection of circulating tumor DNA (ctDNA) from plasma samples at satisfactory sensitivity, specificity, and detection concordance to tumor tissues have facilitated the approval of ctDNA-based genomic profiling to be integrated into regular clinical practice. The recent approval of both single-gene and multigene assays to detect genetic biomarkers from plasma cell-free DNA (cfDNA) as companion diagnostic tools for molecular targeted therapies has transformed the therapeutic decision-making procedure for advanced solid tumors. Despite the increasing use of cfDNA-based molecular profiling, there is an ongoing debate about a 'plasma first' or 'tissue first' approach toward genomic testing for advanced solid malignancies. Both approaches present possible advantages and disadvantages, and these factors should be carefully considered to personalize and select the most appropriate genomic assay. This review focuses on the recent advancements of cfDNA-based genomic profiling assays in advanced solid tumors while highlighting the major challenges that should be tackled to formulate evidence-based guidelines in recommending the 'right assay for the right patient at the right time'.

Serial circulating tumor DNA monitoring of CDK4/6 inhibitors response in metastatic breast cancer

Cyclin‐dependent kinase 4/6 inhibitors (CDK4/6i) significantly improve progression‐free survival and have become the standard therapy for estrogen receptor‐positive/human epidermal growth factor receptor 2‐negative metastatic breast cancer patients. Treatment surveillance by radiological imaging has some limitations in detection and repeated biopsy genomic profiling is not clinically feasible. Serial circulating tumor DNA (ctDNA) analysis may provide insights into treatment response. Here we performed serial ctDNA analysis (n = 178) on 33 patients. Serial ctDNA analysis identified disease progression with sensitivity of 75% and specificity of 92%. In eight of 12 patients (61%) responding to CDK4/6i who eventually developed progressive disease, serial sampling every 3 or 6 months captured the initial rise of ctDNA with an average lead time of 3 months. In three of eight patients that did not respond to CDK4/6i (progressive disease at first radiological assessment, 3 months), biweekly sequencing within the first cycle of CDK4/6i treatment (1 month) detected sustained ctDNA levels (≥0.2% variant allele frequency), with lead time of 2 months. Serial ctDNA analysis tracked RECIST response, including clinically challenging scenarios (bone metastases or small‐sized target lesions), as well as detecting acquired genetic alterations linked to CDK4/6i resistance in the G₁ to S transition phase. Circulating tumor DNA analysis was more sensitive than carcinoembryonic antigen or cancer antigen 15‐3 serum tumor markers at monitoring tumor response to CDK4/6i treatment. Our findings indicated the possible clinical utility of serial ctDNA analysis for earlier progressive disease detection and real‐time monitoring of CDK4/6i response.

Plasma or Serum: Which Is Preferable for Mutation Detection in Liquid Biopsy?

BACKGROUND

Blood-based analysis of circulating tumor DNA (ctDNA) is a promising tool for cancer screening, monitoring relapse/recurrence and evaluating response to treatment. Although plasma is widely used to obtain ctDNA, biorepositories worldwide possess a huge number of serum samples and comparative studies on the use of serum vs plasma as ctDNA sources are essential.

METHODS

We analyzed cell-free DNA (cfDNA) from matched EDTA-plasma and serum samples from healthy donors and patients with colorectal or lung cancer, and used targeted next-generation sequencing to evaluate mutation detection efficiency and reproducibility. Matched samples from healthy individuals were spiked with reference oligonucleotides and sequenced using the Ion-S5 Oncomine-Pan-Cancer panel. Detection efficiency in matched samples from patients with cancer was evaluated using 2 distinct gene panels and compared to mutations found in tissue-biopsy samples at diagnosis.

RESULTS

Mean total cfDNA was 55% higher in serum samples and the presence of longer DNA fragments was significantly increased in serum compared with plasma samples (P = 0.0001 to 0.015). Spiked mutated nucleotides were detected in both samples, but allele frequencies (AF) were approximately half in serum compared with plasma, suggesting ctDNA from serum was more diluted by DNA of noncancerous origins. Matched samples from patients with cancer revealed that up to 44.8% of mutations with low AF were missed in serum samples and concordance rates with somatic mutations found in tissue biopsy at diagnosis was better in plasma samples.

CONCLUSION

The use of serum in retrospective studies should consider the limitations for detecting low AF mutations. Plasma is clearly preferable for prospective clinical applications of liquid biopsy.

Rapid genomic profiling of circulating tumor DNA in non-small cell lung cancer using Oncomine Precision Assay with GenexusTM integrated sequencer

Background

Genomic profiling of tumors from cancer patients facilitates molecular-guided therapy. The turnaround time is one of important issues to deliver results timely for clinical decisions. The Ion Torrent™ Genexus™ Integrated Sequencer automates all next generation sequencing (NGS) workflows and delivers results within a day.

Methods

In this study, we conducted a feasibility study to evaluate the detection rate of genomic alterations from cell-free total nucleic acid (cfTNA, containing cfDNA and cfRNA) of 119 non-small cell lung cancer using Oncomine Precision Assay on Genexus™ Integrated Sequencer. Oncomine Precision Assay (OPA) covers actionable mutations, copy number variations and fusion genes and that are applicable for the selection of targeted therapy. cfTNA isolated from plasma (derived from 14 ml of blood) were subjected to the Genexus system for library construction, templating, sequencing, and data analyses.

Results

The sequencing resulted in median overall depth of 35,773× and median molecular coverage of 2,192× with cfTNA input ranged from 11 to 36 ng. Among the 119 samples evaluated, we detected at least one genomic alteration in plasma cfTNA of 79 cases (66%). When comparing to standard-of-care testing, the sensitivity and specificity of mutation detection in non-small cell lung cancer related genes using liquid biopsy with Genexus-OPA ranged between 49–67% and 93–100%, respectively. 59% of actionable mutations, which were present in tumor tissues, were detected by the Genexus- Oncomine Precision Assay using plasma cfTNA. Among the 5 mutations detected from liquid biopsy only, three mutations are of level 1 evidence according to OncoKB database, highlighting the clinical utilities of liquid biopsy in addressing tumor heterogeneity. Extrathoracic metastasis and levels of lactate dehydrogenase (LDH), C-reactive protein (CRP) and Carcinoembryonic Antigen (CEA) are found to be associated with increased circulating tumor DNA detection.

Conclusions

The Genexus™ Integrated Sequencer system is an automated, accurate NGS system with short turnaround time (TAT) that could assist clinicians to make more timely decision.

Ultradeep targeted sequencing of circulating tumor DNA in plasma of early and advanced breast cancer

We present a study to evaluate the feasibility and clinical utility of amplicon‐based Oncomine Pan‐Cancer cell‐free assay to detect circulating tumor DNA (ctDNA) in patients with early or advanced breast cancer. In this study, 109 early and metastatic breast cancer patients were recruited before the initiation of treatment. ctDNA mutation profiles were assessed through unique molecular tagging (UMT) and ultradeep next generation sequencing (NGS). For patients with mutations, DNA from corresponding white blood cells (WBC) was sequenced to exclude variants of clonal‐hematopoietic (CH) origin. UMT targeted sequencing from plasma of 109 patients achieved a median total coverage of 55 498X and a median molecular coverage of 4187X. Among 53 ctDNA positive samples, 38% were mutation positive by WBC sequencing, indicating potentially false‐positive results contributed by CH origin. Prevalence of CH‐related mutations was associated with age (P = 7.51 × 10⁻⁴). After exclusion of CH mutations, ctDNA detection rates were 37% for local or locally advanced breast cancer (stage I‐III) and 81% for metastatic or recurrent breast cancer. The ctDNA detection rate correlated with disease stage (P = 2.60 × 10⁻⁴), nodal spread (P = 6.49 × 10⁻³) and the status of distant metastases (P = 5.00 × 10⁻⁴). ctDNA variants were detected mostly in TP53, PIK3CA and AKT1 genes, with variants showing therapeutic relevance. This pilot study endorses the use of targeted NGS for non‐invasive molecular profiling of breast cancer. Paired sequencing of plasma ctDNA and WBC should be implemented to improve accurate interpretation of liquid biopsy.

Abstract 3102: Analysis of plasma and serum as a source of circulating tumor DNA for hotspot mutations detection in liquid biopsy

Blood-based analysis of ctDNA is a promising tool for cancer screening, drug selection, detection of minimum residual disease, monitoring release/recurrence and response to treatment. Although plasma is widely used to obtain ctDNA, biorepositories worldwide possess highly-valuable serum samples collection and comparative studies on the use of serum vs plasma as ctDNA source are still essential. Here we analyzed cell free DNA (cfDNA) from matched plasma and serum samples from healthy donors, colorectal and lung cancer patients to evaluate the differences of serum and plasma on mutation detection efficacy and reproducibility by targeted NGS. We initially addressed the difference of both analytes on the quality of cfDNA recovery and on sequencing performance. We then compared mutation detection using matched samples from healthy individuals spiked-in with standard oligonucleotides including common mutations. The amount of cfDNA was more abundant in serum than plasma and the presence of longer DNA fragments was significantly higher in serum samples. Spiked-in mutated nucleotides were detected in both plasma and serum samples, but allele frequencies (AF) were approximately half in serum samples compared with plasma samples, suggesting ctDNA from serum is more diluted in DNAs of noncancerous origins. We further confirmed this difference in detection efficiency using matched plasma and serum samples from cancer patients and found that mutations with low AF are more frequently missed in serum samples. In addition, concordance with tissue-biopsy mutations found at diagnosis was better in plasma samples. Finally, we examined the use of fragment size selection as an alternative tool to improve mutation detection in serum samples. Our findings clearly demonstrated that the use of serum in retrospective studies should consider the limitations for detecting low AF mutations and indicate the advantages of plasma samples for prospective clinical applications of liquid biopsy.

Citation Format: Fabio Pittella-Silva, Yoon Ming Chin, Hui Ting Chan, Satoshi Nagayama, Eisaku Miyauchi, Siew-Kee Low, Yusuke Nakamura. Analysis of plasma and serum as a source of circulating tumor DNA for hotspot mutations detection in liquid biopsy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3102.

Clonal Hematopoiesis in Liquid Biopsy: From Biological Noise to Valuable Clinical Implications

The use of blood liquid biopsy is being gradually incorporated into the clinical setting of cancer management. The minimally invasive nature of the usage of cell-free DNA (cfDNA) and its ability to capture the molecular alterations of tumors are great advantages for their clinical applications. However, somatic mosaicism in plasma remains an immense challenge for accurate interpretation of liquid biopsy results. Clonal hematopoiesis (CH) is part of the normal process of aging with the accumulation of somatic mutations and clonal expansion of hematopoietic stem cells. The detection of these non-tumor derived CH-mutations has been repeatedly reported as a source of biological background noise of blood liquid biopsy. Incorrect classification of CH mutations as tumor-derived mutations could lead to inappropriate therapeutic management. CH has also been associated with an increased risk of developing cardiovascular disease and hematological malignancies. Cancer patients, who are CH carriers, are more prone to develop therapy-related myeloid neoplasms after chemotherapy than non-carriers. The detection of CH mutations from plasma cfDNA analysis should be cautiously evaluated for their potential pathological relevance. Although CH mutations are currently considered as "false-positives" in cfDNA analysis, future studies should evaluate their clinical significance in healthy individuals and cancer patients.

Clinical significance of clonal hematopoiesis in the interpretation of blood liquid biopsy

As the use of next-generation sequencing (NGS) for plasma cell-free DNA (cfDNA) continues to expand in clinical settings, accurate identification of circulating tumor DNA mutations is important to validate its use in the clinical management for cancer patients. Here, we aimed to characterize mutations including clonal hematopoiesis (CH)-related mutations in plasma cfDNA and tumor tissues using the same ultradeep NGS assay and evaluate the clinical significance of CH-related mutations on the interpretation of liquid biopsy results. Ultradeep targeted NGS using Oncomine Pan-Cancer Panel was performed on matched surgically resected tumor tissues, peripheral blood cells (PBCs), and 120 plasma cfDNA samples from 38 colorectal cancer patients. The clinical significance of the CH-related mutations in plasma cfDNA was evaluated by longitudinal monitoring of the postoperative plasma samples. Among the 38 patients, 74 nonsynonymous mutations were identified from tumor tissues and 64 mutations from the preoperative plasma samples. Eleven (17%) of the 64 mutations identified in plasma cfDNA were also detected in PBC DNA and were identified to be CH-related mutations. Overall, 11 of 38 (29%) patients in this cohort harbored at least one CH-related mutation in plasma cfDNA. These CH-related mutations were continuously detected in subsequent postoperative plasma samples from three patients which could be misinterpreted as the presence of residual disease or as lack of treatment response. Our results indicated that it is essential to integrate the mutational information of PBCs to differentiate tumor-derived from CH-related mutations in liquid biopsy analysis. This would prevent the misinterpretation of results to avoid misinformed clinical management for cancer patients.

Abstract A29: Next-generation sequencing of circulating tumor DNA to monitor treatment response to CDK4/6 inhibitors in breast cancer

Background: CDK4/6 inhibitors are effective treatment modalities against hormone receptor-positive metastatic breast cancer (MBC). However, monitoring of clinical responses relies solely on conventional tumor markers that are insufficiently sensitive and specific as well as imaging methods that could not be performed regularly. In this study, we aimed to evaluate the potential utility of circulating tumor DNA (ctDNA) as a complementary approach to monitor clinical response and to evaluate resistance mechanisms associated with CDK4/6 treatment in MBC.

Method: The monitoring duration of this study is up to 24 months or until patient develops disease progression. In this interim report, a total of 100 samples from 21 MBC patients who received CDK4/6 inhibitors were collected before and after treatment. Cell-free DNA/RNA was extracted from plasma and subjected to ultradeep targeted next-generation sequencing (NGS) using Oncomine Pan-Cancer cell-free assay that incorporates the use of unique molecular index. This panel covers more than 1,000 hotspot mutations, 12 CNVs, and 12 fusions in cancer-related genes. Paired NGS was performed with genomic DNA from buffy coat to exclude clonal-hematopoiesis derived mutations. The changes in mutation allele frequency of ctDNA will be compared with tumor markers CA15-3 and CEA as well as CT-imaging and PET-scan results.

Results: According to RECIST criteria, one patient showed complete response 9 months after start of treatment while 11 patients showed partial response or stable disease within 3-12 months from start of treatment. A total of 9 out of 21 MBC patients developed progression of disease within 9 months of treatment. The total and molecular depth of targeted NGS are ~50,000X and ~4000X, respectively. A total of 20 nonsynonymous mutations and 5 copy number variations (CNV) were detected in 16 of the 21 patients (76%) before treatment for response monitoring. The majority of the mutations are in TP53, PIK3CA, and ESR1 genes. The ctDNA profiles were concordant with clinical responses in the majority of the patients. Mutation allele frequencies of ctDNA showed better dynamic changes compared with tumor biomarkers CEA and CA15-3. NGS of ctDNA was able to detect disease progression 3 months in advance or concurrent with imaging data in this study. Diverse ctDNA profiles were observed, indicating the usefulness of ctDNA in detecting intra- and intertumoral heterogeneity. We observed acquired mutations in AKT1 and PIK3CA in one patient, suggesting these mutations were potential CDK4/6 resistance mutations.

Conclusion: Our results suggest that ctDNA may be applied as a robust biomarker to monitor clinical response to the CDK4/6 treatment.

Citation Format: Yoon Ming Chin, Tomoko Shibayama, Masumi Otaki, Hiu Ting Chan, Makiko Ono, Yoshinori Ito, Shunji Takahashi, Shinji Ohno, Takayuki Ueno, Yusuke Nakamura, Siew-Kee Low. Next-generation sequencing of circulating tumor DNA to monitor treatment response to CDK4/6 inhibitors in breast cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A29.

Abstract A46: Next-generation sequencing of circulating tumor DNA for detecting minimal residual disease and predicting recurrence in colorectal cancer patients

Background: Although the prognosis of colorectal cancer (CRC) has improved in the past decade, a subset of CRC patients may still suffer from relapse due to the progression from minimal residual disease (MRD) after surgical resection. A sensitive and noninvasive method to efficiently detect MRD is essential to further improve clinical prognosis. In this study, we have evaluated the feasibility of circulating tumor DNA (ctDNA) analysis in detecting MRD in CRC patients.

Methods: Plasma samples were prospectively collected from 38 CRC patients, ranging from stage I to IV, who underwent surgical resection. A preoperative blood sample was taken just before surgery and postoperative samples were collected on multiple time-points to monitor the changes of mutation profiles. The extracted nucleic acid from matched surgically resected tumor tissues, peripheral blood cells (PBCs), and plasma were subjected to ultradeep targeted next-generation sequencing (NGS) using Oncomine Pan-Cancer Panel.

Results: Cell-free DNA/RNA (cfDNA/RNA) was extracted from 208 preoperative and postoperative plasma samples with a median input of 20 ng for targeted-NGS (ranged from 8-20 ng). The median of sequencing depth, molecular coverage, and barcode tagging efficiency of the sequencing were 54,000x, 4,642x and 84%, respectively. 74 nonsynonymous mutations were identified from tumor tissues and 64 mutations from the preoperative plasma samples. 41 (64.1%) of the 64 mutations detected in plasma samples were concordantly identified from the tumor tissue DNA. Paired PBCs sequencing identified 11 of the mutations detected from plasma and 4 mutations detected from tumor tissues to be clonal hematopoiesis-related mutations. After the exclusion of clonal hematopoiesis-related mutations, 34 (89.5%) of the 38 patients harbor at least one preoperative mutation either from tumor tissue or plasma to be monitored postoperatively. Fourteen patients were detected with ctDNA mutations from postoperative plasma samples and to date, two of them have developed clinical recurrence. One patient was detected to carry TP53-G245D and KRAS-A146T from both the preoperative plasma and resected-tumor tissue. Both mutations were not detected from plasma during adjuvant chemotherapy. At 4.5 months after the completion of chemotherapy, both mutations were positively detected from plasma with no signs of radiologic or clinical evidence of recurrence. Clinical recurrence was confirmed by PET scan 3 months after the detection of molecular recurrence from ctDNA. Similarly, positive ctDNA mutations also preceded radiologic and clinical evidence of recurrence by 3.5 months in another patient who has developed recurrence.

Conclusions: Our current results indicate that ctDNA analysis allows the detection of MRD in CRC patients. The integration of ctDNA analysis with current standard monitoring guidelines holds great promise in early detection of recurrence to allow clinical intervention to be applied promptly.

Citation Format: Hiu Ting Chan, Satoshi Nagayama, Yoon Ming Chin, Masumi Otaki, Rie Hayashi, Kazuma Kiyotani, Yosuke Fukunaga, Masashi Ueno, Yusuke Nakamura, Siew-Kee Low. Next-generation sequencing of circulating tumor DNA for detecting minimal residual disease and predicting recurrence in colorectal cancer patients [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A46.

The application of dynamic monitoring of circulating tumor DNA for detecting minimal residual disease and predicting recurrence in colorectal cancer patients

e15531

Background: Although the prognosis of colorectal cancer (CRC) has improved in the past decade, a subset of CRC patients may still suffer from relapse due to the progression from minimal residual disease (MRD) after surgical resection. A sensitive and non-invasive method to detect MRD and early diagnosis of recurrence disease is warranted to start therapeutic interventions at an earlier timing and improving the overall survival rate. In this study, we have evaluated the feasibility of circulating tumor DNA (ctDNA) analysis to detect MRD and early detection of recurrence in CRC patients. Methods: Plasma samples were collected prospectively from 38 CRC patients (stage I to IV), who underwent surgical resection. Preoperative blood samples were obtained just before surgery and post-operative samples were collected at multiple time-points to monitor the changes of tumor mutation profiles. Tumor-derived mutations were detected in preoperative blood samples as well as surgically resected-tumor tissues using ultradeep targeted next generation sequencing. Patient-paired peripheral blood cells (PBCs) were sequenced concurrently to exclude clonal hematopoiesis-related mutations. Results: Among the 38 patients, 74 non-synonymous mutations were identified in tumor tissues and 64 mutations in the preoperative plasma samples. Paired PBCs sequencing identified 11 mutations in plasma samples to be clonal hematopoiesis-related mutations. After the exclusion of clonal hematopoiesis-related mutations, 34 (89.5%) of the 38 patients harbors at least one somatic mutation either from tumor tissues or plasma samples to be monitored longitudinally. ctDNA was detectable in 5 of 14 (36%) post-surgical samples of patients who did not receive adjuvant chemotherapy and in 9 of 18 (50%) post-chemotherapy samples. Up to date, 6 patients have been detected with clinical recurrence and ctDNA analysis identified all 6 recurrences before imaging. Serial ctDNA analyses were able to detect disease recurrence up to 6 months before imaging tests. Furthermore, all patients that were ctDNA negative post-operative or post-chemotherapy showed no signs of clinical relapse. Conclusions: Our current results indicate that ctDNA analysis allows the detection of MRD in CRC patients. The integration of ctDNA analysis with current standard monitoring guidelines holds great promise in early detection of recurrence to allow clinical intervention to be applied promptly.

Monitoring of therapeutic efficacy to CDK4/6 inhibitors and early detection of metastatic relapse in breast cancer by ultra-deep sequencing of plasma cell-free DNA

e15544

Background: CDK4/6 inhibition substantially improves progression-free survival for women with advanced estrogen receptor-positive breast cancer. Despite this, most patients experience acquired resistance. The analyses of cancer specific genomic aberrations in plasma cell free DNA, or commonly referred to as ‘liquid biopsy’, has generated immense interest. The role of liquid biopsy enables monitoring of therapeutic efficacy to detect relapse in a minimally invasive manner. It would drastically impact risk stratification, treatment selection and patient clinical outcome in advanced stage breast cancer. Methods: We have recruited consecutive patients with metastatic breast cancer who received CDK4/6 inhibitor treatment in combination with endocrine therapy between April 2018 and December 2019. Somatic mutations identified by the Oncomine Pan-Cancer cell free assay were used to assess the mutation profiles of circulating tumor DNA (ctDNA) by ultra-deep sequencing (~56,000 depth) of the plasma DNA. Plasma samples (N = 146) were collected before and during treatment (2 years) or until disease progression. Paired white blood cells (WBC) were also sequenced to exclude clonal hematopoiesis-derived mutations. Results: Twenty-eight patients were enrolled. Based on RECIST criteria, 1 patient showed complete response (CR) within 18 months of treatment, 5 patients showed partial response (PR) 6-18 months from start of treatment, 9 patients showed stable disease (SD) condition within 3-18 months and 13 patients developed progressive disease (PD) within 1-12 months. In 22 of 28 patients (79%), ctDNA was detected prior to start of treatment (12 responders; 10 PD) and used as a monitoring marker. Majority of mutations detected in pre-treatment samples were TP53, PIK3CA and ESR1. Among the 12 ctDNA positive responders, ctDNA levels of 9 patients were undetectable within 2 weeks to 6 months from start of treatment (median 3 months). ctDNA profiles were more reflective of clinical response compared to the tumor markers CEA and CA15-3. In 7 of the 10 PD patients with ctDNA monitoring markers, ctDNA showed higher sensitivity to predict disease progression compared to tumor markers that remained stagnant or below normal threshold. ctDNA also predicted PD earlier than radiological images with a median lead time of 3 months. Conclusions: ctDNA assessment for therapy monitoring and early relapse detection in advanced breast cancer is feasible and provides a basis to evaluate early therapeutic interventions.

Abstract P5-01-15: Monitoring of CDK4/6 inhibitor treatment response through blood liquid biopsy in metastatic breast cancer

Background: Hormone receptor positive breast cancers accounts for approximately 70% of metastatic breast cancers (MBCs), and it is often treated with an anti-hormonal agent as long as possible unless with visceral and aggressive metastasis.CDK4/6 inhibitorsare effective as first- or second-line treatments for metastatic hormone receptor positive HER2 negative breast cancer (HR+ HER2-). When disease progression due to resistance to CDK4/6 treatment occurs, treatment modification is required. Currently, monitoring of treatment response relies solely on imaging.Therefore, through thisstudy, we aim to evaluate ctDNA as a potential biomarker to monitor response to CDK4/6 treatment. Materials & Methods: Patients were recruited from the Cancer Institute Hospital of Japan Foundation for Cancer Research (JFCR).Hormone positive HER2 negative (HR+ HER2-) MBC patients treated with CDK4/6 inhibitors were collected at different timepoints up till 24 months or if patient develops disease progression. These samples were sequenced using a targeted pan-cancer panel that utilizes ultradeep NGS with molecular barcodes.This panel is able to detect all classes of mutations such as single nucleotide variants (SNV), copy number variants (CNV) and fusions. Results:A total of 78 samples from 20patients was sequenced. CDK4/6 was administered as early line treatments. The average total coverage was 56,933X and average molecular coverage was 4,442X.The majority of mutations detected prior to CDK4/6 treatment were TP53, PIK3CAand ESR1. The ctDNA profile is consistent with the clinical status in most patients. ctDNA showed greater dynamics of tumor response to CDK4/6 inhibitor compared to tumor markers CEA and CA15-3.ctDNA was also more sensitive at detecting onset of progression disease compared to imaging. We observed an increase in ctDNA mutation frequency 2-3 months earlier than imaging in 2 patients. From the 20 patients, 7 patients developed progression disease(PD) during our evaluation and required a different treatment. 5 of the 7 patients (71.4%) have ESR1 mutations prior to start of treatment and these patients developed PD within 6 months of treatment. In contrast, no ESR1 mutations were detected in patients who did not develop disease progression. Discussion: In this study, we observed that ctDNA was more sensitive at detecting onset of progression disease compared to imaging. This is essential as early detection of poor response enables timely change of treatment for patients. Patients carrying ESR1mutations respond poorly to CDK4/6 treatment. This might be due to resistance of ESR1mutants to fulvestrant or aromatase inhibitor component of the CDK4/6 treatment regimen. Conclusion: Monitoring of ctDNA is useful to assess treatment response of CDK4/6 inhibitors in metastatic breast cancer patients.

Citation Format: Tomoko Shibayama, Yoon Ming Chin, Makiko Ono, Takayuki Kobayashi, Hiu Ting Chan, Fumitaka Hara, Mari Hosonaga, Kokoro Kobayashi, Rina Inagaki, Yoshinori Ito, Takayuki Ueno, Shunji Takahashi, Shinji Oono, Yusuke Nakamura, Siew Kee Low. Monitoring of CDK4/6 inhibitor treatment response through blood liquid biopsy in metastatic breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-01-15.

Abstract 1338: The application of circulating tumor DNA analysis for detecting minimal residual disease and predicting recurrence in colorectal cancer patients

Background: Although the prognosis of colorectal cancer (CRC) has improved in the past decade, a subset of CRC patients may still suffer from relapse due to the progression from minimal residual disease (MRD) after surgical resection. A sensitive and non-invasive method to efficiently detect MRD is critically essential to further improve the cure rate. In this study, we have evaluated the feasibility of circulating tumor DNA (ctDNA) analysis in detecting MRD in CRC patients. Methods: Plasma samples were prospectively collected from 45 CRC patients, ranged from stage I to IV, who underwent surgical resection. A preoperative blood sample was taken just before surgery and post-operative samples were collected on multiple time-points to monitor the changes of mutation profiles. Cell-free DNA/RNA (cfDNA/RNA) were extracted for library construction using Oncomine Pan-Cancer Cell-Free Assay and were subjected to next-generation sequencing. Results: Sufficient amount of cfDNA/RNA was extracted from 39 of the 45 pre-operatively samples for sequencing. The median input was 19 ng (ranged from 8-20 ng). The median of molecular coverage and barcode tagging efficiency of the sequencing were 4,344x and 83%, respectively. Twenty-seven (69%) of 39 pre-operative patients were found to have at least 2 copies of somatic mutations. Seven samples (ranged from stage I to IV) showed an increase in mutant allele frequency (MAF) postoperatively. The median increase in MAF ranged from 1.2-fold to 7.9-fold with a median of 2.0-fold. One of the 7 patients showed an increase in MAF relapsed 6 months after the primary tumor resection. This stage IIIb patient carried BRAF-V600E with a MAF of 0.067% pre-operatively, showed an 8-fold increase (0.530%) in MAF at the time of diagnosis of recurrence, and showed further increase in MAF to 0.685% at the time of surgical removal of the metastatic lesions. The MAF of BRAF-V600E was reduced to 0.1759% one month after the surgery. The dynamic changes in the MAF detected in ctDNA appears to reflect the recurrence status which might not be detected by imaging tests or currently available biomarkers such as CEA (&lt; 5ng/mL before and after tumor resection in this case). Conclusions: Our current results indicate that ctDNA analysis before and after resection allows the detection of MRD in CRC patients. The integration of ctDNA analysis with current standard monitoring guidelines holds great promise in the early detection of recurrence to allow clinical intervention to be applied promptly.

Citation Format: Hiu Ting Chan, Satoshi Nagayama, Yoon Ming Chin, Rie Hayashi, Kazuma Kiyotani, Yusuke Nakamura, Siew-Kee Low. The application of circulating tumor DNA analysis for detecting minimal residual disease and predicting recurrence in colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1338.

The Roles of Common Variation and Somatic Mutation in Cancer Pharmacogenomics

Cancer pharmacogenomics is the science concerned with understanding genetic alterations and its effects on the pharmacokinetics and pharmacodynamics of anti-cancer drugs, with the aim to provide cancer patients with the precise medication that will achieve a good response and cause low/no incidence of adverse events. Advances in biotechnology and bioinformatics have enabled genomic research to evolve from the evaluation of alterations at the single-gene level to studies on the whole-genome scale using large-scale genotyping and next generation sequencing techniques. International collaborative efforts have resulted in the construction of databases to curate the identified genetic alterations that are clinically significant, and these are currently utilized in clinical sequencing and liquid biopsy screening/monitoring. Furthermore, countless clinical studies have accumulated sufficient evidence to match cancer patients to therapies by utilizing the information of clinical-relevant alterations. In this review we summarize the importance of germline alterations that act as predictive biomarkers for drug-induced toxicity and drug response as well as somatic mutations in cancer cells that function as drug targets. The integration of genomics into the medical field has transformed the era of cancer therapy from one-size-fits-all to cancer precision medicine.

A Genome Wide Study of Copy Number Variation Associated with Nasopharyngeal Carcinoma in Malaysian Chinese Identifies CNVs at 11q14.3 and 6p21.3 as Candidate Loci

Background

Nasopharyngeal carcinoma (NPC) is a neoplasm of the epithelial lining of the nasopharynx. Despite various reports linking genomic variants to NPC predisposition, very few reports were done on copy number variations (CNV). CNV is an inherent structural variation that has been found to be involved in cancer predisposition.

Methods

A discovery cohort of Malaysian Chinese descent (NPC patients, n = 140; Healthy controls, n = 256) were genotyped using Illumina^® HumanOmniExpress BeadChip. PennCNV and cnvPartition calling algorithms were applied for CNV calling. Taqman CNV assays and digital PCR were used to validate CNV calls and replicate candidate copy number variant region (CNVR) associations in a follow-up Malaysian Chinese (NPC cases, n = 465; and Healthy controls, n = 677) and Malay cohort (NPC cases, n = 114; Healthy controls, n = 124).

Results

Six putative CNVRs overlapping GRM5, MICA/HCP5/HCG26, LILRB3/LILRA6, DPY19L2, RNase3/RNase2 and GOLPH3 genes were jointly identified by PennCNV and cnvPartition. CNVs overlapping GRM5 and MICA/HCP5/HCG26 were subjected to further validation by Taqman CNV assays and digital PCR. Combined analysis in Malaysian Chinese cohort revealed a strong association at CNVR on chromosome 11q14.3 (P_combined = 1.54x10^-5; odds ratio (OR) = 7.27; 95% CI = 2.96–17.88) overlapping GRM5 and a suggestive association at CNVR on chromosome 6p21.3 (P_combined = 1.29x10^-3; OR = 4.21; 95% CI = 1.75–10.11) overlapping MICA/HCP5/HCG26 genes.

Conclusion

Our results demonstrated the association of CNVs towards NPC susceptibility, implicating a possible role of CNVs in NPC development.

Significant impact of gene polymorphisms on tacrolimus but not cyclosporine dosing in Asian renal transplant recipients

Calcineurin inhibitors (CNI) are metabolized by cytochrome-P4503A (CYP3A) enzymes and extruded into the intestinal lumen by the drug efflux pump, P-glycoprotein (P-gp). The impact of single nucleotide polymorphisms (SNPs) of genes encoding CYP3A5 and P-gp on CNI dosing was examined among Asian renal transplant recipients. Frequencies of CYP3A5*1 versus *3 and MDR1-C3435T were correlated with tacrolimus (TAC) and cyclosporine (CSA) concentration-to-dose (C/D) ratios. Among 82 recipients (49% male; 88% Chinese), the majority were CYP3A5 expressors (*1*1 and *1*3, 11% and 40%, respectively) and 49% were nonexpressors (*3/*3). The prevalence of MDR-1-C3435T variants was 3435CC (41%), 3435CT (46%), and 3435TT (13%). Among 18 TAC-treated recipients, all receiving Diltiazem (DTZ), the median C/D ratio was lower for CYP3A5 *1/*1 versus *1/*3 versus *3/*3 (1.9, 4.6, and 13.5 ng/mL per 0.1 mg/kg/d, respectively; P = .001). The median C/D ratio was higher for TAC-treated patients with MDR-1-3435CC (14.1, 7.3, and 2.2 ng/mL per 0.1 mg/kg/d for CC, CT, and TT, respectively; P = .023). Neither CYP3A5 nor MDR-1-C3435T variants had an impact on CSA C/D ratios. Thus, CYP3A5 SNP has a significant impact on TAC dosing in Asian renal transplant recipients, which was likely to facilitate TAC metabolism. Although MDR-1-3435CC with higher P-gp expression should experience more TAC efflux and, therefore, lower TAC C/D ratios, all MDR-1-3435CC carriers were CYP3A5 nonexpressors; the latter ultimately contributed to the observed higher TAC C/D ratios in this population. This study advocates starting with a higher TAC dose for CYP3A5 expressors. Coadministration of DTZ may further optimize the TAC level through preferential P-gp binding and CYP3A4 inhibition.

Clinical features and treatment outcome of children with myeloid antigen coexpression in B-lineage acute lymphoblastic leukemia: a study of 151 Malaysian children

The purpose of the study was to evaluate the incidence of myeloid antigen coexpression and its prognostic significance in childhood acute lymphoblastic leukemia (ALL) in Malaysia. A retrospective study was conducted of all ALL cases (< or = 12 years old) diagnosed and treated in University Hospital, Kuala Lumpur, Malaysia between 1 January 1992 and 30 May 1995, with available immunophenotype data. Presenting features and treatment outcome of 39 B-lineage ALL patients with myeloid antigen coexpression (My+B) were compared with 112 B-lineage ALL patients without myeloid antigen coexpression (My-B) for similarity in demographic, clinical and laboratory features and their treatment outcome. My+B and My-B patients were treated with a uniform treatment protocol. Myeloid antigen coexpression was defined as more than 30% isolated leukemic cells positive for CD13 and/or CD33. The ages at diagnoses ranged from 2 months to 12 years. Median age was 4 years. The incidence of myeloid antigen coexpression was 23 per cent. Univariate analyses showed that presenting features were similar between My+B and My-B with regard to age, sex, race, FAB morphology, white cell count, hemoglobin level, platelet count, liver/spleen size, central nervous system or mediastinal involvement, presence of lymphadenopathy, and proportion of blast cells detected in the marrow. Treatment outcome were not significant between the two groups. The 2-year event free survival was achieved in 44 per cent of My+B and 57 per cent of My-B (p = 0.11). The 2-year overall survival rates were 62 per cent for My+B vs. 77 per cent for My-B (p = 0.08). This study demonstrates that myeloid antigen coexpression is fairly common and constitutes 23 per cent of childhood ALL within the Malaysian population and that it is not an adverse risk factor in childhood ALL.

The changing pattern of glomerulonephritis in Singapore over the past two decades

This study reviews the pattern of glomerulonephritis (GN) in Singapore over the past 2 decades. In the earlier decade the pattern was typical of most Asian countries with mesangial proliferative GN (Mes GN) (56%) as the most common form of primary GN including the nephrotic syndrome (40%). In the 2nd decade the pattern undergoes a change. Though Mes GN is the commonest primary GN (42%), the commonest form of nephrotic syndrome is now minimal change disease (30%) with Mes GN decreasing to 25% among all primary nephrotic syndromes. Both minimal change and focal global sclerosis account for 50% of steroid/cyclophosphamide responsive GN today. Membranous GN though still uncommon, has increased from 3% (1st decade) to 6% (2nd decade) (p < 0.01). IgA nephritis is still the commonest primary GN occurring in Singapore (42% of all primary GN in the 1st decade and 45% in the 2nd decade). The present pattern of GN in Singapore, though, still predominantly Asian with the preponderance of mesangial proliferative GN with a relatively low incidence of membranous GN contrasts with the pattern in the West where membranous GN is the commonest form of primary GN. Even the incidence of FSGS has not increased as in the West where there is a rising incidence. The underlying basis for most GN in Singapore as in other Asian countries and elsewhere is antigen-driven: infective antigen as well as food or other allergens.

Concordant childhood acute lymphoblastic leukemia in monozygotic twins

Two 4-year-old monozygotic Chinese, female twins developed concordant childhood acute lymphoblastic leukemia (ALL) within an interval of about 2 weeks. Based on morphology and cytochemistry findings of the bone marrow blast cells, a diagnosis of ALL, L1 was made. Immunophenotyping showed the blast cells of both twins expressed similar antigens, i.e. HLA-DR, CD10, CD13, CD19, CD22 and CD34. Identical blood group, same HLA (human leucocyte antigen) genotype, sex and similar appearance suggest that the twins are monozygotic. Since the bone marrow leukemic cells of both twins were identical in morphology and expressed the same antigens with almost similar percentages of positivity, it is likely that the blast cells were derived from the same single clone. Based on the single clone hypothesis, the leukemogenic event must have arisen in utero in one twin and the cells from the abnormal clone then spread to the other twin via shared placental anastomoses.

Isoelectric focusing and selectivity index in IgA nephrotic syndrome

Proteinuria in 13 patients with IgA nephritis with nephrotic syndrome (IgANS) was analysed by isoelectric focusing (IEF) and compared with 12 patients with minimal change nephrotic syndrome (MCNS) (n = 8) or focal global sclerosis nephrotic syndrome (FGS) (n = 4) to determine the pattern of proteinuria on IEF and to assess the value of IEF and protein selectivity index (SI) as predictors of response to therapy with predisolone or cyclophosphamide. Steroid/cyclophosphamide responsive patients with IgANS had SC:UA (cationic serum albumin with anionic urine albumin) or SA:UC (anionic serum albumin with cationic urine albumin) IEF patterns and steroid/cyclophosphamide unresponsive patients with IgANS had an SC:UC (cationic serum albumin with cationic urine albumin) IEF pattern. The majority of patients with MCNS or FGS who had an SA:UC IEF pattern were steroid responsive. SI was a better predictor of steroid/cyclophosphamide responsiveness in patients with IgANS (r = 0.78, p < 0.002 compared to IEF, r = 0.64, p < 0.02).

The impact of percutaneous renal biopsies on clinical management

Percutaneous renal biopsy (PRB) is now standard practice in clinical nephrology. One hundred consecutive non-transplant PRBs performed on adult patients at the Department of Renal Medicine, Singapore General Hospital, between January and August 1990, were analysed to examine the impact and complications of PRBs in a single institution. The study population consisted of 37 male and 63 female patients with a mean age of 32 +/- 11.9 years. The most frequent indications for PRB were systemic lupus erythematosus with renal involvement (41 patients), haematuria and proteinuria (27 patients) and the nephrotic syndrome (26 patients). Histological diagnoses included lupus nephritis in 45 patients, IgA nephritis in 19 patients, minimal change/focal global sclerosis in 14, non-IgA mesangioproliferative glomerulonephritis in seven and other histologies in the remainder. Eighty-two of our patients received renal-specific therapy, including 72 who received prednisolone or other immunosuppression, and 11 who received persantin and warfarin, in contrast to only 18 patients who received non-specific therapy including diuretics, antihypertensive drugs or dialysis. PRB led to change in therapy in 54% of all our patients, including 42 who had immunosuppressive drugs added to their therapeutic regimen and 11 who were commenced on persantin and/or warfarin. Complications of the procedure were minimal with flank pain in 6% and gross haematuria in 4%. As the inherent risks of inappropriate immunosuppression are well established, these results suggest that PRBs have a major impact on clinical management.

Breakpoint cluster region (BCR) gene rearrangement studies in chronic myeloid and acute lymphoblastic leukemias

Deoxyribonucleic acid (DNA) of twenty chronic myeloid leukemia (CML) and thirty acute lymphoblastic leukemia (ALL) patients were analysed by Southern hybridization. The DNA was digested with BglII and hybridized with a 4.5-kilobase (kb) ph1/bcr-3 DNA probe. All the 20 CML patients showed gene rearrangement within a 5.8-kb segment (the major breakpoint cluster region, M-bcr) of the breakpoint cluster region (bcr) gene of chromosome 22, indicating the presence of the Philadelphia chromosome. M-bcr rearrangement at the bcr gene of chromosome twenty-two was not detected in all the thirty ALL patients (nine adults and twenty-one children) and two normal controls.

Biphenotypic hybrid acute leukaemia detected by two colour flow cytometry

Immunophenotypic studies using immunofluorescent flow cytometry were performed on the blast cells of 36 patients with acute leukaemia using a panel of eight monoclonal antibodies. Six patients had blasts which co-expressed markers for lymphoid and myeloid differentiation, and which were therefore defined as biphenotypic hybrid acute leukaemia. Of the six, three patients were in the paediatric age group (below 12 years old) while the other three were more than 12 years old. Peripheral blood counts were variable; however, bone marrow infiltration was extensive (blasts > or = 75% in all). At the time of study, remission was achieved in only two patients. The authors' data show that biphenotypic hybrid acute leukaemia is not rare in Malaysia. This represents a subgroup of acute leukaemia identifiable by immunophenotyping but not by the French-American-British classification based on morphological and basic cytochemical studies alone. The recognition of this subgroup is important for both practical and theoretical reasons. There are implications for treatment of the individual patient because treatment directed at a single lineage may not be effective. The two colour flow cytometry proved to be a useful tool for diagnosis and classification of acute leukaemia.

Analysis of ras gene mutations in acute myeloid leukemia by the polymerase chain reaction and oligonucleotide probes

In vitro deoxyribonucleic acid (DNA) amplification by the polymerase chain reaction (PCR) followed by hybridization with oligonucleotide probes were used to study ras gene mutations in acute myeloid leukemia (AML). The DNA of 30 AML patients at presentation of the disease at the University of Malaya Hospital, Kuala Lumpur were screened for ras gene mutations in codons 12, 13 and 61 of the N-ras, K-ras and H-ras genes. Four patients (13.3%) had ras gene mutations. They were all below their early thirties in age. Of the four patients with ras gene mutations, three were M3 and one was M4 according to the French American British (FAB) classification of AML.

Cytogenetic studies in women with primary amenorrhea

Cytogenetic investigations were carried out on 117 women with primary amenorrhea who had been referred to our Genetics Laboratory by clinicians throughout Malaysia, after exclusion of other causes of the disorder. Thirty-six cases (31%) showed numerical or structural abnormalities of the sex chromosomes. These can be broadly classified into 4 main types, namely, presence of a Y chromosome (14%), X-chromosome aneuploidies (8%), structural anomalies of the X-chromosome (7%) and lastly, presence of a marker chromosome (2%). Mosaics constituted 17% of the abnormalities observed, always in association with a 45,X cell line. There was no observable correlation between the phenotype of the patients and their respective abnormal karyotypes. The aetiological role of sex chromosomal abnormalities in these amenorrheic women is discussed.

Three cases of partial trisomy 9q in one generation due to maternal reciprocal t(6;8;9) translocation

A family is described in which three siblings had congenital abnormalities consistent with partial trisomy 9q syndrome. Karyotyping indicated that the mother was a carrier of two separate balanced reciprocal translocations involving three chromosomes (46,XX,t (6;8;9)(6q27;8p23;9q32;9q13] resulting from four breakpoints. The three siblings had inherited the der(8) from their mother and hence were partially trisomic for 9q32----9qter and partially monosomic for 8p23----8pter (46,XX,der(8),t(8;9)(p23;q32)mat). The clinical features of the three cases were comparable to those reported in the literature.