Liquid biopsies for residual disease and recurrence

Despite the intensive efforts dedicated to cancer diagnosis and treatment, lung cancer (LCa) remains the leading cause of cancer-related mortality, worldwide. The poor survival rate among lung cancer patients commonly results from diagnosis at late-stage, limitations in characterizing tumor heterogeneity and the lack of non-invasive tools for detection of residual disease and early recurrence. Henceforth, research on liquid biopsies has been increasingly devoted to overcoming these major limitations and improving management of LCa patients. Liquid biopsy is an emerging field that has evolved significantly in recent years due its minimally invasive nature and potential to assess various disease biomarkers. Several strategies for characterization of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have been developed. With the aim of standardizing diagnostic and follow-up practices, microfluidic devices have been introduced to improve biomarkers isolation efficiency and specificity. Nonetheless, implementation of lab-on-a-chip platforms in clinical practice may face some challenges, considering its recent application to liquid biopsies. In this review, recent advances and strategies for the use of liquid biopsies in LCa management are discussed, focusing on high-throughput microfluidic devices applied for CTCs and ctDNA isolation and detection, current clinical validation studies and potential clinical utility.

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Rationale for Early Detection of EWSR1 Translocation-Associated Sarcoma Biomarkers in Liquid Biopsy

Cancers ◽

10.3390/cancers13040824 ◽

2021 ◽

Vol 13 (4) ◽

pp. 824

Author(s):

Felix I. L. Clanchy

Keyword(s):

Early Detection ◽

Liquid Biopsy ◽

Residual Disease ◽

Surgical Excision ◽

Molecular Techniques ◽

Rt Pcr ◽

Liquid Biopsies ◽

Societal Burden ◽

Recent Developments ◽

Mesenchymal Tumours

Sarcomas are mesenchymal tumours that often arise and develop as a result of chromosomal translocations, and for several forms of sarcoma the EWSR1 gene is a frequent translocation partner. Sarcomas are a rare form of malignancy, which arguably have a proportionally greater societal burden that their prevalence would suggest, as they are more common in young people, with survivors prone to lifelong disability. For most forms of sarcoma, histological diagnosis is confirmed by molecular techniques such as FISH or RT-PCR. Surveillance after surgical excision, or ablation by radiation or chemotherapy, has remained relatively unchanged for decades, but recent developments in molecular biology have accelerated the progress towards routine analysis of liquid biopsies of peripheral blood. The potential to detect evidence of residual disease or metastasis in the blood has been demonstrated by several groups but remains unrealized as a routine diagnostic for relapse during remission, for disease monitoring during treatment, and for the detection of occult, residual disease at the end of therapy. An update is provided on research relevant to the improvement of the early detection of relapse in sarcomas with EWSR1-associated translocations, in the contexts of biology, diagnosis, and liquid biopsy.

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Implementing ctDNA Analysis in the Clinic: Challenges and Opportunities in Non-Small Cell Lung Cancer

Cancers ◽

10.3390/cancers12113112 ◽

2020 ◽

Vol 12 (11) ◽

pp. 3112

Author(s):

Elisa Gobbini ◽

Aurélie Swalduz ◽

Matteo Giaj Levra ◽

Sandra Ortiz-Cuaran ◽

Anne-Claire Toffart ◽

...

Keyword(s):

Lung Cancer ◽

Small Cell Lung Cancer ◽

Cell Lung Cancer ◽

Clinical Relevance ◽

Residual Disease ◽

Locally Advanced ◽

Small Cell ◽

Small Cell Lung ◽

Liquid Biopsies ◽

Ctdna Analysis

Tumor genomic profiling has a dramatic impact on the selection of targeted treatment and for the identification of resistance mechanisms at the time of progression. Solid tissue biopsies are sometimes challenging, and liquid biopsies are used as a non-invasive alternative when tissue is limiting. The clinical relevance of tumor genotyping through analysis of ctDNA is now widely recognized at all steps of the clinical evaluation process in metastatic non-small cell lung cancer (NSCLC) patients. ctDNA analysis through liquid biopsy has recently gained increasing attention as well in the management of early and locally advanced, not oncogene-addicted, NSCLC. Its potential applications in early disease detection and the response evaluation to radical treatments are promising. The aim of this review is to summarize the landscape of liquid biopsies in clinical practice and also to provide an overview of the potential perspectives of development focusing on early detection and screening, the assessment of minimal residual disease, and its potential role in predicting response to immunotherapy. In addition to available studies demonstrating the clinical relevance of liquid biopsies, there is a need for standardization and well-designed clinical trials to demonstrate its clinical utility.

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ctDNA monitoring using patient-specific sequencing and integration of variant reads

Science Translational Medicine ◽

10.1126/scitranslmed.aaz8084 ◽

2020 ◽

Vol 12 (548) ◽

pp. eaaz8084 ◽

Cited By ~ 13

Author(s):

Jonathan C. M. Wan ◽

Katrin Heider ◽

Davina Gale ◽

Suzanne Murphy ◽

Eyal Fisher ◽

...

Keyword(s):

Residual Disease ◽

Early Stage ◽

Area Under The Curve ◽

Patient Specific ◽

Sequencing Data ◽

Liquid Biopsies ◽

Whole Exome ◽

Mutation Burden ◽

Median Area ◽

Personalized Cancer

Circulating tumor-derived DNA (ctDNA) can be used to monitor cancer dynamics noninvasively. Detection of ctDNA can be challenging in patients with low-volume or residual disease, where plasma contains very few tumor-derived DNA fragments. We show that sensitivity for ctDNA detection in plasma can be improved by analyzing hundreds to thousands of mutations that are first identified by tumor genotyping. We describe the INtegration of VAriant Reads (INVAR) pipeline, which combines custom error-suppression methods and signal-enrichment approaches based on biological features of ctDNA. With this approach, the detection limit in each sample can be estimated independently based on the number of informative reads sequenced across multiple patient-specific loci. We applied INVAR to custom hybrid-capture sequencing data from 176 plasma samples from 105 patients with melanoma, lung, renal, glioma, and breast cancer across both early and advanced disease. By integrating signal across a median of >105 informative reads, ctDNA was routinely quantified to 1 mutant molecule per 100,000, and in some cases with high tumor mutation burden and/or plasma input material, to parts per million. This resulted in median area under the curve (AUC) values of 0.98 in advanced cancers and 0.80 in early-stage and challenging settings for ctDNA detection. We generalized this method to whole-exome and whole-genome sequencing, showing that INVAR may be applied without requiring personalized sequencing panels so long as a tumor mutation list is available. As tumor sequencing becomes increasingly performed, such methods for personalized cancer monitoring may enhance the sensitivity of cancer liquid biopsies.

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Current Status of Circulating Tumor Cells, Circulating Tumor DNA, and Exosomes in Breast Cancer Liquid Biopsies

International Journal of Molecular Sciences ◽

10.3390/ijms21249457 ◽

2020 ◽

Vol 21 (24) ◽

pp. 9457

Author(s):

Marta Tellez-Gabriel ◽

Erik Knutsen ◽

Maria Perander

Keyword(s):

Breast Cancer ◽

Residual Disease ◽

Early Stage ◽

Clonal Evolution ◽

Current Status ◽

Primary Therapy ◽

Liquid Biopsies ◽

Diagnose Breast Cancer ◽

Early Stage Disease ◽

Cancer Management

Breast cancer is the most common cancer among women worldwide. Although the five-, ten- and fifteen-year survival rates are good for breast cancer patients diagnosed with early-stage disease, some cancers recur many years after completion of primary therapy. Tumor heterogeneity and clonal evolution may lead to distant metastasis and therapy resistance, which are the main causes of breast cancer-associated deaths. In the clinic today, imaging techniques like mammography and tissue biopsies are used to diagnose breast cancer. Even though these methods are important in primary diagnosis, they have limitations when it comes to longitudinal monitoring of residual disease after treatment, disease progression, therapy responses, and disease recurrence. Over the last few years, there has been an increasing interest in the diagnostic, prognostic, and predictive potential of circulating cancer-derived material acquired through liquid biopsies in breast cancer. Thanks to the development of sensitive devices and platforms, a variety of tumor-derived material, including circulating cancer cells (CTCs), circulating DNA (ctDNA), and biomolecules encapsulated in extracellular vesicles, can now be extracted and analyzed from body fluids. Here we will review the most recent studies on breast cancer, demonstrating the clinical potential and utility of CTCs and ctDNA. We will also review literature illustrating the potential of circulating exosomal RNA and proteins as future biomarkers in breast cancer. Finally, we will discuss some of the advantages and limitations of liquid biopsies and the future perspectives of this field in breast cancer management.

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ctDNAtools: An R package to work with sequencing data of circulating tumor DNA

10.1101/2020.01.27.912790 ◽

2020 ◽

Author(s):

Amjad Alkodsi ◽

Leo Meriranta ◽

Annika Pasanen ◽

Sirpa Leppä

Keyword(s):

Residual Disease ◽

Fragment Size ◽

R Package ◽

Monte Carlo Sampling ◽

Circulating Tumor Dna ◽

Cancer Diagnostics ◽

Sequencing Data ◽

Liquid Biopsies ◽

Tumor Dna

AbstractSummarySequencing of cell-free DNA (cfDNA) including circulating tumor DNA (ctDNA) in minimally-invasive liquid biopsies is rapidly maturing towards clinical utility for cancer diagnostics. However, the publicly available bioinformatics tools for the specialized analysis of ctDNA sequencing data are still scarce. Here, we present the ctDNAtools R package, which provides functionalities for testing minimal residual disease (MRD) and analyzing cfDNA fragmentation. MRD detection in ctDNAtools utilizes a Monte Carlo sampling approach to test ctDNA positivity through tracking a set of pre-detected reporter mutations in follow-up samples. Additionally, ctDNAtools includes various functionalities to study cfDNA fragment size histograms, profiles and fragment ends patterns.AvailabilityThe ctDNAtools package is freely available under MIT license at https://github.com/alkodsi/ctDNAtools.

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Relapsed Medulloblastoma in Pre-Irradiated Patients: Current Practice for Diagnostics and Treatment

Cancers ◽

10.3390/cancers14010126 ◽

2021 ◽

Vol 14 (1) ◽

pp. 126

Author(s):

Rebecca M. Hill ◽

Sabine L. A. Plasschaert ◽

Beate Timmermann ◽

Christelle Dufour ◽

Kristian Aquilina ◽

...

Keyword(s):

Residual Disease ◽

Primary Tumour ◽

Treatment Resistance ◽

Signs And Symptoms ◽

Treatment Modalities ◽

Diagnostic Process ◽

Liquid Biopsies ◽

Early Therapy ◽

Paediatric Tumours ◽

Molecular Group

Relapsed medulloblastoma (rMB) accounts for a considerable, and disproportionate amount of childhood cancer deaths. Recent advances have gone someway to characterising disease biology at relapse including second malignancies that often cannot be distinguished from relapse on imaging alone. Furthermore, there are now multiple international early-phase trials exploring drug–target matches across a range of high-risk/relapsed paediatric tumours. Despite these advances, treatment at relapse in pre-irradiated patients is typically non-curative and focuses on providing life-prolonging and symptom-modifying care that is tailored to the needs and wishes of the individual and their family. Here, we describe the current understanding of prognostic factors at disease relapse such as principal molecular group, adverse molecular biology, and timing of relapse. We provide an overview of the clinical diagnostic process including signs and symptoms, staging investigations, and molecular pathology, followed by a summary of treatment modalities and considerations. Finally, we summarise future directions to progress understanding of treatment resistance and the biological mechanisms underpinning early therapy-refractory and relapsed disease. These initiatives include development of comprehensive and collaborative molecular profiling approaches at relapse, liquid biopsies such as cerebrospinal fluid (CSF) as a biomarker of minimal residual disease (MRD), modelling strategies, and the use of primary tumour material for real-time drug screening approaches.

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MAESTRO affords ‘breadth and depth’ for mutation testing

10.1101/2021.01.22.427323 ◽

2021 ◽

Author(s):

Gregory Gydush ◽

Erica Nguyen ◽

Jin H. Bae ◽

Justin Rhoades ◽

Sarah C. Reed ◽

...

Keyword(s):

Residual Disease ◽

Low Frequency ◽

Mutation Testing ◽

Liquid Biopsies ◽

Cancer Genome Sequencing ◽

Large Numbers ◽

Powerful Approach ◽

Sequencing Studies ◽

Duplex Sequencing ◽

Parallel Mutation

AbstractThe ability to assay large numbers of low-abundance mutations is crucial in biomedicine. Yet, the technical hurdles of sequencing multiple mutations at extremely high depth and accuracy remain daunting. For sequencing low-level mutations, it’s either ‘depth or breadth’ but not both. Here, we report a simple and powerful approach to accurately track thousands of distinct mutations with minimal reads. Our technique called MAESTRO (minor allele enriched sequencing through recognition oligonucleotides) employs massively-parallel mutation enrichment to empower duplex sequencing—one of the most accurate methods—to track up to 10,000 low-frequency mutations with up to 100-fold less sequencing. In example use cases, we show that MAESTRO could enable mutation validation from cancer genome sequencing studies. We also show that it could track thousands of mutations from a patient’s tumor in cell-free DNA, which may improve detection of minimal residual disease from liquid biopsies. In all, MAESTRO improves the breadth, depth, accuracy, and efficiency of mutation testing.

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Circulating Tumor DNA as a Biomarker for Outcomes Prediction in Colorectal Cancer Patients

Current Drug Targets ◽

10.2174/1389450121999201103194248 ◽

2020 ◽

Vol 21 ◽

Author(s):

Angelica Petrillo ◽

Massimiliano Salati ◽

Dario Trapani ◽

Michele Ghidini

Keyword(s):

Colorectal Cancer ◽

Residual Disease ◽

Early Stage ◽

Recurrence Risk ◽

Early Response ◽

Circulating Tumor Dna ◽

Response To Treatment ◽

Molecular Profile ◽

Liquid Biopsies ◽

Tissue Biopsy

Abstract:: Circulating tumour DNA (ctDNA) is a novel tool that has being investigated in several types of tumours, includ-ing colorectal cancer (CRC). In fact, the techniques based on liquid biopsies are proposed as appealing non-invasive alter-natives to tissue biopsy, adding more insights into tumour molecular profile, heterogeneity and for cancer detection and monitoring. Additionally, some analysis showed that in CRC patients ctDNA seems to act as biomarker able to predict the outcome (prognostic role) and the response to treatments (predictive role). In particular, in the early stage CRC (stage I-III) it could represent a time marker of adjuvant therapy benefit as well as a marker of minimal residual disease and recurrence risk in addition to the already recognized risk factors. In metastatic CRC, the analysis of molecular tumour profile by ctDNA has shown to have high concordance with the tissue biopsy at diagnosis. Additionally, some studies demonstrated that ctDNA level during the treatment was linked with early response to treatment and prognosis. Finally, the quantitative anal-ysis of ctDNA and copy number alterations may be useful in order to detect resistance to therapy at the time of progression of disease and to help in finding new therapeutic targets.

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Coupled liquid biopsy and bioinformatics for pancreatic cancer early detection and precision prognostication

Molecular Cancer ◽

10.1186/s12943-021-01309-7 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Jun Hou ◽

XueTao Li ◽

Ke-Ping Xie

Keyword(s):

Pancreatic Cancer ◽

Early Detection ◽

Residual Disease ◽

Liquid Biopsies ◽

Tissue Samples ◽

Complete Representation ◽

Minimal Invasiveness ◽

Cancer Early Detection ◽

Pancreatic Cancer Cells ◽

Repeated Sampling

AbstractEarly detection and diagnosis are the key to successful clinical management of pancreatic cancer and improve the patient outcome. However, due to the absence of early symptoms and the aggressiveness of pancreatic cancer, its 5-year survival rate remains below 5 %. Compared to tissue samples, liquid biopsies are of particular interest in clinical settings with respect to minimal invasiveness, repeated sampling, complete representation of the entire or multi-site tumor bulks. The potential of liquid biopsies in pancreatic cancer has been demonstrated by many studies which prove that liquid biopsies are able to detect early emergency of pancreatic cancer cells, residual disease, and recurrence. More interestingly, they show potential to delineate the heterogeneity, spatial and temporal, of pancreatic cancer. However, the performance of liquid biopsies for the diagnosis varies largely across different studies depending of the technique employed and also the type and stage of the tumor. One approach to improve the detect performance of liquid biopsies is to intensively inspect circulome and to define integrated biomarkers which simultaneously profile circulating tumor cells and DNA, extracellular vesicles, and circulating DNA, or cell free DNA and proteins. Moreover, the diagnostic validity and accuracy of liquid biopsies still need to be comprehensively demonstrated and validated.

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