Abstract 1286: Analytical validation of an integrated next-generation sequencing pan-cancer liquid biopsy approach for detection of microsatellite instability

Background: Microsatellite instability (MSI) is a prognostic biomarker used to guide medication selection in multiple cancers, such as colorectal cancer. Traditional PCR with capillary electrophoresis and next-generation sequencing using paired tumor tissue and leukocyte samples are the main approaches for MSI detection due to their high sensitivity and specificity. Currently, patient tissue samples are obtained through puncture or surgery, which causes injury and risk of concurrent disease, further illustrating the need for MSI detection by liquid biopsy. Methods: We propose an analytic method using paired plasma/leukocyte samples and MSI detection using next-generation sequencing technology. Based on the theoretical progress of oncogenesis, we hypothesized that the microsatellite site length in plasma equals the combination of the distribution of tumor tissue and leukocytes. Thus, we defined a window-judgement method to identify whether biomarkers were stable. Results: Compared to traditional PCR as the standard, we evaluated three methods in 20 samples (MSI-H:3/MSS:17): peak shifting method using tissue vs. leukocytes, peak shifting method using plasma vs. leukocytes, and our method using plasma vs. leukocytes. Compared to traditional PCR, we observed a sensitivity of 100%, 0%, and 100%, and a specificity of 100.00%, 94.12%, and 88.24%, respectively. Conclusion: Our method has the advantage of possibly detecting MSI in a liquid biopsy and provides a novel direction for future studies to increase the specificity of the method.

Download Full-text

Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC’s Analytical Variables Working Group

Clinical Chemistry ◽

10.1093/clinchem/hvaa164 ◽

2020 ◽

Vol 66 (9) ◽

pp. 1156-1166 ◽

Cited By ~ 1

Author(s):

James H Godsey ◽

Angela Silvestro ◽

J Carl Barrett ◽

Kelli Bramlett ◽

Darya Chudova ◽

...

Keyword(s):

Next Generation Sequencing ◽

Liquid Biopsy ◽

Working Group ◽

Circulating Tumor Dna ◽

Next Generation ◽

Analytical Validation ◽

Consensus Recommendation ◽

Next Generation Sequencing Ngs ◽

Development And Validation ◽

Generation Sequencing

Abstract Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has demonstrated considerable promise for numerous clinical intended uses. Successful validation and commercialization of novel ctDNA tests have the potential to improve the outcomes of patients with cancer. The goal of the Blood Profiling Atlas Consortium (BloodPAC) is to accelerate the development and validation of liquid biopsy assays that will be introduced into the clinic. To accomplish this goal, the BloodPAC conducts research in the following areas: Data Collection and Analysis within the BloodPAC Data Commons; Preanalytical Variables; Analytical Variables; Patient Context Variables; and Reimbursement. In this document, the BloodPAC’s Analytical Variables Working Group (AV WG) attempts to define a set of generic analytical validation protocols tailored for ctDNA-based Next-Generation Sequencing (NGS) assays. Analytical validation of ctDNA assays poses several unique challenges that primarily arise from the fact that very few tumor-derived DNA molecules may be present in circulation relative to the amount of nontumor-derived cell-free DNA (cfDNA). These challenges include the exquisite level of sensitivity and specificity needed to detect ctDNA, the potential for false negatives in detecting these rare molecules, and the increased reliance on contrived samples to attain sufficient ctDNA for analytical validation. By addressing these unique challenges, the BloodPAC hopes to expedite sponsors’ presubmission discussions with the Food and Drug Administration (FDA) with the protocols presented herein. By sharing best practices with the broader community, this work may also save the time and capacity of FDA reviewers through increased efficiency.

Download Full-text

An enhanced next-generation sequencing liquid biopsy assay for simultaneous detection of somatic variants, microsatellite instability and viral DNA.

Journal of Clinical Oncology ◽

10.1200/jco.2018.36.15_suppl.e24107 ◽

2018 ◽

Vol 36 (15_suppl) ◽

pp. e24107-e24107

Author(s):

Yukti Choudhury ◽

Hao Chen ◽

Farah Fadhlullah ◽

Daniel Kian Hin Tan ◽

Kim Tien Ng ◽

...

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Instability ◽

Liquid Biopsy ◽

Simultaneous Detection ◽

Next Generation ◽

Viral Dna ◽

Generation Sequencing

Download Full-text

Analytical validation of a next generation sequencing liquid biopsy assay for high sensitivity broad molecular profiling

PLoS ONE ◽

10.1371/journal.pone.0193802 ◽

2018 ◽

Vol 13 (3) ◽

pp. e0193802 ◽

Cited By ~ 45

Author(s):

Vincent Plagnol ◽

Samuel Woodhouse ◽

Karen Howarth ◽

Stefanie Lensing ◽

Matt Smith ◽

...

Keyword(s):

Next Generation Sequencing ◽

Liquid Biopsy ◽

High Sensitivity ◽

Molecular Profiling ◽

Next Generation ◽

Analytical Validation ◽

Generation Sequencing

Download Full-text

Detection of activating mutations in liquid biopsy of Egyptian breast cancer patients using targeted next-generation sequencing: a pilot study

Journal of the Egyptian National Cancer Institute ◽

10.1186/s43046-021-00067-3 ◽

2021 ◽

Vol 33 (1) ◽

Author(s):

Neemat Kassem ◽

Hebatallah Kassem ◽

Loay Kassem ◽

Mohamed Hassan

Keyword(s):

Breast Cancer ◽

Next Generation Sequencing ◽

Microsatellite Instability ◽

Cancer Patients ◽

Liquid Biopsy ◽

Missense Mutations ◽

Next Generation ◽

Breast Cancer Patients ◽

Activating Mutations ◽

Generation Sequencing

Abstract Background Breast cancer (BC) is the 2nd most prevalent malignancy worldwide and is the most prevalent cancer among Egyptian women. The number of newly described cancer-associated genes has grown exponentially since the emergence of next-generation sequencing (NGS) technology. We aim to identify activating mutations in liquid biopsy of Egyptian breast cancer patients using targeted NGS technology. We also demonstrate the microsatellite instability (MSI) status using BAT25, BAT26, and NR27 markers which are tested on the Bioanalyzer 2100 system. Results Twenty-one variants were detected in 15 genes: 7 Substitution-Missense, 12 Substitution-coding silent, and 2 Substitution-intronic. Regarding ClinVar database, out of 21 variants there were 14 benign variants, 3 variants with conflicting interpretations of pathogenicity, 3 variants not reported, and 1 drug response variant. TP53 p.(Pro72Arg) missense mutations were found in 75% of patients. PIK3CA p.(Ile391Met), KDR p.(Gln472His) missense mutations were detected in 25% of patients each. Two patients revealed APC gene missense mutation with p.(Ile1307Lys) and p.(Glu1317Gln) variants. Only one patient showed ATM p.(Phe858Leu) gene mutation and one showed FGFR3 p.(Ala719Thr) variant. Regarding microsatellite instability (MSI) status, 2/8 (25%) patients were MSS, 3/8 (37.5%) patients were MSI-L, and 3/8 (37.5%) patients were MSI-HI. Conclusion It is essential to use and validate minimally invasive liquid biopsy for activating mutations detection by next-generation sequencing especially in patients with inoperable disease or bone metastasis. This work should be extended with larger patient series with comparison of genetic mutations in liquid-based versus tissue-based biopsy and longer follow up period.

Download Full-text