We use cookies to understand how you use our site and to improve your experience. This includes personalizing content and advertising. To learn more, click here. By continuing to use our site, you accept our use of cookies. Cookie Policy.

Features Partner Sites Information LinkXpress
Sign In
Advertise with Us
INTEGRA BIOSCIENCES AG

Roche Diagnostics

Develops, manufactures, and markets a wide range of in vitro diagnostic systems, instruments, reagents, and tests read more Featured Products: More products

Download Mobile App




Representative Tumor Sampling Method Lessens Molecular Analyses Bias

By LabMedica International staff writers
Posted on 25 May 2020
Print article
Image: Schematic diagram of how the representative tumor sampling method lessens bias in molecular analyses (Photo courtesy of Francis Crick Institute).
Image: Schematic diagram of how the representative tumor sampling method lessens bias in molecular analyses (Photo courtesy of Francis Crick Institute).
Over the past decade, clinical scientists have demonstrated the inability of an individual biopsy or formalin-fixed paraffin-embedded (FFPE) block to capture the genetic diversity of a solid tumor.

When pathologists extract tumor tissue to identify potential biomarkers for downstream therapy, they deal with issues related to tumor heterogeneity. By analyzing a single sample from a fixed location, they do not always get a representative sample of the cancer, and a tissue biopsy usually only presents less than 0.0005% of the tumor.

Clinical Scientists at the Francis Crick Institute (London, UK) and at Roche Tissue Diagnostics (Tucson, AZ, USA) and their international colleagues have developed a method that they believe could improve clinical tumor molecular profiling by generating accurate tumor mutation burden scores. The team first analyzed data for 1,667 samples across six tumor types from the National Cancer Institute's Cancer Genome Atlas (TCGA). For each sample, they assessed how much of each tumor was sampled.

The system, called Rep-Seq requires at least 1 gram of patient leftover tissue following pathology extraction. The process starts with a pathologist macro-dissecting a sample to remove normal tissue that is at least 5 cm away from the tumor. Tumor and normal tissue are separately incubated and then blended with a specific solution inside a homogenizer. Tumor and immune cells are further separated using fluorescence-activated cell sorting, enriching the representative sample for tumor cells. The group found that tumor sequencing protocols had a high under-sampling bias. Sampling bias was likely also affected by the levels of heterogeneity and purity of tumor cells in the sample.

To determine the effect of spatial bias in single-biopsy sampling, the team pooled extracted DNA from 1,184 multi-region biopsies, taken from 79 primary renal carcinomas (RCCs), to create "cocktail samples." Subjecting the samples to next-generation sequencing (NGS), the team compared mutation calls with previously generated single-biopsy and multi-region biopsy data. They found that the cocktail samples discovered all of the true-set mutations, compared with single biopsies, which only discovered 73%. The team therefore believes that a more representative sample can lead to improved variant detection.

The investigators used tumor masses from leftover material post-surgery, and then applied Rep-Seq on 11 tumors from breast, lung, colorectal, and RCC cancers. Choosing a large clear cell RCC tumor (RS1), the team collected 68 fresh-frozen biopsies from the primary tumor and later homogenized the rest using Rep-Seq. The team performed whole-exome sequencing (WES) on seven biopsies and the Rep-Seq sample, identifying 76 unique mutations. They then compared the Rep-Seq results to the single-biopsy regions and found that the variant allele frequencies (VAFs) from Rep-Seq closely matched the overall tumor VAFs in the 68 biopsies. The group only failed to detect three of the 76 mutations in the Rep-Seq sample.

Samra Turajlic, MBBS, PhD, a Consultant Medical Oncologist and corresponding author of the study, said, “Taking a small sample from a solid cancer, which contains millions or billions of cells, is very problematic, as you deal with the issue of reproducibility. Beyond seeing if there's enough leftover tumor to create a homogenized sample, we wanted to see if the sample will allow you to predict both prognostic and therapeutic markers robustly and accurately.” The study was published on May 5, 2020 in the journal Cell Reports.


Platinum Member
COVID-19 Rapid Test
OSOM COVID-19 Antigen Rapid Test
One Step HbA1c Measuring System
GREENCARE A1c
Anti-Cyclic Citrullinated Peptide Test
GPP-100 Anti-CCP Kit
Gold Member
Xylazine Immunoassay Test
Xylazine ELISA

Print article

Channels

Clinical Chemistry

view channel
Image: Reaching speeds up to 6,000 RPM, this centrifuge forms the basis for a new type of inexpensive, POC biomedical test (Photo courtesy of Duke University)

POC Biomedical Test Spins Water Droplet Using Sound Waves for Cancer Detection

Exosomes, tiny cellular bioparticles carrying a specific set of proteins, lipids, and genetic materials, play a crucial role in cell communication and hold promise for non-invasive diagnostics.... Read more

Molecular Diagnostics

view channel
Image: The study showed the blood-based cancer screening test detects 83% of people with colorectal cancer with specificity of 90% (Photo courtesy of Guardant Health)

Blood Test Shows 83% Accuracy for Detecting Colorectal Cancer

Colorectal cancer is the second biggest cause of cancer deaths among adults in the U.S., with forecasts suggesting 53,010 people might die from it in 2024. While fewer older adults are dying from this... Read more

Hematology

view channel
Image: The Gazelle Hb Variant Test (Photo courtesy of Hemex Health)

First Affordable and Rapid Test for Beta Thalassemia Demonstrates 99% Diagnostic Accuracy

Hemoglobin disorders rank as some of the most prevalent monogenic diseases globally. Among various hemoglobin disorders, beta thalassemia, a hereditary blood disorder, affects about 1.5% of the world's... Read more

Microbiology

view channel
Image: The new platform is designed to perform blood-based diagnoses of nontuberculosis mycobacteria (Photo courtesy of 123RF)

New Blood Test Cuts Diagnosis Time for Nontuberculous Mycobacteria Infections from Months to Hours

Breathing in nontuberculous mycobacteria (NTM) is a common experience for many people. These bacteria are present in water systems, soil, and dust all over the world and usually don't cause any problems.... Read more

Industry

view channel
Image: These new assays are being developed for use on the recently introduced DxI 9000 Immunoassay Analyzer (Photo courtesy of Beckman Coulter)

Beckman Coulter and Fujirebio Expand Partnership on Neurodegenerative Disease Diagnostics

Beckman Coulter Diagnostics (Brea, CA, USA) and Fujirebio Diagnostics (Tokyo, Japan) have expanded their partnership focused on the development, manufacturing and clinical adoption of neurodegenerative... Read more
Copyright © 2000-2024 Globetech Media. All rights reserved.