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

Illumina

Illumina develops, manufactures and markets integrated systems for the analysis of genetic variations and biological ... read more Featured Products: More products

Download Mobile App




DNA Sequencing Technique Unravels Genetic Diversity of Cancer Tumors

By LabMedica International staff writers
Posted on 07 Jul 2020
Print article
Image: Single-cell copy number profiling: Chromium Single Cell CNV Solution provides a comprehensive, scalable solution for revealing genome heterogeneity and understanding clonal evolution (Photo courtesy of 10X Genomics).
Image: Single-cell copy number profiling: Chromium Single Cell CNV Solution provides a comprehensive, scalable solution for revealing genome heterogeneity and understanding clonal evolution (Photo courtesy of 10X Genomics).
The ability to sequence the genome of a tumor has revolutionized cancer treatment by identifying drivers of cancer at the molecular level. However, understanding the genetic diversity of individual cells within a tumor and how that might impact the disease progression has remained a challenge, due to the current limitations of genomic sequencing.

The standard paradigm is bulk sequencing of genomic DNA derived from millions of heterogeneous cells. In bulk sequencing, the ability to resolve sub-clonality is confounded relying on indirect inference, frequently resulting in an ensemble view dominated by the majority clone. Methods for sequencing DNA of single-cells using next-generation sequencing approaches have often been laborious or limited to multiplexing hundreds of cells or nuclei.

Molecular Biologist at the Keck School of Medicine (Los Angeles, CA, USA) and their colleagues performed shallow single-cell sequencing of genomic DNA across 1,475 cells from a cell-line, COLO829, to resolve overall complexity and clonality. This melanoma tumor-line has been previously characterized by multiple technologies and is a benchmark for evaluating somatic alterations. Cells were then analyzed and sorted on a flow cytometer using 488 nm excitation and green emission gating on cells in the G1 phase of the cell cycle. Cells were counted post-sorting to ensure accurate concentration.

The scientists used an emerging technique called "single-cell copy number profiling." developed by 10X Genomics (Pleasanton, CA, USA) with novel analysis methods that integrated these results with those of historical methods The single-cell suspension was processed using chromium single-cell CNV solution (10× Genomics). Sequencing libraries were quantified by qPCR before sequencing on the Illumina platform (San Diego, CA, USA) using NovaSeq S4 chemistry with 2 × 100 paired-end reads. Paired-end reads were processed using version 1.0 of the 10× Genomics’ Cell Ranger DNA Pipeline. Single-cell CNV calls were extracted from a BED file generated by the Cell Ranger DNA Pipeline for 1,373 cell barcodes.

The team reported that following shallow single-cell sequencing, they first identified at least four major sub-clones by discriminant analysis of principal components of single-cell copy number data. Based on clustering, break-point and loss of heterozygosity analysis of aggregated data from sub-clones, they identified distinct hallmark events that were validated within bulk sequencing and spectral karyotyping.

Enrique Velazquez-Villarreal, lead author and assistant professor of translational genomics, said, “Instead of analyzing tissue DNA that is the average of thousands of cells, we analyzed the individual DNA of close to 1,500 cells within a single trial. Studying cancer at this higher resolution, we can discover information that lower-resolution bulk sequencing misses.” The study was published on June 25, 2020 in the journal Nature Communications Biology.


Platinum Member
COVID-19 Rapid Test
OSOM COVID-19 Antigen Rapid Test
HLX
Anti-Cyclic Citrullinated Peptide Test
GPP-100 Anti-CCP Kit
New
Gold Member
Systemic Autoimmune Testing Assay
BioPlex 2200 ANA Screen with MDSS

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

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.