Features Partner Sites Information LinkXpress hp
Sign In
Advertise with Us

Download Mobile App




New Method Simplifies Preparation of Tumor Genomic DNA Libraries

By LabMedica International staff writers
Posted on 28 Oct 2019
A method has been described that simplifies preparation of tumor genomic DNA libraries by employing restriction enzymes and in vitro transcription to barcode and amplify genomic DNA prior to library construction.

In general, a genomic library is the collection of the total genomic DNA from a single organism. More...
The DNA is stored in a population of identical vectors, each containing a different insert of DNA. In order to construct a genomic library, the organism's DNA is extracted from cells and then digested with a restriction enzyme to cut the DNA into fragments of a specific size. The fragments are then inserted into the vector using DNA ligase.

Copy number alterations or variations are common features of cancer cells. Within the same tumor, cells belonging to different anatomical areas of the tumor may carry different variations. Tumors with many variations are typically very aggressive and tend to be resistant to treatment.

Current strategies for massively parallel sequencing of tumor genomic DNA mainly rely on library indexing in the final steps of library preparation. This procedure is costly and time-consuming, since a library must be generated separately for each sample. Furthermore, whole-genome amplification requires intact DNA and thus is problematic in fixed tissue samples, in particular formalin-fixed, paraffin-embedded (FFPE) specimens, which still represent a cornerstone in pathology.

To overcome these limitations, investigators at the Karolinska Institutet (Solna, Sweden) developed a method, which they named CUTseq, that combined restriction endonucleases with in vitro transcription (IVT) to construct highly multiplexed DNA libraries for reduced representation genome sequencing of multiple samples in parallel.

The investigators showed that CUTseq could be used to barcode gDNA extracted from both non-fixed and fixed samples, including old archival FFPE tissue sections. They benchmarked CUTseq by comparing it with a widely used method of DNA library preparation and demonstrated that CUTseq could be used for reduced representation genome and exome sequencing, enabling reproducible DNA copy number profiling and single-nucleotide variant (SNV) calling in both cell and low-input FFPE tissue samples.

The investigators demonstrated an application of CUTseq for assessing genetic differences within tumors by profiling DNA copy number levels in multiple small regions of individual FFPE tumor sections. Finally, they described a workflow for rapid and cost-effective preparation of highly multiplexed CUTseq libraries, which could be applied in the context of high-throughput genetic screens and for cell line authentication.

"I expect that CUTseq will find many useful applications in cancer diagnostics," said senior author Dr. Nicola Crosetto, senior researcher in medical biochemistry and biophysics at the Karolinska Institutet. "Multi-region tumor sequencing is going to be increasingly used in the diagnostic setting, in order to identify patients with highly heterogeneous tumors that need to be treated more aggressively. I believe that our method can play a leading role here."

The study was published in the October 18, 2019, online edition of the journal Nature Communications.

Related Links:
Karolinska Institutet


Gold Member
Quantitative POC Immunoassay Analyzer
EASY READER+
Serological Pipet Controller
PIPETBOY GENIUS
New
Hemodynamic System Monitor
OptoMonitor
New
Specimen Radiography System
TrueView 200 Pro
Read the full article by registering today, it's FREE! It's Free!
Register now for FREE to LabMedica.com and get access to news and events that shape the world of Clinical Laboratory Medicine.
  • Free digital version edition of LabMedica International sent by email on regular basis
  • Free print version of LabMedica International magazine (available only outside USA and Canada).
  • Free and unlimited access to back issues of LabMedica International in digital format
  • Free LabMedica International Newsletter sent every week containing the latest news
  • Free breaking news sent via email
  • Free access to Events Calendar
  • Free access to LinkXpress new product services
  • REGISTRATION IS FREE AND EASY!
Click here to Register








Channels

Molecular Diagnostics

view channel
Image: The ONC IN-CYT platform leverages cross indication biomarker cyto-signatures (Photo courtesy of OraLiva)

AI-Powered Cytology Tool Detects Early Signs of Oral Cancer

Each year, 54,000 Americans are diagnosed with oral cancer, yet only 28% of cases are identified at an early stage, when the five-year survival rate exceeds 85%. Most diagnoses occur in later stages, when... Read more

Hematology

view channel
Image: The microfluidic device for passive separation of platelet-rich plasma from whole blood (Photo courtesy of University of the Basque Country)

Portable and Disposable Device Obtains Platelet-Rich Plasma Without Complex Equipment

Platelet-rich plasma (PRP) plays a crucial role in regenerative medicine due to its ability to accelerate healing and repair tissue. However, obtaining PRP traditionally requires expensive centrifugation... Read more

Immunology

view channel
Image: PD-1 protein blockade is the standard treatment for advanced melanoma among the different types of immunotherapy (Photo courtesy of 123RF)

Precision Tool Predicts Immunotherapy Treatment Failure in Melanoma Patients

Melanoma, though accounting for only about 4% of skin tumors, is the deadliest form of skin cancer due to its high potential to metastasize. While immunotherapy, especially PD-1 protein blockade, has revolutionized... Read more

Pathology

view channel
Image: Researchers have developed a novel method to analyze tumor growth rates (Photo courtesy of Adobe Stock)

Novel Method To Analyze Tumor Growth Rates Helps Tracks Progression Between Diagnosis and Surgery

Patients diagnosed with breast cancer often worry about how quickly their tumors grow while they wait for surgery, and whether delays in treatment might allow the disease to spread beyond the point of cure.... Read more
Copyright © 2000-2025 Globetech Media. All rights reserved.