Mapping Genes Could Improve Cancer Diagnosis
By LabMedica International staff writers Posted on 20 Jul 2017 |
Image: A 3D model of a chromosome, using the Hi-C visualization technique (Photo courtesy of Babraham Institute).
Large-scale changes to the structure of the genome are often seen in cancer cells and scientists have found a way to detect these changes, which could enhance cancer diagnosis and aid the use of targeted treatments.
Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly detrimental in oncology where rearrangements play diagnostic and prognostic roles.
A team of medical scientists led by those at the Babraham Institute (Cambridge, UK) has developed a new application of a technique called Hi-C, which allows scientists to map how genetic material is arranged inside cells. By analyzing this information, investigators can reliably identify major genetic changes that other methods may miss. This all comes at a lower cost than standard DNA sequencing methods.
Hi-C can detect chromosome rearrangements, where large sections of DNA are exchanged or moved between pieces of the genome called chromosomes, and also copy number variation, where genetic material gets copied or deleted. Both of these changes can have drastic effects on how the cell behaves. The team used Hi-C to examine the genome of cancer cells from six people with brain tumors. They were able to identify major genome changes, often with pinpoint accuracy. Uniquely, this approach allows doctors and scientists to study genetic changes in the wider context of the whole genome. Hi-C could become a powerful tool for understanding the complex genetic changes found in many cancers.
The use of Hi-C on the six primary tumor samples revealed amplifications of known oncogenes, deletions of a tumor suppressor gene and many structural rearrangements, both balanced and unbalanced. One balanced rearrangement studied in detail was shown to result in the fusion of two genes known to be involved in cancer. Hi-C does not rely on the presence of dividing cells and can be used on all nucleated cell types. It is therefore a powerful tool in the analysis of solid tumors, where cytogenetic analysis is difficult and rarely performed as part of routine diagnosis/analysis, yet fusion genes can play a critical clinical role. Hi-C allows these tumors to be interrogated and provides a means to alleviate the bias in detection of both chromosomal rearrangements and fusion genes towards blood borne cancers.
Peter Fraser, PhD, a professor and the lead investigator of the study said, “Hi-C could play a pivotal role in the detection of chromosomal abnormalities and may aid the discovery of new fusion genes. The technique works with much lower quality samples than current techniques and has the additional advantage of being able to provide copy number information from the same data. This all comes at a significantly lower cost than standard methods that use DNA sequencing.” The study was published on June 27, 2017, in the journal Genome Biology.
Related Links:
Babraham Institute
Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly detrimental in oncology where rearrangements play diagnostic and prognostic roles.
A team of medical scientists led by those at the Babraham Institute (Cambridge, UK) has developed a new application of a technique called Hi-C, which allows scientists to map how genetic material is arranged inside cells. By analyzing this information, investigators can reliably identify major genetic changes that other methods may miss. This all comes at a lower cost than standard DNA sequencing methods.
Hi-C can detect chromosome rearrangements, where large sections of DNA are exchanged or moved between pieces of the genome called chromosomes, and also copy number variation, where genetic material gets copied or deleted. Both of these changes can have drastic effects on how the cell behaves. The team used Hi-C to examine the genome of cancer cells from six people with brain tumors. They were able to identify major genome changes, often with pinpoint accuracy. Uniquely, this approach allows doctors and scientists to study genetic changes in the wider context of the whole genome. Hi-C could become a powerful tool for understanding the complex genetic changes found in many cancers.
The use of Hi-C on the six primary tumor samples revealed amplifications of known oncogenes, deletions of a tumor suppressor gene and many structural rearrangements, both balanced and unbalanced. One balanced rearrangement studied in detail was shown to result in the fusion of two genes known to be involved in cancer. Hi-C does not rely on the presence of dividing cells and can be used on all nucleated cell types. It is therefore a powerful tool in the analysis of solid tumors, where cytogenetic analysis is difficult and rarely performed as part of routine diagnosis/analysis, yet fusion genes can play a critical clinical role. Hi-C allows these tumors to be interrogated and provides a means to alleviate the bias in detection of both chromosomal rearrangements and fusion genes towards blood borne cancers.
Peter Fraser, PhD, a professor and the lead investigator of the study said, “Hi-C could play a pivotal role in the detection of chromosomal abnormalities and may aid the discovery of new fusion genes. The technique works with much lower quality samples than current techniques and has the additional advantage of being able to provide copy number information from the same data. This all comes at a significantly lower cost than standard methods that use DNA sequencing.” The study was published on June 27, 2017, in the journal Genome Biology.
Related Links:
Babraham Institute
Latest Molecular Diagnostics News
- Novel Biomarkers to Improve Diagnosis of Renal Cell Carcinoma Subtypes
- RNA-Powered Molecular Test to Help Combat Early-Age Onset Colorectal Cancer
- Advanced Blood Test to Spot Alzheimer's Before Progression to Dementia
- Multi-Omic Noninvasive Urine-Based DNA Test to Improve Bladder Cancer Detection
- First of Its Kind NGS Assay for Precise Detection of BCR::ABL1 Fusion Gene to Enable Personalized Leukemia Treatment
- Urine Test to Revolutionize Lyme Disease Testing
- Simple Blood Test Could Enable First Quantitative Assessments for Future Cerebrovascular Disease
- New Genetic Testing Procedure Combined With Ultrasound Detects High Cardiovascular Risk
- Blood Samples Enhance B-Cell Lymphoma Diagnostics and Prognosis
- Blood Test Predicts Knee Osteoarthritis Eight Years Before Signs Appears On X-Rays
- Blood Test Accurately Predicts Lung Cancer Risk and Reduces Need for Scans
- Unique Autoantibody Signature to Help Diagnose Multiple Sclerosis Years before Symptom Onset
- Blood Test Could Detect HPV-Associated Cancers 10 Years before Clinical Diagnosis
- Low-Cost Point-Of-Care Diagnostic to Expand Access to STI Testing
- 18-Gene Urine Test for Prostate Cancer to Help Avoid Unnecessary Biopsies
- Urine-Based Test Detects Head and Neck Cancer