Ligation-mediated PCR whole genome amplification speeds up detection of copy number alterations
The complexities of whole genome sequencing for single cells make it a time-consuming affair – not ideal for resource-stretched clinical laboratories. Now, a more streamlined protocol – ligation-mediated PCR whole genome amplification – aims to speed up low-pass sequencing and detection of copy number alterations (1). The European research team behind the method put it to the test by analyzing single circulating tumor cells (CTCs) and white blood cells – successfully, they say; the protocol detected copy number alterations in single tumor cells with as few as 200,000 reads. To learn more about the technique, we spoke with Nicolò Manaresi, CSO of Menarani Silicon Biosystems.
Why focus on detection of copy number alterations?
Copy number alterations (CNAs) are a hallmark of cancer, and further evidence has pointed to the importance of investigating CNAs in several settings. For example, researchers at the University of Manchester discovered CTC CNA profiles that predict chemoresistance/chemosensitivity in small cell lung carcinoma patients (2). Another hot topic is immune oncology; given the high cost of treatments and risk of severe adverse reactions, immunotherapies are in desperate need for better predictive biomarkers and companion diagnostic options – and copy number losses appear to be relevant. There are several other examples of the effect CNAs have on disease research.
What do your findings mean for tumor cell studies going forward?
As our new method streamlines the process of library preparation for genome-wide CNA profiling, we anticipate that investigation of CNA and their heterogeneity across CTCs from patients will become more and more affordable to researchers, and will drive new discoveries. Moreover, we anticipate the potential adoption of the workflow, which is currently for research use only, in the clinical setting after further investigation.
To foster adoption in the clinic, actionability and clinical utility are key, and this is our current focus. We believe that our cell-based liquid biopsy workflow may play an important role in oncology precision medicine, by supplying longitudinal, accurate CTC molecular profile.
- A Ferrarini et al., “A streamlined workflow for single-cells genome-wide copy-number profiling by low-pass sequencing of LM-PCR whole-genome amplification products”, PLoS One, 13 (2018). PMID: 29494651.
- L Carter et al., “Molecular analysis of circulating tumor cells identifies distinct copy-number profiles in patients with chemosensitive and chemorefractory small-cell lung cancer”, Nat Med, 23, 114–119 (2018). PMID: 27869802.
My fascination with science, gaming, and writing led to my studying biology at university, while simultaneously working as an online games journalist. After university, I travelled across Europe, working on a novel and developing a game, before finding my way to Texere. As Associate Editor, I’m evolving my loves of science and writing, while continuing to pursue my passion for gaming and creative writing in a personal capacity.