Advancing cancer research with plasma-seq

Early detection of cancer is critical for screening populations and improving the survival and quality of life of patients because it allows for earlier implementation of alternative therapies. Circulating tumor DNA (ctDNA) originates from apoptotic or necrotic tumor cells and is characteristic of the malignant process. ctDNA isolated from plasma offers the potential of a sensitive and specific biomarker for a host of applications, including diagnosis or early detection of tumors and prognostic information on overall or disease-free survival. Besides, it can be used to get predictive information on resistance and probability of lack of response to treatment. Recently, two groups published papers using ctDNA and plasma-seq technology to profile biomarkers for prostate cancer and to analyze copy number variations (CNVs) and DNA fragmentation patterns for glioma.

Profiling prostate cancer biomarkers

Researchers at the Karolinska Institute in Stockholm, Sweden, have authored an excellent paper on the profiling of metastatic castration-resistant prostate cancer (mCRPC) from cell-free DNA using the ThruPLEX Plasma-Seq Kit.

The authors performed a large-scale study of over 200 patients to demonstrate how cell-free DNA can be used to detect markers for prostate cancer, compared to germline DNA from white blood cells and other studies using DNA from a cancer tissue biopsy. Their comprehensive profiling of the androgen receptor (AR) revealed a continuous evolution of genetic alterations with intra-AR structural variations detected in a significantly lower fraction of first-line mCRPC therapy patients compared to fourth-line patients (Figure 1). They performed low-depth whole genome sequencing, as well as targeted enrichment to achieve greater depth on specific regions of interest. They used inputs ranging from 0.1–50 ng cell-free DNA (that is as low as 100 pg of cell-free DNA!).

Why is this important?

Cell-free DNA is a highly attractive sample type for cancer diagnosis, prognosis, and marker identification. Using cell-free DNA from plasma samples is much less invasive than obtaining a tissue biopsy and is showing great promise as a more viable technique for understanding the progression of a disease. High-throughput compatibility of the chosen sequencing chemistry for studies involving clinical samples is critical because they often require large-scale preps to minimize batch effects and improve sensitivity.

Discerning glioma CNVs and DNA fragmentation patterns

The next paper used our ThruPLEX Plasma-Seq Kit to develop a fast, low-cost assay to screen patients for glioma (tumors from glial cells found in the brain and spinal cord).

In their latest publication in EMBO Molecular Medicine, Cancer UK scientists demonstrated a new low-cost glioma screening method that uses cell-free tumor DNA (cftDNA) from cerebrospinal fluid (CSF) for CNV detection in patients with glioma. Their technique uses CSF cftDNA as the input (since glioma is challenging to detect in plasma) for analyzing somatic copy number alterations (SCNAs) and DNA fragmentation patterns with shallow sequencing to screen for cell-free tumor DNA (Figure 2).

Why is this important?

This assay helps to solve a significant problem: sequencing cost. By looking at copy number variation and DNA fragmentation, instead of mutations, the sequencing depth requirements are substantially lower. In other words, researchers can reliably get 'candidate' samples from low-cost screening, then follow up with deeper and more costly sequencing only on the patients with a high likelihood of disease. It is possible that this approach may be applied to other conditions or other forms of cancer. It is essential that the chosen sequencing chemistry has a fast and simple workflow that ensures quick turnaround and minimizes sequencing cost.

Future of cftDNA analysis

Recent technological advances in genetic sequencing methods have opened new avenues for cancer diagnosis and tumor monitoring that are minimally invasive. Biopsies of single sites do not address intra-tumoral heterogeneity that is captured by liquid biopsies. Using these alternative sample types could potentially eliminate the need for invasive tissue biopsies in some instances. However, analyzing liquid biopsies has its own challenges and having technologies such as ThruPLEX Plasma-seq that are optimized for cfDNA analysis with features such as a simple workflow, high-throughput compatibility, and high-quality readout with minimal sequencing depth will be instrumental in facilitating a broader application of liquid biopsies.

References

Mayrhofer, M. et al., Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis. Genome Med. 10, (2018).

Mouliere, F. et al., Detection of cell‐free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients. EMBO Mol. Med. e9323, (2018).