Toward more streamlined testing in pediatric oncology

Abstract

Gene sequencing of blood plasma simultaneously detects cancer and infectious disease in pediatric leukemia patients.

Over the last six decades, the outcomes of children with acute lymphoblastic leukemia (ALL) have improved because of advances in the clinical care of these young patients. ALL cure rates have increased from 5% in 1962 to greater than 90% currently (1). This tremendous swing results from progress in treating infectious disease and iterative clinical trials maximizing chemotherapeutic and targeted therapies, which achieve better antileukemic activity. Historically and, to an extent currently, prognosis for pediatric patients with ALL is determined by white blood cell count at presentation, age at presentation, gender, and the presence or absence of central nervous system disease. With advances in molecular techniques and genomics, assessment for remaining disease or measurable residual disease weighs considerably in determining risk. Moreover, the ability of children to tolerate treatment depends on surviving periods of immune suppression and managing infection.

Next-generation sequencing (NGS) technology enables identification of genetic sequences from humans, cancers, and contagions (2, 3). Recent advances in pediatric cancer have drawn upon this technology for classifying, prognosticating, treating, and preventing disease (4–6). Over a decade ago, McDermott et al. and Relman (2, 3) described applying genomics toward understanding cancer and infectious diseases. In this issue of Science Advances, Barsan et al. (7) discuss a means to monitor the two leading contributors to death in pediatric ALL patients: (i) disease persistence or relapse and (ii) infectious microbes in the setting of a dampened immune system. The authors studied the plasma of ALL patients for gene changes and evidence of viruses using a sensitive sequencing approach.

In a prospective manner, the authors collected samples from 20 newly diagnosed ALL patients over a 6-week period. A total of 168 samples were sequenced. To test their methods, Barsan et al. looked at cellular and plasma fractions from blood and bone marrow. They also examined leukemia gene–associated variants and infectious microbial DNA. The team observed an increase in cell-free DNA (cfDNA) from peripheral blood after starting chemotherapy and a later increase in bone marrow with normal blood cell count recovery. Leukemia gene–associated variants found in the patient samples were followed over time and assessed for clearance. Microbes were also evaluated over time. This approach holds promise for reducing the number of invasive bone marrow biopsies and aspirations children may be required to undergo, as comparative analysis of samples from these different sources suggest an informative yield from peripheral blood alone and will suffice at certain time points for disease surveillance decreasing the frequency of bone marrow studies needed, but this will require continued improvements in methods and standardization.

Methods used by the study were limited in their ability to detect all types of genomic alterations, and evidence was not sufficient to recommend stop drawing blood culture and viral titers. Nonetheless, Barsan et al. did take an important step in showing the benefit of deploying a custom panel–based circulating tumor DNA NGS assay for clinical purposes. Fusions or structural variations shown through whole-genome sequencing or fusion-specific assays require additional workflows and allow for broad genomic testing, which is critical in a leukemia population. Nonetheless, this pilot study pushes the field beyond the status quo illustrating the power of sequencing respective cfDNAs to simultaneously detect leukemia, molecular markers of treatment resistance, and infectious microbes and viruses (Fig. 1).

Fig. 1. Tandem genome sequencing detects residual leukemia and viral pathogens in cfDNA.

A custom blood test showing genetic disease variants and infection, the two factors implicated in negative prognosis, could reduce the number of invasive bone marrow biopsies and aspirations pediatric leukemia patients may be required to undergo. ctDNA, circulating tumor DNA. cfDNA, cell-free DNA. Credit: Ashley Mastin/Science Advances.

Barsan et al. chose to use cfDNA and a custom NGS panel to identify relevant human and microbial sequences. As medical centers increasingly use whole-genome sequencing and as technical and analytical costs drop, NGS assays will evolve and be customizable to capture multiple lines of information such as known driver genomic tumor and germline variants, novel genetic changes, and large viral genomes. Such a standalone test will help improve patient outcomes (8, 9).