Targeted Next-Generation Sequencing of Cell-Free DNA to Detect
MYC
-Immunoglobulin Translocation and Epstein-Barr Virus DNA in Plasma of Burkitt Lymphoma Patients in East Africa
Authors: Chamba Clara , Jennings Daisy , Shungu Rehema , Christopher Heavenlight , Josephat Emmanuel , Howard Kieran , Dreau Helene , Burns Adam , Mawalla William , Mapendo Priscus , Mnango Leah , Legason Ismail , Elias Edrick , Achola Caroline , Cutts Anthony , Balandya Emmanuel , Schuh Anna ,   AI-REAL Consortium, Kamanga Jacqueline , Schroeder Kristin , Ntemi Paul Sharack , Sseruyange Julius , Ayitwala Alisen , Mremi Alex , Kahakwa Atukuzwe , Mbwambo Daniel , Mkwizu Elifuraha , Henke Oliver , Goodluck Philomena , Nabalende Hadija , Otim Isaac , Ogwang Martin D. , Atim Pamela , Marogosa Erick , Chiwanga Faraja , Sandi Godlove , Mwamtemi Hadija , Chirande Lulu , Scanlan Patricia , Mahawi Salama , Ruhago George , Mwita Liberata , Tungu Malale , Sangeda Raphael , Mbulaiteye Sam M. , El Moulden Claire , Vavoulis Dimitris , Jiang Jingjing , Ridout Kate , Pascua Laura Lopez , Morrell Liz , Leonte Mihaela , Wordsworth Sarah 
Published: January 2025

PURPOSE

Epstein-Barr virus (EBV)–positive Burkitt lymphoma (BL) affects children in sub-Saharan Africa, but diagnosis via tissue biopsy is challenging. We explored a liquid biopsy approach using targeted next-generation sequencing to detect the
MYC
-immunoglobulin (
MYC
-Ig) translocation and EBV DNA, assessing its potential for minimally invasive BL diagnosis.

MATERIALS AND METHODS

The panel included targets for the characteristic
MYC
-Ig translocation, mutations in intron 1 of
MYC
, mutations in exon 2 of
MYC
, and three EBV genes: EBV-encoded RNA (EBER)1, EBER2, and EBV nuclear antigen 2. It was first tested in a small derivation cohort of four precharacterized BL-derived cell lines with known translocation status and eight precharacterized plasma samples with known EBV DNA status by quantitative polymerase chain reaction (qPCR). These different data modalities were combined to assess the accuracy of this approach in the diagnosis of BL in 20 patient plasma samples in Tanzania and Uganda.

RESULTS

The next-generation sequencing panel detected three of four
MYC
-Ig translocations in the BL-derived cell lines. EBV viral load by targeted sequencing correlated strongly with qPCR results (Spearman's rho = 0.94) in precharacterized plasma samples. Using the patient plasma samples, mutations in
MYC
intron 1 were associated with the presence of a
MYC
translocation with 25 or more mutations being predictive of a translocation with AUC, sensitivity, and specificity of 1. Overall, liquid biopsy parameters associated with a diagnosis of BL (
P
< .05) included cell-free DNA concentration, circulating tumor DNA concentration,
MYC
intron 1 mutations,
MYC
-Ig translocation, and autosome entropy. Integrating these parameters into a diagnostic model demonstrated excellent performance with an AUC of 0.95, sensitivity of 0.9, and specificity of 1.

CONCLUSION

This analysis demonstrates the potential of liquid biopsy to improve BL diagnosis in settings with limited pathology resources. Validation of our approach in a larger data set is needed.