The effect of unique molecular identifier family size using tumor-informed circulating tumor-DNA analysis in childhood cancers.

Authors

Tobias Österlund, Daniel Andersson, Raghda R Ibrahim, Elisabeth Mellström, Jenny Lundmark, Junrui Li, Stefan Filges, Peter Micallef, Manuel Luna Santamaría, Mandy Escobar, Pia Mouhanna, Firaol Tamiru Kebede, Christoffer Vannas, Ida Rahmqvist, Fani Pujol Calderón, Agnes Dahlstrand Rudin, Wilma Franssila, Åsa Torinsson Naluai, Serik Sagitov, Joakim Håkansson, Henrik Fagman, Martin Dalin, Anders Ståhlberg

Published in

The Journal of molecular diagnostics : JMD. Sep 11, 2026. Epub Sep 11, 2026.

Abstract

Analysis of circulating tumor-DNA (ctDNA) provides a molecular assessment that can complement routine imaging in childhood cancer management. Detailed monitoring of ctDNA levels may provide information on treatment efficacy and resistance, minimal residual disease and allows for early detection of relapse. Here, tumor-informed ctDNA analysis was applied to 90 blood plasma samples collected from eight children with malignant tumors. Four to ten tumor-specific mutations per patient were assessed using SiMSen-Seq, a digital sequencing approach utilizing unique molecular identifiers (UMIs). The effects of individual SiMSen-Seq assays and plasma samples were evaluated in relation to their impact on background error rate, number of detected target molecules and mutant calling using different UMI family size cutoff settings. The use of at least two sequencing reads per UMI provided the best overall performance by generating the highest number of detected target molecules and hence the optimal chance to detect low-frequent mutations. Data were consistent between SiMSen-Seq assays and plasma samples, providing robust ctDNA profiling over time for all patients. In conclusion, the results show that optimal use of UMIs in tumor-informed ctDNA analysis enables sensitive molecular readout that can assist in management of childhood cancers.

PMID:
42727690
Bibliographic data and abstract were imported from PubMed on 12 Sep 2026.

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