neomerDB: a comprehensive database of neomer biomarkers in cancer
Provatas, Kimonas Chan, Candace SY Kerasiotis, Ioannis Bochalis, Eleftherios Nayak, Akshatha Zacharia, Brad E Pavlopoulos, Georgios A Li, Wei Georgakopoulos-Soares, Ilias
Provatas, Kimonas
Chan, Candace SY
Kerasiotis, Ioannis
Bochalis, Eleftherios
Nayak, Akshatha
Zacharia, Brad E
Pavlopoulos, Georgios A
Li, Wei
Georgakopoulos-Soares, Ilias
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Computational Biology
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Journal article
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Abstract
The development of biomarkers for population screening, early cancer detection, monitoring, and recurrence surveillance offers substantial potential to improve patient outcomes and save lives. Nullomers are short k-mers that are absent from a human genome, and neomers are the subset of nullomers that emerge recurrently due to somatic mutations during cancer development. Here, we have developed neomerDB, a database that encompasses a catalogue of neomers across cancer types and organs. We examined 10 000 whole exome sequencing and 2658 whole genome sequencing tumour-matched samples and identified the set of neomers associated with each cancer type and organ. We also analysed 76 215 whole genomes and 730 947 whole exomes of individuals from diverse ancestries, from which we removed nullomers and neomers that can arise due to germline variants in the population. Finally, we conducted a case study demonstrating that neomers can be utilized to detect glioblastoma from liquid biopsy samples (n = 38), utilizing cell-free DNA and cell-free RNA, achieving a Receiver Operating Characteristic - Area Under the Curve score of 0.98 and a precision-recall score of 0.99. neomerDB is a user-friendly database that enables advanced searches, provides interactive visualizations, and download options for neomer biomarkers. neomerDB is publicly available at https://neomerDB.com/.
Citation
K. Provatas, C.S.Y. Chan, I. Kerasiotis, E. Bochalis, A. Nayak, B.E. Zacharia , et al., "neomerDB: a comprehensive database of neomer biomarkers in cancer," Database : the journal of biological databases and curation, vol. 2026, pp. baag006-baag006, 2026, https://doi.org/10.1093/database/baag006.
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Database : the journal of biological databases and curation
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31 Biological Sciences, 3102 Bioinformatics and Computational Biology, 3105 Genetics, Biomarkers, Tumor, Databases, Genetic, Genome, Human, Humans, Mutation, Neoplasms, 3 Good Health and Well Being
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Oxford University Press