References
- Vujanić GM, Sandstedt B, Kelsey A, et al. Central pathology review in multicenter trials and studies. Cancer. 2009;115:1977–1983.
- Parkes S, Muir KR, Cameron AH, et al. The need for specialist review of pathology in paediatric cancer. Br J Cancer. 1997;75:1156–1159.
- Shamberger RC, Guthrie KA, Ritchey ML, et al. Surgery-related factors and local recurrence of Wilms tumor in National Wilms Tumor Study 4. Ann Surg. 1999;229:292–297.
- van den Heuvel-eibrink MM, Hol JA, Pritchard-Jones K, et al. Rationale for the treatment of Wilms tumour in the UMBRELLA SIOP–RTSG 2016 protocol. Nat Rev Urol. 2017;14:743–752.
- Kundaje A, Meuleman W, Ernst J, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518:317–330.
- Schultz MD, He Y, Whitaker JW, et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 2015;523:212–216.
- Fernandez AF, Assenov Y, Martin-Subero JI, et al. A DNA methylation fingerprint of 1628 human samples. Genome Res. 2012;22(2):407–419.
- Kang S, Li Q, Chen Q, et al. CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA. Genome Biol. 2017;18(1):53.
- Hoadley KA, Yau C, Hinoue T, et al. Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer. Cell. 2018;173(291–304.e6):291–304.e6.
- Koelsche C, Hartmann W, Schrimpf D, et al. Array-based DNA-methylation profiling in sarcomas with small blue round cell histology provides valuable diagnostic information. Mod Pathol. 2018;31(8):1246–1256.
- Sturm D, Orr B, Toprak U, et al. new brain tumor entities emerge from molecular classification of CNS-PNETs. Cell. 2016;164:1060–1072.
- Capper D, Jones DTW, Sill M, et al. DNA methylation-based classification of central nervous system tumours. Nature. 2018;555:469–474.
- Siravegna G, Marsoni S, Siena S, et al. Integrating liquid biopsies into the management of cancer. Nat Rev Clin Oncol. 2017;14(9):531–548.
- Van Paemel R, Vlug R, De Preter K, et al. The pitfalls and promise of liquid biopsies for diagnosing and treating solid tumors in children: a review. Eur J Pediatr. 2020;179(2):191–202.
- Moss J, Magenheim J, Neiman D, et al. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat Commun. 2018;9:5068.
- Guo S, Diep D, Plongthongkum N, et al. Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA. Nat Genet. 2017;49:635–642.
- Meer A. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005;33:5868–5877.
- De Koker A, Van Paemel R, De Wilde B, et al. A versatile method for circulating cell-free DNA methylome profiling by reduced representation bisulfite sequencing. bioRxiv. 2019;663195. DOI:10.1101/663195.
- Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010.
- Krueger F Trim Galore! 2012.
- Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17:10.
- Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27:1571–1572.
- Raman L, Dheedene A, De Smet M, et al. WisecondorX: improved copy number detection for routine shallow whole-genome sequencing. Nucleic Acids Res. 2019;47:1605–1614.
- Seki M, Nishimura R, Yoshida K, et al. Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma. Nature Communications. 2015;6(1):7557.
- Huertas-Martínez J, Court F, Rello-Varona S, et al. DNA methylation profiling identifies PTRF/Cavin-1 as a novel tumor suppressor in Ewing sarcoma when co-expressed with caveolin-1. Cancer Lett. 2017;386:196–207.
- Wu SP, Cooper, BT, Bu, F, et al. DNA methylation-based classifier for accurate molecular diagnosis of bone sarcomas. JCO Precis Oncol. 2017;2017.
- Pinto EM, Hamideh D, Bahrami A, et al. Malignant rhabdoid tumors originating within and outside the central nervous system are clinically and molecularly heterogeneous. Acta Neuropathol. 2018;136:315–326.
- Almstrup K, Lindhardt Johansen M, Busch AS, et al. Pubertal development in healthy children is mirrored by DNA methylation patterns in peripheral blood. Sci Rep. 2016;6(1):28657.
- Chan KCA, Jiang P, Chan CWM, et al. Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc Natl Acad Sci U S A. 2013;110:18761–18768.
- Chatterjee A, Stockwell PA, Rodger EJ, et al. Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Res. 2012;40:e79–e79.
- Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–842.
- Van Roy N, Van Der Linden M, Menten B, et al. Shallow whole genome sequencing on circulating cell-free DNA allows reliable noninvasive copy-number profiling in neuroblastoma patients. Clin Cancer Res. 2017;23(20):6305–6314.
- Klega K, Imamovic-Tuco, A, Ha, G, et al. Detection of somatic structural variants enables quantification and characterization of circulating tumor DNA in children with solid tumors. JCO Precis Oncol. 2018;1–13. DOI:10.1200/PO.17.00285.
- Chicard M, Colmet-Daage L, Clement N, et al. Whole-exome sequencing of cell-free DNA reveals temporo-spatial heterogeneity and identifies treatment-resistant clones in neuroblastoma. Clin Cancer Res. 2018;24:939–949.
- Gröbner SN, Worst BC, Weischenfeldt J, et al. The landscape of genomic alterations across childhood cancers. Nature. 2018;555:321–327.
- Klein EA, Hubbell E, Maddala T, et al. ASCO abstract 12021: development of a comprehensive cell-free DNA (cfDNA) assay for early detection of multiple tumor types: the Circulating Cell-free Genome Atlas (CCGA) study. J Clin Oncol (suppl; abstr 12021). 2018. DOI:10.1200/JCO.2018.36.15_suppl.12021.
- Choudhury AD, Werner L, Francini E, et al. Tumor fraction in cell-free DNA as a biomarker in prostate cancer. JCI Insight. 2018;3. DOI:10.1172/jci.insight.122109.
- Shen SY, Singhania R, Fehringer G, et al. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature. 2018;563:579–583.
- Lentini A, Lagerwall C, Vikingsson S, et al. A reassessment of DNA-immunoprecipitation-based genomic profiling. Nat Methods. 2018;15:499–504.