Kilgour E, Rothwell DG, Brady G, Dive C. Liquid biopsy-based biomarkers of treatment response and resistance. Cancer Cell. 2020;37:485–95.

Article  PubMed  Google Scholar 

Alix-Panabieres C, Pantel K. Liquid biopsy: from discovery to clinical application. Cancer Discov. 2021;11:858–73.

Article  PubMed  Google Scholar 

Roschewski M, Rossi D, Kurtz DM, Alizadeh AA, Wilson WH. Circulating tumor DNA in lymphoma: principles and future directions. Blood Cancer Discov. 2022;3:5–15.

Article  PubMed  PubMed Central  Google Scholar 

Alig SK, Shahrokh Esfahani M, Garofalo A, Li MY, Rossi C, Flerlage T, et al. Distinct Hodgkin lymphoma subtypes defined by noninvasive genomic profiling. Nature. 2024;625:778–87.

Article  PubMed  Google Scholar 

Doculara L, Trahair TN, Bayat N, Lock RB. Circulating tumor DNA in pediatric cancer. Front Mol Biosci. 2022;9:885597.

Article  PubMed  PubMed Central  Google Scholar 

Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, et al. Pan-cancer genome and transcriptome analyses of 1699 paediatric leukaemias and solid tumours. Nature. 2018;555:371–6.

Article  PubMed  PubMed Central  Google Scholar 

Sweet-Cordero EA, Biegel JA. The genomic landscape of pediatric cancers: implications for diagnosis and treatment. Science. 2019;363:1170–5.

Article  PubMed  PubMed Central  Google Scholar 

Gao Q, Ryan SL, Iacobucci I, Ghate PS, Cranston RE, Schwab C, et al. The genomic landscape of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21. Blood. 2023;142:711–23.

Article  PubMed  PubMed Central  Google Scholar 

Umeda M, Ma J, Huang BJ, Hagiwara K, Westover T, Abdelhamed S, et al. Integrated genomic analysis identifies UBTF tandem duplications as a recurrent lesion in pediatric acute myeloid leukemia. Blood Cancer Discov. 2022;3:194–207.

Article  PubMed  PubMed Central  Google Scholar 

Christodoulou E, Yellapantula V, O’Halloran K, Xu L, Berry JL, Cotter JA, et al. Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors. NPJ Precis Oncol. 2023;7:21.

Article  PubMed  PubMed Central  Google Scholar 

Stankunaite R, George SL, Gallagher L, Jamal S, Shaikh R, Yuan L, et al. Circulating tumour DNA sequencing to determine therapeutic response and identify tumour heterogeneity in patients with paediatric solid tumours. Eur J Cancer. 2022;162:209–20.

Article  PubMed  Google Scholar 

Rusch M, Nakitandwe J, Shurtleff S, Newman S, Zhang Z, Edmonson MN, et al. Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome. Nat Commun. 2018;9:3962.

Article  PubMed  PubMed Central  Google Scholar 

Newman AM, Lovejoy AF, Klass DM, Kurtz DM, Chabon JJ, Scherer F, et al. Integrated digital error suppression for improved detection of circulating tumor DNA. Nat Biotechnol. 2016;34:547–55.

Article  PubMed  PubMed Central  Google Scholar 

Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, et al. SJPedPanel: a pan-cancer gene panel for childhood malignancies to enhance cancer monitoring and early detection. Clin Cancer Res. 2024;30:4100–14.

Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.

Article  PubMed  PubMed Central  Google Scholar 

Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95.

Article  PubMed  PubMed Central  Google Scholar 

Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31:213–9.

Article  PubMed  PubMed Central  Google Scholar 

Wilm A, Aw PP, Bertrand D, Yeo GH, Ong SH, Wong CH, et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012;40:11189–201.

Article  PubMed  PubMed Central  Google Scholar 

Edmonson MN, Patel AN, Hedges DJ, Wang Z, Rampersaud E, Kesserwan CA, et al. Pediatric cancer variant pathogenicity information exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants. Genome Res. 2019;29:1555–65.

Article  PubMed  PubMed Central  Google Scholar 

Robinson JT, Thorvaldsdottir H, Wenger AM, Zehir A, Mesirov JP. Variant review with the integrative genomics viewer. Cancer Res. 2017;77:e31–4.

Article  PubMed  PubMed Central  Google Scholar 

Kent WJ. BLAT–the BLAST-like alignment tool. Genome Res. 2002;12:656–64.

PubMed  PubMed Central  Google Scholar 

Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Kallberg M, et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016;32:1220–2.

Article  PubMed  Google Scholar 

Collins RL, Brand H, Karczewski KJ, Zhao X, Alfoldi J, Francioli LC, et al. A structural variation reference for medical and population genetics. Nature. 2020;581:444–51.

Article  PubMed  PubMed Central  Google Scholar 

Zhou X, Wang J, Patel J, Valentine M, Shao Y, Newman S, et al. Exploration of coding and non-coding variants in cancer using GenomePaint. Cancer Cell. 2021;39:83–95.e4.

Article  PubMed  PubMed Central  Google Scholar 

Belyeu JR, Chowdhury M, Brown J, Pedersen BS, Cormier MJ, Quinlan AR, et al. Samplot: a platform for structural variant visual validation and automated filtering. Genome Biol. 2021;22:161.

Article  PubMed  PubMed Central  Google Scholar 

Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A. et al. From FastQ data to high confidence variant calls: the genome analysis toolkit best practices pipeline. Curr Protoc Bioinform. 2013;43:1101–33.

Google Scholar 

Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alfoldi J, Wang Q, et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020;581:434–43.

Article  PubMed  PubMed Central  Google Scholar 

Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, et al. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed program. Nature. 2021;590:290–9.

Article  PubMed  PubMed Central  Google Scholar 

Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics. 2007;23:657–63.

Article  PubMed  Google Scholar 

Ramirez F, Ryan DP, Gruning B, Bhardwaj V, Kilpert F, Richter AS, et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016;44:W160–5.

Article  PubMed  PubMed Central  Google Scholar 

Talevich E, Shain AH, Botton T, Bastian BC. CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing. PLoS Comput Biol. 2016;12:e1004873.

Article  PubMed  PubMed Central  Google Scholar 

Ma X, Arunachalam S, Liu Y. Applications of probability and statistics in cancer genomics. Quant Biol. 2020;8:95–108.

Article  Google Scholar 

Putnam DK, Ma X, Rice SV, Liu Y, Newman S, Zhang J, et al. VCF2CNA: a tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity. Sci Rep. 2019;9:10357.

Article  PubMed  PubMed Central  Google Scholar 

Adalsteinsson, Ha VA, Freeman G, Choudhury SS, Stover AD, Parsons HA DG, et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun. 2017;8:1324.