High intensity sequencing of plasma cfDNA and WBC gDNA

We sought to define the technical feasibility of a high-intensity sequencing assay of cfDNA and matched white-blood cell (WBC) DNA covering a large genomic region (508 genes, 2Mb, 60,000x raw-depth) in a prospective study of 124 metastatic cancer patients, with contemporaneous matched metastatic tumor tissue biopsies, and age-matched 47 non-cancer controls.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 4 Publications

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Dataset ID	Description	Technology	Samples
EGAD00001005302	Metadata summarizes participants (n=198), samples (n=396), basic clinical information, and analysis. analysis1: raw sequencing reference alignment files (bam/bai) analysis2: error-corrected sequencing reference alignment files (bam/bai) analysis3: variant calling using error-corrected sequencing reference alignment (vcf)		396

Publications	Citations
High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants. Razavi P, Li BT, Brown DN, Jung B, Hubbell E, Shen R, Abida W, Juluru K, De Bruijn I, Hou C, Venn O, Lim R, Anand A, Maddala T, Gnerre S, Vijaya Satya R, Liu Q, Shen L, Eattock N, Yue J, Blocker AW, Lee M, Sehnert A, Xu H, Hall MP, Santiago-Zayas A, Novotny WF, Isbell JM, Rusch VW, Plitas G, Heerdt AS, Ladanyi M, Hyman DM, Jones DR, Morrow M, Riely GJ, Scher HI, Rudin CM, Robson ME, Diaz LA, Solit DB, Aravanis AM, Reis-Filho JS. Nat Med 25: 2019 1928-1937	321
Combining variant detection and fragment length analysis improves detection of minimal residual disease in postsurgery circulating tumour DNA of stage II-IIIA NSCLC patients. Vessies DCL, Schuurbiers MMF, van der Noort V, Schouten I, Linders TC, Lanfermeijer M, Ramkisoensing KL, Hartemink KJ, Monkhorst K, van den Heuvel MM, van den Broek D. Mol Oncol 16: 2022 2719-2732	11
Fragmentomic analysis of circulating tumor DNA-targeted cancer panels. Helzer KT, Sharifi MN, Sperger JM, Shi Y, Annala M, Bootsma ML, Reese SR, Taylor A, Kaufmann KR, Krause HK, Schehr JL, Sethakorn N, Kosoff D, Kyriakopoulos C, Burkard ME, Rydzewski NR, Yu M, Harari PM, Bassetti M, Blitzer G, Floberg J, Sjöström M, Quigley DA, Dehm SM, Armstrong AJ, Beltran H, McKay RR, Feng FY, O'Regan R, Wisinski KB, Emamekhoo H, Wyatt AW, Lang JM, Zhao SG. Ann Oncol 34: 2023 813-825	4
Aging clock based on nucleosome reorganisation derived from cell-free DNA. Shtumpf M, Jeong S, Bikova M, Mamayusupova H, Ruje L, Teif VB. Aging Cell 23: 2024 e14100	3