1. Enhanced detection of circulating tumor DNA by fragment size analysis
- Author
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Nitzan Rosenfeld, Christopher Smith, Charles E. Massie, Florent Mouliere, Ioannis Gounaris, Irena Hudecova, Lise Barlebo Ahlborn, Kevin M. Brindle, Christine Parkinson, Grant D. Stewart, Francesco Marass, Pippa Corrie, Richard D. Baird, Mercedes Jimenez-Linan, Dineika Chandrananda, James D. Brenton, Suzanne Murphy, Wendy N. Cooper, Johanna Burge, Matthew D. Eldridge, Anna Supernat, Olga Østrup, Morten Mau-Sørensen, Javier Garcia-Corbacho, Keval M. Patel, Elizabeth Moore, Davina Gale, James Morris, Simon Pacey, Michiel S. van der Heijden, Anna M. Piskorz, Katrin Heider, Jonathan C. M. Wan, Colin Watts, Richard Mair, Susana Ros, Teodora Goranova, Pathology, Mouliere, Florent [0000-0001-7043-0514], Chandrananda, Dineika [0000-0002-8834-9500], Piskorz, Anna M [0000-0002-7171-1120], Moore, Elizabeth K [0000-0002-2728-3202], Goranova, Teodora [0000-0003-3848-2968], Marass, Francesco [0000-0002-8993-7320], Heider, Katrin [0000-0003-4035-1668], Wan, Jonathan CM [0000-0003-0001-1802], Hudecova, Irena [0000-0003-3823-9896], Eldridge, Matthew D [0000-0002-5799-8911], Gale, Davina [0000-0002-4521-8199], Stewart, Grant D [0000-0003-3188-9140], Cooper, Wendy N [0000-0003-3416-9982], Massie, Charles E [0000-0003-2314-4843], Watts, Colin [0000-0003-3531-8791], Corrie, Pippa [0000-0003-4875-7021], Brindle, Kevin M [0000-0003-3883-6287], Baird, Richard D [0000-0001-7071-6483], Mau-Sørensen, Morten [0000-0003-2235-1250], Smith, Christopher G [0000-0001-7357-2737], Brenton, James D [0000-0002-5738-6683], Rosenfeld, Nitzan [0000-0002-2825-4788], and Apollo - University of Cambridge Repository
- Subjects
0301 basic medicine ,DNA Copy Number Variations ,In silico ,Copy number analysis ,Biology ,medicine.disease_cause ,Deep sequencing ,Circulating Tumor DNA ,Machine Learning ,03 medical and health sciences ,chemistry.chemical_compound ,Mice ,medicine ,Animals ,Humans ,Whole genome sequencing ,Mutation ,Whole Genome Sequencing ,Genome, Human ,Cancer ,General Medicine ,medicine.disease ,Molecular biology ,030104 developmental biology ,chemistry ,Human genome ,DNA - Abstract
Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for noninvasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 patients with cancer using low-pass whole-genome sequencing (0.4×). To establish the size distribution of mutant ctDNA, tumor-guided personalized deep sequencing was performed in 19 patients. We detected enrichment of ctDNA in fragment sizes between 90 and 150 bp and developed methods for in vitro and in silico size selection of these fragments. Selecting fragments between 90 and 150 bp improved detection of tumor DNA, with more than twofold median enrichment in >95% of cases and more than fourfold enrichment in >10% of cases. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alterations that were otherwise not detected. Identification of plasma samples from patients with advanced cancer was improved by predictive models integrating fragment length and copy number analysis of cfDNA, with area under the curve (AUC) >0.99 compared to AUC 0.91 compared to AUC < 0.5 without fragmentation features. Fragment size analysis and selective sequencing of specific fragment sizes can boost ctDNA detection and could complement or provide an alternative to deeper sequencing of cfDNA.
- Published
- 2018
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