Genome-wide cell-free DNA fragmentation in patients with cancer
Stephen Cristiano, Alessandro Leal, Jillian Phallen, Jacob Fiksel, Vilmos Adleff, Daniel C Bruhm, Sarah Østrup Jensen, Jamie E Medina, Carolyn Hruban, James R White, Doreen N Palsgrove, Noushin Niknafs, Valsamo Anagnostou, Patrick Forde, Jarushka Naidoo, Kristen Marrone, Julie Brahmer, Brian D Woodward, Hatim Husain, Karlijn L van Rooijen, Mai-Britt Worm Ørntoft, Anders Husted Madsen, Cornelis J H van de Velde, Marcel Verheij, Annemieke Cats, Cornelis J A Punt, Geraldine R Vink, Nicole C T van Grieken, Miriam Koopman, Remond J A Fijneman, Julia S Johansen, Hans Jørgen Nielsen, Gerrit A Meijer, Claus Lindbjerg Andersen, Robert B Scharpf, Victor E Velculescu, Stephen Cristiano, Alessandro Leal, Jillian Phallen, Jacob Fiksel, Vilmos Adleff, Daniel C Bruhm, Sarah Østrup Jensen, Jamie E Medina, Carolyn Hruban, James R White, Doreen N Palsgrove, Noushin Niknafs, Valsamo Anagnostou, Patrick Forde, Jarushka Naidoo, Kristen Marrone, Julie Brahmer, Brian D Woodward, Hatim Husain, Karlijn L van Rooijen, Mai-Britt Worm Ørntoft, Anders Husted Madsen, Cornelis J H van de Velde, Marcel Verheij, Annemieke Cats, Cornelis J A Punt, Geraldine R Vink, Nicole C T van Grieken, Miriam Koopman, Remond J A Fijneman, Julia S Johansen, Hans Jørgen Nielsen, Gerrit A Meijer, Claus Lindbjerg Andersen, Robert B Scharpf, Victor E Velculescu
Abstract
Cell-free DNA in the blood provides a non-invasive diagnostic avenue for patients with cancer1. However, characteristics of the origins and molecular features of cell-free DNA are poorly understood. Here we developed an approach to evaluate fragmentation patterns of cell-free DNA across the genome, and found that profiles of healthy individuals reflected nucleosomal patterns of white blood cells, whereas patients with cancer had altered fragmentation profiles. We used this method to analyse the fragmentation profiles of 236 patients with breast, colorectal, lung, ovarian, pancreatic, gastric or bile duct cancer and 245 healthy individuals. A machine learning model that incorporated genome-wide fragmentation features had sensitivities of detection ranging from 57% to more than 99% among the seven cancer types at 98% specificity, with an overall area under the curve value of 0.94. Fragmentation profiles could be used to identify the tissue of origin of the cancers to a limited number of sites in 75% of cases. Combining our approach with mutation-based cell-free DNA analyses detected 91% of patients with cancer. The results of these analyses highlight important properties of cell-free DNA and provide a proof-of-principle approach for the screening, early detection and monitoring of human cancer.
Conflict of interest statement
Competing interests: S.C., A.L., J.P., J.F., V. Adleff, R.B.S., and V.E.V.. are inventors on patent applications (62/673,516 and 62/795,900) submitted by Johns Hopkins University related to cell-free DNA for cancer detection. V.E.V. is a founder of Delfi Diagnostics and Personal Genome Diagnostics, a member of their Scientific Advisory Boards and Boards of Directors, and owns Delfi Diagnostics and Personal Genome Diagnostics stock, which are subject to certain restrictions under university policy. Within the last five years, V.E.V. has been an advisor to Daiichi Sankyo, Janssen Diagnostics, Ignyta, and Takeda Pharmaceuticals. The terms of these arrangements are managed by Johns Hopkins University in accordance with its conflict of interest policies.
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References
- Wan JCM et al. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer 17, 223–238, doi:10.1038/nrc.2017.7 (2017).
- Bray F et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 68, 394–424, doi:10.3322/caac.21492 (2018).
- World Health Organization. Guide to Cancer Early Diagnosis. Guide to Cancer Early Diagnosis (2017).
- National Comprehensive Cancer Network (NCCN) clinical practice guidelines in oncology. Accessed 16 April 2019.
- Phallen J et al. Direct detection of early-stage cancers using circulating tumor DNA. Sci Transl Med 9, doi:10.1126/scitranslmed.aan2415 (2017).
- Cohen JD et al. Detection and localization of surgically resectable cancers with a multi-analyte blood test. Science 359, 926–930, doi:10.1126/science.aar3247 (2018).
- Newman AM et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med 20, 548–554, doi:10.1038/nm.3519 (2014).
- Bettegowda C et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med 6, 224ra224, doi:10.1126/scitranslmed.3007094 (2014).
- Leary RJ et al. Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med 2, 20ra14, doi:2/20/20ra14 [pii] 10.1126/scitranslmed.3000702 [doi] (2010).
- Leary RJ et al. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med 4, 162ra154, doi:10.1126/scitranslmed.3004742 (2012).
- Chan KC 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 110, 18761–18768, doi:10.1073/pnas.1313995110 (2013).
- Jiang P et al. Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients. Proc Natl Acad Sci U S A 112, E1317–1325, doi:10.1073/pnas.1500076112 (2015).
- Wang BG et al. Increased plasma DNA integrity in cancer patients. Cancer Res 63, 3966–3968 (2003).
- Umetani N et al. Prediction of breast tumor progression by integrity of free circulating DNA in serum. J Clin Oncol 24, 4270–4276, doi:10.1200/JCO.2006.05.9493 (2006).
- Chan KC, Leung SF, Yeung SW, Chan AT & Lo YM Persistent aberrations in circulating DNA integrity after radiotherapy are associated with poor prognosis in nasopharyngeal carcinoma patients. Clin Cancer Res 14, 4141–4145, doi:10.1158/1078-0432.CCR-08-0182 (2008).
- Mouliere F et al. High fragmentation characterizes tumour-derived circulating DNA. PLoS One 6, e23418, doi:10.1371/journal.pone.0023418 (2011).
- Mouliere F et al. Enhanced detection of circulating tumor DNA by fragment size analysis. Sci Transl Med 10, doi:10.1126/scitranslmed.aat4921 (2018).
- Snyder MW, Kircher M, Hill AJ, Daza RM & Shendure J Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. Cell 164, 57–68, doi:10.1016/j.cell.2015.11.050 (2016).
- Underhill HR et al. Fragment Length of Circulating Tumor DNA. PLoS Genet 12, e1006162, doi:10.1371/journal.pgen.1006162 (2016).
- Ulz P et al. Inferring expressed genes by whole-genome sequencing of plasma DNA. Nat Genet 48, 1273–1278, doi:10.1038/ng.3648 (2016).
- Ivanov M, Baranova A, Butler T, Spellman P & Mileyko V Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation. BMC Genomics 16 Suppl 13, S1, doi:10.1186/1471-2164-16-S13-S1 (2015).
- Jiang P et al. Preferred end coordinates and somatic variants as signatures of circulating tumor DNA associated with hepatocellular carcinoma. Proc Natl Acad Sci U S A, doi:10.1073/pnas.1814616115 (2018).
- Shen SY et al. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature, doi:10.1038/s41586-018-0703-0 (2018).
- Corces MR et al. The chromatin accessibility landscape of primary human cancers. Science 362, doi:10.1126/science.aav1898 (2018).
- Polak P et al. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature 518, 360–364, doi:10.1038/nature14221 (2015).
- Lieberman-Aiden E et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293, doi:10.1126/science.1181369 (2009).
- Fortin JP & Hansen KD Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. Genome Biol 16, 180, doi:10.1186/s13059-015-0741-y (2015).
- Diehl F et al. Circulating mutant DNA to assess tumor dynamics. Nat Med 14, 985–990 (2008).
- Phallen J et al. Early noninvasive detection of response to targeted therapy in non-small cell lung cancer. Cancer Research 15, 1204–1213, doi:DOI: 10.1158/0008-5472.CAN-18-1082 (2019).
- Burnham P et al. Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma. Scientific reports 6, 27859, doi:10.1038/srep27859 (2016).
- Sanchez C, Snyder MW, Tanos R, Shendure J & Thierry AR New insights into structural features and optimal detection of circulating tumor DNA determined by single-strand DNA analysis. NPJ genomic medicine 3, 31, doi:10.1038/s41525-018-0069-0 (2018).
- Fisher S et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol 12, R1, doi:10.1186/gb-2011-12-1-r1 (2011).
- Jones S et al. Personalized genomic analyses for cancer mutation discovery and interpretation. Sci Transl Med 7, 283ra253, doi:10.1126/scitranslmed.aaa7161 (2015).
- Benjamini Y & Speed TP Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 40, e72, doi:10.1093/nar/gks001 (2012).
- Langmead B & Salzberg SL Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359, doi:10.1038/nmeth.1923 (2012).
- Friedman JH Greedy function approximation: A gradient boosting machine. Ann Stat 29, 1189–1232, doi:DOI 10.1214/aos/1013203451 (2001).
- Friedman JH Stochastic gradient boosting. Comput Stat Data An 38, 367–378, doi:Doi 10.1016/S0167-9473(01)00065-2 (2002).
- Efron B & Tibshirani R Improvements on cross-validation: The .632+ bootstrap method. J Am Stat Assoc 92, 548–560, doi:Doi 10.2307/2965703 (1997).
- Zurbenko IG The spectral analysis of time series. (Elsevier, 1986).
- Robin X et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC bioinformatics 12, 77, doi:10.1186/1471-2105-12-77 (2011).
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