Author
Listed:
- Johannes G. Reiter
(Program for Evolutionary Dynamics, Harvard University
IST (Institute of Science and Technology) Austria)
- Alvin P. Makohon-Moore
(The David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center
Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center)
- Jeffrey M. Gerold
(Program for Evolutionary Dynamics, Harvard University)
- Ivana Bozic
(Program for Evolutionary Dynamics, Harvard University
Harvard University)
- Krishnendu Chatterjee
(IST (Institute of Science and Technology) Austria)
- Christine A. Iacobuzio-Donahue
(The David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center
Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center
Memorial Sloan Kettering Cancer Center)
- Bert Vogelstein
(The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine
The Ludwig Center and Howard Hughes Medical Institute at The Johns Hopkins University School of Medicine)
- Martin A. Nowak
(Program for Evolutionary Dynamics, Harvard University
Harvard University
Harvard University)
Abstract
Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods.
Suggested Citation
Johannes G. Reiter & Alvin P. Makohon-Moore & Jeffrey M. Gerold & Ivana Bozic & Krishnendu Chatterjee & Christine A. Iacobuzio-Donahue & Bert Vogelstein & Martin A. Nowak, 2017.
"Reconstructing metastatic seeding patterns of human cancers,"
Nature Communications, Nature, vol. 8(1), pages 1-10, April.
Handle:
RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14114
DOI: 10.1038/ncomms14114
Download full text from publisher
Citations
Citations are extracted by the
CitEc Project, subscribe to its
RSS feed for this item.
Cited by:
- Zicheng Wang & Yunong Xia & Lauren Mills & Athanasios N. Nikolakopoulos & Nicole Maeser & Scott M. Dehm & Jason M. Sheltzer & Ruping Sun, 2024.
"Evolving copy number gains promote tumor expansion and bolster mutational diversification,"
Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Haochen Zhang & Elias-Ramzey Karnoub & Shigeaki Umeda & Ronan Chaligné & Ignas Masilionis & Caitlin A. McIntyre & Palash Sashittal & Akimasa Hayashi & Amanda Zucker & Katelyn Mullen & Jungeui Hong & A, 2023.
"Application of high-throughput single-nucleus DNA sequencing in pancreatic cancer,"
Nature Communications, Nature, vol. 14(1), pages 1-14, December.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14114. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
We have no bibliographic references for this item. You can help adding them by using this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through
the various RePEc services.