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Research: Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer
- Marco L. Leung,
- Alexander Davis,
- Ruli Gao,
- Anna Casasent,
- Yong Wang,
- Emi Sei,
- Eduardo Vilar,
- Dipen Maru,
- Scott Kopetz,
- and Nicholas E. Navin
Genome Res. August 2017 27: 1287-1299; Published in Advance May 25, 2017, doi:10.1101/gr.209973.116
..., USA ↵6 These authors contributed equally to this work. Corresponding author: nnavin@mdanderson.orgAbstractMetastasis is a complex biological process that has been difficult to delineate in human colorectal cancer (CRC) patients. A major obstacle in understanding metastatic lineages is the extensive...
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Methods: Identification of rare cancer driver mutations by network reconstruction
- Ali Torkamani and
- Nicholas J. Schork
Genome Res. September 2009 19: 1570-1578; Published in Advance July 2, 2009, doi:10.1101/gr.092833.109
...Acad Sci 97: 4262–4266. Lin J, Gan CM, Zhang X, Jones S, Sjo¨blom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, et al. 2007. A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res 17: 1304–1318. Margolin AA, Nemenman I, Basso K, Wiggins C...
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Research: Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity
- Zdenek Andrysik,
- Matthew D. Galbraith,
- Anna L. Guarnieri,
- Sara Zaccara,
- Kelly D. Sullivan,
- Ahwan Pandey,
- Morgan MacBeth,
- Alberto Inga,
- and Joaquín M. Espinosa
Genome Res. October 2017 27: 1645-1657; Published in Advance September 13, 2017, doi:10.1101/gr.220533.117
...of Trento, 38123 Trento, TN, Italy; 5Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA The tumor suppressor TP53 is the most frequently mutated gene product in human cancer. Close to half of all solid tumors carry inactivating mutations in the TP53 gene, while in the remaining cases, TP...
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Perspective: Translating cancer ‘omics’ to improved outcomes
- Emily A. Vucic,
- Kelsie L. Thu,
- Keith Robison,
- Leszek A. Rybaczyk,
- Raj Chari,
- Carlos E. Alvarez,
- and Wan L. Lam
Genome Res. February 2012 22: 188-195; doi:10.1101/gr.124354.111
...to targeted cancer therapy Alongside the widespread use of early detection and screening programs, particularly for breast, cervical, prostate, testicular, and colorectal cancers, targeted therapies have been instrumental in extending the lives of millions of cancer patients (Etzioni et al. 2003). A summary...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
..., Wilcoxon rank-sum test, P-value = 1.8 × 10−24). To further assess the cancer cell fraction (CCF) of these shared HBV-induced SVs, we modified the existing algorithm SVclone (Cmero et al. 2020) to suit LRS data. By integrating established timing algorithms MutationTimeR (Gerstung et al. 2020), these shared...
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Research: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. May 2024 34: 680-695; Published in Advance May 22, 2024, doi:10.1101/gr.278565.123
...-STAD patients have a mutation in GATA4 according to cBioPortal (Gao et al. 2013), GATA4 CN alterations are more frequent in TCGA-STAD (Fig. 3B). Further, an interval of Chr 8p containing GATA4 is frequently deleted in human epithelial cancers (Cai and Sablina 2016). Thus, GATA CN alterations are a potential...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
.... 2021), and immunotherapy response (Wang et al. 2020a). Therapeutic promise through m6A can be found in two recently developed METTL3 inhibitors: STM2457 (Yankova et al. 2021) and STM3006 (Guirguis et al. 2023). METTL3 inhibition with STM2457 in AT3 TNBC cells (triple-negative breast cancer mouse cell...
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Method: SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
- Hamim Zafar,
- Nicholas Navin,
- Ken Chen,
- and Luay Nakhleh
Genome Res. November 2019 29: 1847-1859; Published in Advance October 18, 2019, doi:10.1101/gr.243121.118
...mutations in a Darwinian framework result in intra-tumor heterogeneity (ITH) that poses significant challenges to the diagnosis and clinical therapy of cancer. Identification of the tumor cell populations (clones) and reconstruction of their evolutionary relationship can elucidate this heterogeneity...
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Method: Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies
- Paul Geeleher,
- Zhenyu Zhang,
- Fan Wang,
- Robert F. Gruener,
- Aritro Nath,
- Gladys Morrison,
- Steven Bhutra,
- Robert L. Grossman,
- and R. Stephanie Huang
Genome Res. October 2017 27: 1743-1751; Published in Advance August 28, 2017, doi:10.1101/gr.221077.117
.... The next important factor is that ERBB2 amplification is well represented in TCGA. There are 164 ERBB2+ breast cancer samples in TCGA, providing sufficient statistical power. Also, ERBB2 amplification has a substantial effect on gene expression, with breast cancer samples harboring this mutation associated...
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Research: Enduring epigenetic landmarks define the cancer microenvironment
- Ruth Pidsley,
- Mitchell G. Lawrence,
- Elena Zotenko,
- Birunthi Niranjan,
- Aaron Statham,
- Jenny Song,
- Roman M. Chabanon,
- Wenjia Qu,
- Hong Wang,
- Michelle Richards,
- Shalima S. Nair,
- Nicola J. Armstrong,
- Hieu T. Nim,
- Melissa Papargiris,
- Preetika Balanathan,
- Hugh French,
- Timothy Peters,
- Sam Norden,
- Andrew Ryan,
- John Pedersen,
- James Kench,
- Roger J. Daly,
- Lisa G. Horvath,
- Phillip Stricker,
- Mark Frydenberg,
- Renea A. Taylor,
- Clare Stirzaker,
- Gail P. Risbridger,
- and Susan J. Clark
Genome Res. May 2018 28: 625-638; Published in Advance April 12, 2018, doi:10.1101/gr.229070.117
...(EHF), Mutated in Colorectal Cancer (MCC), and STEAP2 (Prostate Cancer Associated Protein 1) genes (Supplemental Fig. S8). These tsDMRs all had consistent changes in DNA methylation across WGBS data from CAFs, LNCaP cells, and tumor tissue, and 450K data from TCGA. Unlike previous studies of prostate...
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