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Anjanappa M, Hao Y, Simpson ER, Bhat-Nakshatri P, Nelson JB, Tersey SA, Mirmira RG, Cohen-Gadol AA, Saadatzadeh MR, Li L, Fang F, Nephew KP, Miller KD, Liu Y, Nakshatri H. A system for detecting high impact-low frequency mutations in primary tumors and metastases. Oncogene 2017; 37:185-196. [PMID: 28892047 DOI: 10.1038/onc.2017.322] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 12/14/2022]
Abstract
Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis. Comparative Ampliseq Comprehensive Cancer Panel sequence analyses were performed on DNA from unprocessed breast tumor and tumor cells propagated from the same tumor. We identified previously uncharacterized mutations present only in the cultured tumor cells, a subset of which has been reported in brain metastatic but not primary breast tumors. In addition, whole-genome sequencing identified mutations enriched in liver metastases of various cancers, including Notch pathway mutations/chromosomal inversions in 5/5 liver metastases, irrespective of cancer types. Mutations/rearrangements in FHIT, involved in purine metabolism, were detected in 4/5 liver metastases, and the same four liver metastases shared mutations in 32 genes, including mutations of different HLA-DR family members affecting OX40 signaling pathway, which could impact the immune response to metastatic cells. Pathway analyses of all mutated genes in liver metastases showed aberrant tumor necrosis factor and transforming growth factor signaling in metastatic cells. Epigenetic regulators including KMT2C/MLL3 and ARID1B, which are mutated in >50% of hepatocellular carcinomas, were also mutated in liver metastases. Thus, irrespective of cancer types, organ-specific metastases may share common genomic aberrations. Since recent studies show independent evolution of primary tumors and metastases and in most cases mutation burden is higher in metastases than primary tumors, the method described here may allow early detection of subclonal somatic alterations associated with metastatic progression and potentially identify therapeutically actionable, metastasis-specific genomic aberrations.
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Affiliation(s)
- M Anjanappa
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Y Hao
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN, USA
| | - E R Simpson
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN, USA
| | - P Bhat-Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - J B Nelson
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - S A Tersey
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - R G Mirmira
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - A A Cohen-Gadol
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - M R Saadatzadeh
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - L Li
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
| | - F Fang
- Medical Science Program, Indiana University, Bloomington, IN, USA
| | - K P Nephew
- Medical Science Program, Indiana University, Bloomington, IN, USA
| | - K D Miller
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Y Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
| | - H Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Roudebush VA Medical Center, Indianapolis, IN, USA
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Hao Y, Xuei X, Li L, Nakshatri H, Edenberg HJ, Liu Y. RareVar: A Framework for Detecting Low-Frequency Single-Nucleotide Variants. J Comput Biol 2017; 24:637-646. [PMID: 28541743 DOI: 10.1089/cmb.2017.0057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Accurate identification of low-frequency somatic point mutations in tumor samples has important clinical utilities. Although high-throughput sequencing technology enables capturing such variants while sequencing primary tumor samples, our ability for accurate detection is compromised when the variant frequency is close to the sequencer error rate. Most current experimental and bioinformatic strategies target mutations with ≥5% allele frequency, which limits our ability to understand the cancer etiology and tumor evolution. We present an experimental and computational modeling framework, RareVar, to reliably identify low-frequency single-nucleotide variants from high-throughput sequencing data under standard experimental protocols. RareVar protocol includes a benchmark design by pooling DNAs from already sequenced individuals at various concentrations to target variants at desired frequencies, 0.5%-3% in our case. By applying a generalized, linear model-based, position-specific error model, followed by machine-learning-based variant calibration, our approach outperforms existing methods. Our method can be applied on most capture and sequencing platforms without modifying the experimental protocol.
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Affiliation(s)
- Yangyang Hao
- 1 Department of Medical and Molecular Genetics, Indiana University School of Medicine , Indianapolis, Indiana.,2 Center for Computational Biology and Bioinformatics, Indiana University School of Medicine , Indianapolis, Indiana
| | - Xiaoling Xuei
- 3 Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana.,4 Center for Medical Genomics, Indiana University School of Medicine , Indianapolis, Indiana
| | - Lang Li
- 1 Department of Medical and Molecular Genetics, Indiana University School of Medicine , Indianapolis, Indiana.,2 Center for Computational Biology and Bioinformatics, Indiana University School of Medicine , Indianapolis, Indiana
| | - Harikrishna Nakshatri
- 5 Department of Surgery, Indiana University School of Medicine , Indianapolis, Indiana.,6 IU Simon Cancer Center, Indiana University School of Medicine , Indianapolis, Indiana
| | - Howard J Edenberg
- 1 Department of Medical and Molecular Genetics, Indiana University School of Medicine , Indianapolis, Indiana.,3 Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana.,4 Center for Medical Genomics, Indiana University School of Medicine , Indianapolis, Indiana
| | - Yunlong Liu
- 1 Department of Medical and Molecular Genetics, Indiana University School of Medicine , Indianapolis, Indiana.,2 Center for Computational Biology and Bioinformatics, Indiana University School of Medicine , Indianapolis, Indiana.,4 Center for Medical Genomics, Indiana University School of Medicine , Indianapolis, Indiana.,6 IU Simon Cancer Center, Indiana University School of Medicine , Indianapolis, Indiana
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Huang K, Liu Y, Huang Y, Li L, Cooper L, Ruan J, Zhao Z. Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science. BMC Genomics 2016; 17 Suppl 7:524. [PMID: 27556295 PMCID: PMC5001210 DOI: 10.1186/s12864-016-2893-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We summarize the 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) and the editorial report of the supplement to BMC Genomics. The supplement includes 20 research articles selected from the manuscripts submitted to ICIBM 2015. The conference was held on November 13-15, 2015 at Indianapolis, Indiana, USA. It included eight scientific sessions, three tutorials, four keynote presentations, three highlight talks, and a poster session that covered current research in bioinformatics, systems biology, computational biology, biotechnologies, and computational medicine.
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Affiliation(s)
- Kun Huang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210 USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Yufei Huang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Lang Li
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Lee Cooper
- Department of Biomedical Informatics, Emory University, Atlanta, GA 30322 USA
- Department of Biomedical Engineering, Emory University / Georgia Institute of Technology, Atlanta, GA 30322 USA
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
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