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De Marchi T, Pyl PT, Sjöström M, Reinsbach SE, DiLorenzo S, Nystedt B, Tran L, Pekar G, Wärnberg F, Fredriksson I, Malmström P, Fernö M, Malmström L, Malmstöm J, Niméus E. Proteogenomics decodes the evolution of human ipsilateral breast cancer. Commun Biol 2023; 6:139. [PMID: 36732562 PMCID: PMC9894938 DOI: 10.1038/s42003-023-04526-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/24/2023] [Indexed: 02/04/2023] Open
Abstract
Ipsilateral breast tumor recurrence (IBTR) is a clinically important event, where an isolated in-breast recurrence is a potentially curable event but associated with an increased risk of distant metastasis and breast cancer death. It remains unclear if IBTRs are associated with molecular changes that can be explored as a resource for precision medicine strategies. Here, we employed proteogenomics to analyze a cohort of 27 primary breast cancers and their matched IBTRs to define proteogenomic determinants of molecular tumor evolution. Our analyses revealed a relationship between hormonal receptors status and proliferation levels resulting in the gain of somatic mutations and copy number. This in turn re-programmed the transcriptome and proteome towards a highly replicating and genomically unstable IBTRs, possibly enhanced by APOBEC3B. In order to investigate the origins of IBTRs, a second analysis that included primaries with no recurrence pinpointed proliferation and immune infiltration as predictive of IBTR. In conclusion, our study shows that breast tumors evolve into different IBTRs depending on hormonal status and proliferation and that immune cell infiltration and Ki-67 are significantly elevated in primary tumors that develop IBTR. These results can serve as a starting point to explore markers to predict IBTR formation and stratify patients for adjuvant therapy.
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Affiliation(s)
- Tommaso De Marchi
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden.
| | - Paul Theodor Pyl
- grid.452834.c0000 0004 5911 2402Department of Laboratory Medicine, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund, Sweden
| | - Martin Sjöström
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden ,grid.266102.10000 0001 2297 6811Department of Radiation Oncology, University of California San Francisco, San Francisco, USA
| | - Susanne Erika Reinsbach
- grid.5371.00000 0001 0775 6028Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, Sweden
| | - Sebastian DiLorenzo
- grid.8993.b0000 0004 1936 9457National Bioinformatics Infrastructure Sweden, Uppsala University, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala, Sweden
| | - Björn Nystedt
- grid.8993.b0000 0004 1936 9457National Bioinformatics Infrastructure Sweden, Uppsala University, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala, Sweden
| | - Lena Tran
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Gyula Pekar
- grid.411843.b0000 0004 0623 9987Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Fredrik Wärnberg
- grid.8761.80000 0000 9919 9582Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Irma Fredriksson
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Breast, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden
| | - Per Malmström
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden ,grid.411843.b0000 0004 0623 9987Department of Haematology, Oncology, and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Mårten Fernö
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Lars Malmström
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Johan Malmstöm
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Emma Niméus
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden. .,Department of Surgery, Skåne University Hospital, Lund, Sweden.
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2
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Paulsson JO, Rafati N, DiLorenzo S, Chen Y, Haglund F, Zedenius J, Juhlin CC. Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8. J Clin Endocrinol Metab 2021; 106:3265-3282. [PMID: 34171097 PMCID: PMC8530729 DOI: 10.1210/clinem/dgab471] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND The genomic and transcriptomic landscape of widely invasive follicular thyroid carcinomas (wiFTCs) and Hürthle cell carcinoma (HCC) are poorly characterized, and subsets of these tumors lack information on genetic driver events. OBJECTIVE The aim of this study was to bridge this gap. METHODS We performed whole-genome and RNA sequencing and subsequent bioinformatic analyses of 11 wiFTCs and 2 HCCs with a particularly poor prognosis, and matched normal tissue. RESULTS All wiFTCs exhibited one or several mutations in established thyroid cancer genes, including TERT (n = 4), NRAS (n = 3), HRAS, KRAS, AKT, PTEN, PIK3CA, MUTYH, TSHR, and MEN1 (n = 1 each). MutSig2CV analysis revealed recurrent somatic mutations in FAM72D (n = 3, in 2 wiFTCs and in a single HCC), TP53 (n = 3, in 2 wiFTCs and a single HCC), and EIF1AX (n = 3), with DGCR8 (n = 2) as borderline significant. The DGCR8 mutations were recurrent p.E518K missense alterations, known to cause familial multinodular goiter via disruption of microRNA (miRNA) processing. Expression analyses showed reduced DGCR8 messenger RNA expression in FTCs in general, and the 2 DGCR8 mutants displayed a distinct miRNA profile compared to DGCR8 wild-types. Copy number analyses revealed recurrent gains on chromosomes 4, 6, and 10, and fusion gene analyses revealed 27 high-quality events. Both HCCs displayed hyperploidy, which was fairly unusual in the FTC cohort. Based on the transcriptome data, tumors amassed in 2 principal clusters. CONCLUSION We describe the genomic and transcriptomic landscape in wiFTCs and HCCs and identify novel recurrent mutations and copy number alterations with possible driver properties and lay the foundation for future studies.
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Affiliation(s)
- Johan O Paulsson
- Department of Oncology-Pathology, Karolinska Institutet, 171 64, Solna-Stockholm, Sweden
- Correspondence: Johan O. Paulsson, MD, Department of Oncology-Pathology, BioClinicum J6:20, Karolinska Institutet, 171 64, Solna-Stockholm, Stockholm, Sweden.
| | - Nima Rafati
- National Bioinformatics Infrastructure Sweden, Uppsala University, SciLifeLab, Department of Medical Biochemistry and Microbiology, 751 23 Uppsala, Sweden
| | - Sebastian DiLorenzo
- National Bioinformatics Infrastructure Sweden, Uppsala University, SciLifeLab, Department of Cell and Molecular Biology, 751 23 Uppsala, Sweden
| | - Yi Chen
- Department of Oncology-Pathology, Karolinska Institutet, 171 64, Solna-Stockholm, Sweden
| | - Felix Haglund
- Department of Oncology-Pathology, Karolinska Institutet, 171 64, Solna-Stockholm, Sweden
- Department of Pathology and Cytology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Jan Zedenius
- Department of Breast, Endocrine Tumors and Sarcoma, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet, 171 64, Solna-Stockholm, Sweden
- Department of Pathology and Cytology, Karolinska University Hospital, 171 76 Stockholm, Sweden
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3
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Garcia M, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, Díaz De Ståhl T, Ewels P, Wirta V, Nistér M, Käller M, Nystedt B. Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. F1000Res 2020; 9:63. [PMID: 32269765 PMCID: PMC7111497 DOI: 10.12688/f1000research.16665.2] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at
https://github.com/nf-core/sarek and at
https://nf-co.re/sarek/.
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Affiliation(s)
- Maxime Garcia
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Szilveszter Juhos
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden.,Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121, Sweden.,Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
| | - Malin Larsson
- Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Linköping University, Linköping, 58183, Sweden
| | - Pall I Olason
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
| | - Marcel Martin
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121, Sweden
| | - Jesper Eisfeldt
- Clinical Genetics, Department of Molecular Medicine and Surgery, Karolinska Institutet, MMK L1:00, Karolinska University Hospital at Solna, Stockholm, 171 76, Sweden
| | - Sebastian DiLorenzo
- Department of Medical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Teresita Díaz De Ståhl
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Philip Ewels
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121, Sweden
| | - Valtteri Wirta
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Science for Life Laboratory, Karolinska Institutet, Box 1031, Solna, 171 21, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Max Käller
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, Solna, 17121, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
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4
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Garcia M, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, Díaz De Ståhl T, Ewels P, Wirta V, Nistér M, Käller M, Nystedt B. Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. F1000Res 2020; 9:63. [DOI: 10.12688/f1000research.16665.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/23/2020] [Indexed: 01/08/2023] Open
Abstract
Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.
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5
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Mesmar F, Dai B, Ibrahim A, Hases L, Jafferali MH, Jose Augustine J, DiLorenzo S, Kang Y, Zhao Y, Wang J, Kim M, Lin CY, Berkenstam A, Fleming J, Williams C. Clinical candidate and genistein analogue AXP107-11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein-coupled estrogen receptor signaling. Cancer Med 2019; 8:7705-7719. [PMID: 31568691 PMCID: PMC6912054 DOI: 10.1002/cam4.2581] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/13/2019] [Accepted: 09/13/2019] [Indexed: 12/17/2022] Open
Abstract
Despite advances in cancer therapeutics, pancreatic cancer remains difficult to treat and often develops resistance to chemotherapies. We have evaluated a bioavailable genistein analogue, AXP107-11 which has completed phase Ib clinical trial, as an approach to sensitize tumor cells to chemotherapy. Using organotypic cultures of 14 patient-derived xenografts (PDX) of pancreatic ductal adenocarcinoma, we found that addition of AXP107-11 indeed sensitized 57% of cases to gemcitabine treatment. Results were validated using PDX models in vivo. Further, RNA-Seq from responsive and unresponsive tumors proposed a 41-gene treatment-predictive signature. Functional and molecular assays were performed in cell lines and demonstrated that the effect was synergistic. Transcriptome analysis indicated activation of G-protein-coupled estrogen receptor (GPER1) as the main underlying mechanism of action, which was corroborated using GPER1-selective agonists and antagonists. GPER1 expression in pancreatic tumors was indicative of survival, and our study proposes that activation of GPER1 may constitute a new avenue for pancreatic cancer therapeutics.
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Affiliation(s)
- Fahmi Mesmar
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA.,Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Bingbing Dai
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ahmed Ibrahim
- Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Linnea Hases
- Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Mohammed Hakim Jafferali
- Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Jithesh Jose Augustine
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sebastian DiLorenzo
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ya'an Kang
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yang Zhao
- Department of Bioinformatics and Computing Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Department of Bioinformatics and Computing Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Kim
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chin-Yo Lin
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | | | - Jason Fleming
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cecilia Williams
- Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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6
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Bersani C, Sivars L, Haeggblom L, DiLorenzo S, Mints M, Ährlund-Richter A, Tertipis N, Munck-Wikland E, Näsman A, Ramqvist T, Dalianis T. Targeted sequencing of tonsillar and base of tongue cancer and human papillomavirus positive unknown primary of the head and neck reveals prognostic effects of mutated FGFR3. Oncotarget 2018; 8:35339-35350. [PMID: 28525363 PMCID: PMC5471059 DOI: 10.18632/oncotarget.15240] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/24/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Human papillomavirus positive (HPV+) tonsillar cancer (TSCC), base of tongue cancer (BOTSCC) and unknown primary cancer of the head and neck (HNCUP) have better outcome than corresponding HPV- cancers. To find predictive markers for response to treatment, and correlations and differences in mutated oncogenes and suppressor genes between HPV+ TSCC/BOTSSCC and HPV+ HNCUP and HPV- TSCC/BOTSCC targeted next-generation sequencing was performed of frequently mutated regions in 50 cancer related genes. PATIENTS AND METHODS DNA from 348 TSCC/BOTSCC and 20 HNCUP from patients diagnosed 2000-2011, was sequenced by the Ion Proton sequencing platform using the Ion AmpliSeq Cancer Hotspot Panel v2 to identify frequently mutated regions in 50 cancer related genes. Ion Torrent Variant Caller software was used to call variants. RESULTS 279 HPV+ TSCC/BOTSCC, 46 HPV- TSCC/BOTSCC and 19 HPV+ HNCUP samples qualified for further analysis. Mutations/tumor were fewer in HPV+ TSCC/BOTSCC and HNCUP, compared to HPV- tumors (0.92 vs. 1.32 vs. 1.68). Differences in mutation frequency of TP53 and PIK3CA were found between HPV+ TSCC/BOTSCC and HNCUP and HPV- TSCC/BOTSCC. In HPV+ TSCC/BOTSCC presence of FGFR3 mutations correlated to worse prognosis. Other correlations to survival within the groups were not disclosed. CONCLUSIONS In HPV+ TSCC/BOTSCC mutation of PIK3CA was most frequently observed, while TP53 mutations dominated in HPV- TSCC/BOTSCC. In HPV+ TSCC/BOTSCC and HNCUP, mutations/tumor were similar in frequency and fewer compared to that in HPV- TSCC/BOTSCC. Notably, FGFR3 mutations in HPV+ TSCC/BOTSCC indicated worse prognosis.
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Affiliation(s)
- Cinzia Bersani
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Lars Sivars
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Linnea Haeggblom
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian DiLorenzo
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Michael Mints
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | | | - Nikolaos Tertipis
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Eva Munck-Wikland
- Department of Clinical Science and Technology, Karolinska Institutet, Stockholm, Sweden.,Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Näsman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Torbjörn Ramqvist
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Tina Dalianis
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
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7
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Mayrhofer M, DiLorenzo S, Isaksson A. Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue. Genome Biol 2013; 14:R24. [PMID: 23531354 PMCID: PMC4053982 DOI: 10.1186/gb-2013-14-3-r24] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 02/27/2013] [Accepted: 03/25/2013] [Indexed: 12/28/2022] Open
Abstract
Whole-genome sequencing of tumor tissue has the potential to provide comprehensive characterization of genomic alterations in tumor samples. We present Patchwork, a new bioinformatic tool for allele-specific copy number analysis using whole-genome sequencing data. Patchwork can be used to determine the copy number of homologous sequences throughout the genome, even in aneuploid samples with moderate sequence coverage and tumor cell content. No prior knowledge of average ploidy or tumor cell content is required. Patchwork is freely available as an R package, installable via R-Forge (http://patchwork.r-forge.r-project.org/).
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Affiliation(s)
- Markus Mayrhofer
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Sebastian DiLorenzo
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Anders Isaksson
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
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