4
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Ji X, Li P, Fuscoe JC, Chen G, Xiao W, Shi L, Ning B, Liu Z, Hong H, Wu J, Liu J, Guo L, Kreil DP, Łabaj PP, Zhong L, Bao W, Huang Y, He J, Zhao Y, Tong W, Shi T. A comprehensive rat transcriptome built from large scale RNA-seq-based annotation. Nucleic Acids Res 2020; 48:8320-8331. [PMID: 32749457 PMCID: PMC7470976 DOI: 10.1093/nar/gkaa638] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 01/01/2023] Open
Abstract
The rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts. We also found that 11 715 genes and 15 852 transcripts were expressed in all 11 tissues and that 849 house-keeping genes expressed different isoforms among tissues. This comprehensive transcriptome is freely available at http://www.unimd.org/rtr/. Our new rat transcriptome provides essential reference for genetics and gene expression studies in rat disease and toxicity models.
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Affiliation(s)
- Xiangjun Ji
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Peng Li
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,Massachusetts General Hospital, Harvard Medical School, 51 Blossom St, Boston, MA 02114, USA
| | - James C Fuscoe
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Geng Chen
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wenzhong Xiao
- Massachusetts General Hospital, Harvard Medical School, 51 Blossom St, Boston, MA 02114, USA
| | - Leming Shi
- Center for Pharmacogenomics, School of Pharmacy, Fudan University, Shanghai, 200438, China
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Zhichao Liu
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jinghua Liu
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Lei Guo
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - David P Kreil
- Department of Biotechnology, Boku University Vienna, 1190 Muthgasse 18, Austria
| | - Paweł P Łabaj
- Department of Biotechnology, Boku University Vienna, 1190 Muthgasse 18, Austria.,Małopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7A, 30-387 Kraków, Poland
| | - Liping Zhong
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Wenjun Bao
- SAS Institute Inc., Cary, NC, 27513, USA
| | - Yong Huang
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Jian He
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Weida Tong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China
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6
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Laskar RS, Muller DC, Li P, Machiela MJ, Ye Y, Gaborieau V, Foll M, Hofmann JN, Colli L, Sampson JN, Wang Z, Bacq-Daian D, Boland A, Abedi-Ardekani B, Durand G, Le Calvez-Kelm F, Robinot N, Blanche H, Prokhortchouk E, Skryabin KG, Burdett L, Yeager M, Radojevic-Skodric S, Savic S, Foretova L, Holcatova I, Janout V, Mates D, Rascu S, Mukeria A, Zaridze D, Bencko V, Cybulski C, Fabianova E, Jinga V, Lissowska J, Lubinski J, Navratilova M, Rudnai P, Świątkowska B, Benhamou S, Cancel-Tassin G, Cussenot O, Trichopoulou A, Riboli E, Overvad K, Panico S, Ljungberg B, Sitaram RT, Giles GG, Milne RL, Severi G, Bruinsma F, Fletcher T, Koppova K, Larsson SC, Wolk A, Banks RE, Selby PJ, Easton DF, Pharoah P, Andreotti G, Beane Freeman LE, Koutros S, Albanes D, Männistö S, Weinstein S, Clark PE, Edwards TL, Lipworth L, Carol H, Freedman ML, Pomerantz MM, Cho E, Kraft P, Preston MA, Wilson KM, Michael Gaziano J, Sesso HD, Black A, Freedman ND, Huang WY, Anema JG, Kahnoski RJ, Lane BR, Noyes SL, Petillo D, Teh BT, Peters U, White E, Anderson GL, Johnson L, Luo J, Chow WH, Moore LE, Choueiri TK, Wood C, Johansson M, McKay JD, Brown KM, Rothman N, Lathrop MG, Deleuze JF, Wu X, Brennan P, Chanock SJ, Purdue MP, Scelo G. Sex specific associations in genome wide association analysis of renal cell carcinoma. Eur J Hum Genet 2019; 27:1589-1598. [PMID: 31231134 PMCID: PMC6777615 DOI: 10.1038/s41431-019-0455-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 12/15/2022] Open
Abstract
Renal cell carcinoma (RCC) has an undisputed genetic component and a stable 2:1 male to female sex ratio in its incidence across populations, suggesting possible sexual dimorphism in its genetic susceptibility. We conducted the first sex-specific genome-wide association analysis of RCC for men (3227 cases, 4916 controls) and women (1992 cases, 3095 controls) of European ancestry from two RCC genome-wide scans and replicated the top findings using an additional series of men (2261 cases, 5852 controls) and women (1399 cases, 1575 controls) from two independent cohorts of European origin. Our study confirmed sex-specific associations for two known RCC risk loci at 14q24.2 (DPF3) and 2p21(EPAS1). We also identified two additional suggestive male-specific loci at 6q24.3 (SAMD5, male odds ratio (ORmale) = 0.83 [95% CI = 0.78-0.89], Pmale = 1.71 × 10-8 compared with female odds ratio (ORfemale) = 0.98 [95% CI = 0.90-1.07], Pfemale = 0.68) and 12q23.3 (intergenic, ORmale = 0.75 [95% CI = 0.68-0.83], Pmale = 1.59 × 10-8 compared with ORfemale = 0.93 [95% CI = 0.82-1.06], Pfemale = 0.21) that attained genome-wide significance in the joint meta-analysis. Herein, we provide evidence of sex-specific associations in RCC genetic susceptibility and advocate the necessity of larger genetic and genomic studies to unravel the endogenous causes of sex bias in sexually dimorphic traits and diseases like RCC.
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Affiliation(s)
- Ruhina S Laskar
- International Agency for Research on Cancer (IARC), Lyon, France
| | - David C Muller
- Faculty of Medicine, School of Public Health, Imperial College London, London, UK
| | - Peng Li
- Max Planck Institute for Demographic Research, Rostock, Germany
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Yuanqing Ye
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Matthieu Foll
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Leandro Colli
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine, , Institut de biologie François Jacob, CEA, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, , Institut de biologie François Jacob, CEA, Evry, France
| | | | - Geoffroy Durand
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | | | - Helene Blanche
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Egor Prokhortchouk
- Center 'Bioengineering' of the Russian Academy of Sciences, Moscow, Russian Federation
- Kurchatov Scientific Center, Moscow, Russian Federation
| | - Konstantin G Skryabin
- Center 'Bioengineering' of the Russian Academy of Sciences, Moscow, Russian Federation
- Kurchatov Scientific Center, Moscow, Russian Federation
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | | | - Slavisa Savic
- Department of Urology, University Hospital "Dr D. Misovic" Clinical Center, Belgrade, Serbia
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ivana Holcatova
- 2nd Faculty of Medicine, Institute of Public Health and Preventive Medicine, Charles University, Prague, Czech Republic
| | - Vladimir Janout
- Department of Preventive Medicine, Faculty of Medicine, Palacky University, Olomouc, Czech Republic
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Stefan Rascu
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, Bucharest, Romania
| | - Anush Mukeria
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Vladimir Bencko
- First Faculty of Medicine, Institute of Hygiene and Epidemiology, Charles University, Prague, Czech Republic
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Eleonora Fabianova
- Regional Authority of Public Health in BanskaBystrica, BanskaBystrica, Slovakia
| | - Viorel Jinga
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, Bucharest, Romania
| | - Jolanta Lissowska
- The M Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Peter Rudnai
- National Public Health Institute, Budapest, Hungary
| | - Beata Świątkowska
- Department of Epidemiology, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Simone Benhamou
- INSERM U946, Paris, France
- CNRS UMR8200, Institute Gustave Roussy, Villejuif, France
| | - Geraldine Cancel-Tassin
- Sorbonne Université, GRC no. 5, ONCOTYPE-URO, AP-HP, Tenon Hospital, Paris, France
- CeRePP, Paris, France
| | - Olivier Cussenot
- Sorbonne Université, GRC no. 5, ONCOTYPE-URO, AP-HP, Tenon Hospital, Paris, France
- CeRePP, Paris, France
| | | | - Elio Riboli
- Faculty of Medicine, School of Public Health, Imperial College London, London, UK
| | - Kim Overvad
- Department of Public Health, Section for Epidemiology, Aarhus University, Aarhus C, Denmark
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | - Borje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Raviprakash T Sitaram
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Graham G Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council of Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville Victoria, 3010, Australia
| | - Roger L Milne
- Cancer Epidemiology & Intelligence Division, Cancer Council of Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville Victoria, 3010, Australia
| | - Gianluca Severi
- Cancer Epidemiology & Intelligence Division, Cancer Council of Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia
- Inserm U1018, Center for Research in Epidemiology and Population Health (CESP), Facultés de Medicine, Université Paris-Saclay, Université Paris-Sud, UVSQ, Gustave Roussy, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
| | - Fiona Bruinsma
- Cancer Epidemiology & Intelligence Division, Cancer Council of Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia
| | - Tony Fletcher
- London School of Hygiene and Tropical Medicine, University of London, London, UK
| | - Kvetoslava Koppova
- Regional Authority of Public Health in BanskaBystrica, BanskaBystrica, Slovakia
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rosamonde E Banks
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds, UK
| | - Peter J Selby
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds, UK
| | - Douglas F Easton
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul Pharoah
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Satu Männistö
- National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | | | | | | | | | | | | | | | - Peter Kraft
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark A Preston
- Brigham and Women's Hospital and VA Boston, Boston, MA, USA
| | | | | | - Howard D Sesso
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - John G Anema
- Division of Urology, Spectrum Health, Grand Rapids, MI, USA
| | | | - Brian R Lane
- Division of Urology, Spectrum Health, Grand Rapids, MI, USA
- College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Sabrina L Noyes
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - David Petillo
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - Bin Tean Teh
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - Ulrike Peters
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emily White
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Lisa Johnson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Juhua Luo
- Department of Epidemiology and Biostatistics, School of Public Health Indiana University Bloomington, Bloomington, IN, USA
| | - Wong-Ho Chow
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lee E Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | | | - Christopher Wood
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - James D McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Mark G Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine, , Institut de biologie François Jacob, CEA, Evry, France
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France.
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