1
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Chan SH, Bylstra Y, Teo JX, Kuan JL, Bertin N, Gonzalez-Porta M, Hebrard M, Tirado-Magallanes R, Tan JHJ, Jeyakani J, Li Z, Chai JF, Chong YS, Davila S, Goh LL, Lee ES, Wong E, Wong TY, Prabhakar S, Liu J, Cheng CY, Eisenhaber B, Karnani N, Leong KP, Sim X, Yeo KK, Chambers JC, Tai ES, Tan P, Jamuar SS, Ngeow J, Lim WK, Gluckman PD, Goh DLM, Jain K, Kam S, Kassam I, Lakshmanan LN, Lee CG, Lee J, Lee SC, Lee YS, Li H, Lim CW, Lim TH, Loh M, Maurer-Stroh S, Mina TH, Mok SQ, Ng HK, Pua CJ, Riboli E, Rim TH, Sabanayagam C, Sim WC, Subramaniam T, Tan ES, Tan EK, Tantoso E, Tay D, Teo YY, Tham YC, Toh LXG, Tsai PK, van Dam RM, Veeravalli L, Khin-lin GW, Wilm A, Yang C, Yap F, Yew YW, Prabhakar S, Liu J, Cheng CY, Eisenhaber B, Karnani N, Leong KP, Sim X, Yeo KK, Chambers JC, Tai ES, Tan P, Jamuar SS, Ngeow J, Lim WK. Analysis of clinically relevant variants from ancestrally diverse Asian genomes. Nat Commun 2022; 13:6694. [PMID: 36335097 PMCID: PMC9637116 DOI: 10.1038/s41467-022-34116-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 04/14/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Asian populations are under-represented in human genomics research. Here, we characterize clinically significant genetic variation in 9051 genomes representing East Asian, South Asian, and severely under-represented Austronesian-speaking Southeast Asian ancestries. We observe disparate genetic risk burden attributable to ancestry-specific recurrent variants and identify individuals with variants specific to ancestries discordant to their self-reported ethnicity, mostly due to cryptic admixture. About 27% of severe recessive disorder genes with appreciable carrier frequencies in Asians are missed by carrier screening panels, and we estimate 0.5% Asian couples at-risk of having an affected child. Prevalence of medically-actionable variant carriers is 3.4% and a further 1.6% harbour variants with potential for pathogenic classification upon additional clinical/experimental evidence. We profile 23 pharmacogenes with high-confidence gene-drug associations and find 22.4% of Asians at-risk of Centers for Disease Control and Prevention Tier 1 genetic conditions concurrently harbour pharmacogenetic variants with actionable phenotypes, highlighting the benefits of pre-emptive pharmacogenomics. Our findings illuminate the diversity in genetic disease epidemiology and opportunities for precision medicine for a large, diverse Asian population.
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Affiliation(s)
- Sock Hoai Chan
- grid.410724.40000 0004 0620 9745Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610 Singapore ,grid.428397.30000 0004 0385 0924Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore
| | - Yasmin Bylstra
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore
| | - Jing Xian Teo
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore
| | - Jyn Ling Kuan
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore
| | - Nicolas Bertin
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Mar Gonzalez-Porta
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Maxime Hebrard
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Roberto Tirado-Magallanes
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Joanna Hui Juan Tan
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Justin Jeyakani
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Zhihui Li
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Jin Fang Chai
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549 Singapore
| | - Yap Seng Chong
- grid.4280.e0000 0001 2180 6431Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.452264.30000 0004 0530 269XSingapore Institute for Clinical Sciences, Singapore, 117609 Singapore
| | - Sonia Davila
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.428397.30000 0004 0385 0924Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Genomic Medicine Centre, Singapore, 168582 Singapore
| | - Liuh Ling Goh
- grid.240988.f0000 0001 0298 8161Personalized Medicine Service, Tan Tock Seng Hospital, Singapore, 308433 Singapore
| | - Eng Sing Lee
- grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore ,grid.466910.c0000 0004 0451 6215National Healthcare Group Polyclinics, Singapore, 138543 Singapore
| | - Eleanor Wong
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Tien Yin Wong
- grid.419272.b0000 0000 9960 1711Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 168751 Singapore
| | | | - Shyam Prabhakar
- grid.418377.e0000 0004 0620 715XLaboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Jianjun Liu
- grid.418377.e0000 0004 0620 715XHuman Genomics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore
| | - Ching-Yu Cheng
- grid.419272.b0000 0000 9960 1711Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 168751 Singapore ,grid.428397.30000 0004 0385 0924Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, 169857 Singapore
| | - Birgit Eisenhaber
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore ,grid.418325.90000 0000 9351 8132Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 138671 Singapore
| | - Neerja Karnani
- grid.452264.30000 0004 0530 269XHuman Development, Singapore Institute for Clinical Sciences, Singapore, 117609 Singapore ,grid.418325.90000 0000 9351 8132Clinical Data Engagement, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 138671 Singapore ,grid.4280.e0000 0001 2180 6431Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596 Singapore
| | - Khai Pang Leong
- grid.240988.f0000 0001 0298 8161Personalized Medicine Service, Tan Tock Seng Hospital, Singapore, 308433 Singapore ,grid.240988.f0000 0001 0298 8161Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, 308433 Singapore
| | - Xueling Sim
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549 Singapore
| | - Khung Keong Yeo
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.419385.20000 0004 0620 9905Department of Cardiology, National Heart Centre Singapore, Singapore, 169609 Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, 169857 Singapore
| | - John C. Chambers
- grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore ,Precision Health Research Singapore (PRECISE), Singapore, 139234 Singapore ,grid.7445.20000 0001 2113 8111Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG UK
| | - E-Shyong Tai
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549 Singapore ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, 169857 Singapore ,Precision Health Research Singapore (PRECISE), Singapore, 139234 Singapore
| | - Patrick Tan
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore ,Precision Health Research Singapore (PRECISE), Singapore, 139234 Singapore ,grid.428397.30000 0004 0385 0924Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore
| | - Saumya S. Jamuar
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Genomic Medicine Centre, Singapore, 168582 Singapore ,grid.414963.d0000 0000 8958 3388Genetics Service, Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore, 229899 Singapore ,grid.428397.30000 0004 0385 0924Paediatric Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857 Singapore
| | - Joanne Ngeow
- grid.410724.40000 0004 0620 9745Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610 Singapore ,grid.428397.30000 0004 0385 0924Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore ,grid.185448.40000 0004 0637 0221Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, 138673 Singapore
| | - Weng Khong Lim
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Genomic Medicine Centre, Singapore, 168582 Singapore ,grid.428397.30000 0004 0385 0924Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857 Singapore
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2
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Nahar R, Zhai W, Zhang T, Takano A, Khng AJ, Lee YY, Liu X, Lim CH, Koh TPT, Aung ZW, Lim TKH, Veeravalli L, Yuan J, Teo ASM, Chan CX, Poh HM, Chua IML, Liew AA, Lau DPX, Kwang XL, Toh CK, Lim WT, Lim B, Tam WL, Tan EH, Hillmer AM, Tan DSW. Elucidating the genomic architecture of Asian EGFR-mutant lung adenocarcinoma through multi-region exome sequencing. Nat Commun 2018; 9:216. [PMID: 29335443 PMCID: PMC5768770 DOI: 10.1038/s41467-017-02584-z] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 12/11/2017] [Indexed: 12/14/2022] Open
Abstract
EGFR-mutant lung adenocarcinomas (LUAD) display diverse clinical trajectories and are characterized by rapid but short-lived responses to EGFR tyrosine kinase inhibitors (TKIs). Through sequencing of 79 spatially distinct regions from 16 early stage tumors, we show that despite low mutation burdens, EGFR-mutant Asian LUADs unexpectedly exhibit a complex genomic landscape with frequent and early whole-genome doubling, aneuploidy, and high clonal diversity. Multiple truncal alterations, including TP53 mutations and loss of CDKN2A and RB1, converge on cell cycle dysregulation, with late sector-specific high-amplitude amplifications and deletions that potentially beget drug resistant clones. We highlight the association between genomic architecture and clinical phenotypes, such as co-occurring truncal drivers and primary TKI resistance. Through comparative analysis with published smoking-related LUAD, we postulate that the high intra-tumor heterogeneity observed in Asian EGFR-mutant LUAD may be contributed by an early dominant driver, genomic instability, and low background mutation rates. EGFR mutant lung adenocarcinoma (LUAD) exhibit diverse clinical outcomes in response to targeted therapies. Here the authors show that these LUADs involve a complex genomic landscape with high intratumor heterogeneity, providing insights into the evolutionary trajectory of oncogene-driven LUAD and potential mediators of EGFR TKI resistance.
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Affiliation(s)
- Rahul Nahar
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Weiwei Zhai
- Human Genetics, Genome Institute of Singapore, Singapore, 138672, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Tong Zhang
- Human Genetics, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Angela Takano
- Department of Pathology, Singapore General Hospital, Singapore, 169608, Singapore
| | - Alexis J Khng
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Yin Yeng Lee
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Xingliang Liu
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Chong Hee Lim
- Department of Cardiothoracic Surgery, National Heart Centre Singapore, Singapore, 169609, Singapore
| | - Tina P T Koh
- Department of Cardiothoracic Surgery, National Heart Centre Singapore, Singapore, 169609, Singapore
| | - Zaw Win Aung
- Division of Clinical Trials and Epidemiological Sciences, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Tony Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore, 169608, Singapore
| | - Lavanya Veeravalli
- Research Pipeline Development, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Ju Yuan
- Cancer Stem Cell Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Audrey S M Teo
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Cheryl X Chan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Huay Mei Poh
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Ivan M L Chua
- Next Generation Sequencing Platform, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Audrey Ann Liew
- Cancer Stem Cell Biology, Genome Institute of Singapore, Singapore, 138672, Singapore.,Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore.,Cancer Therapeutics Research Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Dawn Ping Xi Lau
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore.,Cancer Therapeutics Research Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Xue Lin Kwang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore.,Cancer Therapeutics Research Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Chee Keong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Wan-Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Bing Lim
- Cancer Stem Cell Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Wai Leong Tam
- Cancer Stem Cell Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Eng-Huat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Axel M Hillmer
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, 138672, Singapore. .,Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany.
| | - Daniel S W Tan
- Cancer Stem Cell Biology, Genome Institute of Singapore, Singapore, 138672, Singapore. .,Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore. .,Cancer Therapeutics Research Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, 169610, Singapore.
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3
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Yao F, Kausalya JP, Sia YY, Teo ASM, Lee WH, Ong AGM, Zhang Z, Tan JHJ, Li G, Bertrand D, Liu X, Poh HM, Guan P, Zhu F, Pathiraja TN, Ariyaratne PN, Rao J, Woo XY, Cai S, Mulawadi FH, Poh WT, Veeravalli L, Chan CS, Lim SS, Leong ST, Neo SC, Choi PSD, Chew EGY, Nagarajan N, Jacques PÉ, So JBY, Ruan X, Yeoh KG, Tan P, Sung WK, Hunziker W, Ruan Y, Hillmer AM. Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity. Cell Rep 2015; 12:272-85. [PMID: 26146084 DOI: 10.1016/j.celrep.2015.06.020] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 04/21/2015] [Accepted: 06/06/2015] [Indexed: 12/21/2022] Open
Abstract
Genome rearrangements, a hallmark of cancer, can result in gene fusions with oncogenic properties. Using DNA paired-end-tag (DNA-PET) whole-genome sequencing, we analyzed 15 gastric cancers (GCs) from Southeast Asians. Rearrangements were enriched in open chromatin and shaped by chromatin structure. We identified seven rearrangement hot spots and 136 gene fusions. In three out of 100 GC cases, we found recurrent fusions between CLDN18, a tight junction gene, and ARHGAP26, a gene encoding a RHOA inhibitor. Epithelial cell lines expressing CLDN18-ARHGAP26 displayed a dramatic loss of epithelial phenotype and long protrusions indicative of epithelial-mesenchymal transition (EMT). Fusion-positive cell lines showed impaired barrier properties, reduced cell-cell and cell-extracellular matrix adhesion, retarded wound healing, and inhibition of RHOA. Gain of invasion was seen in cancer cell lines expressing the fusion. Thus, CLDN18-ARHGAP26 mediates epithelial disintegration, possibly leading to stomach H(+) leakage, and the fusion might contribute to invasiveness once a cell is transformed.
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Affiliation(s)
- Fei Yao
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore
| | - Jaya P Kausalya
- Epithelial Cell Biology Laboratory, Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Yee Yen Sia
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore
| | - Audrey S M Teo
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore
| | - Wah Heng Lee
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Alicia G M Ong
- Epithelial Cell Biology Laboratory, Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Zhenshui Zhang
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Joanna H J Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Denis Bertrand
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Xingliang Liu
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Huay Mei Poh
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Peiyong Guan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore; School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Feng Zhu
- The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Thushangi Nadeera Pathiraja
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore
| | - Pramila N Ariyaratne
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jaideepraj Rao
- Department of General Surgery, Tan Tock Seng Hospital, Singapore 308433, Singapore
| | - Xing Yi Woo
- Personal Genomic Solutions, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Shaojiang Cai
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Fabianus H Mulawadi
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Wan Ting Poh
- Personal Genomic Solutions, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Lavanya Veeravalli
- Research Computing, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Chee Seng Chan
- Research Computing, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Seong Soo Lim
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - See Ting Leong
- Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Say Chuan Neo
- Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Poh Sum D Choi
- Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Elaine G Y Chew
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Niranjan Nagarajan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Jimmy B Y So
- The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; National University Health System, Singapore 119228, Singapore
| | - Xiaoan Ruan
- Personal Genomic Solutions, Genome Institute of Singapore, Singapore 138672, Singapore; Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Khay Guan Yeoh
- The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; National University Health System, Singapore 119228, Singapore
| | - Patrick Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore; Duke-NUS Graduate Medical School, Singapore 169857, Singapore; Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Wing-Kin Sung
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore; School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Walter Hunziker
- Epithelial Cell Biology Laboratory, Institute of Molecular and Cell Biology, Singapore 138673, Singapore; Department of Physiology, National University of Singapore, Singapore 117597, Singapore.
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Axel M Hillmer
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore.
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4
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Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2013; 22:1775-89. [PMID: 22955988 PMCID: PMC3431493 DOI: 10.1101/gr.132159.111] [Citation(s) in RCA: 3740] [Impact Index Per Article: 340.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to investigate these genes have been hampered by the lack of comprehensive lncRNA annotation. Here, we present and analyze the most complete human lncRNA annotation to date, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts. Our analyses indicate that lncRNAs are generated through pathways similar to that of protein-coding genes, with similar histone-modification profiles, splicing signals, and exon/intron lengths. In contrast to protein-coding genes, however, lncRNAs display a striking bias toward two-exon transcripts, they are predominantly localized in the chromatin and nucleus, and a fraction appear to be preferentially processed into small RNAs. They are under stronger selective pressure than neutrally evolving sequences—particularly in their promoter regions, which display levels of selection comparable to protein-coding genes. Importantly, about one-third seem to have arisen within the primate lineage. Comprehensive analysis of their expression in multiple human organs and brain regions shows that lncRNAs are generally lower expressed than protein-coding genes, and display more tissue-specific expression patterns, with a large fraction of tissue-specific lncRNAs expressed in the brain. Expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of lncRNAs.
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Affiliation(s)
- Thomas Derrien
- Bioinformatics and Genomics, Centre for Genomic Regulation and UPF, 08003 Barcelona, Catalonia, Spain
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