1
|
Westrin KJ, Kretzschmar WW, Emanuelsson O. ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs. BMC Bioinformatics 2024; 25:54. [PMID: 38302873 PMCID: PMC10836024 DOI: 10.1186/s12859-024-05663-3] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Transcriptome assembly from RNA-sequencing data in species without a reliable reference genome has to be performed de novo, but studies have shown that de novo methods often have inadequate ability to reconstruct transcript isoforms. We address this issue by constructing an assembly pipeline whose main purpose is to produce a comprehensive set of transcript isoforms. RESULTS We present the de novo transcript isoform assembler ClusTrast, which takes short read RNA-seq data as input, assembles a primary assembly, clusters a set of guiding contigs, aligns the short reads to the guiding contigs, assembles each clustered set of short reads individually, and merges the primary and clusterwise assemblies into the final assembly. We tested ClusTrast on real datasets from six eukaryotic species, and showed that ClusTrast reconstructed more expressed known isoforms than any of the other tested de novo assemblers, at a moderate reduction in precision. For recall, ClusTrast was on top in the lower end of expression levels (<15% percentile) for all tested datasets, and over the entire range for almost all datasets. Reference transcripts were often (35-69% for the six datasets) reconstructed to at least 95% of their length by ClusTrast, and more than half of reference transcripts (58-81%) were reconstructed with contigs that exhibited polymorphism, measuring on a subset of reliably predicted contigs. ClusTrast recall increased when using a union of assembled transcripts from more than one assembly tool as primary assembly. CONCLUSION We suggest that ClusTrast can be a useful tool for studying isoforms in species without a reliable reference genome, in particular when the goal is to produce a comprehensive transcriptome set with polymorphic variants.
Collapse
Affiliation(s)
- Karl Johan Westrin
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 65, Solna, Sweden
| | - Warren W Kretzschmar
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 65, Solna, Sweden
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine (HERM), Karolinska Institute, 141 52, Flemingsberg, Sweden
| | - Olof Emanuelsson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 65, Solna, Sweden.
| |
Collapse
|
2
|
Moura PL, Mortera-Blanco T, Hofman IJ, Todisco G, Kretzschmar WW, Björklund AC, Creignou M, Hagemann-Jensen M, Ziegenhain C, Cabrerizo Granados D, Barbosa I, Walldin G, Jansson M, Ashley N, Mead AJ, Lundin V, Dimitriou M, Yoshizato T, Woll PS, Ogawa S, Sandberg R, Jacobsen SEW, Hellström-Lindberg E. Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts. Cancer Res 2024; 84:211-225. [PMID: 37921711 PMCID: PMC10790130 DOI: 10.1158/0008-5472.can-23-3038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
Abstract
Myelodysplastic syndromes with ring sideroblasts (MDS-RS) commonly develop from hematopoietic stem cells (HSC) bearing mutations in the splicing factor SF3B1 (SF3B1mt). Direct studies into MDS-RS pathobiology have been limited by a lack of model systems that fully recapitulate erythroid biology and RS development and the inability to isolate viable human RS. Here, we combined successful direct RS isolation from patient samples, high-throughput multiomics analysis of cells encompassing the SF3B1mt stem-erythroid continuum, and functional assays to investigate the impact of SF3B1mt on erythropoiesis and RS accumulation. The isolated RS differentiated, egressed into the blood, escaped traditional nonsense-mediated decay (NMD) mechanisms, and leveraged stress-survival pathways that hinder wild-type hematopoiesis through pathogenic GDF15 overexpression. Importantly, RS constituted a contaminant of magnetically enriched CD34+ cells, skewing bulk transcriptomic data. Mis-splicing in SF3B1mt cells was intensified by erythroid differentiation through accelerated RNA splicing and decreased NMD activity, and SF3B1mt led to truncations in several MDS-implicated genes. Finally, RNA mis-splicing induced an uncoupling of RNA and protein expression, leading to critical abnormalities in proapoptotic p53 pathway genes. Overall, this characterization of erythropoiesis in SF3B1mt RS provides a resource for studying MDS-RS and uncovers insights into the unexpectedly active biology of the "dead-end" RS. SIGNIFICANCE Ring sideroblast isolation combined with state-of-the-art multiomics identifies survival mechanisms underlying SF3B1-mutant erythropoiesis and establishes an active role for erythroid differentiation and ring sideroblasts themselves in SF3B1-mutant myelodysplastic syndrome pathogenesis.
Collapse
Affiliation(s)
- Pedro L. Moura
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Teresa Mortera-Blanco
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Isabel J. Hofman
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Gabriele Todisco
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Warren W. Kretzschmar
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Ann-Charlotte Björklund
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Maria Creignou
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Medicine, Division of Hematology, Karolinska University Hospital, Huddinge, Sweden
| | - Michael Hagemann-Jensen
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Xpress Genomics AB, Stockholm, Sweden
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Xpress Genomics AB, Stockholm, Sweden
| | - David Cabrerizo Granados
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Indira Barbosa
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Gunilla Walldin
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Monika Jansson
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Neil Ashley
- Hematopoietic Stem Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Adam J. Mead
- Hematopoietic Stem Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Vanessa Lundin
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Marios Dimitriou
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Tetsuichi Yoshizato
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Petter S. Woll
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Seishi Ogawa
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Rickard Sandberg
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Xpress Genomics AB, Stockholm, Sweden
| | - Sten Eirik W. Jacobsen
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Division of Hematology, Karolinska University Hospital, Huddinge, Sweden
- Hematopoietic Stem Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Eva Hellström-Lindberg
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Medicine, Division of Hematology, Karolinska University Hospital, Huddinge, Sweden
| |
Collapse
|
3
|
Rodriguez-Meira A, Norfo R, Wen S, Chédeville AL, Rahman H, O'Sullivan J, Wang G, Louka E, Kretzschmar WW, Paterson A, Brierley C, Martin JE, Demeule C, Bashton M, Sousos N, Moralli D, Subha Meem L, Carrelha J, Wu B, Hamblin A, Guermouche H, Pasquier F, Marzac C, Girodon F, Vainchenker W, Drummond M, Harrison C, Chapman JR, Plo I, Jacobsen SEW, Psaila B, Thongjuea S, Antony-Debré I, Mead AJ. Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution. Nat Genet 2023; 55:1531-1541. [PMID: 37666991 PMCID: PMC10484789 DOI: 10.1038/s41588-023-01480-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/20/2023] [Indexed: 09/06/2023]
Abstract
Understanding the genetic and nongenetic determinants of tumor protein 53 (TP53)-mutation-driven clonal evolution and subsequent transformation is a crucial step toward the design of rational therapeutic strategies. Here we carry out allelic resolution single-cell multi-omic analysis of hematopoietic stem/progenitor cells (HSPCs) from patients with a myeloproliferative neoplasm who transform to TP53-mutant secondary acute myeloid leukemia (sAML). All patients showed dominant TP53 'multihit' HSPC clones at transformation, with a leukemia stem cell transcriptional signature strongly predictive of adverse outcomes in independent cohorts, across both TP53-mutant and wild-type (WT) AML. Through analysis of serial samples, antecedent TP53-heterozygous clones and in vivo perturbations, we demonstrate a hitherto unrecognized effect of chronic inflammation, which suppressed TP53 WT HSPCs while enhancing the fitness advantage of TP53-mutant cells and promoted genetic evolution. Our findings will facilitate the development of risk-stratification, early detection and treatment strategies for TP53-mutant leukemia, and are of broad relevance to other cancer types.
Collapse
Affiliation(s)
- Alba Rodriguez-Meira
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK.
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
| | - Ruggiero Norfo
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Centre for Regenerative Medicine 'Stefano Ferrari', Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Sean Wen
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Medical Research Council Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Agathe L Chédeville
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
- Université Paris Cité, Paris, France
| | - Haseeb Rahman
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Jennifer O'Sullivan
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Guanlin Wang
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Medical Research Council Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Eleni Louka
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Warren W Kretzschmar
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Aimee Paterson
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Charlotte Brierley
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Center for Hematological Malignancies, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Jean-Edouard Martin
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
- Université Paris Cité, Paris, France
| | | | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Nikolaos Sousos
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | | | - Joana Carrelha
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Bishan Wu
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Angela Hamblin
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Helene Guermouche
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, AP-HP, Hôpital Saint-Antoine, Service d'hématologie biologique, Paris, France
| | - Florence Pasquier
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
- Département d'Hématologie, Gustave Roussy, Villejuif, France
| | - Christophe Marzac
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
- Laboratoire d'Immuno-Hématologie, Gustave Roussy, Villejuif, France
| | - François Girodon
- Laboratoire d'Hématologie, CHU Dijon, Dijon, France
- INSERM, UMR 1231, Centre de Recherche, Dijon, France
| | - William Vainchenker
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | | | | | - J Ross Chapman
- Genome Integrity Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Isabelle Plo
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | - Sten Eirik W Jacobsen
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Bethan Psaila
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Supat Thongjuea
- Medical Research Council Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Iléana Antony-Debré
- INSERM, UMR 1287, Villejuif, France.
- Gustave Roussy, Villejuif, France.
- Université Paris Saclay, Gif-sur-Yvette, France.
| | - Adam J Mead
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK.
| |
Collapse
|
4
|
Walters RG, Millwood IY, Lin K, Schmidt Valle D, McDonnell P, Hacker A, Avery D, Edris A, Fry H, Cai N, Kretzschmar WW, Ansari MA, Lyons PA, Collins R, Donnelly P, Hill M, Peto R, Shen H, Jin X, Nie C, Xu X, Guo Y, Yu C, Lv J, Clarke RJ, Li L, Chen Z. Genotyping and population characteristics of the China Kadoorie Biobank. Cell Genom 2023; 3:100361. [PMID: 37601966 PMCID: PMC10435379 DOI: 10.1016/j.xgen.2023.100361] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 02/09/2023] [Accepted: 06/24/2023] [Indexed: 08/22/2023]
Abstract
The China Kadoorie Biobank (CKB) is a population-based prospective cohort of >512,000 adults recruited from 2004 to 2008 from 10 geographically diverse regions across China. Detailed data from questionnaires and physical measurements were collected at baseline, with additional measurements at three resurveys involving ∼5% of surviving participants. Analyses of genome-wide genotyping, for >100,000 participants using custom-designed Axiom arrays, reveal extensive relatedness, recent consanguinity, and signatures reflecting large-scale population movements from recent Chinese history. Systematic genome-wide association studies of incident disease, captured through electronic linkage to death and disease registries and to the national health insurance system, replicate established disease loci and identify 14 novel disease associations. Together with studies of candidate drug targets and disease risk factors and contributions to international genetics consortia, these demonstrate the breadth, depth, and quality of the CKB data. Ongoing high-throughput omics assays of collected biosamples and planned whole-genome sequencing will further enhance the scientific value of this biobank.
Collapse
Affiliation(s)
- Robin G. Walters
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Iona Y. Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Dan Schmidt Valle
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Pandora McDonnell
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Alex Hacker
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Daniel Avery
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Ahmed Edris
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Hannah Fry
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Na Cai
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | - M. Azim Ansari
- Nuffield Department of Medicine, Oxford University, Oxford OX1 3SY, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Paul A. Lyons
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rory Collins
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Michael Hill
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Richard Peto
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Hongbing Shen
- Department of Epidemiology, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211116, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chao Nie
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yu Guo
- Fuwai Hospital, Chinese Academy of Medical Sciences, Beijing 100037, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing 100191, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing 100191, China
| | - Robert J. Clarke
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing 100191, China
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - China Kadoorie Biobank Collaborative Group
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Nuffield Department of Medicine, Oxford University, Oxford OX1 3SY, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
- Department of Epidemiology, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211116, China
- BGI-Shenzhen, Shenzhen 518083, China
- Fuwai Hospital, Chinese Academy of Medical Sciences, Beijing 100037, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing 100191, China
| |
Collapse
|
5
|
Akhter S, Westrin KJ, Zivi N, Nordal V, Kretzschmar WW, Delhomme N, Street NR, Nilsson O, Emanuelsson O, Sundström JF. Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway. New Phytol 2022; 236:1951-1963. [PMID: 36076311 PMCID: PMC9825996 DOI: 10.1111/nph.18449] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.
Collapse
Affiliation(s)
- Shirin Akhter
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
| | - Karl Johan Westrin
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologySE‐171 65SolnaSweden
| | - Nathan Zivi
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
- Skogforsk, Uppsala Science ParkUppsalaSE‐751 83Sweden
| | - Veronika Nordal
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
| | - Warren W. Kretzschmar
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologySE‐171 65SolnaSweden
| | - Nicolas Delhomme
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural Sciences (SLU)SE‐901 83UmeåSweden
| | - Nathaniel R. Street
- Department of Plant Physiology, Umeå Plant Science CentreUmeå UniversitySE‐901 87UmeåSweden
| | - Ove Nilsson
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural Sciences (SLU)SE‐901 83UmeåSweden
| | - Olof Emanuelsson
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologySE‐171 65SolnaSweden
| | - Jens F. Sundström
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
| |
Collapse
|
6
|
Ingelshed K, Spiegelberg D, Kannan P, Påvénius L, Hacheney J, Jiang L, Eisinger S, Lianoudaki D, Lama D, Castillo F, Bosdotter C, Kretzschmar WW, Al-Radi O, Fritz N, Villablanca EJ, Karlsson MCI, Wermeling F, Nestor M, Lane DP, Sedimbi SK. The MDM2 Inhibitor Navtemadlin Arrests Mouse Melanoma Growth In Vivo and Potentiates Radiotherapy. Cancer Res Commun 2022; 2:1075-1088. [PMID: 36922937 PMCID: PMC10010373 DOI: 10.1158/2767-9764.crc-22-0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/21/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
The tumor suppressor protein p53 is mutated in close to 50% of human tumors and is dysregulated in many others, for instance by silencing or loss of p14ARF. Under steady-state conditions, the two E3 ligases MDM2/MDM4 interact with and inhibit the transcriptional activity of p53. Inhibition of p53-MDM2/4 interaction to reactivate p53 in tumors with wild-type (WT) p53 has therefore been considered a therapeutic strategy. Moreover, studies indicate that p53 reactivation may synergize with radiation and increase tumor immunogenicity. In vivo studies of most MDM2 inhibitors have utilized immunodeficient xenograft mouse models, preventing detailed studies of action of these molecules on the immune response. The mouse melanoma cell line B16-F10 carries functional, WT p53 but does not express the MDM2 regulator p19ARF. In this study, we tested a p53-MDM2 protein-protein interaction inhibitor, the small molecule Navtemadlin, which is currently being tested in phase II clinical trials. Using mass spectrometry-based proteomics and imaging flow cytometry, we identified specific protein expression patterns following Navtemadlin treatment of B16-F10 melanoma cells compared with their p53 CRISPR-inactivated control cells. In vitro, Navtemadlin induced a significant, p53-dependent, growth arrest but little apoptosis in B16-F10 cells. When combined with radiotherapy, Navtemadlin showed synergistic effects and increased apoptosis. In vivo, Navtemadlin treatment significantly reduced the growth of B16-F10 melanoma cells implanted in C57Bl/6 mice. Our data highlight the utility of a syngeneic B16-F10 p53+/+ mouse melanoma model for assessing existing and novel p53-MDM2/MDM4 inhibitors and in identifying new combination therapies that can efficiently eliminate tumors in vivo. Significance The MDM2 inhibitor Navtemadlin arrests mouse tumor growth and potentiates radiotherapy. Our results support a threshold model for apoptosis induction that requires a high, prolonged p53 signaling for cancer cells to become apoptotic.
Collapse
Affiliation(s)
- Katrine Ingelshed
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Diana Spiegelberg
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Pavitra Kannan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Linnéa Påvénius
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jessica Hacheney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Long Jiang
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Stockholm, Sweden
| | - Silke Eisinger
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Danai Lianoudaki
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Francisca Castillo
- Center for Molecular Medicine, Stockholm, Sweden
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Bosdotter
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Omayma Al-Radi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Nicolas Fritz
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Eduardo J. Villablanca
- Center for Molecular Medicine, Stockholm, Sweden
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Mikael C. I. Karlsson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Wermeling
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Stockholm, Sweden
| | - Marika Nestor
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - David P. Lane
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Corresponding Authors: Saikiran K. Sedimbi and David P. Lane, Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Nobels Väg 16, Stockholm, SE-17177, Sweden. Phone: +46 852 448 6452; E-mail: ; Phone: +46 852 448 6452; E-mail:
| | - Saikiran K. Sedimbi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Corresponding Authors: Saikiran K. Sedimbi and David P. Lane, Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Nobels Väg 16, Stockholm, SE-17177, Sweden. Phone: +46 852 448 6452; E-mail: ; Phone: +46 852 448 6452; E-mail:
| |
Collapse
|
7
|
Pain O, Hodgson K, Trubetskoy V, Ripke S, Marshe VS, Adams MJ, Byrne EM, Campos AI, Carrillo-Roa T, Cattaneo A, Als TD, Souery D, Dernovsek MZ, Fabbri C, Hayward C, Henigsberg N, Hauser J, Kennedy JL, Lenze EJ, Lewis G, Müller DJ, Martin NG, Mulsant BH, Mors O, Perroud N, Porteous DJ, Rentería ME, Reynolds CF, Rietschel M, Uher R, Wigmore EM, Maier W, Wray NR, Aitchison KJ, Arolt V, Baune BT, Biernacka JM, Bondolfi G, Domschke K, Kato M, Li QS, Liu YL, Serretti A, Tsai SJ, Turecki G, Weinshilboum R, McIntosh AM, Lewis CM, Kasper S, Zohar J, Souery D, Montgomery S, Albani D, Forloni G, Ferentinos P, Rujescu D, Mendlewicz J, Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TF, Bacanu SA, Bækvad-Hansen M, Beekman AT, Bigdeli TB, Binder EB, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke TK, Coleman JR, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Davies G, Deary IJ, Degenhardt F, Derks EM, Direk N, Dolan CV, Dunn EC, Eley TC, Escott-Price V, Hassan Kiadeh FF, Finucane HK, Foo JC, Forstner AJ, Frank J, Gaspar HA, Gill M, Goes FS, Gordon SD, Grove J, Hall LS, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga JJ, Hougaard DM, Howard DM, Ising M, Jansen R, Jones I, Jones LA, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Kutalik Z, Li Y, Lind PA, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, Marchini J, Mbarek H, McGrath P, McGuffin P, Medland SE, Mehta D, Middeldorp CM, Mihailov E, Milaneschi Y, Milani L, Mondimore FM, Montgomery GW, Mostafavi S, Mullins N, Nauck M, Ng B, Nivard MG, Nyholt DR, O’Reilly PF, Oskarsson H, Owen MJ, Painter JN, Pedersen CB, Pedersen MG, Peterson RE, Peyrot WJ, Pistis G, Posthuma D, Quiroz JA, Qvist P, Rice JP, Riley BP, Rivera M, Mirza SS, Schoevers R, Schulte EC, Shen L, Shi J, Shyn SI, Sigurdsson E, Sinnamon GC, Smit JH, Smith DJ, Stefansson H, Steinberg S, Streit F, Strohmaier J, Tansey KE, Teismann H, Teumer A, Thompson W, Thomson PA, Thorgeirsson TE, Traylor M, Treutlein J, Trubetskoy V, Uitterlinden AG, Umbricht D, Van der Auwera S, van Hemert AM, Viktorin A, Visscher PM, Wang Y, Webb BT, Weinsheimer SM, Wellmann J, Willemsen G, Witt SH, Wu Y, Xi HS, Yang J, Zhang F, Arolt V, Baune BT, Berger K, Boomsma DI, Cichon S, Dannlowski U, de Geus E, DePaulo JR, Domenici E, Domschke K, Esko T, Grabe HJ, Hamilton SP, Hayward C, Heath AC, Kendler KS, Kloiber S, Lewis G, Li QS, Lucae S, Madden PA, Magnusson PK, Martin NG, McIntosh AM, Metspalu A, Mors O, Mortensen PB, Müller-Myhsok B, Nordentoft M, Nöthen MM, O’Donovan MC, Paciga SA, Pedersen NL, Penninx BW, Perlis RH, Porteous DJ, Potash JB, Preisig M, Rietschel M, Schaefer C, Schulze TG, Smoller JW, Stefansson K, Tiemeier H, Uher R, Völzke H, Weissman MM, Werge T, Lewis CM, Levinson DF, Breen G, Børglum AD, Sullivan PF. Identifying the Common Genetic Basis of Antidepressant Response. Biol Psychiatry Glob Open Sci 2022; 2:115-126. [PMID: 35712048 PMCID: PMC9117153 DOI: 10.1016/j.bpsgos.2021.07.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 01/20/2023] Open
Abstract
Background Antidepressants are a first-line treatment for depression. However, only a third of individuals experience remission after the first treatment. Common genetic variation, in part, likely regulates antidepressant response, yet the success of previous genome-wide association studies has been limited by sample size. This study performs the largest genetic analysis of prospectively assessed antidepressant response in major depressive disorder to gain insight into the underlying biology and enable out-of-sample prediction. Methods Genome-wide analysis of remission (n remit = 1852, n nonremit = 3299) and percentage improvement (n = 5218) was performed. Single nucleotide polymorphism-based heritability was estimated using genome-wide complex trait analysis. Genetic covariance with eight mental health phenotypes was estimated using polygenic scores/AVENGEME. Out-of-sample prediction of antidepressant response polygenic scores was assessed. Gene-level association analysis was performed using MAGMA and transcriptome-wide association study. Tissue, pathway, and drug binding enrichment were estimated using MAGMA. Results Neither genome-wide association study identified genome-wide significant associations. Single nucleotide polymorphism-based heritability was significantly different from zero for remission (h 2 = 0.132, SE = 0.056) but not for percentage improvement (h 2 = -0.018, SE = 0.032). Better antidepressant response was negatively associated with genetic risk for schizophrenia and positively associated with genetic propensity for educational attainment. Leave-one-out validation of antidepressant response polygenic scores demonstrated significant evidence of out-of-sample prediction, though results varied in external cohorts. Gene-based analyses identified ETV4 and DHX8 as significantly associated with antidepressant response. Conclusions This study demonstrates that antidepressant response is influenced by common genetic variation, has a genetic overlap schizophrenia and educational attainment, and provides a useful resource for future research. Larger sample sizes are required to attain the potential of genetics for understanding and predicting antidepressant response.
Collapse
|
8
|
Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman EC, Galloway JG, Gladstein AL, Gorjanc G, Guo B, Jeffery B, Kretzschmar WW, Lohse K, Matschiner M, Nelson D, Pope NS, Quinto-Cortés CD, Rodrigues MF, Saunack K, Sellinger T, Thornton K, van Kemenade H, Wohns AW, Wong Y, Gravel S, Kern AD, Koskela J, Ralph PL, Kelleher J. Efficient ancestry and mutation simulation with msprime 1.0. Genetics 2021; 220:6460344. [PMID: 34897427 PMCID: PMC9176297 DOI: 10.1093/genetics/iyab229] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [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: 09/22/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and the tskit library. We summarize msprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.
Collapse
Affiliation(s)
- Franz Baumdicker
- Cluster of Excellence "Controlling Microbes to Fight Infections", Mathematical and Computational Population Genetics, University of Tübingen, 72076 Tübingen, Germany
| | - Gertjan Bisschop
- Institute of Evolutionary Biology,The University of Edinburgh, EH9 3FL, UK
| | - Daniel Goldstein
- Khoury College of Computer Sciences, Northeastern University, MA 02115, USA.,No affiliation
| | - Graham Gower
- Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Aaron P Ragsdale
- Department of Integrative Biology, University of Wisconsin-Madison, WI 53706, USA
| | - Georgia Tsambos
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Victoria, 3010, Australia
| | - Sha Zhu
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Bjarki Eldon
- Leibniz Institute for Evolution and Biodiversity Science,Museum für Naturkunde Berlin, 10115, Germany
| | | | - Jared G Galloway
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA.,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Ariella L Gladstein
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599-7264, USA.,Embark Veterinary, Inc., Boston, MA 02111, USA
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, UK
| | - Bing Guo
- Institute for Genome Sciences,University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ben Jeffery
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Warren W Kretzschmar
- Center for Hematology and Regenerative Medicine, Karolinska Institute, 141 83 Huddinge, Sweden
| | - Konrad Lohse
- Institute of Evolutionary Biology,The University of Edinburgh, EH9 3FL, UK
| | | | - Dominic Nelson
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Nathaniel S Pope
- Department of Entomology, Pennsylvania State University, PA 16802, USA
| | - Consuelo D Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato, Mexico
| | - Murillo F Rodrigues
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA
| | - Kumar Saunack
- IIT Bombay, Powai, Mumbai 400 076, Maharashtra, India
| | - Thibaut Sellinger
- Professorship for Population Genetics, Department of Life Science Systems, Technical University of Munich, 85354 Freising, Germany
| | - Kevin Thornton
- Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | | | - Anthony W Wohns
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Simon Gravel
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Andrew D Kern
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA
| | - Jere Koskela
- Department of Statistics, University of Warwick, CV4 7AL, UK
| | - Peter L Ralph
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA.,Department of Mathematics, University of Oregon, OR 97403-5289 USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| |
Collapse
|
9
|
Paczkowski M, Kretzschmar WW, Markelc B, Liu SK, Kunz-Schughart LA, Harris AL, Partridge M, Byrne HM, Kannan P. Reciprocal interactions between tumour cell populations enhance growth and reduce radiation sensitivity in prostate cancer. Commun Biol 2021; 4:6. [PMID: 33398023 PMCID: PMC7782740 DOI: 10.1038/s42003-020-01529-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/24/2020] [Indexed: 01/29/2023] Open
Abstract
Intratumoural heterogeneity (ITH) contributes to local recurrence following radiotherapy in prostate cancer. Recent studies also show that ecological interactions between heterogeneous tumour cell populations can lead to resistance in chemotherapy. Here, we evaluated whether interactions between heterogenous populations could impact growth and response to radiotherapy in prostate cancer. Using mixed 3D cultures of parental and radioresistant populations from two prostate cancer cell lines and a predator-prey mathematical model to investigate various types of ecological interactions, we show that reciprocal interactions between heterogeneous populations enhance overall growth and reduce radiation sensitivity. The type of interaction influences the time of regrowth after radiation, and, at the population level, alters the survival and cell cycle of each population without eliminating either one. These interactions can arise from oxygen constraints and from cellular cross-talk that alter the tumour microenvironment. These findings suggest that ecological-type interactions are important in radiation response and could be targeted to reduce local recurrence.
Collapse
Affiliation(s)
| | - Warren W Kretzschmar
- School of Engineering Sciences in Chemistry Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine (HERM), Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine (HERM), Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Bostjan Markelc
- CRUK and MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Stanley K Liu
- Sunnybrook Research Institute and Departments of Medical Biophysics and Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Leoni A Kunz-Schughart
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz-Zentrum, Dresden, Rossendorf, Germany
- National Center for Tumor Diseases (NCT), Partner Site, Dresden, Germany
| | - Adrian L Harris
- CRUK and MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mike Partridge
- CRUK and MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Helen M Byrne
- Mathematical Institute, University of Oxford, Oxford, UK.
| | - Pavitra Kannan
- CRUK and MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
10
|
Cai N, Bigdeli TB, Kretzschmar WW, Li Y, Liang J, Hu J, Peterson RE, Bacanu S, Webb BT, Riley B, Li Q, Marchini J, Mott R, Kendler KS, Flint J. Retraction Note: 11,670 whole-genome sequences representative of the Han Chinese population from the CONVERGE project. Sci Data 2020; 7:123. [PMID: 32300216 PMCID: PMC7162935 DOI: 10.1038/s41597-020-0430-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
11
|
Kannan P, Kretzschmar WW, Winter H, Warren D, Bates R, Allen PD, Syed N, Irving B, Papiez BW, Kaeppler J, Markelc B, Kinchesh P, Gilchrist S, Smart S, Schnabel JA, Maughan T, Harris AL, Muschel RJ, Partridge M, Sharma RA, Kersemans V. Functional Parameters Derived from Magnetic Resonance Imaging Reflect Vascular Morphology in Preclinical Tumors and in Human Liver Metastases. Clin Cancer Res 2018; 24:4694-4704. [PMID: 29959141 PMCID: PMC6171743 DOI: 10.1158/1078-0432.ccr-18-0033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/11/2018] [Accepted: 06/25/2018] [Indexed: 12/13/2022]
Abstract
Purpose: Tumor vessels influence the growth and response of tumors to therapy. Imaging vascular changes in vivo using dynamic contrast-enhanced MRI (DCE-MRI) has shown potential to guide clinical decision making for treatment. However, quantitative MR imaging biomarkers of vascular function have not been widely adopted, partly because their relationship to structural changes in vessels remains unclear. We aimed to elucidate the relationships between vessel function and morphology in vivo Experimental Design: Untreated preclinical tumors with different levels of vascularization were imaged sequentially using DCE-MRI and CT. Relationships between functional parameters from MR (iAUC, K trans, and BATfrac) and structural parameters from CT (vessel volume, radius, and tortuosity) were assessed using linear models. Tumors treated with anti-VEGFR2 antibody were then imaged to determine whether antiangiogenic therapy altered these relationships. Finally, functional-structural relationships were measured in 10 patients with liver metastases from colorectal cancer.Results: Functional parameters iAUC and K trans primarily reflected vessel volume in untreated preclinical tumors. The relationships varied spatially and with tumor vascularity, and were altered by antiangiogenic treatment. In human liver metastases, all three structural parameters were linearly correlated with iAUC and K trans For iAUC, structural parameters also modified each other's effect.Conclusions: Our findings suggest that MR imaging biomarkers of vascular function are linked to structural changes in tumor vessels and that antiangiogenic therapy can affect this link. Our work also demonstrates the feasibility of three-dimensional functional-structural validation of MR biomarkers in vivo to improve their biological interpretation and clinical utility. Clin Cancer Res; 24(19); 4694-704. ©2018 AACR.
Collapse
Affiliation(s)
- Pavitra Kannan
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom.
| | - Warren W Kretzschmar
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Helen Winter
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Daniel Warren
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Russell Bates
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Philip D Allen
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Nigar Syed
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
- NHS, Department of Radiology, Churchill Hospital, Oxford, United Kingdom
| | - Benjamin Irving
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Bartlomiej W Papiez
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Jakob Kaeppler
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Bosjtan Markelc
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Paul Kinchesh
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Stuart Gilchrist
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Sean Smart
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Julia A Schnabel
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, United Kingdom
| | - Tim Maughan
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Adrian L Harris
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Ruth J Muschel
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Mike Partridge
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Ricky A Sharma
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
- NIHR University College London Hospitals Biomedical Research Centre, University College London, London, United Kingdom
| | - Veerle Kersemans
- CRUK and MRC Oxford Institute for Radiation Oncology Department of Oncology, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
12
|
Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TMF, Bacanu SA, Bækvad-Hansen M, Beekman AFT, Bigdeli TB, Binder EB, Blackwood DRH, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke TK, Coleman JIR, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Crowley CA, Dashti HS, Davies G, Deary IJ, Degenhardt F, Derks EM, Direk N, Dolan CV, Dunn EC, Eley TC, Eriksson N, Escott-Price V, Kiadeh FHF, Finucane HK, Forstner AJ, Frank J, Gaspar HA, Gill M, Giusti-Rodríguez P, Goes FS, Gordon SD, Grove J, Hall LS, Hannon E, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga JJ, Hougaard DM, Hu M, Hyde CL, Ising M, Jansen R, Jin F, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Krogh J, Kutalik Z, Lane JM, Li Y, Li Y, Lind PA, Liu X, Lu L, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, Marchini J, Mbarek H, McGrath P, McGuffin P, Medland SE, Mehta D, Middeldorp CM, Mihailov E, Milaneschi Y, Milani L, Mill J, Mondimore FM, Montgomery GW, Mostafavi S, Mullins N, Nauck M, Ng B, Nivard MG, Nyholt DR, O'Reilly PF, Oskarsson H, Owen MJ, Painter JN, Pedersen CB, Pedersen MG, Peterson RE, Pettersson E, Peyrot WJ, Pistis G, Posthuma D, Purcell SM, Quiroz JA, Qvist P, Rice JP, Riley BP, Rivera M, Saeed Mirza S, Saxena R, Schoevers R, Schulte EC, Shen L, Shi J, Shyn SI, Sigurdsson E, Sinnamon GBC, Smit JH, Smith DJ, Stefansson H, Steinberg S, Stockmeier CA, Streit F, Strohmaier J, Tansey KE, Teismann H, Teumer A, Thompson W, Thomson PA, Thorgeirsson TE, Tian C, Traylor M, Treutlein J, Trubetskoy V, Uitterlinden AG, Umbricht D, Van der Auwera S, van Hemert AM, Viktorin A, Visscher PM, Wang Y, Webb BT, Weinsheimer SM, Wellmann J, Willemsen G, Witt SH, Wu Y, Xi HS, Yang J, Zhang F, Arolt V, Baune BT, Berger K, Boomsma DI, Cichon S, Dannlowski U, de Geus ECJ, DePaulo JR, Domenici E, Domschke K, Esko T, Grabe HJ, Hamilton SP, Hayward C, Heath AC, Hinds DA, Kendler KS, Kloiber S, Lewis G, Li QS, Lucae S, Madden PFA, Magnusson PK, Martin NG, McIntosh AM, Metspalu A, Mors O, Mortensen PB, Müller-Myhsok B, Nordentoft M, Nöthen MM, O'Donovan MC, Paciga SA, Pedersen NL, Penninx BWJH, Perlis RH, Porteous DJ, Potash JB, Preisig M, Rietschel M, Schaefer C, Schulze TG, Smoller JW, Stefansson K, Tiemeier H, Uher R, Völzke H, Weissman MM, Werge T, Winslow AR, Lewis CM, Levinson DF, Breen G, Børglum AD, Sullivan PF. Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression. Nat Genet 2018; 50:668-681. [PMID: 29700475 PMCID: PMC5934326 DOI: 10.1038/s41588-018-0090-3] [Citation(s) in RCA: 1625] [Impact Index Per Article: 270.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/14/2018] [Indexed: 12/12/2022]
Abstract
Major depressive disorder (MDD) is a common illness accompanied by considerable morbidity, mortality, costs, and heightened risk of suicide. We conducted a genome-wide association meta-analysis based in 135,458 cases and 344,901 controls and identified 44 independent and significant loci. The genetic findings were associated with clinical features of major depression and implicated brain regions exhibiting anatomical differences in cases. Targets of antidepressant medications and genes involved in gene splicing were enriched for smaller association signal. We found important relationships of genetic risk for major depression with educational attainment, body mass, and schizophrenia: lower educational attainment and higher body mass were putatively causal, whereas major depression and schizophrenia reflected a partly shared biological etiology. All humans carry lesser or greater numbers of genetic risk factors for major depression. These findings help refine the basis of major depression and imply that a continuous measure of risk underlies the clinical phenotype.
Collapse
Affiliation(s)
- Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.
| | - Stephan Ripke
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry and Psychotherapy, Universitätsmedizin Berlin Campus Charité Mitte, Berlin, Germany
| | - Manuel Mattheisen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Maciej Trzaskowski
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Enda M Byrne
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Abdel Abdellaoui
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Esben Agerbo
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Tracy M Air
- Discipline of Psychiatry, University of Adelaide, Adelaide, South Australia, Australia
| | - Till M F Andlauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Silviu-Alin Bacanu
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Marie Bækvad-Hansen
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Aartjan F T Beekman
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Tim B Bigdeli
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Virginia Institute for Psychiatric and Behavior Genetics, Richmond, VA, USA
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Henriette N Buttenschøn
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Clinical Medicine, Translational Neuropsychiatry Unit, Aarhus University, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Na Cai
- Statistical Genomics and Systems Genetics, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Human Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Enrique Castelao
- Department of Psychiatry, University Hospital of Lausanne, Prilly, Switzerland
| | - Jane Hvarregaard Christensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Toni-Kim Clarke
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Jonathan I R Coleman
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Lucía Colodro-Conde
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Baptiste Couvy-Duchesne
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Centre for Advanced Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - Nick Craddock
- Psychological Medicine, Cardiff University, Cardiff, UK
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
| | - Cheynna A Crowley
- Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hassan S Dashti
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
| | - Eske M Derks
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Nese Direk
- Psychiatry, Dokuz Eylul University School of Medicine, Izmir, Turkey
- Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Conor V Dolan
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erin C Dunn
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Massachusetts General Hospital, Boston, MA, USA
| | - Thalia C Eley
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | | | | | | | - Hilary K Finucane
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
- Department of Psychiatry (UPK), University of Basel, Basel, Switzerland
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Héléna A Gaspar
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Michael Gill
- Department of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | | | - Fernando S Goes
- Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Scott D Gordon
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Lynsey S Hall
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | | | - Christine Søholm Hansen
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas F Hansen
- Danish Headache Centre, Department of Neurology, Rigshospitalet, Glostrup, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Psychiatric Research, Copenhagen, Denmark
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Ian B Hickie
- Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine and Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Carsten Horn
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Jouke-Jan Hottenga
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - David M Hougaard
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Ming Hu
- Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Craig L Hyde
- Statistics, Pfizer Global Research and Development, Groton, CT, USA
| | - Marcus Ising
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Rick Jansen
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Fulai Jin
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - James A Knowles
- Psychiatry and Behavioral Sciences, University of Southern California, Los Angeles, CA, USA
| | - Isaac S Kohane
- Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Julia Kraft
- Department of Psychiatry and Psychotherapy, Universitätsmedizin Berlin Campus Charité Mitte, Berlin, Germany
| | | | - Jesper Krogh
- Department of Endocrinology at Herlev University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Social and Preventive Medicine (IUMSP), University Hospital of Lausanne, Lausanne, Switzerland
| | - Jacqueline M Lane
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yihan Li
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yun Li
- Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Penelope A Lind
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Xiaoxiao Liu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Leina Lu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Donald J MacIntyre
- Mental Health, NHS 24, Glasgow, UK
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Dean F MacKinnon
- Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Robert M Maier
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Wolfgang Maier
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | | | - Hamdi Mbarek
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Patrick McGrath
- Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Peter McGuffin
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Sarah E Medland
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Divya Mehta
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- School of Psychology and Counseling, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Christel M Middeldorp
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Child and Youth Mental Health Service, Children's Health Queensland Hospital and Health Service, South Brisbane, Queensland, Australia
- Child Health Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | | | - Yuri Milaneschi
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | - Francis M Mondimore
- Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Grant W Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Sara Mostafavi
- Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Niamh Mullins
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Matthias Nauck
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, University Medicine, University Medicine Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Bernard Ng
- Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michel G Nivard
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dale R Nyholt
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Paul F O'Reilly
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | | | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Jodie N Painter
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Carsten Bøcker Pedersen
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Marianne Giørtz Pedersen
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Roseann E Peterson
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Erik Pettersson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Wouter J Peyrot
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Giorgio Pistis
- Department of Psychiatry, University Hospital of Lausanne, Prilly, Switzerland
| | - Danielle Posthuma
- Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Clinical Genetics, Vrije Universiteit Medical Center, Amsterdam, The Netherlands
| | - Shaun M Purcell
- Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Per Qvist
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - John P Rice
- Department of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Brien P Riley
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Margarita Rivera
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- Department of Biochemistry and Molecular Biology II, Institute of Neurosciences, Center for Biomedical Research, University of Granada, Granada, Spain
| | | | - Richa Saxena
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert Schoevers
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Eva C Schulte
- Department of Psychiatry and Psychotherapy, Medical Center of the University of Munich, Campus Innenstadt, Munich, Germany
- Institute of Psychiatric Phenomics and Genomics (IPPG), Medical Center of the University of Munich, Campus Innenstadt, Munich, Germany
| | - Ling Shen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stanley I Shyn
- Behavioral Health Services, Kaiser Permanente Washington, Seattle, WA, USA
| | - Engilbert Sigurdsson
- Faculty of Medicine, Department of Psychiatry, University of Iceland, Reykjavik, Iceland
| | - Grant B C Sinnamon
- School of Medicine and Dentistry, James Cook University, Townsville, Queensland, Australia
| | - Johannes H Smit
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Daniel J Smith
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | | | | | - Craig A Stockmeier
- Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Katherine E Tansey
- College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Henning Teismann
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Wesley Thompson
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- KG Jebsen Centre for Psychosis Research, Norway Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Pippa A Thomson
- Medical Genetics Section, CGEM, IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Chao Tian
- Research, 23andMe, Inc., Mountain View, CA, USA
| | - Matthew Traylor
- Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vassily Trubetskoy
- Department of Psychiatry and Psychotherapy, Universitätsmedizin Berlin Campus Charité Mitte, Berlin, Germany
| | | | - Daniel Umbricht
- Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery and Translational Medicine Area, Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Albert M van Hemert
- Department of Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander Viktorin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Yunpeng Wang
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- KG Jebsen Centre for Psychosis Research, Norway Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Bradley T Webb
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Shantel Marie Weinsheimer
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
| | - Jürgen Wellmann
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Gonneke Willemsen
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Yang Wu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Hualin S Xi
- Computational Sciences Center of Emphasis, Pfizer Global Research and Development, Cambridge, MA, USA
| | - Jian Yang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Futao Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Volker Arolt
- Department of Psychiatry, University of Münster, Munster, Germany
| | - Bernhard T Baune
- Discipline of Psychiatry, University of Adelaide, Adelaide, South Australia, Australia
| | - Klaus Berger
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Dorret I Boomsma
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Juelich, Germany
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Udo Dannlowski
- Department of Psychiatry, University of Münster, Munster, Germany
| | - E C J de Geus
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Institute, Vrije Universiteit Medical Center, Amsterdam, The Netherlands
| | - J Raymond DePaulo
- Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Enrico Domenici
- Centre for Integrative Biology, Università degli Studi di Trento, Trento, Italy
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tõnu Esko
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Steven P Hamilton
- Psychiatry, Kaiser Permanente Northern California, San Francisco, CA, USA
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew C Heath
- Department of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | | | - Kenneth S Kendler
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Stefan Kloiber
- Max Planck Institute of Psychiatry, Munich, Germany
- Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Glyn Lewis
- Division of Psychiatry, University College London, London, UK
| | - Qingqin S Li
- Neuroscience Therapeutic Area, Janssen Research and Development, LLC, Titusville, NJ, USA
| | | | - Pamela F A Madden
- Department of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Patrik K Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas G Martin
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Ole Mors
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Aarhus, Denmark
| | - Preben Bo Mortensen
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Merete Nordentoft
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Mental Health Center Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Sara A Paciga
- Human Genetics and Computational Biomedicine, Pfizer Global Research and Development, Groton, CT, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Brenda W J H Penninx
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Roy H Perlis
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Psychiatry, Harvard Medical School, Boston, MA, USA
| | - David J Porteous
- Medical Genetics Section, CGEM, IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Martin Preisig
- Department of Psychiatry, University Hospital of Lausanne, Prilly, Switzerland
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Catherine Schaefer
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thomas G Schulze
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
- Institute of Psychiatric Phenomics and Genomics (IPPG), Medical Center of the University of Munich, Campus Innenstadt, Munich, Germany
- Human Genetics Branch, NIMH Division of Intramural Research Programs, Bethesda, MD, USA
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Jordan W Smoller
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Massachusetts General Hospital, Boston, MA, USA
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Henning Tiemeier
- Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Child and Adolescent Psychiatry, Erasmus MC, Rotterdam, The Netherlands
- Psychiatry, Erasmus MC, Rotterdam, The Netherlands
| | - Rudolf Uher
- Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Myrna M Weissman
- Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Division of Epidemiology, New York State Psychiatric Institute, New York, NY, USA
| | - Thomas Werge
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ashley R Winslow
- Human Genetics and Computational Biomedicine, Pfizer Global Research and Development, Cambridge, MA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cathryn M Lewis
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Douglas F Levinson
- Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Gerome Breen
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- NIHR BRC for Mental Health, King's College London, London, UK
| | - Anders D Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
13
|
Akhter S, Kretzschmar WW, Nordal V, Delhomme N, Street NR, Nilsson O, Emanuelsson O, Sundström JF. Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies. Front Plant Sci 2018; 9:1625. [PMID: 30483285 PMCID: PMC6243048 DOI: 10.3389/fpls.2018.01625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/18/2018] [Indexed: 05/06/2023]
Abstract
Recent efforts to sequence the genomes and transcriptomes of several gymnosperm species have revealed an increased complexity in certain gene families in gymnosperms as compared to angiosperms. One example of this is the gymnosperm sister clade to angiosperm TM3-like MADS-box genes, which at least in the conifer lineage has expanded in number of genes. We have previously identified a member of this sub-clade, the conifer gene DEFICIENS AGAMOUS LIKE 19 (DAL19), as being specifically upregulated in cone-setting shoots. Here, we show through Sanger sequencing of mRNA-derived cDNA and mapping to assembled conifer genomic sequences that DAL19 produces six mature mRNA splice variants in Picea abies. These splice variants use alternate first and last exons, while their four central exons constitute a core region present in all six transcripts. Thus, they are likely to be transcript isoforms. Quantitative Real-Time PCR revealed that two mutually exclusive first DAL19 exons are differentially expressed across meristems that will form either male or female cones, or vegetative shoots. Furthermore, mRNA in situ hybridization revealed that two mutually exclusive last DAL19 exons were expressed in a cell-specific pattern within bud meristems. Based on these findings in DAL19, we developed a sensitive approach to transcript isoform assembly from short-read sequencing of mRNA. We applied this method to 42 putative MADS-box core regions in P. abies, from which we assembled 1084 putative transcripts. We manually curated these transcripts to arrive at 933 assembled transcript isoforms of 38 putative MADS-box genes. 152 of these isoforms, which we assign to 28 putative MADS-box genes, were differentially expressed across eight female, male, and vegetative buds. We further provide evidence of the expression of 16 out of the 38 putative MADS-box genes by mapping PacBio Iso-Seq circular consensus reads derived from pooled sample sequencing to assembled transcripts. In summary, our analyses reveal the use of mutually exclusive exons of MADS-box gene isoforms during early bud development in P. abies, and we find that the large number of identified MADS-box transcripts in P. abies results not only from expansion of the gene family through gene duplication events but also from the generation of numerous splice variants.
Collapse
Affiliation(s)
- Shirin Akhter
- Linnean Center for Plant Biology, Uppsala BioCenter, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Warren W. Kretzschmar
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Biotechnology, Chemistry and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Veronika Nordal
- Linnean Center for Plant Biology, Uppsala BioCenter, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Nathaniel R. Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Ove Nilsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Olof Emanuelsson
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Biotechnology, Chemistry and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Jens F. Sundström
- Linnean Center for Plant Biology, Uppsala BioCenter, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- *Correspondence: Jens F. Sundström,
| |
Collapse
|
14
|
Kannan P, Schain M, Kretzschmar WW, Weidner L, Mitsios N, Gulyás B, Blom H, Gottesman MM, Innis RB, Hall MD, Mulder J. An automated method measures variability in P-glycoprotein and ABCG2 densities across brain regions and brain matter. J Cereb Blood Flow Metab 2017; 37:2062-2075. [PMID: 27488911 PMCID: PMC5464701 DOI: 10.1177/0271678x16660984] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 06/01/2016] [Accepted: 06/22/2016] [Indexed: 12/13/2022]
Abstract
Changes in P-glycoprotein and ABCG2 densities may play a role in amyloid-beta accumulation in Alzheimer's disease. However, previous studies report conflicting results from different brain regions, without correcting for changes in vessel density. We developed an automated method to measure transporter density exclusively within the vascular space, thereby correcting for vessel density. We then examined variability in transporter density across brain regions, matter, and disease using two cohorts of post-mortem brains from Alzheimer's disease patients and age-matched controls. Changes in transporter density were also investigated in capillaries near plaques and on the mRNA level. P-glycoprotein density varied with brain region and matter, whereas ABCG2 density varied with brain matter. In temporal cortex, P-glycoprotein density was 53% lower in Alzheimer's disease samples than in controls, and was reduced by 35% in capillaries near plaque deposits within Alzheimer's disease samples. ABCG2 density was unaffected in Alzheimer's disease. No differences were detected at the transcript level. Our study indicates that region-specific changes in transporter densities can occur globally and locally near amyloid-beta deposits in Alzheimer's disease, providing an explanation for conflicting results in the literature. When differences in region and matter are accounted for, changes in density can be reproducibly measured using our automated method.
Collapse
Affiliation(s)
- Pavitra Kannan
- Molecular Imaging Branch, National Institute of Mental Health, Bethesda, MD, USA
- Karolinska Institutet, Department of Clinical Neuroscience, Stockholm, Sweden
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Martin Schain
- Karolinska Institutet, Department of Clinical Neuroscience, Stockholm, Sweden
| | | | - Lora Weidner
- Molecular Imaging Branch, National Institute of Mental Health, Bethesda, MD, USA
- Karolinska Institutet, Department of Neuroscience, Science for Life Laboratory, Stockholm, Sweden
| | - Nicholas Mitsios
- Karolinska Institutet, Department of Neuroscience, Science for Life Laboratory, Stockholm, Sweden
| | - Balázs Gulyás
- Karolinska Institutet, Department of Clinical Neuroscience, Stockholm, Sweden
| | - Hans Blom
- Karolinska Institutet, Department of Neuroscience, Science for Life Laboratory, Stockholm, Sweden
| | | | - Robert B Innis
- Molecular Imaging Branch, National Institute of Mental Health, Bethesda, MD, USA
| | - Matthew D Hall
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD, USA
| | - Jan Mulder
- Karolinska Institutet, Department of Neuroscience, Science for Life Laboratory, Stockholm, Sweden
| |
Collapse
|
15
|
Pessler F, Ogdie AR, Mayer CT, Kretzschmar WW, Dai L, Elsaman AM, Einhorn E, Krenn V, Schumacher HR. Amyloid arthropathy associated with multiple myeloma: polyarthritis without synovial infiltration of CD20+ or CD38+ cells. Amyloid 2014; 21:28-34. [PMID: 24286442 PMCID: PMC3956491 DOI: 10.3109/13506129.2013.862229] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To describe histological, immunohistochemical and ultrastructural features of synovial biopsies of amyloid arthropathy associated with multiple myeloma (MM). METHODS Synovial biopsies from affected joints of two patients with MM and amyloid arthropathy were examined with light and electron microscopy, and immunohistochemically for expression of CD3, CD8, CD20, CD38, CD68, Ki-67 and vWF. Results were compared to values from osteoarthritis (OA, n = 26), rheumatoid arthritis (RA, n = 24) and normal (n = 15) synovial membranes. RESULTS There was no or only mild lining hyperplasia. Vascular density was not elevated, and there were few Ki-67+ proliferating cells in the stroma. The Krenn synovitis score classified one specimen as "low-grade" and one as "high-grade" synovitis. CD68+ and CD3+ cells were the predominant mononuclear inflammatory cells, whereas CD20+ and CD38+ cells were absent from both synovial membrane and synovial fluid sediment. Electron microscopy demonstrated amyloid phagocytosis by synovial macrophages. In hierarchical clustering the two amyloid arthropathy specimens were more closely related to OA than to RA or normal synovium. CONCLUSIONS This first detailed immunohistological analysis of MM-associated amyloid arthropathy suggests that it is a chronic synovitis that evolves despite the loss of humoral immunity seen in advanced MM. Instead, amyloid phagocytosis by synovial macrophages likely triggers and perpetuates local disease.
Collapse
Affiliation(s)
- Frank Pessler
- TWINCORE Center for Experimental and Clinical Infection Research , Hannover , Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Ferreira Z, Hurle B, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Gonder MK, Stone AC, Tishkoff S, Swanson WJ, Green ED, Clark AG, Seixas S. Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity. Genome Biol Evol 2013; 5:2512-23. [PMID: 24356879 PMCID: PMC3879984 DOI: 10.1093/gbe/evt198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Indexed: 01/02/2023] Open
Abstract
Recent efforts have attempted to describe the population structure of common chimpanzee, focusing on four subspecies: Pan troglodytes verus, P. t. ellioti, P. t. troglodytes, and P. t. schweinfurthii. However, few studies have pursued the effects of natural selection in shaping their response to pathogens and reproduction. Whey acidic protein (WAP) four-disulfide core domain (WFDC) genes and neighboring semenogelin (SEMG) genes encode proteins with combined roles in immunity and fertility. They display a strikingly high rate of amino acid replacement (dN/dS), indicative of adaptive pressures during primate evolution. In human populations, three signals of selection at the WFDC locus were described, possibly influencing the proteolytic profile and antimicrobial activities of the male reproductive tract. To evaluate the patterns of genomic variation and selection at the WFDC locus in chimpanzees, we sequenced 17 WFDC genes and 47 autosomal pseudogenes in 68 chimpanzees (15 P. t. troglodytes, 22 P. t. verus, and 31 P. t. ellioti). We found a clear differentiation of P. t. verus and estimated the divergence of P. t. troglodytes and P. t. ellioti subspecies in 0.173 Myr; further, at the WFDC locus we identified a signature of strong selective constraints common to the three subspecies in WFDC6—a recent paralog of the epididymal protease inhibitor EPPIN. Overall, chimpanzees and humans do not display similar footprints of selection across the WFDC locus, possibly due to different selective pressures between the two species related to immune response and reproductive biology.
Collapse
Affiliation(s)
- Zélia Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Ferreira Z, Seixas S, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Swanson WJ, Clark AG, Green ED, Hurle B. Reproduction and immunity-driven natural selection in the human WFDC locus. Mol Biol Evol 2013; 30:938-50. [PMID: 23292442 DOI: 10.1093/molbev/mss329] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The whey acidic protein (WAP) four-disulfide core domain (WFDC) locus located on human chromosome 20q13 spans 19 genes with WAP and/or Kunitz domains. These genes participate in antimicrobial, immune, and tissue homoeostasis activities. Neighboring SEMG genes encode seminal proteins Semenogelin 1 and 2 (SEMG1 and SEMG2). WFDC and SEMG genes have a strikingly high rate of amino acid replacement (dN/dS), indicative of responses to adaptive pressures during vertebrate evolution. To better understand the selection pressures acting on WFDC genes in human populations, we resequenced 18 genes and 54 noncoding segments in 71 European (CEU), African (YRI), and Asian (CHB + JPT) individuals. Overall, we identified 484 single-nucleotide polymorphisms (SNPs), including 65 coding variants (of which 49 are nonsynonymous differences). Using classic neutrality tests, we confirmed the signature of short-term balancing selection on WFDC8 in Europeans and a signature of positive selection spanning genes PI3, SEMG1, SEMG2, and SLPI. Associated with the latter signal, we identified an unusually homogeneous-derived 100-kb haplotype with a frequency of 88% in Asian populations. A putative candidate variant targeted by selection is Thr56Ser in SEMG1, which may alter the proteolytic profile of SEMG1 and antimicrobial activities of semen. All the well-characterized genes residing in the WDFC locus encode proteins that appear to have a role in immunity and/or fertility, two processes that are often associated with adaptive evolution. This study provides further evidence that the WFDC and SEMG loci have been under strong adaptive pressure within the short timescale of modern humans.
Collapse
Affiliation(s)
- Zélia Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Noda A, Hirai Y, Kodama Y, Kretzschmar WW, Hamasaki K, Kusunoki Y, Mitani H, Cullings HM, Nakamura N. Easy detection of GFP-positive mutants following forward mutations at specific gene locus in cultured human cells. Mutat Res 2011; 721:101-7. [PMID: 21215816 DOI: 10.1016/j.mrgentox.2010.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 11/19/2010] [Accepted: 12/29/2010] [Indexed: 10/18/2022]
Abstract
We have generated a new mutation assay system using HT1080 human fibrosarcoma cells, which consists of a combination of tetracycline-operator dependent GFP gene (TetO-EGFP) and tetracycline repressor (TetR) genes, where the expression of GFP gene is under strict control of TetR protein, and the TetR gene is located within the endogenous HPRT gene. In this system, any inactivating mutation at the TetR gene or large deletions including the gene itself results in high expression of GFP gene (>200-fold increase) in the cells, which can be readily scored not only by a flow cytometer but also under a fluorescent microscope. With this new cell line, we show that the spontaneous mutation rate at the TetR locus was 2.8-3.4×10(-6)/cell division, slightly lower than the rate at the endogenous HPRT gene of HT1080 cells, and has a dose response to X rays as a mutagen. We also isolated variant clones with elevated spontaneous mutation rate (i.e., genetically unstable cells) following X irradiation. Spontaneous GFP-positive mutants were predominantly base-change mutations at the TetR gene while those obtained after X irradiation often contained large deletions which spanned up to 6Mb. The results indicate that the bacterial TetR/TetO regulatory units work extremely well as a mutation detection system in human cells, and any part of the human genome may be tested for mutation sensitivity following targeted insertion of the TetR gene in a stably expressing gene.
Collapse
Affiliation(s)
- Asao Noda
- Department of Genetics, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-Ku, Hiroshima 732-0815, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Andrés AM, Dennis MY, Kretzschmar WW, Cannons JL, Lee-Lin SQ, Hurle B, Schwartzberg PL, Williamson SH, Bustamante CD, Nielsen R, Clark AG, Green ED. Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. PLoS Genet 2010; 6:e1001157. [PMID: 20976248 PMCID: PMC2954825 DOI: 10.1371/journal.pgen.1001157] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 09/13/2010] [Indexed: 11/18/2022] Open
Abstract
A remarkable characteristic of the human major histocompatibility complex (MHC) is its extreme genetic diversity, which is maintained by balancing selection. In fact, the MHC complex remains one of the best-known examples of natural selection in humans, with well-established genetic signatures and biological mechanisms for the action of selection. Here, we present genetic and functional evidence that another gene with a fundamental role in MHC class I presentation, endoplasmic reticulum aminopeptidase 2 (ERAP2), has also evolved under balancing selection and contains a variant that affects antigen presentation. Specifically, genetic analyses of six human populations revealed strong and consistent signatures of balancing selection affecting ERAP2. This selection maintains two highly differentiated haplotypes (Haplotype A and Haplotype B), with frequencies 0.44 and 0.56, respectively. We found that ERAP2 expressed from Haplotype B undergoes differential splicing and encodes a truncated protein, leading to nonsense-mediated decay of the mRNA. To investigate the consequences of ERAP2 deficiency on MHC presentation, we correlated surface MHC class I expression with ERAP2 genotypes in primary lymphocytes. Haplotype B homozygotes had lower levels of MHC class I expressed on the surface of B cells, suggesting that naturally occurring ERAP2 deficiency affects MHC presentation and immune response. Interestingly, an ERAP2 paralog, endoplasmic reticulum aminopeptidase 1 (ERAP1), also shows genetic signatures of balancing selection. Together, our findings link the genetic signatures of selection with an effect on splicing and a cellular phenotype. Although the precise selective pressure that maintains polymorphism is unknown, the demonstrated differences between the ERAP2 splice forms provide important insights into the potential mechanism for the action of selection. It has long been known that the extremely high levels of genetic diversity present in the major histocompatibility locus (MHC) are due to balancing selection, a type of natural selection that maintains advantageous genetic diversity in populations. The MHC encodes for molecules required for a type of antigen presentation that mediates detection of infected and cancerous cells by the immune system; the genetic diversity of the MHC thus ensures an adequate response to the wide variety of pathogens that humans encounter. Here, we show that other genes involved in the same antigen-presentation pathway are also subject to balancing selection in humans. Specifically, we show that balancing selection acts to maintain two forms of the endoplasmic reticulum aminopeptidase 2 gene (ERAP2), which encodes a protein also involved in antigen presentation. Although the two ERAP2 forms are present in a similar frequency (close to 0.5), they are associated with differences with respect to the levels of MHC molecules on the cell surface of immune cells. In summary, our findings show that natural selection maintains variants of ERAP2 that affect immune surveillance; they also establish ERAP2 as one of the few examples of balancing selection in humans where the selected variant, its functional consequences, and its influence in interpersonal diversity are known.
Collapse
Affiliation(s)
- Aida M Andrés
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|