Literature DB >> 32777102

The Musculoskeletal Knowledge Portal: Making Omics Data Useful to the Broader Scientific Community.

Douglas P Kiel1,2,3,4, John P Kemp5,6, Fernando Rivadeneira7, Jennifer J Westendorf8, David Karasik1,9, Emma L Duncan10, Yuuki Imai11, Ralph Müller12, Jason Flannick3,13, Lynda Bonewald14, Noël Burtt4.   

Abstract

The development of high-throughput genotyping technologies and large biobank collections, complemented with rapid methodological advances in statistical genetics, has enabled hypothesis-free genome-wide association studies (GWAS), which have identified hundreds of genetic variants across many loci associated with musculoskeletal conditions. Similarly, basic scientists have valuable molecular cellular and animal data based on musculoskeletal disease that would be enhanced by being able to determine the human translation of their findings. By integrating these large-scale human genomic musculoskeletal datasets with complementary evidence from model organisms, new and existing genetic loci can be statistically fine-mapped to plausibly causal variants, candidate genes, and biological pathways. Genes and pathways identified using this approach can be further prioritized as drug targets, including side-effect profiling and the potential for new indications. To bring together these big data, and to realize the vision of creating a knowledge portal, the International Federation of Musculoskeletal Research Societies (IFMRS) established a working group to collaborate with scientists from the Broad Institute to create the Musculoskeletal Knowledge Portal (MSK-KP)(http://mskkp.org/). The MSK consolidates omics datasets from humans, cellular experiments, and model organisms into a central repository that can be accessed by researchers. The vision of the MSK-KP is to enable better understanding of the biological mechanisms underlying musculoskeletal disease and apply this knowledge to identify and develop new disease interventions.
© 2020 American Society for Bone and Mineral Research (ASBMR). © 2020 American Society for Bone and Mineral Research (ASBMR).

Entities:  

Keywords:  DISEASES AND DISORDERS OF/RELATED TO BONE; EPIGENETICS; GENETIC RESEARCH; OSTEOARTHRITIS; OSTEOPOROSIS

Mesh:

Year:  2020        PMID: 32777102      PMCID: PMC8114232          DOI: 10.1002/jbmr.4147

Source DB:  PubMed          Journal:  J Bone Miner Res        ISSN: 0884-0431            Impact factor:   6.741


  47 in total

1.  Use of genome-wide association studies for drug repositioning.

Authors:  Philippe Sanseau; Pankaj Agarwal; Michael R Barnes; Tomi Pastinen; J Brent Richards; Lon R Cardon; Vincent Mooser
Journal:  Nat Biotechnol       Date:  2012-04-10       Impact factor: 54.908

2.  Population genomics in a disease targeted primary cell model.

Authors:  Elin Grundberg; Tony Kwan; Bing Ge; Kevin C L Lam; Vonda Koka; Andreas Kindmark; Hans Mallmin; Joana Dias; Dominique J Verlaan; Manon Ouimet; Daniel Sinnett; Fernando Rivadeneira; Karol Estrada; Albert Hofman; Joyce M van Meurs; André Uitterlinden; Patrick Beaulieu; Alexandru Graziani; Eef Harmsen; Osten Ljunggren; Claes Ohlsson; Dan Mellström; Magnus K Karlsson; Olle Nilsson; Tomi Pastinen
Journal:  Genome Res       Date:  2009-08-04       Impact factor: 9.043

Review 3.  Statistical power and significance testing in large-scale genetic studies.

Authors:  Pak C Sham; Shaun M Purcell
Journal:  Nat Rev Genet       Date:  2014-05       Impact factor: 53.242

4.  Meta-analysis of how well measures of bone mineral density predict occurrence of osteoporotic fractures.

Authors:  D Marshall; O Johnell; H Wedel
Journal:  BMJ       Date:  1996-05-18

5.  Topological domains in mammalian genomes identified by analysis of chromatin interactions.

Authors:  Jesse R Dixon; Siddarth Selvaraj; Feng Yue; Audrey Kim; Yan Li; Yin Shen; Ming Hu; Jun S Liu; Bing Ren
Journal:  Nature       Date:  2012-04-11       Impact factor: 49.962

6.  The open targets post-GWAS analysis pipeline.

Authors:  Gareth Peat; William Jones; Michael Nuhn; José Carlos Marugán; William Newell; Ian Dunham; Daniel Zerbino
Journal:  Bioinformatics       Date:  2020-05-01       Impact factor: 6.937

7.  Assessment of the genetic and clinical determinants of fracture risk: genome wide association and mendelian randomisation study.

Authors:  Katerina Trajanoska; John A Morris; Ling Oei; Hou-Feng Zheng; David M Evans; Douglas P Kiel; Claes Ohlsson; J Brent Richards; Fernando Rivadeneira
Journal:  BMJ       Date:  2018-08-29

Review 8.  Genetics of Bone and Muscle Interactions in Humans.

Authors:  Katerina Trajanoska; Fernando Rivadeneira; Douglas P Kiel; David Karasik
Journal:  Curr Osteoporos Rep       Date:  2019-04       Impact factor: 5.096

9.  Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.

Authors:  Hou-Feng Zheng; Vincenzo Forgetta; Yi-Hsiang Hsu; Karol Estrada; Alberto Rosello-Diez; Paul J Leo; Chitra L Dahia; Kyung Hyun Park-Min; Jonathan H Tobias; Charles Kooperberg; Aaron Kleinman; Unnur Styrkarsdottir; Ching-Ti Liu; Charlotta Uggla; Daniel S Evans; Carrie M Nielson; Klaudia Walter; Ulrika Pettersson-Kymmer; Shane McCarthy; Joel Eriksson; Tony Kwan; Mila Jhamai; Katerina Trajanoska; Yasin Memari; Josine Min; Jie Huang; Petr Danecek; Beth Wilmot; Rui Li; Wen-Chi Chou; Lauren E Mokry; Alireza Moayyeri; Melina Claussnitzer; Chia-Ho Cheng; Warren Cheung; Carolina Medina-Gómez; Bing Ge; Shu-Huang Chen; Kwangbom Choi; Ling Oei; James Fraser; Robert Kraaij; Matthew A Hibbs; Celia L Gregson; Denis Paquette; Albert Hofman; Carl Wibom; Gregory J Tranah; Mhairi Marshall; Brooke B Gardiner; Katie Cremin; Paul Auer; Li Hsu; Sue Ring; Joyce Y Tung; Gudmar Thorleifsson; Anke W Enneman; Natasja M van Schoor; Lisette C P G M de Groot; Nathalie van der Velde; Beatrice Melin; John P Kemp; Claus Christiansen; Adrian Sayers; Yanhua Zhou; Sophie Calderari; Jeroen van Rooij; Chris Carlson; Ulrike Peters; Soizik Berlivet; Josée Dostie; Andre G Uitterlinden; Stephen R Williams; Charles Farber; Daniel Grinberg; Andrea Z LaCroix; Jeff Haessler; Daniel I Chasman; Franco Giulianini; Lynda M Rose; Paul M Ridker; John A Eisman; Tuan V Nguyen; Jacqueline R Center; Xavier Nogues; Natalia Garcia-Giralt; Lenore L Launer; Vilmunder Gudnason; Dan Mellström; Liesbeth Vandenput; Najaf Amin; Cornelia M van Duijn; Magnus K Karlsson; Östen Ljunggren; Olle Svensson; Göran Hallmans; François Rousseau; Sylvie Giroux; Johanne Bussière; Pascal P Arp; Fjorda Koromani; Richard L Prince; Joshua R Lewis; Bente L Langdahl; A Pernille Hermann; Jens-Erik B Jensen; Stephen Kaptoge; Kay-Tee Khaw; Jonathan Reeve; Melissa M Formosa; Angela Xuereb-Anastasi; Kristina Åkesson; Fiona E McGuigan; Gaurav Garg; Jose M Olmos; Maria T Zarrabeitia; Jose A Riancho; Stuart H Ralston; Nerea Alonso; Xi Jiang; David Goltzman; Tomi Pastinen; Elin Grundberg; Dominique Gauguier; Eric S Orwoll; David Karasik; George Davey-Smith; Albert V Smith; Kristin Siggeirsdottir; Tamara B Harris; M Carola Zillikens; Joyce B J van Meurs; Unnur Thorsteinsdottir; Matthew T Maurano; Nicholas J Timpson; Nicole Soranzo; Richard Durbin; Scott G Wilson; Evangelia E Ntzani; Matthew A Brown; Kari Stefansson; David A Hinds; Tim Spector; L Adrienne Cupples; Claes Ohlsson; Celia M T Greenwood; Rebecca D Jackson; David W Rowe; Cynthia A Loomis; David M Evans; Cheryl L Ackert-Bicknell; Alexandra L Joyner; Emma L Duncan; Douglas P Kiel; Fernando Rivadeneira; J Brent Richards
Journal:  Nature       Date:  2015-09-14       Impact factor: 49.962

10.  The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.

Authors:  Judy Sprague; Leyla Bayraktaroglu; Yvonne Bradford; Tom Conlin; Nathan Dunn; David Fashena; Ken Frazer; Melissa Haendel; Douglas G Howe; Jonathan Knight; Prita Mani; Sierra A T Moxon; Christian Pich; Sridhar Ramachandran; Kevin Schaper; Erik Segerdell; Xiang Shao; Amy Singer; Peiran Song; Brock Sprunger; Ceri E Van Slyke; Monte Westerfield
Journal:  Nucleic Acids Res       Date:  2007-11-08       Impact factor: 16.971

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  11 in total

1.  Prioritization of Genes Relevant to Bone Fragility Through the Unbiased Integration of Aging Mouse Bone Transcriptomics and Human GWAS Analyses.

Authors:  Serra Kaya; Charles A Schurman; Neha S Dole; Daniel S Evans; Tamara Alliston
Journal:  J Bone Miner Res       Date:  2022-02-28       Impact factor: 6.390

2.  The Musculoskeletal Knowledge Portal: improving access to multi-omics data.

Authors:  Jennifer J Westendorf; Lynda F Bonewald; Douglas P Kiel; Noël P Burtt
Journal:  Nat Rev Rheumatol       Date:  2022-01       Impact factor: 32.286

Review 3.  Single Cell Omics for Musculoskeletal Research.

Authors:  Muhammad Farooq Rai; Chia-Lung Wu; Terence D Capellini; Farshid Guilak; Amanda R Dicks; Pushpanathan Muthuirulan; Fiorella Grandi; Nidhi Bhutani; Jennifer J Westendorf
Journal:  Curr Osteoporos Rep       Date:  2021-02-09       Impact factor: 5.096

4.  Genome-wide Association Studies Reveal Novel Locus With Sex-/Therapy-Specific Fracture Risk Effects in Childhood Cancer Survivors.

Authors:  Cindy Im; Nan Li; Wonjong Moon; Qi Liu; Lindsay M Morton; Wendy M Leisenring; Rebecca M Howell; Eric J Chow; Charles A Sklar; Carmen L Wilson; Zhaoming Wang; Yadav Sapkota; Wassim Chemaitilly; Kirsten K Ness; Melissa M Hudson; Leslie L Robison; Smita Bhatia; Gregory T Armstrong; Yutaka Yasui
Journal:  J Bone Miner Res       Date:  2020-12-30       Impact factor: 6.741

Review 5.  Opportunities and Challenges in Functional Genomics Research in Osteoporosis: Report From a Workshop Held by the Causes Working Group of the Osteoporosis and Bone Research Academy of the Royal Osteoporosis Society on October 5th 2020.

Authors:  Jonathan H Tobias; Emma L Duncan; Erika Kague; Chrissy L Hammond; Celia L Gregson; Duncan Bassett; Graham R Williams; Josine L Min; Tom R Gaunt; David Karasik; Claes Ohlsson; Fernando Rivadeneira; James R Edwards; Fadil M Hannan; John P Kemp; Sophie J Gilbert; Nerea Alonso; Neelam Hassan; Juliet E Compston; Stuart H Ralston
Journal:  Front Endocrinol (Lausanne)       Date:  2021-02-15       Impact factor: 5.555

Review 6.  A Roadmap to Gene Discoveries and Novel Therapies in Monogenic Low and High Bone Mass Disorders.

Authors:  Melissa M Formosa; Dylan J M Bergen; Celia L Gregson; Antonio Maurizi; Anders Kämpe; Natalia Garcia-Giralt; Wei Zhou; Daniel Grinberg; Diana Ovejero Crespo; M Carola Zillikens; Graham R Williams; J H Duncan Bassett; Maria Luisa Brandi; Luca Sangiorgi; Susanna Balcells; Wolfgang Högler; Wim Van Hul; Outi Mäkitie
Journal:  Front Endocrinol (Lausanne)       Date:  2021-08-13       Impact factor: 5.555

Review 7.  The "GEnomics of Musculo Skeletal Traits TranslatiOnal NEtwork": Origins, Rationale, Organization, and Prospects.

Authors:  Fjorda Koromani; Nerea Alonso; Ines Alves; Maria Luisa Brandi; Ines Foessl; Melissa M Formosa; Milana Frenkel Morgenstern; David Karasik; Mikhail Kolev; Outi Makitie; Evangelia Ntzani; Barbara Obermayer Pietsch; Claes Ohlsson; Martina Rauner; Kent Soe; Ivan Soldatovic; Anna Teti; Amina Valjevac; Fernando Rivadeneira
Journal:  Front Endocrinol (Lausanne)       Date:  2021-08-16       Impact factor: 5.555

8.  Whole Genome Sequencing Unravels New Genetic Determinants of Early-Onset Familial Osteoporosis and Low BMD in Malta.

Authors:  Chanelle Cilia; Donald Friggieri; Josanne Vassallo; Angela Xuereb-Anastasi; Melissa Marie Formosa
Journal:  Genes (Basel)       Date:  2022-01-23       Impact factor: 4.096

Review 9.  Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques.

Authors:  Martina Rauner; Ines Foessl; Melissa M Formosa; Erika Kague; Vid Prijatelj; Nerea Alonso Lopez; Bodhisattwa Banerjee; Dylan Bergen; Björn Busse; Ângelo Calado; Eleni Douni; Yankel Gabet; Natalia García Giralt; Daniel Grinberg; Nika M Lovsin; Xavier Nogues Solan; Barbara Ostanek; Nathan J Pavlos; Fernando Rivadeneira; Ivan Soldatovic; Jeroen van de Peppel; Bram van der Eerden; Wim van Hul; Susanna Balcells; Janja Marc; Sjur Reppe; Kent Søe; David Karasik
Journal:  Front Endocrinol (Lausanne)       Date:  2021-11-30       Impact factor: 5.555

Review 10.  The Polygenic and Monogenic Basis of Paediatric Fractures.

Authors:  S Ghatan; A Costantini; R Li; C De Bruin; N M Appelman-Dijkstra; E M Winter; L Oei; Carolina Medina-Gomez
Journal:  Curr Osteoporos Rep       Date:  2021-05-04       Impact factor: 5.096

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