Literature DB >> 28904183

The TB Portals: an Open-Access, Web-Based Platform for Global Drug-Resistant-Tuberculosis Data Sharing and Analysis.

Alex Rosenthal1, Andrei Gabrielian2, Eric Engle2, Darrell E Hurt2, Sofia Alexandru3, Valeriu Crudu3, Eugene Sergueev4, Valery Kirichenko4, Vladzimir Lapitskii4, Eduard Snezhko4, Vassili Kovalev4, Andrei Astrovko5, Alena Skrahina5, Jessica Taaffe2, Michael Harris2, Alyssa Long2, Kurt Wollenberg2, Irada Akhundova6, Sharafat Ismayilova6, Aliaksandr Skrahin7, Elcan Mammadbayov6, Hagigat Gadirova6, Rafik Abuzarov6, Mehriban Seyfaddinova6, Zaza Avaliani8, Irina Strambu9, Dragos Zaharia9, Alexandru Muntean9, Eugenia Ghita9, Miron Bogdan9, Roxana Mindru9, Victor Spinu9, Alexandra Sora9, Catalina Ene9, Sergo Vashakidze8, Natalia Shubladze8, Ucha Nanava8, Alexander Tuzikov4, Michael Tartakovsky2.   

Abstract

The TB Portals program is an international consortium of physicians, radiologists, and microbiologists from countries with a heavy burden of drug-resistant tuberculosis working with data scientists and information technology professionals. Together, we have built the TB Portals, a repository of socioeconomic/geographic, clinical, laboratory, radiological, and genomic data from patient cases of drug-resistant tuberculosis backed by shareable, physical samples. Currently, there are 1,299 total cases from five country sites (Azerbaijan, Belarus, Moldova, Georgia, and Romania), 976 (75.1%) of which are multidrug or extensively drug resistant and 38.2%, 51.9%, and 36.3% of which contain X-ray, computed tomography (CT) scan, and genomic data, respectively. The top Mycobacterium tuberculosis lineages represented among collected samples are Beijing, T1, and H3, and single nucleotide polymorphisms (SNPs) that confer resistance to isoniazid, rifampin, ofloxacin, and moxifloxacin occur the most frequently. These data and samples have promoted drug discovery efforts and research into genomics and quantitative image analysis to improve diagnostics while also serving as a valuable resource for researchers and clinical providers. The TB Portals database and associated projects are continually growing, and we invite new partners and collaborations to our initiative. The TB Portals data and their associated analytical and statistical tools are freely available at https://tbportals.niaid.nih.gov/.

Entities:  

Keywords:  MDR-TB; Mycobacterium tuberculosis; XDR-TB; digital health; drug-resistant TB; interactive portals; query; tuberculosis

Mesh:

Year:  2017        PMID: 28904183      PMCID: PMC5654911          DOI: 10.1128/JCM.01013-17

Source DB:  PubMed          Journal:  J Clin Microbiol        ISSN: 0095-1137            Impact factor:   5.948


  18 in total

1.  Identifying Mycobacterium tuberculosis complex strain families using spoligotypes.

Authors:  Inna Vitol; Jeffrey Driscoll; Barry Kreiswirth; Natalia Kurepina; Kristin P Bennett
Journal:  Infect Genet Evol       Date:  2006-05-02       Impact factor: 3.342

2.  Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance.

Authors:  Hongtai Zhang; Dongfang Li; Lili Zhao; Joy Fleming; Nan Lin; Ting Wang; Zhangyi Liu; Chuanyou Li; Nicholas Galwey; Jiaoyu Deng; Ying Zhou; Yuanfang Zhu; Yunrong Gao; Tong Wang; Shihua Wang; Yufen Huang; Ming Wang; Qiu Zhong; Lin Zhou; Tao Chen; Jie Zhou; Ruifu Yang; Guofeng Zhu; Haiying Hang; Jia Zhang; Fabin Li; Kanglin Wan; Jun Wang; Xian-En Zhang; Lijun Bi
Journal:  Nat Genet       Date:  2013-09-01       Impact factor: 38.330

3.  CARS 2015-Computer Assisted Radiology and Surgery Proceedings of the 29th International Congress and Exhibition Barcelona, Spain, June 24-27, 2015.

Authors: 
Journal:  Int J Comput Assist Radiol Surg       Date:  2015-06       Impact factor: 2.924

4.  PET/CT imaging correlates with treatment outcome in patients with multidrug-resistant tuberculosis.

Authors:  Ray Y Chen; Lori E Dodd; Myungsun Lee; Praveen Paripati; Dima A Hammoud; James M Mountz; Doosoo Jeon; Nadeem Zia; Homeira Zahiri; M Teresa Coleman; Matthew W Carroll; Jong Doo Lee; Yeon Joo Jeong; Peter Herscovitch; Saher Lahouar; Michael Tartakovsky; Alexander Rosenthal; Sandeep Somaiyya; Soyoung Lee; Lisa C Goldfeder; Ying Cai; Laura E Via; Seung-Kyu Park; Sang-Nae Cho; Clifton E Barry
Journal:  Sci Transl Med       Date:  2014-12-03       Impact factor: 17.956

5.  Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis.

Authors:  Maha R Farhat; B Jesse Shapiro; Karen J Kieser; Razvan Sultana; Karen R Jacobson; Thomas C Victor; Robin M Warren; Elizabeth M Streicher; Alistair Calver; Alex Sloutsky; Devinder Kaur; Jamie E Posey; Bonnie Plikaytis; Marco R Oggioni; Jennifer L Gardy; James C Johnston; Mabel Rodrigues; Patrick K C Tang; Midori Kato-Maeda; Mark L Borowsky; Bhavana Muddukrishna; Barry N Kreiswirth; Natalia Kurepina; James Galagan; Sebastien Gagneux; Bruce Birren; Eric J Rubin; Eric S Lander; Pardis C Sabeti; Megan Murray
Journal:  Nat Genet       Date:  2013-09-01       Impact factor: 38.330

6.  Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.

Authors:  Bruce J Walker; Thomas Abeel; Terrance Shea; Margaret Priest; Amr Abouelliel; Sharadha Sakthikumar; Christina A Cuomo; Qiandong Zeng; Jennifer Wortman; Sarah K Young; Ashlee M Earl
Journal:  PLoS One       Date:  2014-11-19       Impact factor: 3.240

7.  Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance.

Authors:  Abigail L Manson; Keira A Cohen; Thomas Abeel; Christopher A Desjardins; Derek T Armstrong; Clifton E Barry; Jeannette Brand; Sinéad B Chapman; Sang-Nae Cho; Andrei Gabrielian; James Gomez; Andreea M Jodals; Moses Joloba; Pontus Jureen; Jong Seok Lee; Lesibana Malinga; Mamoudou Maiga; Dale Nordenberg; Ecaterina Noroc; Elena Romancenco; Alex Salazar; Willy Ssengooba; A A Velayati; Kathryn Winglee; Aksana Zalutskaya; Laura E Via; Gail H Cassell; Susan E Dorman; Jerrold Ellner; Parissa Farnia; James E Galagan; Alex Rosenthal; Valeriu Crudu; Daniela Homorodean; Po-Ren Hsueh; Sujatha Narayanan; Alexander S Pym; Alena Skrahina; Soumya Swaminathan; Martie Van der Walt; David Alland; William R Bishai; Ted Cohen; Sven Hoffner; Bruce W Birren; Ashlee M Earl
Journal:  Nat Genet       Date:  2017-01-16       Impact factor: 38.330

8.  Evolution and transmission of drug-resistant tuberculosis in a Russian population.

Authors:  Nicola Casali; Vladyslav Nikolayevskyy; Yanina Balabanova; Simon R Harris; Olga Ignatyeva; Irina Kontsevaya; Jukka Corander; Josephine Bryant; Julian Parkhill; Sergey Nejentsev; Rolf D Horstmann; Timothy Brown; Francis Drobniewski
Journal:  Nat Genet       Date:  2014-01-26       Impact factor: 38.330

9.  Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance.

Authors:  Christopher A Desjardins; Keira A Cohen; Vanisha Munsamy; Thomas Abeel; Kashmeel Maharaj; Bruce J Walker; Terrance P Shea; Deepak V Almeida; Abigail L Manson; Alex Salazar; Nesri Padayatchi; Max R O'Donnell; Koleka P Mlisana; Jennifer Wortman; Bruce W Birren; Jacques Grosset; Ashlee M Earl; Alexander S Pym
Journal:  Nat Genet       Date:  2016-04-11       Impact factor: 38.330

10.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

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  26 in total

1.  Differentiating between drug-sensitive and drug-resistant tuberculosis with machine learning for clinical and radiological features.

Authors:  Feng Yang; Hang Yu; Karthik Kantipudi; Manohar Karki; Yasmin M Kassim; Alex Rosenthal; Darrell E Hurt; Ziv Yaniv; Stefan Jaeger
Journal:  Quant Imaging Med Surg       Date:  2022-01

Review 2.  Bridging gaps between images and data: a systematic update on imaging biobanks.

Authors:  Michela Gabelloni; Lorenzo Faggioni; Rita Borgheresi; Giuliana Restante; Jorge Shortrede; Lorenzo Tumminello; Camilla Scapicchio; Francesca Coppola; Dania Cioni; Ignacio Gómez-Rico; Luis Martí-Bonmatí; Emanuele Neri
Journal:  Eur Radiol       Date:  2022-01-10       Impact factor: 5.315

3.  Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections.

Authors:  Miguel Moreno-Molina; Natalia Shubladze; Iza Khurtsilava; Zaza Avaliani; Nino Bablishvili; Manuela Torres-Puente; Luis Villamayor; Andrei Gabrielian; Alex Rosenthal; Cristina Vilaplana; Sebastien Gagneux; Russell R Kempker; Sergo Vashakidze; Iñaki Comas
Journal:  Nat Commun       Date:  2021-05-11       Impact factor: 17.694

4.  Patterns of genomic interrelatedness of publicly available samples in the TB portals database.

Authors:  Kurt R Wollenberg; Brendan M Jeffrey; Michael A Harris; Andrei Gabrielian; Darrell E Hurt; Alex Rosenthal
Journal:  Tuberculosis (Edinb)       Date:  2022-01-24       Impact factor: 3.131

5.  Open Health Imaging Foundation Viewer: An Extensible Open-Source Framework for Building Web-Based Imaging Applications to Support Cancer Research.

Authors:  Erik Ziegler; Trinity Urban; Danny Brown; James Petts; Steve D Pieper; Rob Lewis; Chris Hafey; Gordon J Harris
Journal:  JCO Clin Cancer Inform       Date:  2020-04

6.  TB DEPOT (Data Exploration Portal): A multi-domain tuberculosis data analysis resource.

Authors:  Andrei Gabrielian; Eric Engle; Michael Harris; Kurt Wollenberg; Octavio Juarez-Espinosa; Alexander Glogowski; Alyssa Long; Lisa Patti; Darrell E Hurt; Alex Rosenthal; Mike Tartakovsky
Journal:  PLoS One       Date:  2019-05-23       Impact factor: 3.240

Review 7.  In Silico Strategies in Tuberculosis Drug Discovery.

Authors:  Stephani Joy Y Macalino; Junie B Billones; Voltaire G Organo; Maria Constancia O Carrillo
Journal:  Molecules       Date:  2020-02-04       Impact factor: 4.411

Review 8.  Use of Digital Technology to Enhance Tuberculosis Control: Scoping Review.

Authors:  Yejin Lee; Mario C Raviglione; Antoine Flahault
Journal:  J Med Internet Res       Date:  2020-02-13       Impact factor: 5.428

9.  LINCS Data Portal 2.0: next generation access point for perturbation-response signatures.

Authors:  Vasileios Stathias; John Turner; Amar Koleti; Dusica Vidovic; Daniel Cooper; Mehdi Fazel-Najafabadi; Marcin Pilarczyk; Raymond Terryn; Caty Chung; Afoma Umeano; Daniel J B Clarke; Alexander Lachmann; John Erol Evangelista; Avi Ma'ayan; Mario Medvedovic; Stephan C Schürer
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

10.  Feature selection and prediction of treatment failure in tuberculosis.

Authors:  Christopher Martin Sauer; David Sasson; Kenneth E Paik; Ned McCague; Leo Anthony Celi; Iván Sánchez Fernández; Ben M W Illigens
Journal:  PLoS One       Date:  2018-11-20       Impact factor: 3.240

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