Draft Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium tuberculosis East African Indian Strain OSDD271

Vellarikkal, Shamsudheen Karuthedath; Patowary, Ashok; Singh, Meghna; Periwal, Vinita; Singh, Ajay Vir; Singh, Pravin Kumar; Garg, Prachi; Katoch, V.M.; Katoch, Kiran; Jangir, Pramod Kumar; Sharma, Rakesh; Chauhan, Deepika; Scaria, Vinod; Sivasubbu, Sridhar

doi:10.1128/genomea.00541-13

Cited by 3 publications

(4 citation statements)

References 15 publications

(12 reference statements)

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“…tuberculosis OSDD271 (17). The data were reference aligned as described in the ‘Materials and Methods’ section.…”

Section: Resultsmentioning

confidence: 99%

“…As a proof-of-principle, we have annotated the genome of a recently sequenced Multidrug resistant (MDR) strain of M . tuberculosis OSDD271 ( 17 ). The data were reference aligned as described in the ‘Materials and Methods’ section.…”

Section: Resultsmentioning

confidence: 99%

“…We performed proof-of-principle analysis of a recently sequenced clinical isolate of M . tuberculosis OSDD271 ( 17 ) isolated from India. The variations called from this strain against H37Rv reference genome were provided to annoTB using the interface, and summary report provided by the analysis was retrieved.…”

Section: Datasets and Methodsmentioning

confidence: 99%

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tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis

2014

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Mycobacterium tuberculosis, along with closely related species, commonly known as M. tuberculosis complex (MTBC), causes tuberculosis in humans and other organisms. Tuberculosis is a disease with high morbidity and mortality, especially in the third world. The genetic variability between clinical isolates of MTBC has been poorly understood, although recent years have seen the re-sequencing of a large number of clinical isolates of MTBC from around the world. The availability of genomic data of multiple isolates in public domain would potentially offer a unique opportunity toward understanding the variome of the organism and the functional consequences of the variations. This nevertheless has been limited by the lack of systematic curation and analysis of data sets available in public domain. In this report, we have re-analyzed re-sequencing data sets corresponding to >450 isolates of MTBC available in public domain to create a comprehensive variome map of MTBC comprising >29 000 single nucleotide variations. Using a systematic computational pipeline, we have annotated potential functional variants and drug-resistance-associated variants from the variome. We have made available this data set as a searchable database. Apart from a user-friendly interface, the database also has a novel option to annotate variants from clinical re-sequencing data sets of MTBC. To the best of our knowledge, tbvar is the largest and most comprehensive genome variation resources for MTBC.Database URL: http://genome.igib.res.in/tbvar/

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“…tuberculosis OSDD271 (17). The data were reference aligned as described in the ‘Materials and Methods’ section.…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis

2014

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“…A number of major and minor genotypes have been reported from across the world, of which the major lineages include the East Asian (Beijing), East African-Indian, Indo-Oceanic, Euro-American (Haarlem, LAM, T, and X), West African I, and West African II lineages. The complete or draft genome sequences of many of the members of the major lineages are now available in the public domain ( 2 , 3 ), and they show significant differences in their gene repertoires and sometimes in their genome architectures. It is now imperative to understand the genome structures and gene repertoires of the minor genotypes, which have been less explored.…”

Section: Genome Announcementmentioning

confidence: 99%