Additional file 6: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Additional file 3: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data

Benjamin Sobkowiak (409159)
Judith Glynn (371406)
Rein Houben (5091068)
Kim Mallard (362508)
Jody Phelan (3543014)
JosĂŠ Guerra-AssunĂ§ĂŁo (5632652)
Louis Banda (5632649)
Themba Mzembe (771356)
Miguel Viveiros (69123)
Ruth McNerney (227467)
Julian Parkhill (30393)
Amelia Crampin (272631)
Taane Clark (3507860)

August 2018

Coverage plots illustrating four Regions of Differences (RDs) in clinically-derived Malawi strains. ...

Farhat, Maha

Pooled data on genetic variation. Each row represents an individual Mycobacterium tuberculosis patie...

Additional file 4: of Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms

Tra-My Ngo (6318062)
Yik-Ying Teo (159446)

February 2019

Figure S1. Distribution of sample numbers in three TB databases. Number of isolates with available D...

Additional file 1: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

Isolates Selected for WGS from Clusters Identified by Identical Genetic Fingerprints. This table sum...

Additional file 7: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

Genes Containing Intra-cluster SNPs. This table displays the genes and mutation sites where SNPs tha...

Additional file 4: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

U Cluster 1 Demographics. This table displays the demographics of the patients providing isolates fr...

Additional file 5: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

Comparison of the Sensitivity and Specificity of Standard Mtb Fingerprinting against Whole Genome Se...

Additional file 3: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

Epidemiologically Identified Clusters. This table summarizes the isolates that were selected for WGS...

Additional file 2: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

Clusters Identified by Shared Uncommon Spoligotypes. This table summarizes the isolates that were se...

Additional file 1: of Role of MIRU-VNTR and spoligotyping in assessing the genetic diversity of Mycobacterium tuberculosis in Henan Province, China

Jie Shi (130059)
Danwei Zheng (5712341)
Yankun Zhu (5712344)
Xiaoguang Ma (251269)
Shaohua Wang (1447912)
Hui Li (32376)
Jin Xing (5712347)

September 2018

Figure S1. Genotyping of 668Â M. tuberculosis isolates with 26-locus MIRU-VNTR and spoligotyping. Th...

Additional file 4: of First insights on the genetic diversity of MDR Mycobacterium tuberculosis in Lebanon

Balig Panossian (6164099)
Tamara Salloum (3917417)
George Araj (5059463)
Georges Khazen (171939)
Sima Tokajian (3559616)

December 2018

Loci Information for short MIRU-VNTR. List of Loci taken into account for the analysis of the short ...

Additional file 1: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data

Benjamin Sobkowiak (409159)
Judith Glynn (371406)
Rein Houben (5091068)
Kim Mallard (362508)
Jody Phelan (3543014)
JosĂŠ Guerra-AssunĂ§ĂŁo (5632652)
Louis Banda (5632649)
Themba Mzembe (771356)
Miguel Viveiros (69123)
Ruth McNerney (227467)
Julian Parkhill (30393)
Amelia Crampin (272631)
Taane Clark (3507860)

August 2018

Strain information and full results table for clinically-derived Malawi samples, in silico replicate...

Additional file 3: of First insights on the genetic diversity of MDR Mycobacterium tuberculosis in Lebanon

Balig Panossian (6164099)
Tamara Salloum (3917417)
George Araj (5059463)
Georges Khazen (171939)
Sima Tokajian (3559616)

December 2018

Repeat regions on M. tuberculosis H37Rv genome. Repeat regions of H37Rv excluded from the analysis o...

Additional file 5: of Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

Hollie-Ann Hatherell (2588509)
Caroline Colijn (164960)
Helen Stagg (3480410)
Charlotte Jackson (565035)
Joanne Winter (3507035)
Ibrahim Abubakar (217017)

March 2016

Appendix E. Factors affecting the number of polymorphisms detected in sequences. (DOCX 18 kb

Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent J. Koster
Angela Largen
Jeffrey T. Foster
Kevin P. Drees
Lishi Qian
Ed Desmond
Xuehua Wan
Shaobin Hou
James T. Douglas

December 2018

Abstract Background Tuberculosis (TB) caused an estimated 1.4 million deaths and 10.4 million new ca...

Additional file 3: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data

Benjamin Sobkowiak (409159)
Judith Glynn (371406)
Rein Houben (5091068)
Kim Mallard (362508)
Jody Phelan (3543014)
JosĂŠ Guerra-AssunĂ§ĂŁo (5632652)
Louis Banda (5632649)
Themba Mzembe (771356)
Miguel Viveiros (69123)
Ruth McNerney (227467)
Julian Parkhill (30393)
Amelia Crampin (272631)
Taane Clark (3507860)

August 2018

Coverage plots illustrating four Regions of Differences (RDs) in clinically-derived Malawi strains. ...

genetic variation

Farhat, Maha

Pooled data on genetic variation. Each row represents an individual Mycobacterium tuberculosis patie...

Additional file 4: of Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms

Tra-My Ngo (6318062)
Yik-Ying Teo (159446)

February 2019

Figure S1. Distribution of sample numbers in three TB databases. Number of isolates with available D...

Additional file 1: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

Isolates Selected for WGS from Clusters Identified by Identical Genetic Fingerprints. This table sum...

Additional file 7: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

Genes Containing Intra-cluster SNPs. This table displays the genes and mutation sites where SNPs tha...

Additional file 4: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

U Cluster 1 Demographics. This table displays the demographics of the patients providing isolates fr...

Additional file 5: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

Comparison of the Sensitivity and Specificity of Standard Mtb Fingerprinting against Whole Genome Se...

Additional file 3: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

Epidemiologically Identified Clusters. This table summarizes the isolates that were selected for WGS...

Additional file 2: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent Koster (3916520)
Angela Largen (5545592)
Jeffrey Foster (3532328)
Kevin Drees (3714319)
Lishi Qian (3916529)
Ed Desmond (6039224)
Xuehua Wan (475915)
Shaobin Hou (475914)
James Douglas (1814851)

December 2018

Clusters Identified by Shared Uncommon Spoligotypes. This table summarizes the isolates that were se...

Additional file 1: of Role of MIRU-VNTR and spoligotyping in assessing the genetic diversity of Mycobacterium tuberculosis in Henan Province, China

Jie Shi (130059)
Danwei Zheng (5712341)
Yankun Zhu (5712344)
Xiaoguang Ma (251269)
Shaohua Wang (1447912)
Hui Li (32376)
Jin Xing (5712347)

September 2018

Figure S1. Genotyping of 668Â M. tuberculosis isolates with 26-locus MIRU-VNTR and spoligotyping. Th...

Additional file 4: of First insights on the genetic diversity of MDR Mycobacterium tuberculosis in Lebanon

Balig Panossian (6164099)
Tamara Salloum (3917417)
George Araj (5059463)
Georges Khazen (171939)
Sima Tokajian (3559616)

December 2018

Loci Information for short MIRU-VNTR. List of Loci taken into account for the analysis of the short ...

Additional file 1: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data

Benjamin Sobkowiak (409159)
Judith Glynn (371406)
Rein Houben (5091068)
Kim Mallard (362508)
Jody Phelan (3543014)
JosĂŠ Guerra-AssunĂ§ĂŁo (5632652)
Louis Banda (5632649)
Themba Mzembe (771356)
Miguel Viveiros (69123)
Ruth McNerney (227467)
Julian Parkhill (30393)
Amelia Crampin (272631)
Taane Clark (3507860)

August 2018

Strain information and full results table for clinically-derived Malawi samples, in silico replicate...

Additional file 3: of First insights on the genetic diversity of MDR Mycobacterium tuberculosis in Lebanon

Balig Panossian (6164099)
Tamara Salloum (3917417)
George Araj (5059463)
Georges Khazen (171939)
Sima Tokajian (3559616)

December 2018

Repeat regions on M. tuberculosis H37Rv genome. Repeat regions of H37Rv excluded from the analysis o...

Additional file 5: of Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

Hollie-Ann Hatherell (2588509)
Caroline Colijn (164960)
Helen Stagg (3480410)
Charlotte Jackson (565035)
Joanne Winter (3507035)
Ibrahim Abubakar (217017)

March 2016

Appendix E. Factors affecting the number of polymorphisms detected in sequences. (DOCX 18 kb

Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Kent J. Koster
Angela Largen
Jeffrey T. Foster
Kevin P. Drees
Lishi Qian
Ed Desmond
Xuehua Wan
Shaobin Hou
James T. Douglas

December 2018

Abstract Background Tuberculosis (TB) caused an estimated 1.4 million deaths and 10.4 million new ca...

Additional file 3: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data

Benjamin Sobkowiak (409159)
Judith Glynn (371406)
Rein Houben (5091068)
Kim Mallard (362508)
Jody Phelan (3543014)
JosĂŠ Guerra-AssunĂ§ĂŁo (5632652)
Louis Banda (5632649)
Themba Mzembe (771356)
Miguel Viveiros (69123)
Ruth McNerney (227467)
Julian Parkhill (30393)
Amelia Crampin (272631)
Taane Clark (3507860)

August 2018

Coverage plots illustrating four Regions of Differences (RDs) in clinically-derived Malawi strains. ...

genetic variation

Farhat, Maha

Pooled data on genetic variation. Each row represents an individual Mycobacterium tuberculosis patie...

Additional file 4: of Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms

Tra-My Ngo (6318062)
Yik-Ying Teo (159446)

February 2019

Figure S1. Distribution of sample numbers in three TB databases. Number of isolates with available D...

Additional file 6: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Abstract

Extracted data

Additional file 6: of Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Abstract

Extracted data

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