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/.KEYWORDS tuberculosis, digital health, interactive portals, MDR-TB, Mycobacterium tuberculosis, query, XDR-TB, drug-resistant TB T uberculosis (TB) continues to represent a major health problem worldwide. An estimated one-third of the world's population is living with latent TB (1). In 2015, there were an estimated 10.4 million new (incident) TB cases worldwide, of which 5.9 million (56%) were among men, 3.5 million (34%) were among women, and 1.0 million (10%) were among children. People living with HIV accounted for 1.2 million (11%) of
BackgroundIn the Commonwealth of Independent States (CIS) countries the epidemiology of chronic obstructive pulmonary disease (COPD) is poorly characterized. The objective of this analysis is to present the prevalence, burden and risk factors associated with COPD in three CIS countries as part of the CORE study (Chronic Obstructive Respiratory Diseases), the rationale and design of which have been described elsewhere.MethodsA total of 2842 adults (≥18 years) were recruited (964 in Ukraine, Kiev, 945 in Kazakhstan, Almaty and 933 in Azerbaijan, Baku) between 2013 and 2015 during household visits. Two-step cluster randomization was used for the sampling strategy. All respondents were interviewed about respiratory symptoms, smoking status and medical history, and underwent spirometry with bronchodilator. COPD was defined as (i) “previously diagnosed” when the respondent reported that he/she had previously been diagnosed with COPD by a doctor, (ii) “diagnosed by spirometry” using the GOLD criteria (2011) based on spirometry conducted during the study (FEV1/FVC < 0.70), and (iii) “firstly diagnosed by spirometry”, when the patient had received the COPD diagnosis for the first time based on the spirometry results obtained in this study.ResultsThe prevalence of “previously diagnosed” COPD was 10.4, 13.8 and 4.3 per 1000, and the prevalence of COPD “diagnosed by spirometry” was 31.9, 66.7 and 37.5 per 1000 in Ukraine, Kazakhstan, and Azerbaijan, respectively. Almost all respondents with COPD were diagnosed for the first time during this study. A statistically significant relationship was shown between smoking and COPD in Kazakhstan (odds ratio, OR: 3.75) and Azerbaijan (OR: 2.80); BMI in Ukraine (OR: 2.10); tuberculosis in Ukraine (OR: 32.3); and dusty work in Kazakhstan (OR: 2.30). Co-morbidities like cardiovascular diseases and a history of pneumonia occurred significantly (p < 0.05) more frequently in the COPD population compared to the non-COPD population across all participating countries. For hypertension, this was the case in Ukraine and Azerbaijan.ConclusionIn CIS countries (Ukraine, Kazakhstan and Azerbaijan), the prevalence of COPD “diagnosed by spirometry” was significantly higher than the prevalence of previously diagnosed COPD. Compared to many other countries, the prevalence of COPD seems to be relatively low in CIS countries. Factors such as limited funding from the government; lack of COPD knowledge and the attitude within the population, and of primary care physicians; as well as low access to high-quality spirometry may play a role in this under-diagnosis of COPD. The information provided in this paper will be helpful for healthcare policy makers in CIS countries to instruct COPD management and prevention strategies and to allocate healthcare resources accordingly.
BackgroundMain treatable Chronic Respiratory Diseases (CRDs) like Chronic Obstructive Pulmonary Disease (COPD), Bronchial Asthma (BA) and Allergic Rhinitis (AR) are underdiagnosed and undertreated worldwide. CORE study was aimed to assess the point prevalence of COPD, BA and AR in the adult population of major cities of Commonwealth of Independent States (CIS) countries – Azerbaijan, Kazakhstan, and Ukraine based on study questionnaires and/or spirometry, and to document risk factors, characterize the COPD, BA and AR population to provide a clearer “epidemiological data”.MethodsA descriptive, cross-sectional, population-based epidemiological study conducted from 2013 to 2015 with two-stage cluster geographical randomization. Interviewers conducted face-to-face visits at respondent’s household after informed consent and eligibility assessment including interviews, anthropometry, spirometry (with bronchodilator test) and completion of disease-specific questionnaires.ResultsTwo thousand eight hundred forty-two respondents (Ukraine: 964 from Ukraine; 945 from Kazakhstan; 933 Azerbaijan) were enrolled. Mean age was 40–42 years and males were 37%–42% across three countries. In Kazakhstan 62.8% were Asians, but in Ukraine and in Azerbaijan 99.7% and 100.0%, respectively, were Caucasians. Manual labourers constituted 40.5% in Ukraine, 22.8% in Kazakhstan and 22.0% in Azerbaijan, while office workers were 16.1%, 31.6% and 36.8% respectively. 51.3% respondents in Ukraine, 64.9% in Kazakhstan and 69.7% in Azerbaijan were married.ConclusionCORE study collected information that can be supportive for health policy decision makers in allocating healthcare resources in order to improve diagnosis and management of CRDs. The detailed findings will be described in future publications.Trial registrationStudy Protocol Summary is disclosed at GlaxoSmithKline Clinical Study Register on Jun 06, 2013, study ID 116757.Electronic supplementary materialThe online version of this article (10.1186/s12890-017-0471-x) contains supplementary material, which is available to authorized users.
Motivation Short-read whole genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences, and sequencing bias reduce the performance of variant calling using short-read alignment, but the loss in recall and specificity has not been adequately characterized. To benchmark short-read variant calling, we used 36 diverse clinical Mycobacterium tuberculosis (Mtb) isolates dually sequenced with Illumina short-reads and PacBio long-reads. We systematically studied the short-read variant calling accuracy and the influence of sequence uniqueness, reference bias, and GC content. Results Reference based Illumina variant calling demonstrated a maximum recall of 89.0% and minimum precision of 98.5% across parameters evaluated. The approach that maximized variant recall while still maintaining high precision (<99%) was tuning the mapping quality (MQ) filtering threshold, i.e. confidence of the read mapping (recall = 85.8%, precision = 99.1%, MQ ≥ 40). Additional masking of repetitive sequence content is an alternative conservative approach to variant calling that increases precision at cost to recall (recall = 70.2%, precision = 99.6%, MQ ≥ 40). Of the genomic positions typically excluded for Mtb, 68% are accurately called using Illumina WGS including 52/168 PE/PPE genes (34.5%). From these results we present a refined list of low confidence regions across the Mtb genome, which we found to frequently overlap with regions with structural variation, low sequence uniqueness, and low sequencing coverage. Our benchmarking results have broad implications for the use of WGS in the study of Mtb biology, inference of transmission in public health surveillance systems, and more generally for WGS applications in other organisms. Availability All relevant code is available at https://github.com/farhat-lab/mtb-illumina-wgs-evaluation Supplementary information Supplementary data are available at Bioinformatics online.
Background: Short-read whole genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences, and sequencing bias, reduce the performance of variant calling using short-read alignment, but the loss in recall and specificity has not been adequately characterized. For the clonal pathogen Mycobacterium tuberculosis (Mtb), researchers frequently exclude 10.7% of the genome believed to be repetitive and prone to erroneous variant calls. To benchmark short-read variant calling, we used 36 diverse clinical Mtb isolates dually sequenced with Illumina short-reads and PacBio long-reads. We systematically study the short-read variant calling accuracy and the influence of sequence uniqueness, reference bias, and GC content. Results: Reference based Illumina variant calling had a recall ≥89.0% and precision ≥98.5% across parameters evaluated. The best balance between precision and recall was achieved by tuning the mapping quality (MQ) threshold, i.e. confidence of the read mapping (recall 85.8%, precision 99.1% at MQ ≥ 40). Masking repetitive sequence content is an alternative conservative approach to variant calling that maintains high precision (recall 70.2%, precision 99.6% at MQ≥40). Of the genomic positions typically excluded for Mtb, 68% are accurately called using Illumina WGS including 52 of the 168 PE/PPE genes (34.5%). We present a refined list of low confidence regions and examine the largest sources of variant calling error. Conclusions: Our improved approach to variant calling has broad implications for the use of WGS in the study of Mtb biology, inference of transmission in public health surveillance systems, and more generally for WGS applications in other organisms.
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