scholarly journals Data on genome sequencing, assembly, annotation and genomic analysis of Rhodococcus rhodochrous strain SPC17 isolated from Lonar Lake

Data in Brief ◽  
2020 ◽  
Vol 29 ◽  
pp. 105336
Author(s):  
Satish Kumar ◽  
Dhiraj Paul ◽  
Yogesh Shouche ◽  
Mangesh Suryavanshi
Keyword(s):  
Genome Sequencing ◽  
Genomic Analysis ◽  
Rhodococcus Rhodochrous ◽  
Lonar Lake

scholarly journals Genomic analysis of an outbreak of bovine tuberculosis in a man-made multi-host species system: a call for action on wildlife in Brazil

2021 ◽  
Author(s):  
Daiane A. R. Lima ◽  
Cristina K. Zimpel ◽  
José Salvatore Patané ◽  
Taiana T. Silva-Pereira ◽  
Rodrigo N. Etges ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Genome Sequencing ◽  
Mycobacterium Bovis ◽  
Bovine Tuberculosis ◽  
Genomic Analysis ◽  
Whole Genome ◽  
System A ◽  
Recent Transmission ◽  
And Control ◽  
Tuberculin Tests

We report on a 15-year-long outbreak of bovine tuberculosis (bTB) in wildlife from a Brazilian safari park. A timeline of diagnostic events and whole-genome sequencing (WGS) of 21 Mycobacterium bovis isolates from deer and llamas were analyzed. Accordingly, from 2003 to 2018, at least 16 animals, from 8 species, died due to TB, which is likely an underestimated number. In three occasions since 2013, the deer presented positive tuberculin tests, leading to the park closure and culling of all deer. WGS indicated that multiple M. bovis strains were circulating, with at least three founding introductions since the park inauguration in 1977. Recent transmission events between nearby farms and the park were not found based on WGS. Lastly, by discussing socio-economic and environmental factors escaping current regulatory gaps that were determinant of this outbreak, we pledge for the development of a plan to report and control bTB in wildlife in Brazil.

scholarly journals Genome sequencing, annotation and comparative genomic analysis of Shigella dysenteriae strain SD1D

Gut Pathogens ◽  
2014 ◽  
Vol 6 (1) ◽  
Author(s):  
Gurwinder Kaur ◽  
Sathyaseelan Sathyabama ◽  
Amit Arora ◽  
Sheenam Verma ◽  
Nida Mubin ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Shigella Dysenteriae ◽  
Comparative Genomic

scholarly journals Identification of Pathogenic Structural Variants in Rare Disease Patients through Genome Sequencing

2019 ◽  
Author(s):  
James M. Holt ◽  
Camille L. Birch ◽  
Donna M. Brown ◽  
Manavalan Gajapathy ◽  
Nadiya Sosonkina ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Rare Disease ◽  
Genome Sequencing ◽  
Genomic Analysis ◽  
Whole Genome ◽  
Structural Variants ◽  
Single Nucleotide Variants ◽  
Standard Clinical Practice ◽  
Wide Range ◽  
Genetic Features

AbstractPurposeClinical whole genome sequencing is becoming more common for determining the molecular diagnosis of rare disease. However, standard clinical practice often focuses on small variants such as single nucleotide variants and small insertions/deletions. This leaves a wide range of larger “structural variants” that are not commonly analyzed in patients.MethodsWe developed a pipeline for processing structural variants for patients who received whole genome sequencing through the Undiagnosed Diseases Network (UDN). This pipeline called structural variants, stored them in an internal database, and filtered the variants based on internal frequencies and external annotations. The remaining variants were manually inspected and then interesting findings were reported as research variants to clinical sites in the UDN.ResultsOf 477 analyzed UDN cases, 286 cases (≈ 60%) received at least one structural variant as a research finding. The variants in 16 cases (≈ 4%) are considered “Certain” or “Highly likely” molecularly diagnosed and another 4 cases are currently in review. Of those 20 cases, at least 13 were identified originally through our pipeline with one finding leading to identification of a new disease. As part of this paper, we have also released the collection of variant calls identified in our cohort along with heterozygous and homozygous call counts. This data is available at https://github.com/HudsonAlpha/UDN_SV_export.ConclusionStructural variants are key genetic features that should be analyzed during routine clinical genomic analysis. For our UDN patients, structural variants helped solve ≈ 4% of the total number of cases (≈ 13% of all genome sequencing solves), a success rate we expect to improve with better tools and greater understanding of the human genome.

scholarly journals Diagnosis of Genetic White Matter Disorders by Singleton Whole-Exome and Genome Sequencing Using Interactome-Driven Prioritization

Neurology ◽  
2022 ◽  
pp. 10.1212/WNL.0000000000013278
Author(s):  
Agatha Schlüter ◽  
Agustí Rodríguez-Palmero ◽  
Edgard Verdura ◽  
Valentina Vélez-Santamaría ◽  
Montserrat Ruiz ◽  
...  
Keyword(s):  
White Matter ◽  
Candidate Genes ◽  
Genome Sequencing ◽  
Molecular Diagnosis ◽  
Diagnostic Yield ◽  
Collaborative Study ◽  
Case Series ◽  
Genomic Analysis ◽  
White Matter Disorders ◽  
Whole Exome

Background and Objectives:Genetic white matter disorders (GWMD) are of heterogeneous origin, with more than a hundred causal genes identified to date. Classical targeted approaches achieve a molecular diagnosis in only half of all patients. Here we aim to determine the clinical utility of singleton whole-exome sequencing and whole-genome sequencing (sWES-WGS) interpreted with a phenotype- and interactome-driven prioritization algorithm to diagnose GWMD patients, while identifying novel phenotypes and candidate genes.Methods:A case series of patients of all ages with undiagnosed GWMD despite extensive standard-of-care paraclinical studies were recruited between April 2017 and December 2019 in a collaborative study at the Bellvitge Biomedical Research Institute (IDIBELL) and neurology units of tertiary Spanish hospitals. We ran sWES and WGS and applied our interactome-prioritization algorithm, based on the network expansion of a seed group of GWMD-related genes, derived from the HPO terms of each patient.Results:We received 126 patients (101 children and 25 adults), with ages ranging from 1 month to 74 years. We obtained a first molecular diagnosis by singleton WES in 59% of cases, which increased to 68% after annual reanalysis and reached 72% after WGS was performed in 16 of the remaining negative cases. We identified variants in 57 different genes among 91 diagnosed cases, with the most frequent being RNASEH2B, EIF2B5, POLR3A and PLP1; and a dual diagnosis underlying complex phenotypes in six families, underscoring the importance of genomic analysis to solve these cases. Finally, we discovered 9 candidate genes causing novel diseases, and propose additional putative novel candidate genes for yet-to-be discovered GWMD.Discussion:Our strategy enables a high diagnostic yield and is a good alternative to trio WES/WGS for GWMD. It shortens the time to diagnosis compared to the classical targeted approach, thus optimizing appropriate management. Furthermore, the interactome-driven prioritization pipeline enables the discovery of novel disease-causing genes and phenotypes, and predicts novel putative candidate genes, shedding light on etiopathogenic mechanisms that are pivotal for myelin generation and maintenance.

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