scholarly journals Rapid Diagnosis of Spinocerebellar Ataxia 36 in a Three‐Generation Family Using Short‐Read Whole‐Genome Sequencing Data

2020 ◽  
Vol 35 (9) ◽  
pp. 1675-1679
Author(s):  
Haloom Rafehi ◽  
David J. Szmulewicz ◽  
Kate Pope ◽  
Mathew Wallis ◽  
John Christodoulou ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Spinocerebellar Ataxia ◽  
Genome Sequencing ◽  
Rapid Diagnosis ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Short Read ◽  
Generation Family

scholarly journals Short-Read Whole-Genome Sequencing for Laboratory-Based Surveillance of Bordetella pertussis

2017 ◽  
Vol 55 (5) ◽  
pp. 1446-1453 ◽  
Author(s):  
Alex Marchand-Austin ◽  
Raymond S. W. Tsang ◽  
Jennifer L. Guthrie ◽  
Jennifer H. Ma ◽  
Gillian H. Lim ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bordetella Pertussis ◽  
Vaccine Effectiveness ◽  
Vaccine Antigen ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Short Read ◽  
Content Type

ABSTRACTBordetella pertussisis a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance ofB. pertussisacellular vaccine (aP) antigens is critical for understanding the interaction between evolutionary pressures, disease pathogenesis, and vaccine effectiveness. Methods currently used to characterize aP components are relatively labor-intensive and low throughput. To address this challenge, we sought to derive aP antigen genotypes from minimally processed short-read whole-genome sequencing data generated from 40 clinicalB. pertussisisolates and analyzed using the SRST2 bioinformatic package. SRST2 was able to identify aP antigen genotypes for all antigens with the exception of pertactin, possibly due to low read coverage in GC-rich low-complexity regions of variation. Two main genotypes were observed in addition to a singular third genotype that contained an 84-bp deletion that was identified by SRST2 despite the issues in allele calling. This method has the potential to generate large pools ofB. pertussismolecular data that can be linked to clinical and epidemiological information to facilitate research of vaccine effectiveness and disease severity in the context of emerging vaccine antigen-deficient strains.

scholarly journals Determining Streptococcus suis serotype from short-read whole-genome sequencing data

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Taryn B. T. Athey ◽  
Sarah Teatero ◽  
Sonia Lacouture ◽  
Daisuke Takamatsu ◽  
Marcelo Gottschalk ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Streptococcus Suis ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Short Read ◽  
Suis Serotype

scholarly journals Rapid diagnosis of SCA36 in a three-generation family using short-read whole genome sequencing data

2019 ◽  
Author(s):  
Haloom Rafehi ◽  
David J. Szmulewicz ◽  
Kate Pope ◽  
Mathew Wallis ◽  
John Christodoulou ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Cost Effective ◽  
Repeat Expansion ◽  
Rapid Diagnosis ◽  
Whole Genome Sequencing Data ◽  
Molecular Testing ◽  
Whole Genome ◽  
Sequencing Data

AbstractBackgroundSpinocerebellar ataxias (SCA) are often caused by expansions of short tandem repeats (STRs). Recent methodological advances have made repeat expansion (RE) detection with whole genome sequencing (WGS) feasible.ObjectivesTo determine the genetic basis of ataxia in a multigenerational Australian pedigree, with autosomal dominant inheritance.Methods and ResultsWGS was performed on three affected relatives. The sequence data was screened for known pathogenic REs using two repeat expansion detection tools: exSTRa and ExpansionHunter. This screen provided a clear and rapid diagnosis (<five days from receiving the sequencing data) of SCA36, a rare form of ataxia caused by an intronic GGCCTG RE in NOP56.Conclusionsthe that diagnosis of rare ataxias caused by REs is highly feasible and cost effective with WGS. We propose that WGS be implemented as the frontline, cost effective methodology for molecular testing of individuals with a clinical diagnosis of ataxia.

scholarly journals Deriving Group A Streptococcus Typing Information from Short-Read Whole-Genome Sequencing Data

2014 ◽  
Vol 52 (6) ◽  
pp. 1871-1876 ◽  
Author(s):  
T. B. T. Athey ◽  
S. Teatero ◽  
A. Li ◽  
A. Marchand-Austin ◽  
B. W. Beall ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Group A Streptococcus ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Short Read ◽  
Group A

scholarly journals Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽  
2021 ◽  
Author(s):  
Axel Jensen ◽  
Mette Lillie ◽  
Kristofer Bergström ◽  
Per Larsson ◽  
Jacob Höglund
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Peripheral Populations ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

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