scholarly journals Haplocheck: Phylogeny-based Contamination Detection in Mitochondrial and Whole-Genome Sequencing Studies

2020 ◽  
Author(s):  
Hansi Weissensteiner ◽  
Lukas Forer ◽  
Liane Fendt ◽  
Azin Kheirkhah ◽  
Antonio Salas ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Nuclear Dna ◽  
Nuclear Genome ◽  
Whole Genome ◽  
Sequencing Studies ◽  
Project Data ◽  
The Impact

AbstractWithin-species contamination is a major issue in sequencing studies, especially for mitochondrial studies. Contamination can be detected by analysing the nuclear genome or by inspecting the heteroplasmic sites in the mitochondrial genome. Existing methods using the nuclear genome are computationally expensive, and no suitable tool for detecting contamination in large-scale mitochondrial datasets is available. Here we present haplocheck, a tool that requires only the mitochondrial genome to detect contamination in both mitochondrial and whole-genome sequencing studies. Haplocheck is able to distinguish between contaminated and real heteroplasmic sites using the mitochondrial phylogeny. By applying haplocheck to the 1000 Genomes Project data, we show (1) high concordance in contamination estimates between mitochondrial and nuclear DNA and (2) quantify the impact of mitochondrial copy numbers on the mitochondrial based contamination results. Haplocheck complements leading nuclear DNA based contamination tools, and can therefore be used as a proxy tool in nuclear genome studies.Haplocheck is available both as a command-line tool at https://github.com/genepi/haplocheck and as a cloud web-service producing interactive reports that facilitates the navigation through the phylogeny of contaminated samples.

scholarly journals Efficient Variant Set Mixed Model Association Tests for Continuous and Binary Traits in Large-Scale Whole-Genome Sequencing Studies

2019 ◽  
Vol 104 (2) ◽  
pp. 260-274 ◽  
Author(s):  
Han Chen ◽  
Jennifer E. Huffman ◽  
Jennifer A. Brody ◽  
Chaolong Wang ◽  
Seunggeun Lee ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Mixed Model ◽  
Whole Genome ◽  
Association Tests ◽  
Binary Traits ◽  
Sequencing Studies

scholarly journals Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Kristopher A. Standish ◽  
Tristan M. Carland ◽  
Glenn K. Lockwood ◽  
Wayne Pfeiffer ◽  
Mahidhar Tatineni ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Variant Calling ◽  
Whole Genome ◽  
Next Generation ◽  
Sequencing Studies

scholarly journals A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies

2021 ◽  
Author(s):  
Zilin Li ◽  
Xihao Li ◽  
Hufeng Zhou ◽  
Sheila M Gaynor ◽  
Margaret Sunitha Selvaraj ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Association Analysis ◽  
Genome Sequencing ◽  
Large Scale ◽  
Rare Variants ◽  
Whole Genome ◽  
Computationally Efficient ◽  
Annotation Information ◽  
Sequencing Studies ◽  
Complex Human Traits

Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare variants' (RVs) associations with complex human traits. Variant set analysis is a powerful approach to study RV association, and a key component of it is constructing RV sets for analysis. However, existing methods have limited ability to define analysis units in the noncoding genome. Furthermore, there is a lack of robust pipelines for comprehensive and scalable noncoding RV association analysis. Here we propose a computationally-efficient noncoding RV association-detection framework that uses STAAR (variant-set test for association using annotation information) to group noncoding variants in gene-centric analysis based on functional categories. We also propose SCANG (scan the genome)-STAAR, which uses dynamic window sizes and incorporates multiple functional annotations, in a non-gene-centric analysis. We furthermore develop STAARpipeline to perform flexible noncoding RV association analysis, including gene-centric analysis as well as fixed-window-based and dynamic-window-based non-gene-centric analysis. We apply STAARpipeline to identify noncoding RV sets associated with four quantitative lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several noncoding RV associations in an additional 9,123 TOPMed samples.

0306 Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 146-146
Author(s):  
D. M. Bickhart ◽  
L. Xu ◽  
J. L. Hutchison ◽  
J. B. Cole ◽  
D. J. Null ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Copy Number ◽  
Large Scale ◽  
Copy Number Variants ◽  
Whole Genome

scholarly journals Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Peter Higgins ◽  
Cooper A Grace ◽  
Soon A Lee ◽  
Matthew R Goddard
Keyword(s):  
Saccharomyces Cerevisiae ◽  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Copy Number ◽  
Small Scale ◽  
Whole Genome ◽  
Copy Number Changes ◽  
The Impact

Abstract Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

scholarly journals Piglet Gut and in-Barn Manure from Farms on a Raised without Antibiotics Program Display Reduced Antimicrobial Resistance but an Increased Prevalence of Pathogens

Antibiotics ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1152
Author(s):  
Samuel M. Chekabab ◽  
John R. Lawrence ◽  
Alvin C. Alvarado ◽  
Bernardo Z. Predicala ◽  
Darren R. Korber
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Fecal Samples ◽  
Time Points ◽  
Conventional Farms ◽  
Production Practices ◽  
On Farm ◽  
The Impact

In response to new stringent regulations in Canada regarding the use of antibiotics in animal production, many farms have implemented practices to produce animals that are raised without antibiotics (RWA) from birth to slaughter. This study aims to assess the impact of RWA production practices on reducing the actual total on-farm use of antibiotics, the occurrence of pathogens, and the prevalence of antimicrobial resistance (AMR). A 28-month longitudinal surveillance of farms that adopted the RWA program and conventional farms using antibiotics in accordance with the new regulations (non-RWA) was conducted by collecting fecal samples from 6-week-old pigs and composite manure from the barn over six time points and applying whole-genome sequencing (WGS) to assess the prevalence of AMR genes as well as the abundance of pathogens. Analysis of in-barn drug use records confirmed the decreased consumption of antibiotics in RWA barns compared to non-RWA barns. WGS analyses revealed that RWA barns had reduced the frequency of AMR genes in piglet feces and in-barn manure. However, metagenomic analyses showed that RWA barns had a significant increase in the frequency of pathogenic Firmicutes in fecal samples and pathogenic Proteobacteria in barn manure samples.

scholarly journals Improving tuberculosis surveillance by detecting international transmission using publicly available whole-genome sequencing data

2019 ◽  
Author(s):  
Andrea Sanchini ◽  
Christine Jandrasits ◽  
Julius Tembrockhaus ◽  
Thomas Andreas Kohl ◽  
Christian Utpatel ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Added Value ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
International Transmission ◽  
The Public ◽  
Public Dataset ◽  
Public Repositories

AbstractIntroductionImproving the surveillance of tuberculosis (TB) is especially important for multidrug-resistant (MDR) and extensively drug-resistant (XDR)-TB. The large amount of publicly available whole-genome sequencing (WGS) data for TB gives us the chance to re-use data and to perform additional analysis at a large scale.AimWe assessed the usefulness of raw WGS data of global MDR/XDR-TB isolates available from public repositories to improve TB surveillance.MethodsWe extracted raw WGS data and the related metadata of Mycobacterium tuberculosis isolates available from the Sequence Read Archive. We compared this public dataset with WGS data and metadata of 131 MDR- and XDR-TB isolates from Germany in 2012-2013.ResultsWe aggregated a dataset that includes 1,081 MDR and 250 XDR isolates among which we identified 133 molecular clusters. In 16 clusters, the isolates were from at least two different countries. For example, cluster2 included 56 MDR/XDR isolates from Moldova, Georgia, and Germany. By comparing the WGS data from Germany and the public dataset, we found that 11 clusters contained at least one isolate from Germany and at least one isolate from another country. We could, therefore, connect TB cases despite missing epidemiological information.ConclusionWe demonstrated the added value of using WGS raw data from public repositories to contribute to TB surveillance. By comparing the German and the public dataset, we identified potential international transmission events. Thus, using this approach might support the interpretation of national surveillance results in an international context.

scholarly journals Evaluation of whole genome sequencing for the identification and typing of Vibrio cholerae

2018 ◽  
Author(s):  
David R. Greig ◽  
Ulf Schafer ◽  
Sophie Octavia ◽  
Ebony Hunter ◽  
Marie A. Chattaway ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Vibrio Cholerae ◽  
Species Identification ◽  
Genome Sequencing ◽  
National Level ◽  
Whole Genome ◽  
Surveillance Programs ◽  
El Tor ◽  
The Impact

AbstractEpidemiological and microbiological data on Vibrio cholerae isolated between 2004 and 2017 (n=836) and held in the Public Health England culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome derived species identification and serotype for a sub-set of isolates (n=152). Of the 836 isolates, 750 (89.7%) were from faecal specimens, 206 (24.6%) belonged to serogroup O1 and seven (0.8%) were serogroup O139, and 792 (94.7%) isolates from patients reporting recent travel abroad, most commonly to India (n=209) and Pakistan (n=104). Of the 152 isolates of V. cholerae speciated by kmer identification, 149 (98.1%) were concordant with the traditional biochemical approach. Traditional serotyping results were 100% concordant with the whole genome sequencing (WGS) analysis for identification of serogroups O1 and O139 and Classical and El Tor biotypes. ctxA was detected in all isolates of V. cholerae O1 El Tor and O139 belonging to sequence type (ST) 69, and in V. cholerae O1 Classical variants belonging to ST73. A phylogeny of isolates belonging to ST69 from UK travellers clustered geographically, with isolates from India and Pakistan located on separate branches. Moving forward, WGS data from UK travellers will contribute to global surveillance programs, and the monitoring of emerging threats to public health and the global dissemination of pathogenic lineages. At the national level, these WGS data will inform the timely reinforcement of direct public health messaging to travellers and mitigate the impact of imported infections and the associated risks to public health.

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