Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator

2011 ◽  
Vol 18 (9) ◽  
pp. 1131-1139 ◽  
Author(s):  
Y. Lin ◽  
V. Rajan ◽  
B.M.E. Moret
Keyword(s):  
High Resolution ◽  
Phylogenetic Reconstruction ◽  
Whole Genome ◽  
Genome Data

scholarly journals High Resolution Ancestry Deconvolution for Next Generation Genomic Data

2021 ◽  
Author(s):  
Helgi Hilmarsson ◽  
Arvind S. Kumar ◽  
Richa Rastogi ◽  
Carlos D. Bustamante ◽  
Daniel Mas Montserrat ◽  
...  
Keyword(s):  
High Resolution ◽  
Prediction Models ◽  
Association Studies ◽  
Training Data ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Next Generation ◽  
Genome Data ◽  
Computational Performance ◽  
Genetic Risk Prediction

ABSTRACTAs genome-wide association studies and genetic risk prediction models are extended to globally diverse and admixed cohorts, ancestry deconvolution has become an increasingly important tool. Also known as local ancestry inference (LAI), this technique identifies the ancestry of each region of an individual’s genome, thus permitting downstream analyses to account for genetic effects that vary between ancestries. Since existing LAI methods were developed before the rise of massive, whole genome biobanks, they are computationally burdened by these large next generation datasets. Current LAI algorithms also fail to harness the potential of whole genome sequences, falling well short of the accuracy that such high variant densities can enable. Here we introduce Gnomix, a set of algorithms that address each of these points, achieving higher accuracy and swifter computational performance than any existing LAI method, while also enabling portable models that are particularly useful when training data are not shareable due to privacy or other restrictions. We demonstrate Gnomix (and its swift phase correction counterpart Gnofix) on worldwide whole-genome data from both humans and canids and utilize its high resolution accuracy to identify the location of ancient New World haplotypes in the Xoloitzcuintle, dating back over 100 generations. Code is available at https://github.com/AI-sandbox/gnomix.

scholarly journals Whole-Genome SNP Analysis Identifies Putative Mycobacterium bovis Transmission Clusters in Livestock and Wildlife in Catalonia, Spain

2021 ◽  
Vol 9 (8) ◽  
pp. 1629
Author(s):  
Claudia Perea ◽  
Giovanna Ciaravino ◽  
Tod Stuber ◽  
Tyler C. Thacker ◽  
Suelee Robbe-Austerman ◽  
...  
Keyword(s):  
High Resolution ◽  
Mycobacterium Bovis ◽  
Phylogenetic Reconstruction ◽  
Snp Analysis ◽  
Whole Genome ◽  
Resistance Factors ◽  
Distance Analysis ◽  
Wildlife Reservoirs ◽  
Explanatory Factors ◽  
Low Prevalence

The high-resolution WGS analyses of MTBC strains have provided useful insight for determining sources of infection for animal tuberculosis. In Spain, tuberculosis in livestock is caused by Mycobacterium bovis and Mycobacterium caprae, where wildlife reservoirs play an important role. We analyzed a set of 125 M. bovis isolates obtained from livestock and wildlife from Catalonia to investigate strain diversity and identify possible sources and/or causes of infection. Whole-genome SNP profiles were used for phylogenetic reconstruction and pairwise SNP distance analysis. Additionally, SNPs were investigated to identify virulence and antimicrobial resistance factors to investigate clade-specific associations. Putative transmission clusters (≤12 SNPs) were identified, and associated epidemiological metadata were used to determine possible explanatory factors for transmission. M. bovis distribution was heterogeneous, with 7 major clades and 21 putative transmission clusters. In order of importance, the explanatory factors associated were proximity and neighborhood, residual infection, livestock-wildlife interaction, shared pasture, and movement. Genes related to lipid transport and metabolism showed the highest number of SNPs. All isolates were pyrazinamide resistant, and five were additionally resistant to isoniazid, but no clade-specific associations could be determined. Our findings highlight the importance of high-resolution molecular surveillance to monitor bovine tuberculosis dynamics in a low-prevalence setting.

Extracting a needle from a haystack: reanalysis of whole genome data reveals a readily translatable finding

2009 ◽  
Vol 39 (8) ◽  
pp. 1231-1235 ◽  
Author(s):  
R. Keers ◽  
A. E. Farmer ◽  
K. J. Aitchison
Keyword(s):  
Bipolar Disorder ◽  
Calcium Channel ◽  
Unmet Need ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding ◽  
Genome Data ◽  
Early Results ◽  
Genome Association ◽  
Genome Study

There is significant unmet need for more effective treatments for bipolar disorder. The drug discovery process is becoming prohibitively expensive. Hence, biomarker clues to assist or shortcut this process are now widely sought. Using the publicly available data from the whole genome association study conducted by the Wellcome Trust Case Control Consortium, we sought to identify groups of genetic markers (single nucleotide polymorphisms) in which each marker was independently associated with bipolar disorder, with a less stringent threshold than that set by the original investigators (p⩽1×10−4). We identified a group of markers occurring within the CACNA1C gene (encoding the alpha subunit of the calcium channel Cav1.2). We then ascertained that this locus had been previously associated with the disorder in both a smaller and a whole genome study, and that a number of drugs blocking this channel (including verapamil and diltiazem) had been trialled in the treatment of bipolar disorder. The dihydropyridine-based blockers such as nimodipine that bind specifically to Cav1.2 and are more penetrant to the central nervous system have shown some promising early results; however, further trials are indicated. In addition, migraine is commonly seen in affective disorder, and calcium channel antagonists are successfully used in the treatment of migraine. One such agent, flunarizine, is structurally related to other first-generation derivatives of antihistamines such as antipsychotics. This implies that flunarizine could be useful in the treatment of bipolar disorder, and, furthermore, that other currently licensed drugs should be investigated for antagonism of Cav1.2.

scholarly journals High Resolution Typing by Whole Genome Mapping Enables Discrimination of LA-MRSA (CC398) Strains and Identification of Transmission Events

PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e66493 ◽  
Author(s):  
Thijs Bosch ◽  
Erwin Verkade ◽  
Martijn van Luit ◽  
Bruno Pot ◽  
Paul Vauterin ◽  
...  
Keyword(s):  
High Resolution ◽  
Genome Mapping ◽  
Whole Genome ◽  
Whole Genome Mapping

scholarly journals Population Genomic- and Phylogenomic-Enabled Advances to Increase Insight Into Pathogen Biology and Epidemiology

2021 ◽  
Vol 111 (1) ◽  
pp. 8-11
Author(s):  
Remco Stam ◽  
Pierre Gladieux ◽  
Boris A. Vinatzer ◽  
Erica M. Goss ◽  
Neha Potnis ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Genomics ◽  
Cost Effective ◽  
Whole Genome ◽  
Genome Data ◽  
Sequencing Technologies ◽  
Population Genomic ◽  
High Throughput Dna Sequencing ◽  
Opening Up ◽  
Insight Into

Population genetics has been a key discipline in phytopathology for many years. The recent rise in cost-effective, high-throughput DNA sequencing technologies, allows sequencing of dozens, if not hundreds of specimens, turning population genetics into population genomics and opening up new, exciting opportunities as described in this Focus Issue . Without the limitations of genetic markers and the availability of whole or near whole-genome data, population genomics can give new insights into the biology, evolution and adaptation, and dissemination patterns of plant-associated microbes.

scholarly journals Quantifying the interplay between rapid bacterial evolution within the mouse intestine and transmission between hosts

2020 ◽  
Author(s):  
Kimberly S. Vasquez ◽  
Lisa Willis ◽  
Nate Cira ◽  
Katharine M. Ng ◽  
Miguel F. Pedro ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Population Genetics ◽  
High Resolution ◽  
Evolutionary Dynamics ◽  
Day Treatment ◽  
Whole Genome ◽  
Germ Free ◽  
Selection Dynamics ◽  
Mouse Intestine ◽  
Ciprofloxacin Resistance

SummaryDue to limitations on high-resolution strain tracking, selection dynamics during gut-microbiota colonization and transmission between hosts remain mostly mysterious. Here, we introduced hundreds of barcoded Escherichia coli strains into germ-free mice and quantified strain-level dynamics and metagenomic changes. Mutants involved in motility and utilization of abundant metabolites were reproducibly selected within days. Even with rapid selection, coprophagy enforced similar barcode distributions across co-housed mice. Whole-genome sequencing of hundreds of isolates quantified evolutionary dynamics and revealed linked alleles. A population-genetics model predicted substantial fitness advantages for certain mutants and that migration accounted for ~10% of the resident microbiota each day. Treatment with ciprofloxacin demonstrated the interplay between selection and transmission. While initial colonization was mostly uniform, in two mice a bottleneck reduced diversity and selected for ciprofloxacin resistance in the absence of drug. These findings highlight the interplay between environmental transmission and rapid, deterministic selection during evolution of the intestinal microbiota.

Sign in / Sign up

Export Citation Format

Share Document