GATK Nuclear variant discovery and consensus assembly v1

2020 ◽  
Author(s):  
Graham Etherington
Keyword(s):  
Great Britain ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Legal Protection ◽  
Population Level ◽  
Population Increase ◽  
Whole Genome ◽  
Mustela Putorius ◽  
Variant Discovery ◽  
Mammalian Predator

The European polecat (Mustela putorius) is a mammalian predator which breeds across much of Europe east to central Asia. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as ‘pure’ polecats.

Introgression v1

2021 ◽  
Author(s):  
Graham Etherington
Keyword(s):  
Great Britain ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Legal Protection ◽  
Population Level ◽  
Population Increase ◽  
Whole Genome ◽  
Mustela Putorius ◽  
Mammalian Predator

The European polecat (Mustela putorius) is a mammalian predator which breeds across much of Europe east to central Asia. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as ‘pure’ polecats.

scholarly journals Extensive genome introgression between domestic ferret and European polecat during population recovery in Great Britain.

2021 ◽  
Author(s):  
Graham John Etherington ◽  
Adam Ciezarek ◽  
Rebecca Shaw ◽  
Johan Michaux ◽  
Elizabeth Croose ◽  
...  
Keyword(s):  
Great Britain ◽  
Cognitive Function ◽  
Legal Protection ◽  
Population Level ◽  
Population Increase ◽  
Whole Genome ◽  
Population Recovery ◽  
Ural Mountains ◽  
Mustela Putorius ◽  
Mammalian Predator

The European polecat (Mustela putorius) is a mammalian predator which occurs across much of Europe east to the Ural Mountains. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as pure polecats. We quantify this introgression and find introgressed genes under selection that may assist in cognitive function and sight.

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.

Whole-genome sequencing and variant discovery in C. elegans

2008 ◽  
Vol 5 (2) ◽  
pp. 183-188 ◽  
Author(s):  
LaDeana W Hillier ◽  
Gabor T Marth ◽  
Aaron R Quinlan ◽  
David Dooling ◽  
Ginger Fewell ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
C Elegans ◽  
Variant Discovery

scholarly journals Multiplex SARS-CoV-2 Genotyping PCR for Population-Level Variant Screening and Epidemiologic Surveillance

2021 ◽  
Author(s):  
Hannah Wang ◽  
Jacob A. Miller ◽  
Michelle Verghese ◽  
Mamdouh Sibai ◽  
Daniel Solis ◽  
...  
Keyword(s):  
Public Health ◽  
Nucleic Acid ◽  
Whole Genome Sequencing ◽  
San Francisco ◽  
Genome Sequencing ◽  
High Throughput ◽  
Population Level ◽  
Nucleic Acid Amplification ◽  
Whole Genome ◽  
Epidemiologic Surveillance

ABSTRACTBackgroundEmergence of SARS-CoV-2 variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for pandemic response, but many laboratories do not have the resources to support population-level sequencing. We hypothesized that a spike genotyping nucleic acid amplification test (NAAT) could facilitate high-throughput variant surveillance.MethodsWe designed and analytically validated a one-step multiplex allele-specific reverse transcriptase polymerase chain reaction (RT-qPCR) to detect three non-synonymous spike protein mutations (L452R, E484K, N501Y). Assay specificity was validated with next-generation whole-genome sequencing. We then screened a large cohort of SARS-CoV-2 positive specimens from our San Francisco Bay Area population.ResultsBetween December 1, 2020 and March 1, 2021, we screened 4,049 unique infections by genotyping RT-qPCR, with an assay failure rate of 2.8%. We detected 1,567 L452R mutations (38.7%), 34 N501Y mutations (0.84%), 22 E484K mutations (0.54%), and 3 (0.07%) E484K+N501Y mutations. The assay had near-perfect (98-100%) concordance with whole-genome sequencing in a validation subset of 229 specimens, and detected B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, and P.2 variants, among others. The assay revealed rapid emergence of L452R in our population, with a prevalence of 24.8% in December 2020 that increased to 62.5% in March 2021.ConclusionsWe developed and clinically implemented a genotyping RT-qPCR to conduct high-throughput SARS-CoV-2 variant screening. This approach can be adapted for emerging mutations and immediately implemented in laboratories already performing NAAT worldwide using existing equipment, personnel, and extracted nucleic acid.Summary / Key PointsEmergence of SARS-CoV-2 variants with concerning phenotypes is of public health interest. We developed a multiplex genotyping RT-qPCR to rapidly detect L452R, E484K, and N501Y with high sequencing concordance. This high-throughput alternative to resource-intensive sequencing enabled surveillance of L452R emergence.

scholarly journals Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Masao Nagasaki ◽  
◽  
Jun Yasuda ◽  
Fumiki Katsuoka ◽  
Naoki Nariai ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rare Variant ◽  
Whole Genome ◽  
Variant Discovery

scholarly journals Variant discovery and breakpoint region prediction for studying the human 22q11.2 deletion using BAC clone and whole genome sequencing analysis

2016 ◽  
Vol 25 (17) ◽  
pp. 3754-3767 ◽  
Author(s):  
Xingyi Guo ◽  
Maria Delio ◽  
Nousin Haque ◽  
Raquel Castellanos ◽  
Matthew S. Hestand ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Breakpoint Region ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
22Q11.2 Deletion ◽  
Bac Clone ◽  
Variant Discovery
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