scholarly journals Mapping challenging mutations by whole-genome sequencing

2016 ◽  
Author(s):  
Harold E. Smith ◽  
Amy S. Fabritius ◽  
Aimee Jaramillo-Lambert ◽  
Andy Golden
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Single Gene ◽  
Global Scale ◽  
Model Organisms ◽  
Whole Genome ◽  
Genetic Screens ◽  
Alternative Approach ◽  
Mutation Identification

ABSTRACTWhole-genome sequencing provides a rapid and powerful method for identifying mutations on a global scale, and has spurred a renewed enthusiasm for classical genetic screens in model organisms. The most commonly characterized category of mutation consists of monogenic, recessive traits, due to their genetic tractability. Therefore, most of the mapping methods for mutation identification by whole-genome sequencing are directed toward alleles that fulfill those criteria (i.e., single-gene, homozygous variants). However, such approaches are not entirely suitable for the characterization of a variety of more challenging mutations, such as dominant and semi-dominant alleles or multigenic traits. Therefore, we have developed strategies for the identification of those classes of mutations, using polymorphism mapping in Caenorhabditis elegans as our model for validation. We also report an alternative approach for mutation identification from traditional recombinant crosses, and a solution to the technical challenge of sequencing sterile or terminally arrested strains where population size is limiting. The methods described herein extend the applicability of whole-genome sequencing to a broader spectrum of mutations, including classes that are difficult to map by traditional means.

scholarly journals Micro-costing diagnostics in oncology: from single-gene testing to whole genome sequencing

2021 ◽  
Author(s):  
Clémence TB Pasmans ◽  
Bastiaan BJ Tops ◽  
Elisabeth MP Steeghs ◽  
Veerle MH Coupé ◽  
Katrien Grünberg ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Single Gene ◽  
Whole Genome ◽  
Gene Testing

scholarly journals SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Weili Cai ◽  
Schyler Nunziata ◽  
John Rascoe ◽  
Michael J. Stulberg
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Coverage ◽  
Metagenomic Sample ◽  
Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

Genetics of neuropsychiatric disease

2020 ◽  
pp. 127-140
Author(s):  
Stefania Bruno ◽  
Nayana Lahiri
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Disorders ◽  
Single Gene ◽  
Diagnostic Techniques ◽  
Genetic Influences ◽  
Whole Genome ◽  
Neuropsychiatric Disease ◽  
Genomic Technologies ◽  
Whole Exome

To better understand the intricacies of genetic influences on neuropsychiatric disease, it is important first to have a grounding in the models of human inheritance and current diagnostic techniques. This chapter covers the fundamentals of genetic disorders, giving insights into chromosomal, single-gene, and mitochondrial disorders. Moreover, it explores the changing applications of genomic technologies, such as whole exome and whole genome sequencing, through the lens of their implications for neuropsychiatry. Clinical examples are provided to give an idea of the genetic underpinnings of Alzheimer’s disease, Parkinson’s disease, and other familiar disorders.

First isolation and characterization of Brucella suis from yak

Genome ◽  
2020 ◽  
Vol 63 (8) ◽  
pp. 397-405
Author(s):  
Xiaowen Yang ◽  
Ning Wang ◽  
Xiaofang Cao ◽  
Pengfei Bie ◽  
Zhifeng Xing ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Health And Safety ◽  
Host Cells ◽  
Whole Genome ◽  
Genetic Characteristics ◽  
Qinghai Province ◽  
Isolation And Characterization ◽  
Smooth Strain

Brucella spp., facultative intracellular pathogens that can persistently colonize animal host cells and cause zoonosis, affect public health and safety. A Brucella strain was isolated from yak in Qinghai Province. To detect whether this isolate could cause an outbreak of brucellosis and to reveal its genetic characteristics, several typing and whole-genome sequencing methods were applied to identify its species and genetic characteristics. Phylogenetic analysis based on MLVA and whole-genome sequencing revealed the genetic characteristics of the isolated strain. The results showed that the isolated strain is a B. suis biovar 1 smooth strain, and this isolate was named B. suis QH05. The results of comparative genomics and MLVA showed that B. suis QH05 is not a vaccine strain. Comparison with other B. suis strains isolated from humans and animals indicated that B. suis QH05 may be linked to specific animal and human sources. In conclusion, B. suis QH05 does not belong to the Brucella epidemic species in China, and as the first isolation of B. suis from yak, this strain expands the host range of B. suis.

Characterization of Salmonella enterica Isolates from Selected U.S. Swine Feed Mills by Whole-Genome Sequencing

2020 ◽  
Vol 17 (2) ◽  
pp. 126-136 ◽  
Author(s):  
Valentina Trinetta ◽  
Gabriela Magossi ◽  
Marc W. Allard ◽  
Sandra M. Tallent ◽  
Eric W. Brown ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Whole Genome ◽  
Swine Feed

Whole genome sequencing and characterization of a virulent Newcastle disease virus isolated from an outbreak in Sweden

Virus Genes ◽  
2011 ◽  
Vol 43 (2) ◽  
pp. 261-271 ◽  
Author(s):  
Muhammad Munir ◽  
Anna-Malin Linde ◽  
Siamak Zohari ◽  
Karl Ståhl ◽  
Claudia Baule ◽  
...  
Keyword(s):  
Newcastle Disease Virus ◽  
Whole Genome Sequencing ◽  
Disease Virus ◽  
Genome Sequencing ◽  
Newcastle Disease ◽  
Whole Genome ◽  
Virulent Newcastle Disease Virus

scholarly journals Characterization of SXT/R391 Integrative and Conjugative Elements in Proteus mirabilis Isolates from Food-Producing Animals in China

2016 ◽  
Vol 60 (3) ◽  
pp. 1935-1938 ◽  
Author(s):  
Chang-Wei Lei ◽  
An-Yun Zhang ◽  
Hong-Ning Wang ◽  
Bi-Hui Liu ◽  
Li-Qin Yang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Proteus Mirabilis ◽  
Whole Genome ◽  
Content Type ◽  
Integrative And Conjugative Elements ◽  
Animal Farms

SXT/R391 integrative and conjugative elements (ICEs) were detected in 8 out of 125Proteus mirabilisisolates from food-producing animals in China. Whole-genome sequencing revealed that seven ICEs were identical to ICEPmiJpn1, carrying the cephalosporinase geneblaCMY-2. Another one, designated ICEPmiChn1, carried five resistance genes. All eight ICEs could be transferred toEscherichia colivia conjugation. The results highlight the idea that animal farms are important reservoir of the SXT/R391 ICE-containingP. mirabilis.

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