scholarly journals Target Capture Sequencing of SARS-CoV-2 Genomes Using the ONETest Coronaviruses Plus

2021 ◽  
Author(s):  
Shing H. Zhan ◽  
Sepideh M. Alamouti ◽  
Brian S. Kwok ◽  
Meng-Hsun Lee ◽  
Jaswinder Khattra ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Added Value ◽  
Respiratory Pathogens ◽  
Sequence Coverage ◽  
Pcr Assay ◽  
Genetic Changes ◽  
Target Capture ◽  
Archived Samples ◽  
Target Capture Sequencing ◽  
Generation Sequencing

ABSTRACTBackgroundGenomic sequencing is important to track and monitor genetic changes in SARS-CoV-2. We introduce a target capture next-generation sequencing methodology, the ONETest Coronaviruses Plus, to sequence SARS-CoV-2 genomes and select genes of other respiratory viruses simultaneously.MethodsWe applied the ONETest on 70 respiratory samples (collected in Florida, USA between May and July, 2020), in which SARS-CoV-2 had been detected by a qualitative PCR assay. For 48 (69%) of the samples, we also applied the ARTIC protocol for Illumina sequencing. All the libraries were sequenced as 2×150 nucleotide reads on an Illumina instrument. The ONETest data were analyzed using an in-house pipeline and the ARTIC data using a published pipeline to produce consensus SARS-CoV-2 genome sequences, to which lineages were assigned using pangolin.ResultsOf the 70 ONETest libraries, 45 (64%) had a complete or near-complete SARS-CoV-2 genome sequence (> 29,000 bases and with > 90% of its bases covered by at least 10 reads). Of the 48 ARTIC libraries, 25 (52%) had a complete or near-complete SARS-CoV-2 genome sequence.In 24 out of 34 (71%) samples in which both the ONETest and ARTIC sequences were complete or near-complete and in which lineage could be assigned to both the ONETest and ARTIC sequences, the SARS-CoV-2 lineage identified was the same.ConclusionsThe ONETest can be used to sequence the SARS-CoV-2 genomes in archived samples and thereby enable detection of circulating and emerging SARS-CoV-2 variants. Target capture approaches, such as the ONETest, are less prone to loss of sequence coverage probably due to amplicon dropouts encountered in amplicon approaches, such as ARTIC. With its added value of characterizing other major respiratory pathogens, although not assessed in this study, the ONETest can help to better understand the epidemiology of infectious respiratory disease in the post COVID-19 era.

scholarly journals Three novel mutations of microphthalmos identified in two Chinese families

2020 ◽  
Author(s):  
Yating Tang ◽  
Jie Xu ◽  
Tianyu Zheng ◽  
Yi Lu
Keyword(s):  
Genetic Defect ◽  
Genetic Diagnosis ◽  
Chinese Family ◽  
Novel Mutations ◽  
Chinese Families ◽  
Target Capture ◽  
Disease Related Genes ◽  
Presymptomatic Diagnosis ◽  
Target Capture Sequencing ◽  
Generation Sequencing

Abstract Background: To identify the underlying genetic defect responsible for microphthalmos eyes in two three-generation Chinese families.Methods: In our study, we screened 425 potential eye disease-related genes of the proband of a three-generation Chinese family diagnosed with microphthalmos using next-generation sequencing-based target capture sequencing. Variants were filtered and analyzed to identify possible disease-causing variants before Sanger sequencing validation.Results: We enrolled two families with microphthalmos (Family 1: microphthalmos with congenital ocular coloboma and Family 2: simple microphthalmos). Two novel heterozygous mutations, PXDN c.3165C>T (p.Pro1055Pro) and PXDN c.2640C>G (p.Arg880Arg), were found in Family 1, and CRYBB2 c.481G>A (p.Gly161Arg) was found in Family 2, but none of the mutations were found in the unaffected individuals, who were phenotypically normal. Multiple orthologous sequence alignment (MSA) revealed that the CRYBB2 p.Gly161Arg mutation was a deleterious effect mutation.Conclusions: The three novel mutations found in our study extend our current understanding of the genetic basis of microphthalmos and provide early presymptomatic diagnosis and emphasize the significance of genetic diagnosis of microphthalmos.

scholarly journals Genome Sequences of Three Novel Isolates of Human Parainfluenza Virus 2 Associated with Acute Respiratory Infection

2017 ◽  
Vol 5 (33) ◽  
Author(s):  
J. L. Kennedy ◽  
J. C. Kincaid ◽  
K. C. Schwalm ◽  
A. N. Stoner ◽  
T. J. Abramo ◽  
...  
Keyword(s):  
Respiratory Infection ◽  
Acute Respiratory Infection ◽  
Pediatric Patients ◽  
Parainfluenza Virus ◽  
Accession Number ◽  
Genome Sequences ◽  
Viral Nucleic Acid ◽  
Target Capture ◽  
Human Parainfluenza Virus ◽  
Generation Sequencing

ABSTRACT Using target capture of viral nucleic acid and next-generation sequencing, we generated the genome sequences of three novel human parainfluenza virus 2 isolates. Isolates ACRI_0185 (GenBank accession number MF077311), ACRI_0230 (MF077312), and ACRI_0248 (MF077313) were collected in October 2016, February 2017, and March 2017, respectively, from pediatric patients with acute respiratory infection in Arkansas.

scholarly journals Multiplexed Reverse Transcriptase PCR Assay for Identification of Viral Respiratory Pathogens at the Point of Care

2007 ◽  
Vol 45 (11) ◽  
pp. 3498-3505 ◽  
Author(s):  
S. E. Letant ◽  
J. I. Ortiz ◽  
L. F. Bentley Tammero ◽  
J. M. Birch ◽  
R. W. Derlet ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Point Of Care ◽  
Respiratory Pathogens ◽  
Pcr Assay ◽  
Reverse Transcriptase Pcr ◽  
Viral Respiratory

scholarly journals Draft Genome Sequence of Saccharomyces cerevisiae Strain Awamori Number 101, Commonly Used to Make Awamori, a Traditional Spirit, in Okinawa, Japan

2021 ◽  
Vol 10 (25) ◽  
Author(s):  
Masatoshi Tsukahara ◽  
Kotaro Ise ◽  
Maiko Nezuo ◽  
Haruna Azuma ◽  
Takeshi Akao ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Next Generation ◽  
Industrial Strain ◽  
Content Type ◽  
Short Reads ◽  
Generation Sequencing

We report here the draft genome sequence for Saccharomyces cerevisiae strain Awamori number 101, an industrial strain used for producing awamori, a distilled alcohol beverage. It was constructed by assembling the short reads obtained by next-generation sequencing. The 315 contigs constitute an 11.5-Mbp genome sequence coding 6,185 predicted proteins.

scholarly journals Clinical and genetic diagnosis of thirteen Japanese patients with hereditary spherocytosis

2022 ◽  
Vol 9 (1) ◽  
Author(s):  
Keiko Shimojima Yamamoto ◽  
Taiju Utshigisawa ◽  
Hiromi Ogura ◽  
Takako Aoki ◽  
Takahiro Kawakami ◽  
...  
Keyword(s):  
Hemolytic Anemia ◽  
Hereditary Spherocytosis ◽  
Genetic Diagnosis ◽  
Genomic Analysis ◽  
Japanese Patients ◽  
Asian Countries ◽  
Target Capture ◽  
Detailed Family History ◽  
Target Capture Sequencing ◽  
Chronic Hemolytic Anemia

AbstractHereditary spherocytosis is the most frequent cause of hereditary hemolytic anemia and is classified into five subtypes (SPH1-5) according to OMIM. Because the clinical and laboratory features of patients with SPH1-5 are variable, it is difficult to classify these patients into the five subtypes based only on these features. We performed target capture sequencing in 51 patients with hemolytic anemia associated with/without morphological abnormalities in red blood cells. Thirteen variants were identified in five hereditary spherocytosis-related genes (six in ANK1 [SPH1]; four in SPTB [SPH2]; and one in each of SPTA1 [SPH3], SLC4A1 [SPH4], and EPB42 [SPH5]). Among these variants, seven were novel. The distribution pattern of the variants was different from that reported previously in Japan but similar to those reported in other Asian countries. Comprehensive genomic analysis would be useful and recommended, especially for patients without a detailed family history and those receiving frequent blood transfusions due to chronic hemolytic anemia.

scholarly journals De Novo Genome Assembly of a Foxtail Millet Cultivar Huagu11 Uncovered the Genetic Difference to the Cultivar Yugu1, and the Genetic Mechanism of Imazethapyr Tolerance

2021 ◽  
Author(s):  
Jie Wang ◽  
Shiming Li ◽  
Lei Lan ◽  
Mushan Xie ◽  
Shu Cheng ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Reference Genome ◽  
Foxtail Millet ◽  
Setaria Italica ◽  
Genome Comparison ◽  
Sequencing Technology ◽  
High Quality ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Abstract Background: Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. Results: Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97% and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. Conclusions: A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was found that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.

scholarly journals Modeling the developmental origins of pediatric cancer to improve patient outcomes

2021 ◽  
Vol 14 (2) ◽  
Author(s):  
James F. Amatruda
Keyword(s):  
Patient Outcomes ◽  
Pediatric Cancer ◽  
Molecular Mechanisms ◽  
Cellular Transformation ◽  
Genetic Changes ◽  
Current Therapies ◽  
Physician Scientist ◽  
Improve Patient ◽  
Generation Sequencing

ABSTRACT In the treatment of children and adolescents with cancer, multimodal approaches combining surgery, chemotherapy and radiation can cure most patients, but may cause lifelong health problems in survivors. Current therapies only modestly reflect increased knowledge about the molecular mechanisms of these cancers. Advances in next-generation sequencing have provided unprecedented cataloging of genetic aberrations in tumors, but understanding how these genetic changes drive cellular transformation, and how they can be effectively targeted, will require multidisciplinary collaboration and preclinical models that are truly representative of the in vivo environment. Here, I discuss some of the key challenges in pediatric cancer from my perspective as a physician-scientist, and touch on some promising new approaches that have the potential to transform our understanding of these diseases.

scholarly journals Complete Genome Sequence of Matlo Bat Lyssavirus

2021 ◽  
Vol 10 (20) ◽  
Author(s):  
Colyn S. Grobler ◽  
Jessica Coertse ◽  
Wanda Markotter
Keyword(s):  
South Africa ◽  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Novel Species ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequencing Technologies ◽  
Generation Sequencing

ABSTRACT The genus Lyssavirus includes rabies virus as well as multiple diverse and recently described novel species. Using next-generation sequencing technologies, we have obtained the whole-genome sequence of Matlo bat lyssavirus, which was isolated from a Natal long-fingered bat (Miniopterus natalensis) in South Africa.

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