scholarly journals Novel mutations identified from whole-genome sequencing of SARS-CoV-2 isolated from Noakhali, Bangladesh

2021 ◽  
Author(s):  
Maqsud Hossain ◽  
Tahrima Saiha Huq ◽  
Aura Rahman ◽  
Md. Aminul Islam ◽  
Syeda Naushin Tabassum ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Novel Mutation ◽  
Temporal Distribution ◽  
Eastern Region ◽  
Whole Genome ◽  
Viral Pathogens ◽  
South Eastern ◽  
Study Results ◽  
Variant Analysis

Abstract Whole-genome sequencing is increasingly being used to investigate the spatial and temporal distribution of viral pathogens including the Severe Acute Respiratory Syndrome Coronavirus Variant 2 (SARS-CoV-2) which is responsible for the ongoing COVID-19 pandemic. In this study, we determined 55 complete genome sequences of SARS-CoV-2 strains isolated from patients from Noakhali, a South-Eastern district in Bangladesh. Variant analysis of our sequenced genomes identified sixteen rare variations in S, six in N, two in M, one in E protein and the S protein variation, Y204F, identified in two of our sequenced strains, has not been reported from any other countries in the GISAID database. Comparison of the prevalence pattern across the country showed GH clade lineages B.1.36 and B.1.36.16 to be abundant in Noakhali and the South-Eastern region of Chittagong when compared to the rest of the country. Phylodynamic analysis of our sequenced genomes revealed that the virus was estimated to be evolving at the rate of 1.065 X 10− 4 subs/site/year. The study results demonstrated the necessity of initiating a concerted, country-wide genomics surveillance effort to determine any novel mutation of functional significance, understanding virus evolution, transmission, and spread in Bangladesh. Short running title: Genome sequencing of Noakhali isolates SARS-Cov-2 in Bangladesh

Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing

2010 ◽  
Vol 42 (11) ◽  
pp. 931-936 ◽  
Author(s):  
Akihiro Fujimoto ◽  
Hidewaki Nakagawa ◽  
Naoya Hosono ◽  
Kaoru Nakano ◽  
Tetsuo Abe ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Whole Genome ◽  
Parallel Sequencing ◽  
Variant Analysis ◽  
Japanese Individual

M86 NOVEL MUTATION IN PPEF2 REPORTED IN A FAMILY AFFECTED WITH SCHIZOPHRENIA: WHOLE GENOME SEQUENCING STUDY

2019 ◽  
Vol 29 ◽  
pp. S212-S213
Author(s):  
Sandra Smieszek ◽  
Rosa Torres ◽  
Derek Xiao ◽  
Christos Polymeropoulos ◽  
Gunther Birznieks ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Novel Mutation ◽  
Whole Genome

scholarly journals Whole-Genome Sequencing Reveals Exonic Variation of ASIC5 Gene Results in Recurrent Pregnancy Loss

2021 ◽  
Vol 8 ◽  
Author(s):  
Nourah H. Al Qahtani ◽  
Sayed AbdulAzeez ◽  
Noor B. Almandil ◽  
Norah Fahad Alhur ◽  
Hind Saleh Alsuwat ◽  
...  
Keyword(s):  
Ion Channel ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Pregnancy Loss ◽  
Recurrent Pregnancy Loss ◽  
Interaction Analysis ◽  
Novel Mutation ◽  
Direct Sequencing ◽  
Recessive Mutation ◽  
Whole Genome

Family trio next-generation sequencing-based variant analysis was done to identify the genomic reason on unexplained recurrent pregnancy loss (RPL). A family (dead fetus and parents) from Saudi Arabia with an earlier history of three unexplained RPLs at the ninth week of pregnancy was included in the study. Whole-genome sequencing (WGS) of a dead fetus and the parents was done to identify the pathogenic variation and confirmed through Sanger sequencing. WGS of dead fetus identifies a novel homozygous exonic variation (NM_017419.3:c.680G>T) in ASIC5 (acid-sensing ion channel subunit family member 5) gene; the parents are heterozygous. Newly designed ARMS PCR followed by direct sequencing confirms the presence of heterozygous in one subject and absence of homozygous novel mutation among randomly selected healthy Saudis. The second family with heterozygous was confirmed with three unexplained RPLs. Pathogenicity analysis of R227I amino acid substitution in ASIC5 protein through molecular docking and interaction analysis revealed that the mutations are highly pathogenic, decrease the stability of the protein, and prevent binding of amiloride, which is an activator to open the acid-sensing ion channel of ASIC5. The identified rare and novel autosomal recessive mutation, c.680G>T:p.R227I (ASIC5Saudi), in two families confirm the ASIC5 gene association with RPL and can be fatal to the fetus.

scholarly journals Whole genome sequencing and rare variant analysis in essential tremor families

PLoS ONE ◽  
2019 ◽  
Vol 14 (8) ◽  
pp. e0220512 ◽  
Author(s):  
Zagaa Odgerel ◽  
Shilpa Sonti ◽  
Nora Hernandez ◽  
Jemin Park ◽  
Ruth Ottman ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Essential Tremor ◽  
Genome Sequencing ◽  
Rare Variant ◽  
Whole Genome ◽  
Rare Variant Analysis ◽  
Variant Analysis

scholarly journals Mitochondrial PITRM1 peptidase loss-of-function in childhood cerebellar atrophy

2018 ◽  
Vol 55 (9) ◽  
pp. 599-606 ◽  
Author(s):  
Yeshaya Langer ◽  
Adi Aran ◽  
Suleyman Gulsuner ◽  
Bassam Abu Libdeh ◽  
Paul Renbaum ◽  
...  
Keyword(s):  
Mental Retardation ◽  
Whole Genome Sequencing ◽  
Spinocerebellar Ataxia ◽  
Genome Sequencing ◽  
Novel Mutation ◽  
Cerebellar Atrophy ◽  
Whole Genome ◽  
Loss Of Function ◽  
Childhood Onset ◽  
Whole Exome

ObjectiveTo identify the genetic basis of a childhood-onset syndrome of variable severity characterised by progressive spinocerebellar ataxia, mental retardation, psychotic episodes and cerebellar atrophy.MethodsIdentification of the underlying mutations by whole exome and whole genome sequencing. Consequences were examined in patients’ cells and in yeast.ResultsTwo brothers from a consanguineous Palestinian family presented with progressive spinocerebellar ataxia, mental retardation and psychotic episodes. Serial brain imaging showed severe progressive cerebellar atrophy. Whole exome sequencing revealed a novel mutation: pitrilysin metallopeptidase 1 (PITRM1) c.2795C>T, p.T931M, homozygous in the affected children and resulting in 95% reduction in PITRM1 protein. Whole genome sequencing revealed a chromosome X structural rearrangement that also segregated with the disease. Independently, two siblings from a second Palestinian family presented with similar, somewhat milder symptoms and the same PITRM1 mutation on a shared haplotype. PITRM1T931M carrier frequency was 0.027 (3/110) in the village of the first family evaluated, and 0/300 among Palestinians from other locales. PITRM1 is a mitochondrial matrix enzyme that degrades 10–65 amino acid oligopeptides, including the mitochondrial fraction of amyloid-beta peptide. Analysis of peptide cleavage activity by the PITRM1T931M protein revealed a significant decrease in the degradation capacity specifically of peptides ≥40 amino acids.ConclusionPITRM1T931M results in childhood-onset recessive cerebellar pathology. Severity of PITRM1-related disease may be affected by the degree of impairment in cleavage of mitochondrial long peptides. Disruption and deletion of X linked regulatory segments may also contribute to severity.

scholarly journals SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis.

2021 ◽  
Vol 144 ◽  
pp. 104993
Author(s):  
Jordy P.M. Coolen ◽  
Femke Wolters ◽  
Alma Tostmann ◽  
Lenneke F.J. van Groningen ◽  
Chantal P. Bleeker-Rovers ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Reverse Complement ◽  
Variant Analysis

scholarly journals Multiplex Fragment analysis detects all COVID-19 variants of concern

2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S138-S138
Author(s):  
J A SoRelle ◽  
A Clark ◽  
Z Wang ◽  
J Park
Keyword(s):  
New York ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Fragment Analysis ◽  
Deletion Mutations ◽  
Percent Agreement ◽  
Indian Origin ◽  
Allele Specific ◽  
Variant Analysis

Abstract Introduction/Objective The majority of tracking methods have employed whole genome sequencing, which can be very expensive and time consuming. An alternative method has been to use genotyping of specific mutations to identify variants. However, tracking SARS-CoV-2 variants by targeted methods has been a moving target. Most methods only multiplex four targets per reaction, but we have multiplexed 8 targets in a single tube using fragment analysis. Methods/Case Report Fluorescently labeled primers targeted a combination of insertion/ deletion mutations and single nucleotide mutations. The PCR amplified products, amplicons, were separated by capillary electrophoresis. Primers were designed to detect changes in size indicative of insertion or deletion mutations including: ORF1A:Del3675_3677, S:Del69_70, S:Del144, S:Del157_158, S:Del242_244, ORF8:Del119_120, and ORF8:ins28269-28273. Allele-specific primers were designed to detect both the wild-type and mutated versions of S:N501Y, S:E484K, and S:L452R. Residual nasopharyngeal and nasal specimens testing positive for SARS-CoV-2 by RT-PCR or isothermal amplification (IDnow) methods were selected from May 1- June 24, 2021. Variant analysis was performed by multiplex targeted PCR and whole genome sequencing in parallel on the same specimens to determine positive percent agreement. Results (if a Case Study enter NA) Variant analysis was performed on 250 specimens detecting each of the major variants of concern Alpha (B.1.1.7, U.K. origin, n= 108), Beta (B.1.351, South Africa origin, n=3), Gamma (P.1, Brazil origin, n=12), Delta (B.1.617.2, Indian origin, n=17), and Iota (B.1.526, New York, n=5). Some specimens with low viral load were detected by only PCR (n=18), only WGS (n=41), or neither (n=20). Overall positive percent agreement was 95% (163/171). Conclusion This adjustable method robustly and accurately identifies COVID-19 VOCs utilizing a platform amenable to multiple targets (20-40 targets ranging from 100-500b.p. across four fluorescent channels) using equipment commonly found in routine molecular pathology laboratories. Future directions include adjusting targets to detect new variants.

Whole-genome sequencing of prostate cancer reveals novel mutation-driven processes and molecular subgroups

Life Sciences ◽  
2020 ◽  
Vol 254 ◽  
pp. 117218 ◽  
Author(s):  
Caixia Liang ◽  
Lijuan Niu ◽  
Zejun Xiao ◽  
Cuiling Zheng ◽  
Yinchen Shen ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Novel Mutation ◽  
Whole Genome ◽  
Molecular Subgroups
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