Abstract P224: Whole Genome Sequencing of 8 Indian Asians

Circulation ◽  
2012 ◽  
Vol 125 (suppl_10) ◽  
Author(s):  
John Chambers ◽  
Abtehale Al-Hussaini ◽  
Tsung Tan ◽  
Joban Sehmi ◽  
Mark McCarthy ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Lipid Metabolism ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Variants ◽  
Genetic Factors ◽  
Whole Genome ◽  
The Novel ◽  
Autosomal Snps ◽  
B Vitamin

Background The genetic architecture and variation of Indian Asians, who represent one quarter of the world's population, has not been described. This represents an important obstacle to the identification of the genetic factors contributing to diseases encountered in Indian Asians. Aim To identify and describe the patterns of genetic variation in Indian Asians. Methods We carried out high-depth whole genome sequencing of 8 Indian Asian men, using paired-end and mate-pair libraries, and Illumina GAII x instruments. We used Stampy, with BWA as a pre-mapper, to align reads to Genome Reference Consortium build 37 of the human genome (GRCh37). We used GATK and SAMtools to call SNPs and indels; accepting genetic variants called by both algorithms as confirmed. Results Mean coverage was 28.4x (range 13.9 to 32.5x); 99.8% of the mappable genome was covered by at least one read in each sample. We found 6,602,840 autosomal SNPs (mean 3,318,386 per person) of which 436,823 (6.6%) are novel (not in dbSNP132 or 1000G June 2011). The majority of novel SNPs were singletons (88% vs 20% for known SNPs). There were 50,585 novel SNPs present at least twice (ie MAF>10%), and 2,174 novel SNPs predicted to affect protein coding. Amongst the novel cSNPs that are identified as pathogenic by SIFT or PolyPhen2, 145 are in genes linked by OMIM to human disease, including obesity ( FTO , UCP1 ), diabetes mellitus ( CDKAL1 , GCGR , HNF1B ), lipid metabolism ( APOB ), renal disease ( NPHP4, PKD1 ), hypertension ( NOS2 ), iron and B vitamin metabolism ( CUBN , TCN2, TF ), and susceptibility to malaria and leprosy ( CR1 , FCGR2A , NOS2, TLR1 ). There were 65,613 novel autosomal indels of which 35,097 are present at least twice, and 2,301 novel deletions >100bp. We found that amongst the novel SNPs and indels discovered, >50% are not in high LD (r 2 ≥0.8) with tagSNPs on available high-density microarrays Conclusions Our results reveal 502,436 new genetic variants amongst Indian Asians, including coding SNPs and indels in genes involved in atherosclerosis, carbohydrate and lipid metabolism, immunity and inflammation. The majority of novel variants are in low LD with standard commercial micro-arrays, indicating that these genome-wide arrays do not capture Indian Asian specific genetic variation. Our findings will inform the design of future studies to identify the genetic factors contributing to cardiovascular disease and other disorders that are more common amongst Indian Asians.

Advancing RNA Virus Discovery and Biology with Whole Genome Sequencing

2021 ◽  
Author(s):  
◽  
Mariah Taylor ◽  
Keyword(s):  
Genetic Variation ◽  
Amino Acid ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rna Virus ◽  
Animal Health ◽  
Functional Domains ◽  
Whole Genome ◽  
Coding Region

Two RNA virus families that pose a threat to human and animal health are Hantaviridae and Coronaviridae. These RNA viruses which originate in wildlife continue and will continue to cause disease, and hence, it is critical that scientific research define the mechanisms as to how these viruses spillover and adapt to new hosts to become endemic. One gap in our ability to define these mechanisms is the lack of whole genome sequences for many of these viruses. To address this specific gap, I developed a versatile amplicon-based whole-genome sequencing (WGS) approach to identify viral genomes of hantaviruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within reservoir and spillover hosts. In my research studies, I used the amplicon-based WGS approach to define the genetic plasticity of viral RNA within pathogenic and nonpathogenic hantavirus species. The standing genetic variation of Andes orthohantavirus and Prospect Hill orthohantavirus was mapped out and amino acid changes occurring outside of functional domains were identified within the nucleocapsid and glycoprotein. I observed several amino acid changes in functional domains of the RNA-dependent RNA polymerase, as well as single nucleotide polymorphisms (SNPs) within the 3’ non-coding region (NCR) of the S-segment. To identify whether virus adaptation would occur within the S- and L-segments we attempted to adapt hantaviruses in vitro in a spillover host model through passaging experiments. In early passages we identified few mutations in the M-segment with the majority being identified in the S-segment 3’ NCR and the L-segment. This work suggests that hantavirus adaptation occurs in the S- and L-segments although the effect of these mutants on pathology is yet to be determined. While sequencing laboratory isolates is easily accomplished, sequencing low concentrations of virus within the reservoir is a formidable task. I further translated our amplicon-based WGS approach into a pan-oligonucleotide amplicon-based WGS approach to sequence hantavirus vRNA and mRNA from reservoir and spillover hosts in Ukraine. This approach successfully identified a novel Puumala orthohantavirus (PUUV) strain in Ukraine and using Bayesian phylogenetics we found this strain to be associated with the PUUV Latvian lineage. Early during the SARS-CoV-2 pandemic, I applied the knowledge gained in the hantavirus WGS efforts to sequencing of SARS-CoV-2 from nasopharyngeal swabs collected in April 2020. The genetic diversity of 45 SARS-CoV-2 isolates was evaluated with the methods I developed. We identified D614G, a notable mutation known for increasing transmission, in over 90% of our isolates. Two major lineages distinguish SARS-CoV-2 variants worldwide, lineages A and B. While most of our isolates were found within B lineage, we also identified one isolate within lineage A. We performed in vitro work which confirmed A lineage isolates as having poor replication in the trachea as compared to the nasal cavity. Five of these isolates presented a unique array of mutations which were assessed in the keratin 18 human angiotensin-converting enzyme 2 (K18-hACE2) mouse model for its response immunologically and pathogenically. We identified a distinction of pathogenesis between the A and B lineages with emphysema being common amongst A lineage isolates. Additionally, we discovered a small cohort of likely SNPs that defined the late induction of eosinophils during infection. In summary, this work will further define the dynamics of genetic variation and plasticity within virus populations that cause disease outbreaks and will allow a deeper understanding of the virus-host relationship.

scholarly journals Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

2013 ◽  
Vol 93 (2) ◽  
pp. 249-263 ◽  
Author(s):  
Yong-hui Jiang ◽  
Ryan K.C. Yuen ◽  
Xin Jin ◽  
Mingbang Wang ◽  
Nong Chen ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Variants ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Whole Genome

scholarly journals Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov

2017 ◽  
Vol 5 (42) ◽  
Author(s):  
S. Wesley Long ◽  
Sarah E. Linson ◽  
Matthew Ojeda Saavedra ◽  
Concepcion Cantu ◽  
James J. Davis ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Clinical Isolate ◽  
Genome Sequencing ◽  
Novel Species ◽  
Whole Genome ◽  
The Novel ◽  
Short Read ◽  
Oxford Nanopore ◽  
Long Read

ABSTRACT In a study of 1,777 Klebsiella strains, we discovered KPN1705, which was distinct from all recognized Klebsiella spp. We closed the genome of strain KPN1705 using a hybrid of Illumina short-read and Oxford Nanopore long-read technologies. For this novel species, we propose the name Klebsiella quasivariicola sp. nov.

scholarly journals Cefiderocol Activity against Clinical Pseudomonas aeruginosa Isolates Exhibiting Ceftolozane-Tazobactam Resistance

2021 ◽  
Author(s):  
Patricia J Simner ◽  
Stephan Beisken ◽  
Yehudit Bergman ◽  
Andreas E Posch ◽  
Sara E Cosgrove ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Binding Sites ◽  
Whole Genome ◽  
The Novel ◽  
Broth Microdilution ◽  
Mechanisms Of Resistance ◽  
Fold Reduction ◽  
Target Binding

Abstract Objective Mutations in the AmpC-AmpR region are associated with treatment-emergent ceftolozane-tazobactam (TOL-TAZ) and ceftazidime-avibactam (CAZ-AVI) resistance. We sought to determine if these mutations impact susceptibility to the novel cephalosporin-siderophore compound cefiderocol. Methods Thirty-two paired isolates from 16 patients with index P. aeruginosa isolates susceptible to TOL-TAZ and subsequent P. aeruginosa isolates available after TOL-TAZ exposure from January 2019 to December 2020 were included. TOL-TAZ, CAZ-AVI, imipenem-relebactam (IMI-REL), and cefiderocol minimum inhibitory concentrations (MICs) were determined using broth microdilution. Whole genome sequencing of paired isolates was used to identify mechanisms of resistance to cefiderocol that emerged, focusing on putative mechanisms of resistance to cefiderocol or earlier siderophore-antibiotic conjugates based on the previously published literature. Results Analyzing the 16 pairs of P. aeruginosa isolates, ≥4-fold increases in cefiderocol MICs occurred in 4 of 16 isolates. Cefiderocol non-susceptibility criteria was met for only 1 of the 4 isolates, using Clinical and Laboratory Standards Institute criteria. Specific mechanisms identified included the following: AmpC E247K (2 isolates), MexR A66V and L57D (1 isolate each), and AmpD G116D (1 isolate) substitutions. For both isolates with AmpC E247K mutations, ≥4-fold MIC increases occurred for both TOL-TAZ and CAZ-AVI, while a ≥4-fold reduction in IMI-REL MICs was observed. Conclusions Our findings suggest that alterations in the target binding sites of P. aeruginosa derived AmpC β-lactamases have the potential to reduce the activity of three of four novel β-lactams (i.e., ceftolozane-tazobactam, ceftazidime-avibactam, and cefiderocol) and potentially increase susceptibility to imipenem-relebactam. These findings are in need of validation in a larger cohort.

scholarly journals Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1803
Author(s):  
Jitendra Singh ◽  
Anvita Gupta Malhotra ◽  
Debasis Biswas ◽  
Prem Shankar ◽  
Leena Lokhande ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Spike Protein ◽  
Whole Genome ◽  
The Novel ◽  
Genome Sequences ◽  
Second Wave ◽  
Insight Into

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

scholarly journals OXA-900, a Novel OXA Sub-Family Carbapenemase Identified in Citrobacter freundii, Evades Detection by Commercial Molecular Diagnostics Tests

2021 ◽  
Vol 9 (9) ◽  
pp. 1898
Author(s):  
Sammy Frenk ◽  
Nadya Rakovitsky ◽  
Hadas Kon ◽  
Reut Rov ◽  
Shirin Abramov ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Molecular Diagnostics ◽  
Target Gene ◽  
Whole Genome ◽  
Citrobacter Freundii ◽  
The Novel ◽  
Class D ◽  
Marine Environmental ◽  
Wide Dissemination

Using whole-genome sequencing and cloning of the target gene, we identified blaOXA-900 carbapenemase, a novel blaOXA belonging to a distant and distinct sub-family of blaOXA-48-like. The plasmid-mediated gene was identified in a C. freundii isolate with elevated carbapenem MICs that evaded detection by commercial DNA-based methods. The novel gene, an OXA-48 family carbapenem-hydrolyzing class D β-lactamase, OXA-900, likely originates from marine environmental Shewanella. Since this plasmid-mediated gene has entered a member of the Enterobacterales and evades detection by commonly used tests, it may gain wide dissemination among Enterobacterales.

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