Diagnosis of SLC25A46-related pontocerebellar hypoplasia in two siblings with fulminant neonatal course: role of postmortem CT and whole genomic analysis: a case report

Abstract Background Pontocerebellar hypoplasia (PCH) is increasingly known as a degenerative disease rather than simple “hypoplasia”. At least 21 disease-causing genes have been identified for PCH so far. Because PCH is very heterogenous, prognostic prediction based solely on clinical or radiologic findings is not feasible. Case presentation Here, we report two siblings who had a fulminant neonatal course. The documentation of pontocerebellar hypoplasia by postmortem brain CT imaging in one of the siblings and a subsequent complex and comprehensive whole genome analysis established that both siblings had bi-allelic compound heterozygous variants (a splicing variant and a deletion) in the SLC25A46 gene which encodes a solute carrier protein essential for mitochondrial function. Long-read whole genome sequencing was required to confirm the presence of the deletion. The fulminant courses suggest that SLC25A46-related PCH is an acutely progressive degenerative condition starting in utero, rather than a simple static hypoplasia. Conclusion The genomic analysis was instrumental and essential to solving the enigma of the unexplained neonatal deaths of these two siblings and to provide accurate genetic counseling.

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Comparative Whole-Genome Analysis of Russian Foodborne Multidrug-Resistant Salmonella Infantis Isolates

Microorganisms ◽

10.3390/microorganisms10010089 ◽

2021 ◽

Vol 10 (1) ◽

pp. 89

Author(s):

Anna Egorova ◽

Yulia Mikhaylova ◽

Stepan Saenko ◽

Marina Tyumentseva ◽

Aleksandr Tyumentsev ◽

...

Keyword(s):

Meat Product ◽

Genomic Analysis ◽

Public Health Problem ◽

Multidrug Resistant ◽

Epidemiological Surveillance ◽

Whole Genome ◽

Whole Genome Analysis ◽

Salmonella Infections ◽

Genes Encoding ◽

Long Read

Non-typhoidal Salmonella infections remain a significant public health problem worldwide. In this study, we present the first detailed genomic analysis report based on short-read (Illumina) whole-genome sequencing (WGS) of 45 multidrug-resistant (MDR) Salmonella enterica subsp. enterica serotype Infantis isolates from poultry and meat product samples obtained in Russia during 2018–2020, and long-read (MinION) WGS of five more representative isolates. We sought to determine whether foodborne S. Infantis have acquired new characteristics, traits, and dynamics in MDR growth in recent years. All sequenced isolates belonged to the sequence type ST32 and more than the half of isolates was characterized by six similar antimicrobial susceptibility profiles, most of which corresponded well with the antimicrobial resistance determinants to aminoglycosides, sulphonamides, tetracycline, and chloramphenicol revealed in silico. Some of the isolates were characterized by the presence of several types of plasmids simultaneously. Plasmid typing using WGS revealed Col440I, ColpVC, ColRNAI, IncFIB, IncFII, IncX1, IncHI2, IncHI2A, and IncN replicons. The identified virulence genes for 45 whole genomes of S. Infantis were similar and included 129 genes encoding structural components of the cell, factors responsible for successful invasion of the host, and secreted products. These data will be a valuable contribution to further comparative genomics of S. Infantis circulating in Russia, as well as to epidemiological surveillance of foodborne Salmonella isolates and investigations of Salmonella outbreaks.

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Whole-genome analysis reveals the complex evolutionary dynamics of Kenyan G2P[4] human rotavirus strains

Journal of General Virology ◽

10.1099/vir.0.033001-0 ◽

2011 ◽

Vol 92 (9) ◽

pp. 2201-2208 ◽

Cited By ~ 22

Author(s):

Souvik Ghosh ◽

Noriaki Adachi ◽

Zipporah Gatheru ◽

James Nyangao ◽

Dai Yamamoto ◽

...

Keyword(s):

Genome Analysis ◽

Complete Genome ◽

Evolutionary Dynamics ◽

Genomic Analysis ◽

Whole Genome ◽

Genome Sequences ◽

Whole Genome Analysis ◽

Human Rotavirus ◽

Genotype Constellation ◽

Common Causes

Although G2P[4] rotaviruses are common causes of acute childhood diarrhoea in Africa, to date there are no reports on whole genomic analysis of African G2P[4] strains. In this study, the nearly complete genome sequences of two Kenyan G2P[4] strains, AK26 and D205, detected in 1982 and 1989, respectively, were analysed. Strain D205 exhibited a DS-1-like genotype constellation, whilst strain AK26 appeared to be an intergenogroup reassortant with a Wa-like NSP2 genotype on the DS-1-like genotype constellation. The VP2-4, VP6-7, NSP1, NSP3 and NSP5 genes of strain AK26 and the VP2, VP4, VP7 and NSP1–5 genes of strain D205 were closely related to those of the prototype or other human G2P[4] strains. In contrast, their remaining genes were distantly related, and, except for NSP2 of AK26, appeared to originate from or share a common origin with rotavirus genes of artiodactyl (ruminant and camelid) origin. These observations highlight the complex evolutionary dynamics of African G2P[4] rotaviruses.

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Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping

10.1101/110163 ◽

2017 ◽

Cited By ~ 5

Author(s):

Tslil Gabrieli ◽

Hila Sharim ◽

Yael Michaeli ◽

Yuval Ebenstein

Keyword(s):

Single Molecule ◽

Genome Mapping ◽

Single Point ◽

Read Length ◽

Whole Genome ◽

Sequencing Analysis ◽

Nanopore Sequencing ◽

Sequencing Data ◽

Whole Genome Analysis ◽

Long Read

ABSTRACTVariations in the genetic code, from single point mutations to large structural or copy number alterations, influence susceptibility, onset, and progression of genetic diseases and tumor transformation. Next-generation sequencing analysis is unable to reliably capture aberrations larger than the typical sequencing read length of several hundred bases. Long-read, single-molecule sequencing methods such as SMRT and nanopore sequencing can address larger variations, but require costly whole genome analysis. Here we describe a method for isolation and enrichment of a large genomic region of interest for targeted analysis based on Cas9 excision of two sites flanking the target region and isolation of the excised DNA segment by pulsed field gel electrophoresis. The isolated target remains intact and is ideally suited for optical genome mapping and long-read sequencing at high coverage. In addition, analysis is performed directly on native genomic DNA that retains genetic and epigenetic composition without amplification bias. This method enables detection of mutations and structural variants as well as detailed analysis by generation of hybrid scaffolds composed of optical maps and sequencing data at a fraction of the cost of whole genome sequencing.

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Genomic Analysis of an Indian G8P[1] Caprine Rotavirus-A Strain Revealing Artiodactyl and DS-1-Like Human Multispecies Reassortment

Frontiers in Veterinary Science ◽

10.3389/fvets.2020.606661 ◽

2021 ◽

Vol 7 ◽

Author(s):

Shubhankar Sircar ◽

Yashpal Singh Malik ◽

Prashant Kumar ◽

Mohd Ikram Ansari ◽

Sudipta Bhat ◽

...

Keyword(s):

Genomic Analysis ◽

Complex Nature ◽

Whole Genome ◽

Structural Genes ◽

Whole Genome Analysis ◽

Surveillance Studies ◽

Rotavirus A ◽

Health Significance ◽

Genome Analyses

The surveillance studies for the presence of caprine rotavirus A (RVA) are limited in India, and the data for the whole-genome analysis of the caprine RVA is not available. This study describes the whole-genome-based analysis of a caprine rotavirus A strain, RVA/Goat-wt/IND/K-98/2015, from a goat kid in India. The genomic analysis revealed that the caprine RVA strain K-98, possess artiodactyl-like and DS-1 human-like genome constellation G8P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The three structural genes (VP2, VP4, and VP7) were close to caprine host having nucleotide-based identity range between 97.5 and 98.9%. Apart from them, other gene segments showed similarity with either bovine or human like genes, ultimately pointing toward a common evolutionary origin having an artiodactyl-type backbone of strain K-98. Phylogenetically, the various genes of the current study isolate also clustered inside clades comprising Human-Bovine-Caprine isolates from worldwide. The current findings add to the knowledge on caprine rotaviruses and might play a substantial role in designing future vaccines or different alternative strategies combating such infections having public health significance. To the best of our knowledge, this is the first report on the whole-genome characterization of a caprine RVA G8P[1] strain from India. Concerning the complex nature of the K-98 genome, whole-genome analyses of more numbers of RVA strains from different parts of the country are needed to comprehend the genomic nature and genetic diversity among caprine RVA.

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Establishing the involvement of the novel gene AGBL5 in retinitis pigmentosa by whole genome sequencing

Physiological Genomics ◽

10.1152/physiolgenomics.00101.2016 ◽

2016 ◽

Vol 48 (12) ◽

pp. 922-927 ◽

Cited By ~ 12

Author(s):

Kari Branham ◽

Hiroko Matsui ◽

Pooja Biswas ◽

Aditya A. Guru ◽

Michael Hicks ◽

...

Keyword(s):

Retinitis Pigmentosa ◽

Variant Calling ◽

Field Testing ◽

Copy Number Variations ◽

Whole Genome Sequence ◽

Fundus Photography ◽

Compound Heterozygous ◽

Whole Genome ◽

Illumina Hiseq ◽

Compound Heterozygous Variants

While more than 250 genes are known to cause inherited retinal degenerations (IRD), nearly 40–50% of families have the genetic basis for their disease unknown. In this study we sought to identify the underlying cause of IRD in a family by whole genome sequence (WGS) analysis. Clinical characterization including standard ophthalmic examination, fundus photography, visual field testing, electroretinography, and review of medical and family history was performed. WGS was performed on affected and unaffected family members using Illumina HiSeq X10. Sequence reads were aligned to hg19 using BWA-MEM and variant calling was performed with Genome Analysis Toolkit. The called variants were annotated with SnpEff v4.11, PolyPhen v2.2.2, and CADD v1.3. Copy number variations were called using Genome STRiP (svtoolkit 2.00.1611) and SpeedSeq software. Variants were filtered to detect rare potentially deleterious variants segregating with disease. Candidate variants were validated by dideoxy sequencing. Clinical evaluation revealed typical adolescent-onset recessive retinitis pigmentosa (arRP) in affected members. WGS identified about 4 million variants in each individual. Two rare and potentially deleterious compound heterozygous variants p.Arg281Cys and p.Arg487* were identified in the gene ATP/GTP binding protein like 5 ( AGBL5) as likely causal variants. No additional variants in IRD genes that segregated with disease were identified. Mutation analysis confirmed the segregation of these variants with the IRD in the pedigree. Homology models indicated destabilization of AGBL5 due to the p.Arg281Cys change. Our findings establish the involvement of mutations in AGBL5 in RP and validate the WGS variant filtering pipeline we designed.

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GAAP: A Genome Assembly + Annotation Pipeline

BioMed Research International ◽

10.1155/2019/4767354 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12 ◽

Cited By ~ 2

Author(s):

Jinhwa Kong ◽

Sun Huh ◽

Jung-Im Won ◽

Jeehee Yoon ◽

Baeksop Kim ◽

...

Keyword(s):

Genome Analysis ◽

De Novo ◽

Transcriptome Assembly ◽

Genomic Analysis ◽

Whole Genome ◽

High Throughput Analysis ◽

Whole Genome Analysis ◽

A Genome ◽

Base Sequences ◽

Wide Range

Genomic analysis begins with de novo assembly of short-read fragments in order to reconstruct full-length base sequences without exploiting a reference genome sequence. Then, in the annotation step, gene locations are identified within the base sequences, and the structures and functions of these genes are determined. Recently, a wide range of powerful tools have been developed and published for whole-genome analysis, enabling even individual researchers in small laboratories to perform whole-genome analyses on their objects of interest. However, these analytical tools are generally complex and use diverse algorithms, parameter setting methods, and input formats; thus, it remains difficult for individual researchers to select, utilize, and combine these tools to obtain their final results. To resolve these issues, we have developed a genome analysis pipeline (GAAP) for semiautomated, iterative, and high-throughput analysis of whole-genome data. This pipeline is designed to perform read correction, de novo genome (transcriptome) assembly, gene prediction, and functional annotation using a range of proven tools and databases. We aim to assist non-IT researchers by describing each stage of analysis in detail and discussing current approaches. We also provide practical advice on how to access and use the bioinformatics tools and databases and how to implement the provided suggestions. Whole-genome analysis of Toxocara canis is used as case study to show intermediate results at each stage, demonstrating the practicality of the proposed method.

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