A defect in the NOG gene increases susceptibility to spontaneous superficial chronic corneal epithelial defects (SCCED) in boxer dogs

Abstract Background Superficial chronic corneal epithelial defects (SCCEDs) are spontaneous corneal defects in dogs that share many clinical and pathologic characteristics to recurrent corneal erosions (RCE) in humans. Boxer dogs are predisposed to SCCEDs, therefore a search for a genetic defect was performed to explain this susceptibility. DNA was extracted from blood collected from Boxer dogs with and without SCCEDs followed by whole genome sequencing (WGS). RNA sequencing of corneal tissue and immunostaining of corneal sections from affected SCCED Boxer dogs with a deletion in the NOG gene and affected non-Boxer dogs without the deletion were performed. Results A 30 base pair deletion at a splice site in Noggin (NOG) (Chr 9:31453999) was identified by WGS and was significantly associated (P < 0.0001) with Boxer SCCEDs compared to unaffected non-Boxer dogs. NOG, BMP4, MMP13, and NCAM1 all had significant fold reductions in expression and SHH was significantly increased in Boxers with the NOG deletion as identified by RNA-Seq. Corneal IHC from NOG deletion dogs with SCCEDs had lower NOG and significantly higher scores of BMP2. Conclusions Many Boxer dogs with SCCED have a genetic defect in NOG. NOG is a constitutive protein in the cornea which is a potent inhibitor of BMP, which likely regulate limbal epithelial progenitor cells (LEPC). Dysregulation of LEPC may play a role in the pathogenesis of RCE.

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Comprehensive analysis of RNA-seq and whole genome sequencing data reveals no evidence for SARS-CoV-2 integrating into host genome

10.1101/2021.06.06.447293 ◽

2021 ◽

Author(s):

Yu-Sheng Chen ◽

Shuaiyao Lu ◽

Bing Zhang ◽

Tingfu Du ◽

Wen-Jie Li ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Rna Virus ◽

Comprehensive Analysis ◽

Host Genome ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Rna Seq ◽

Sequencing Data ◽

Infected Cells

SARS-CoV-2, as the causation of severe epidemic of COVID-19, is one kind of positive single-stranded RNA virus with high transmissibility. However, whether or not SARS-CoV-2 can integrate into host genome needs thorough investigation. Here, we performed both RNA sequencing (RNA-seq) and whole genome sequencing on SARS-CoV-2 infected human and monkey cells, and investigated the presence of host-virus chimeric events. Through RNA-seq, we did detect the chimeric host-virus reads in the infected cells. But further analysis using mixed libraries of infected cells and uninfected zebrafish embryos demonstrated that these reads are falsely generated during library construction. In support, whole genome sequencing also didn't identify the existence of chimeric reads in their corresponding regions. Therefore, the evidence for SARS-CoV-2's integration into host genome is lacking.

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The Efficacy of Whole Genome Sequencing and RNA-Seq in the Diagnosis of Whole Exome Sequencing Negative Patients with Complex Neurological Phenotypes

Journal of Pediatric Genetics ◽

10.1055/s-0041-1736610 ◽

2021 ◽

Author(s):

Bianca Blake ◽

Lauren I. Brady ◽

Nicholas A. Rouse ◽

Peter Nagy ◽

Mark A. Tarnopolsky

Keyword(s):

Whole Genome Sequencing ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Genome Sequencing ◽

Diagnostic Yield ◽

Whole Genome ◽

Rna Seq ◽

Complete Coverage ◽

Whole Exome ◽

Chromosome Microarray

AbstractWhole-genome sequencing (WGS) is being increasingly utilized for the diagnosis of neurological disease by sequencing both the exome and the remaining 98 to 99% of the genetic code. In addition to more complete coverage, WGS can detect structural variants (SVs) and intronic variants (SNVs) that cannot be identified by whole exome sequencing (WES) or chromosome microarray (CMA). Other multi-omics tools, such as RNA sequencing (RNA-Seq), can be used in conjunction with WGS to functionally validate certain variants by detecting changes in gene expression and splicing. The objective of this retrospective study was to measure the diagnostic yield of duo/trio-based WGS and RNA-Seq in a cohort of 22 patients (20 families) with pediatric onset neurological phenotypes and negative or inconclusive WES results in lieu of reanalysis. WGS with RNA-Seq resulted in a definite diagnosis of an additional 25% of cases. Sixty percent of these solved cases arose from the identification of variants that were missed by WES. Variants that could not be unequivocally proven to be causative of the patients' condition were identified in an additional 5% of cases.

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Whole genome sequencing reveals a 7 base-pair deletion in DMD exon 42 in a dog with muscular dystrophy

Mammalian Genome ◽

10.1007/s00335-016-9675-2 ◽

2016 ◽

Vol 28 (3-4) ◽

pp. 106-113 ◽

Cited By ~ 13

Author(s):

Peter P. Nghiem ◽

Luca Bello ◽

Cindy Balog-Alvarez ◽

Sara Mata López ◽

Amanda Bettis ◽

...

Keyword(s):

Muscular Dystrophy ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Base Pair ◽

Whole Genome ◽

Base Pair Deletion

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HGG-57. WHOLE-GENOME SEQUENCING, METHYLATION ANALYSIS, AND SINGLE-CELL RNA-SEQ DEFINE UNIQUE CHARACTERISTICS OF PEDIATRIC TREATMENT-INDUCED HIGH-GRADE GLIOMA AND SUGGEST ONCOGENIC MECHANISMS

Neuro-Oncology ◽

10.1093/neuonc/noaa222.336 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii354-iii354

Author(s):

John Lucas ◽

John DeSisto ◽

Ke Xu ◽

Andrew Donson ◽

Tong Lin ◽

...

Keyword(s):

Gene Expression ◽

Whole Genome Sequencing ◽

Single Cell ◽

Genome Sequencing ◽

High Grade Glioma ◽

Whole Genome ◽

High Grade ◽

Rna Seq ◽

Mutational Signatures ◽

Pediatric Treatment

Abstract BACKGROUND Pediatric treatment-induced high-grade glioma (TIHGG) is among the most severe late effects observed in childhood cancer survivors and is uniformly fatal. We previously showed that TIHGG are divergent from de novo pediatric high-grade glioma (pHGG) and cluster into two gene expression subgroups, one stemlike and the other inflammatory. Here we systematically compared TIHGG molecular profiles to pHGG and evaluated expression and single cell sequencing profiles in order to identify oncogenic mechanisms and the cellular basis for the observed TIHGG gene expression subgroups. MATERIALS/ METHODS 450/850K methylation and mutational signature analysis was conducted in 36 TIHGG samples. Resultant data were analyzed for the presence of chromothripsis, distinct molecular alterations, and mutational signatures in a subset of 10 samples with whole genome sequencing data. Five TIHGGs underwent single-cell RNA-Seq analysis (scRNAseq). RESULTS 26/36 TIHGG clustered with the pedRTK1 methylation class. TIHGG were characterized by an increased frequency of chromothripsis relative to pHGG (67% vs. 31%, p=0.036). FISH and WGS revealed frequent PDGFRA amplification secondary to enrichment in ecDNA. TIHGG were enriched for COSMIC mutational signatures 5 and 19 (p=0.0003) relative to pHGG. scRNAseq data showed that TIHGG tumors are composed of stem-like, neuronal, and inflammatory cell populations which may contribute to the previously described dominant expression profiles. CONCLUSIONS TIHGG represents a distinct molecular subtype of pHGG. Chromothripsis, leading to enriched expression of genes in extrachromosomal DNA, likely contribute to TIHGG oncogenesis. The dominant cell type (stem-like vs. inflammatory) may define the expression subgroup derived from bulk RNA-seq in heterogeneous tumors.

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Patients with PMD who are thoroughly screened by Genomic medicine have a considerable chance of benefiting greatly from whole-genome sequencing

10.31219/osf.io/dajft ◽

2021 ◽

Author(s):

Moataz Dowaidar

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Direct Sequencing ◽

Genomic Medicine ◽

Diagnostic Process ◽

Whole Genome ◽

Rna Seq ◽

Tissue Samples ◽

Long Read ◽

Major Transition

It appears that the role of genetics in neurology is undergoing a major transition in the present. The scope of genomic medicine has advanced from the only realm of academic investigation to the well-established and widely accepted instrument for genetic labs. Previously, this test was reserved for the most challenging patients, but today it is being utilized as a first step in looking at rare inherited neurological disorders. Researchers and clinicians working in the field of mitochondrial medicine will need to employ new laboratory techniques and DNA sequencing technology in order to move forward with future diagnosis methods and cut down on research time. Patients with PMD who are thoroughly screened have a considerable chance of benefiting greatly from whole-genome sequencing (WGS) at the beginning of their diagnostic process. Using long-read sequencing, there is the potential to help in the discovery of new genetic causes of PMD, the resolution of phasing issues, and the advancement of RNA and mtDNA investigations by way of direct sequencing. With the use of a great number of tissue samples from patients with PMD, there are significant advantages which can greatly promote the quick implementation of this technique into diagnostic laboratories. As RNA-seq technology is introduced into diagnostic laboratories, it will serve as an accurate means to examine the entire spectrum of disease while providing support for difficult cases. The plentiful supply of tissue samples from patients with PMD further enhances the ability of RNA-seq to rapidly be adopted in these laboratories. Finally, more validation of innovative tRNA approaches will be required in order to determine the pathogenicity of this common group of mtDNA-related PMDs.

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Prioritizing disease-related genes and pathways by integrating patient-specific iPSC-derived RNA-seq and whole genome sequencing in hypoplastic left heart syndrome

BMC Bioinformatics ◽

10.1186/1471-2105-15-s10-p7 ◽

2014 ◽

Vol 15 (Suppl 10) ◽

pp. P7

Author(s):

Xing Li ◽

Almudena Martinez-Fernandez ◽

Jeanne Theis ◽

Jean-Pierre Kocher ◽

Andre Terzic ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Hypoplastic Left Heart Syndrome ◽

Genome Sequencing ◽

Patient Specific ◽

Whole Genome ◽

Left Heart ◽

Rna Seq ◽

Hypoplastic Left Heart ◽

Disease Related Genes ◽

Left Heart Syndrome

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Homozygous duplication identified by whole genome sequencing causes LRBA deficiency

npj Genomic Medicine ◽

10.1038/s41525-021-00263-z ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Daniele Merico ◽

Yehonatan Pasternak ◽

Mehdi Zarrei ◽

Edward J. Higginbotham ◽

Bhooma Thiruvahindrapuram ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Cytotoxic T Lymphocyte ◽

Genetic Defect ◽

Digital Pcr ◽

Comparative Genomic ◽

Whole Genome ◽

Reading Frame ◽

Inherited Immunodeficiency ◽

Genetic Aberration

AbstractIn more than one-third of primary immunodeficiency (PID) patients, extensive genetic analysis including whole-exome sequencing (WES) fails to identify the genetic defect. Whole-genome sequencing (WGS) is able to detect variants missed by other genomics platforms, enabling the molecular diagnosis of otherwise unresolved cases. Here, we report two siblings, offspring of consanguineous parents, who experienced similar severe events encompassing early onset of colitis, lymphoproliferation, and hypogammaglobulinemia, typical of lipopolysaccharide-responsive and beige-like anchor (LRBA) or cytotoxic T lymphocyte antigen 4 (CTLA4) deficiencies. Gene-panel sequencing, comparative genomic hybridization (CGH) array, and WES failed to reveal a genetic aberration in relevant genes. WGS of these patients detected a 12.3 kb homozygous tandem duplication that was absent in control cohorts and is predicted to disrupt the reading frame of the LRBA gene. The variant was validated by PCR and Sanger sequencing, demonstrating the presence of the junction between the reference and the tandem-duplicated sequence. Droplet digital PCR (ddPCR) further confirmed the copy number in the unaffected parents (CN = 3, heterozygous) and affected siblings (CN = 4, homozygous), confirming the expected segregation pattern. In cases of suspected inherited immunodeficiency, WGS may reveal a mutation when other methods such as microarray and WES analysis failed to detect an aberration.

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