Evaluation of the SNP rs2367563 genotyping test as an adjunctive detection tool for dental metal hypersensitivity

Abstract Background Knowledge translation (KT) is challenging to carry out and assess. The content of a program developed to foster KT activities pertaining to the Elder Abuse Suspicion Index (EASI)©, a tool to help identify elder abuse, is described, along with reporting and analysis of some of its outcomes. Methods Enquiries about the use of the EASI were encouraged through completion of a structured questionnaire available on an EASI website. These were submitted by email and guided individualized responses. Descriptive data collated anonymously from the questionnaires described in aggregate corresponders’ occupations, countries of work, information needs about the tool, and intent of use. The processes that generated this data were evaluated as to whether they conformed to established elements of KT. Results One hundred thirty-eight queries were received over 6 years coming from enquirers with 12 different professional backgrounds, working in 25 countries. The information sought aimed to facilitate EASI use in clinical, quality improvement, public health, research, teaching, KT, and commercial ventures. Conclusions This activity, incorporating recognized elements of a KT undertaking, documents specific global interests in elder abuse detection. It suggests a model for researchers to gauge interest in their findings and to promote exchange around them.

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Quick Response Code Validation and Phishing Detection Tool

2021 IEEE 11th IEEE Symposium on Computer Applications & Industrial Electronics (ISCAIE) ◽

10.1109/iscaie51753.2021.9431807 ◽

2021 ◽

Author(s):

Safwati Ismail ◽

Mohammed Hazim Alkawaz ◽

Alvin Ebenazer Kumar

Keyword(s):

Quick Response ◽

Response Code ◽

Detection Tool ◽

Code Validation ◽

Quick Response Code ◽

Phishing Detection

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Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

Scientific Reports ◽

10.1038/s41598-021-83459-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Joseph Tomlinson ◽

Shawn W. Polson ◽

Jing Qiu ◽

Juniper A. Lake ◽

William Lee ◽

...

Keyword(s):

Broiler Chickens ◽

Nucleotide Polymorphisms ◽

Rna Seq ◽

Specific Expression ◽

Single Nucleotide ◽

Allele Specific Expression ◽

Detection Tool ◽

Commercial Broiler ◽

Significant Phenomenon ◽

Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

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FGFR3 overexpression is a useful detection tool for FGFR3 fusions and sequence variations in glioma

Neuro-Oncology Practice ◽

10.1093/nop/npaa075 ◽

2020 ◽

Author(s):

Jens Schittenhelm ◽

Lukas Ziegler ◽

Jan Sperveslage ◽

Michel Mittelbronn ◽

David Capper ◽

...

Keyword(s):

Coiled Coil ◽

Growth Factor Receptor ◽

Gene Mutations ◽

Diagnostic Tools ◽

Wild Type ◽

Rt Pcr ◽

Fgfr3 Gene ◽

Detection Tool ◽

Sequence Variations ◽

Gene Panel Sequencing

Abstract Background Fibroblast growth factor receptor (FGFR) inhibitors are currently used in clinical development. A subset of glioblastomas carries gene fusion of FGFR3 and transforming acidic coiled-coil protein 3. The prevalence of other FGFR3 alterations in glioma is currently unclear. Methods We performed RT-PCR in 101 glioblastoma samples to detect FGFR3-TACC3 fusions (“RT-PCR cohort”) and correlated results with FGFR3 immunohistochemistry (IHC). Further, we applied FGFR3 IHC in 552 tissue microarray glioma samples (“TMA cohort”) and validated these results in two external cohorts with 319 patients. Gene panel sequencing was carried out in 88 samples (“NGS cohort”) to identify other possible FGFR3 alterations. Molecular modeling was performed on newly detected mutations. Results In the “RT-PCR cohort,” we identified FGFR3-TACC3 fusions in 2/101 glioblastomas. Positive IHC staining was observed in 73/1024 tumor samples of which 10 were strongly positive. In the “NGS cohort,” we identified FGFR3 fusions in 9/88 cases, FGFR3 amplification in 2/88 cases, and FGFR3 gene mutations in 7/88 cases in targeted sequencing. All FGFR3 fusions and amplifications and a novel FGFR3 K649R missense mutation were associated with FGFR3 overexpression (sensitivity and specificity of 93% and 95%, respectively, at cutoff IHC score > 7). Modeling of these data indicated that Tyr647, a residue phosphorylated as a part of FGFR3 activation, is affected by the K649R mutation. Conclusions FGFR3 IHC is a useful screening tool for the detection of FGFR3 alterations and could be included in the workflow for isocitrate dehydrogenase (IDH) wild-type glioma diagnostics. Samples with positive FGFR3 staining could then be selected for NGS-based diagnostic tools.

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