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A Multi-detection Assay for Malaria Transmitting Mosquitoes

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Novel biosensor-based microarray assay for detecting rs8099917 and rs12979860 genotypes.

Pei-Yuan Li¹, Xiao-Jun Zhou, Lan Yao

¹Department of Gastroenterology, the Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai 519000, Guangdong Province, China.

World Journal of Gastroenterology

|December 1, 2012

Summary

A novel biosensor-based microarray (BBM) assay accurately detects interleukin 28B-associated polymorphisms (SNPs) rs12979860 and rs8099917. This rapid, specific, and sensitive assay is suitable for clinical use.

Keywords:

Assay Biosensor-based microarray Detection Hepatitis C virus rs12979860 rs8099917

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

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Published on: June 21, 2018

Area of Science:

Genetics
Molecular Biology
Biotechnology

Background:

Interleukin 28B (IL28B) gene polymorphisms, specifically rs12979860 and rs8099917, are crucial in predicting hepatitis C treatment outcomes.
Accurate and efficient genotyping of these single nucleotide polymorphisms (SNPs) is essential for personalized medicine approaches in managing hepatitis C virus (HCV) infection.

Purpose of the Study:

To develop and evaluate a novel biosensor-based microarray (BBM) assay for the simultaneous detection of rs12979860 and rs8099917 genotypes.
To assess the specificity, sensitivity, and clinical applicability of the BBM assay compared to direct sequencing.

Main Methods:

Design and construction of a biosensor microarray with probes specific for rs8099917 (C/T) and rs12979860 (G/T) alleles.
Simultaneous amplification of target fragments using a one-tube polymerase chain reaction (PCR) system.
Hybridization of PCR amplicons to the BBM array and visual or digital camera-based signal detection.

Main Results:

The BBM assay successfully amplified and detected target fragments for both SNPs, with clear and distinct signals visible to the unaided eye.
High agreement was observed between the BBM assay and direct sequencing for both SNPs: 95% for rs8099917 and 92.5% for rs12979860, with substantial kappa values (0.88 and 0.85, respectively).
The assay demonstrated high specificity (100% agreement with plasmids) and sensitivity, capable of detecting SNP sequences in samples with as few as 10(2) white blood cells/μL.

Conclusions:

The developed biosensor microarray assay is a highly specific, sensitive, rapid, and user-friendly method for genotyping rs12979860 and rs8099917.
This BBM assay is compatible with clinical practice and offers a valuable tool for the detection of these important IL28B-associated SNPs.