The MC1R single nucleotide polymorphisms identification by DNA-microarray on miniaturized silicon chip

• Published in: Sensors and actuators. B, Chemical Chemical, 2021-11, Vol.346, p.130514, Article 130514
• Main Authors: Petralia, Salvatore, Vigilanza, Antonella, Sciuto, Emanuele, Maffia, Michele, Romanini, Antonella, Conoci, Sabrina
• Format: Article
• Language: English
• Subjects: Aluminum; Confidence intervals; Discrimination; DNA-microarray; Hybridization; Investigations; MC1R gene; Melanin; Melanoma; Multilayers; Nucleotides; Optical communication; Polymorphism; Silicon dioxide; Single nucleotide polymorphisms
• ISSN: 0925-4005; 1873-3077
• DOI: 10.1016/j.snb.2021.130514

•Innovative miniaturized silicon microarray for t MC1R Single Nucleotide Polymorphisms identification.•Straightforward Discrimination Factor allowing detection of an SNP in an unknown genotype with a >99 % confidence level.•High sensitivity with discrimination factors above 0.4 for all variants investigated rs1805005, rs1805006 and rs885479.•Biosensing strategy suitable for genetic assay in portable format for molecular detection of MC1R gene. The melanocortin 1 receptor (MC1R) gene plays a key role in the control of melanin formation. Polymorphism in the MC1R gene have been associated with Cutaneous melanoma risk and therefore molecular investigation is essential to prevent the pathology and to reduce melanoma mortality. In the current study, we investigated single nucleotide polymorphism for the MC1R target gene using a miniaturized silicon-based microarray-chip. The microarray substrates were properly designed with a multilayer component (Si/Al/SiO2) to enhance the hybridization optical signal by Al layer acting as a mirror while the SiO2 thickness was optimized for light constructive interference. The microarray probe density was found to be 1.900 ± 200 molecules μm−2. The genotyping experiments performed at different wild type and mutated target amount have shown good sensitivity with discrimination factor >4 for all investigated variants namely rs1805005 V60 L (252 C→T), rs1805006 D84E (425 G→A) and rs885479 R163Q (451 C→T). The obtained Discrimination Factor (DF) values highlights that the assay would allow detection of SNP in an unknown genotype with a >99 % confidence level. Results pave the way for future development of genetic assay in portable format for molecular detection of MC1R gene.