An in-house multilocus SNP genotyping assay for evaluation of complex genetic diseases

<p><b>Background:</b> With an increase in the discovery of newer genetic loci/polymorphisms in complex multifactorial diseases, there is also an increased need for methods that can simultaneously genotype multiple loci in a cost-effective manner. Using coronary artery disease (CAD) as a model, the study aimed to develop an in-house multilocus assay for simultaneous detection of 17 genetic variants in 11 genes implicated in CAD.</p> <p><b>Methods:</b> A multiplex polymerase chain reaction (PCR)-based reverse line blot hybridization (MPCR-RLBH) approach was used, where each DNA sample was amplified using two separate MPCRs, and the alleles were genotyped using covalently immobilized, amino-linked sequence-specific oligonucleotide probes using an enhanced chemiluminescence system. The assay performance was tested on 75 healthy controls and 75 angiographically proven CAD cases. Validation was done by automated Sanger sequencing.</p> <p><b>Results:</b> The assay could successfully discriminate both the alleles at <i>CETP</i> (I405V), <i>LPL</i> (D9N), <i>NOS3</i> (T-786G and E298D), <i>LIPC</i> (C-514T), <i>FGB</i> (G-455A), <i>ITGB3</i> (L33P), <i>AGT</i> (M235T), and <i>MTR</i> (A2756G) loci. Certain mutations included in this assay such as ins242G, ins397G, E387K, L393K in the <i>LDLR</i>; N291S in the <i>LPL</i>; D442G in the <i>CETP</i>; and T833C in the <i>CBS</i> genes were found to be absent. The genotype results obtained using this assay showed 100% concordance with sequencing.</p> <p><b>Conclusion:</b> The study demonstrated development and validation of a multiplex SNP genotyping assay that can be used to assess genetic risk factors in CAD. The assay provides a cost-effective alternative to expensive high throughput genotyping systems in common molecular research laboratories.</p

MicroRNA Profiling in Intraocular Medulloepitheliomas

<div><p>Purpose</p><p>To study the differential expression of microRNA (miRNA) profiles between intraocular medulloepithelioma (ME) and normal control tissue (CT).</p><p>Material and Methods</p><p>Total RNA was extracted from formalin fixed paraffin embedded (FFPE) intraocular ME (n=7) and from age matched ciliary body controls (n=8). The clinical history and phenotype was recorded. MiRNA profiles were determined using the Affymetrix GeneChip miRNA Arrays analyzed using expression console 1.3 software. Validation of significantly dysregulated miRNA was confimed by quantitaive real-time PCR. The web-based DNA Intelligent Analysis (DIANA)-miRPath v2.0 was used to perform enrichment analysis of differentially expressed (DE) miRNA gene targets in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway.</p><p>Results</p><p>The pathologic evaluation revealed one benign (benign non-teratoid, n=1) and six malignant tumors (malignant teratoid, n=2; malignant non-teratoid, n = 4). A total of 88 miRNAs were upregulated and 43 miRNAs were downregulated significantly (P<0.05) in the tumor specimens. Many of these significantly dysregulated miRNAs were known to play various roles in carcinogenesis and tumor behavior. RT-PCR validated three significantly upregulated miRNAs and three significantly downregulated miRNAs namely miR-217, miR-216a, miR-216b, miR-146a, miR-509-3p and miR-211. Many DE miRNAs that were significant in ME tumors showed dysregulation in retinoblastoma, glioblastoma, and precursor, normal and reactive human cartilage. Enriched pathway analysis suggested a significant association of upregulated miRNAs with 15 pathways involved in prion disease and several types of cancer. The pathways involving significantly downregulated miRNAs included the toll-like receptor (TLR) (p<4.36E-16) and Nuclear Factor kappa B (NF-κB) signaling pathways (p<9.00E-06).</p><p>Conclusions</p><p>We report significantly dysregulated miRNAs in intraocular ME tumors, which exhibited abnormal profiles in other cancers as well such as retinoblastoma and glioblastoma. Pathway analysis of all dysregulated miRNAs shared commonalities with other cancer pathways.</p></div

MiRNAs differentially regulated in medulloepitheliomas (n = 7), retinoblastoma, glioblastoma, and chondrocytes (precursor, normal, reactive).

<p>^† P: Precursor chondrocytes, N: Normal chondrocytes, R: Reactive chondrocytes, All: All three types of chondrocytes (P, N, and R).</p><p>MiRNAs differentially regulated in medulloepitheliomas (n = 7), retinoblastoma, glioblastoma, and chondrocytes (precursor, normal, reactive).</p

Volcano plot of differentially expressed miRNAs in seven cases of medulloepithelioma.

<p>The x-axis shows the log2 fold-change in miRNA expression and y-axis shows the-Log10 of the p-value from tumor versus control miRNA expression counts. Labelled miRNAs have Log2 fold change greater than 2SD from the mean.</p

Clinical and Demogrpahic details of patients included in the study.

<p>M: Male; F: Female; Y: Years; AC: anterior chamber; OD: right eye; OS: left Eye; HM: hand motion; TRD: tractional retinal detachment.</p><p>Clinical and Demogrpahic details of patients included in the study.</p

MiRNAs significantly overexpressed (p < 0.05) by at least 2 standard deviations in tumors compared to control samples.

<p>MiRNAs significantly overexpressed (p < 0.05) by at least 2 standard deviations in tumors compared to control samples.</p

MiRNAs significantly underexpressed (p < 0.05) by at least 2 standard deviations in tumors compared to control samples.

<p>MiRNAs significantly underexpressed (p < 0.05) by at least 2 standard deviations in tumors compared to control samples.</p

qPCR validation Data.

<p>qPCR validation Data.</p