Genetic Variant Detection in the CALR gene using High Resolution Melting Analysis

• Published in: Journal of visualized experiments no. 162
• Main Authors: Pajič, Tadej, Belčič Mikič, Tanja, Podgornik, Helena, Klun, Jurka, Šućurović, Sandra, Zver, Samo, Sever, Matjaz
• Format: Journal Article
• Language: English
• Published: United States 26-08-2020
• Subjects: Calreticulin - genetics; DNA - genetics; DNA Mutational Analysis - methods; Fluorescence; Genetic Variation; Humans; Limit of Detection; Mutation - genetics; Nucleic Acid Denaturation; Real-Time Polymerase Chain Reaction; Retrospective Studies
• ISSN: 1940-087X
• DOI: 10.3791/61642

High resolution melting analysis (HRM) is a powerful method for genotyping and genetic variation scanning. Most HRM applications depend on saturating DNA dyes that detect sequence differences, and heteroduplexes that change the shape of the melting curve. Excellent instrument resolution and special data analysis software are needed to identify the small melting curve differences that identify a variant or genotype. Different types of genetic variants with diverse frequencies can be observed in the gene specific for patients with a specific disease, especially cancer and in the CALR gene in patients with Philadelphia chromosome-negative myeloproliferative neoplasms. Single nucleotide changes, insertions and/or deletions (indels) in the gene of interest can be detected by the HRM analysis. The identification of different types of genetic variants is mostly based on the controls used in the qPCR HRM assay. However, as the product length increases, the difference between wild-type and heterozygote curves becomes smaller, and the type of genetic variant is more difficult to determine. Therefore, where indels are the prevalent genetic variant expected in the gene of interest, an additional method such as agarose gel electrophoresis can be used for the clarification of the HRM result. In some instances, an inconclusive result must be re-checked/re-diagnosed by standard Sanger sequencing. In this retrospective study, we applied the method to JAK2 V617F-negative patients with MPN.