Genotyping of common SIRPB1 copy number variant using Paralogue Ratio Test coupled to MALDI-MS quantification
Pascual Pons, Mariona
Sanchez Lopez, Isabel
MetadataShow full item record
Copy number variant (CNV) regions have been proven to have a significant impact on gene expression. Some of them have been also found to be associated to different human diseases. CNV genotyping is often prone to error and cross-validation with independent methods is frequently required. The platform of choice depends on whether it is a genome-wide discovery screening or a candidate CNV study, the cohort size and the number of CNVs included in the assay and, finally, the budget available. Here we illustrate a affordable approach to determine the CNV genotype using matrix-assisted laser desorption/ ionization mass spectrometry (MALDI-MS) and based on the quantitative determination of single nucleotide duplicated mismatches (SNDM) mapping the CNV region and a paralogue genomic region that is used as a two-copy reference. We have genotyped nsv436327, a common CNV mapping SIRPB1 intron 1 that has been associated to human personality behavior. SIRP cluster region was subjected to several ancestral duplication events what makes SIRPB1 CNV genotyping technically challenging. We designed three sets of primer pairs that amplified paralogue regions inside and outside the CNV, containing three SNDMs. Post-PCR extension analyses of sequencing oligonucleotides mapping immediately upstream each SNDM allowed us to quantify using MALDI-MS the proportion of PCR products derived from the CNV region versus the external reference. In contrast to other approaches, setting up this genotyping method requires an affordable investment.
Is part ofMolecular and Cellular Probes, 2015, vol. 29, núm. 6, p. 517-521
European research projects
Showing items related by title, author, creator and subject.
A common copy-number variant within SIRPB1 correlates with human Out-of-Africa migration after genetic drift correction Royo Sánchez-Palencia, José Luis; Valls Marsal, Joan; Acemel, Rafael D.; Gómez-Marin, Carlos; Pascual Pons, Mariona; Lupiañez, Arantxa; Gomez-Skarmeta, Jose Luis; Fibla Palazón, Joan (Public Library of Science, 2018)Previous reports have proposed that personality may have played a role on human Out-Of- Africa migration, pinpointing some genetic variants that were positively selected in the migrating populations. In this work, we ...
De novo assembly of the Brown trout (Salmo trutta m. fario) brain and muscle transcriptome: transcript annotation, tissue differential expression profile and SNP discovery Fibla Palazón, Joan; Oromí Farrús, Neus; Pascual Pons, Mariona; Royo Sánchez-Palencia, José Luis; Palau, Antoni; Fibla, M. (BMC, 2020-11-02)Objectives: The Brown trout is a salmonid species with a high commercial value in Europe. Life history and spawning behaviour include resident (Salmo trutta m. fario) and migratory (Salmo trutta m. trutta) ecotypes. The ...
Differential metabolic profiles associated to movement behaviour of stream-resident brown trout (Salmo trutta) Oromí Farrús, Neus; Jové Font, Mariona; Pascual Pons, Mariona; Royo Sánchez-Palencia, José Luis; Rocaspana, Rafel; Aparicio, Enric; Pamplona Gras, Reinald; Palau, Antoni; Sanuy i Castells, Delfí; Fibla Palazón, Joan; Portero Otín, Manuel (Public Library of Science, 2017)The mechanisms that can contribute in the fish movement strategies and the associated behaviour can be complex and related to the physiology, genetic and ecology of each species. In the case of the brown trout (Salmo ...