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Disease associated tandem repeat genotyping from NGS target sequencing data

Repetitive DNA sequence represented a big technical challenge for NGS technologies. Their analysis istraditionally based on PCR-amplification followed by fluorescence capillary electrophoresis to identifyfragment length differences. Theoretically, NGS technology could offer several potential advantages forTandem Repeat Polymorphisms (TRPs) genotyping.Our aim was to test the feasibility of the analysis of TRPs in NGS data. To do this we compared 16 differentdisease-associated TRPs genotypes from short-read NGS data to those derived through fluorescencefragment analysis approach.We sequenced and analyzed 14 DNA samples affected by various neurodegenerative diseases with repeatexpansions of different lengths for 16 disease associated TRPs by Illumina MiSeq sequencing platform (300+300 bp reads). We performed a repeat specific capture probes design (Duitama 2014) which uses theflanking regions of the repeats to design enrichment probes in unique regions. For the target regionsenrichment, we used SureSelect XT Kit, (Agilent technologies). Besides a known bioinformatics tool(lobSTR), a new software procedure was successfully implemented to precisely genotype TRPs from NGSdata to achieve genotype accuracy and efficiency. Overall, we were able to compare 224 genotypes. Locusspecific TRP typing demonstrated a very good correlation (up to 80%) between genotypes derived byfluorescence fragment analysis and those measured by our NGS approach. Even for very large expansionswe have been able to identify the samples carrying a pathological expansion. This pilot experimentdemonstrated the feasibility of the analysis of TRPs in NGS data for a large number of loci.

Abstracts from the 51st European Society of Human Genetics Conference, Milano, 2018

Autori IIT:

Loredana Marialuisa Genovese

Foto di Loredana Marialuisa Genovese

Tipo: Abstract in atti di convegno
Area di disciplina: Computer Science & Engineering
Corrado, L., Geraci, F., Severgnini, M., Di Pierro, A., Frontini, V., Mangano, E., Genovese, L.M., Barizzone, N., D'Aurizio, R., Croce, R. and De Marchi, F., 2019, July. Disease associated tandem repeat genotyping from NGS target sequencing data. In EUROPEAN JOURNAL OF HUMAN GENETICS (Vol. 27, pp. 532-532). MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND: NATURE PUBLISHING GROUP.
File: s41431-019-0404-7 532.pdf

Attività: Biologia computazionale