Computational protocol: Screening for novel hexanucleotide repeat expansions at ALS- and FTD-associated loci

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Protocol publication

[…] G4C2 repeat numbers in the longer allele were determined by repeat-primed PCR as previously reported, followed by capillary electrophoresis and fragment analysis. The primer sequences are included in table e-2. The individual reverse primers for each candidate gene were designed using Primer 3 tools (http://biotools.umassmed.edu/bioapps/primer3_www.cgi) and were labeled with either 6-FAM or 5-HEX fluorescent dye. The PCR products were diluted in highly deionized formamide (HiDi formamide; ThermoFisher Scientific, Waltham, WA) containing size standard ROX-1000 (BioVenture, TN). Fragment analysis was performed at the University of Michigan Sequencing Core facility on an ABI 3730 Sequencer. The data were analyzed using GeneMarker (SoftGenetics, PA) to determine the maximal repeat number. […]

Pipeline specifications

Software tools Biotools, Primer3, GeneMarker
Applications Population genetic analysis, qPCR
Organisms Homo sapiens
Diseases Amyotrophic Lateral Sclerosis, Frontotemporal Dementia