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Pipeline publication

[…] d below were investigated. Informed consent (UCLH: N99/103) was obtained from all individuals and the institutional review boards at the participating medical centers approved the study. Acquired spastic paraplegia was excluded and neurophysiological studies, MRI scans and skin biopsies were performed using standard methods. Genomic DNA samples from the two affected individuals and two unaffected relatives were used for molecular genetic analyses (supplementary material). The mutation in the Cypriot family was previously reported []., Exome sequencing was performed as previously described [–] using the Agilent SureSelect kit and run on the Illumina HiSeq2500. Sequences were aligned with the Burrows-Wheeler Aligner, duplicates were removed with Picard, indels aligned and base quality scores recalibrated with the Genome Analysis Toolkit (GATK). The average sequencing depth was 55-fold with variants being filtered according to pathogenicity, inheritance pattern, and segregation in the family. We confirmed causative variant candidates by the Sanger sequencing method using an automatic genetic analyzer. SPG11 PCR primers were designed using Primer3 so that the PCR products would span whole exons and about 35 bp of flanking introns ( Primer sequences are listed in the supplementary file. Touchdown PCR was done using the PCR Master Mix (Roche) and is described in more detail in the supplementary table. PCR amplification products were cleaned with ExoAp. The purified PCR products was split into two and sequenced bidirectionally with the original primers that were used to amplify the region of interest and Big Dye Terminator Kit v.3.1 (Applied Biosystems) [, ]. Conditions were as follows: 25 cycles of denaturation at 95 °C for 10 s, annealing at 50 °C for 5 s and extension at 60 °C for 4 min. Sequencing reactions were cleaned using CleanSEQ SPRI beads according to the manufacturer’s protocol (Agencourt). Se […]

Pipeline specifications

Software tools BWA, Picard, GATK, Primer3
Diseases Nervous System Diseases, Peripheral Nervous System Diseases, Neurologic Manifestations, Peripheral Nervous System Diseases, Hereditary Sensory and Motor Neuropathy, Heredodegenerative Disorders, Nervous System, Nervous System Malformations, Peripheral Nervous System Diseases