Computational protocol: Exome sequencing in undiagnosed inherited and sporadic ataxias

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Protocol publication

[…] Blood genomic DNA was fragmented, exome enriched and sequenced (Illumina TruSeq™ 62 Mb and HiSeq 2000, 100 bp paired-end reads). Coverage data are summarized in Supplementary Tables 1 and 2. In-house bioinformatic analysis included alignment to UCSC hg19, using Burrows-Wheeler Aligner; duplicate removal (Picard v1.85) and variant detection (Varscan v2.2) (), Dindel v1.01 (). Further analysis was performed on variants with a minor allele frequency <0.01 in several databases: dbSNP137, 1000 Genomes (April 2012 data release), the National Heart, Lung and Blood Institute (NIH) Exome Sequencing Project (ESP) 6500 exomes, and 286 unrelated in-house controls. Rare homozygous and compound heterozygous variants were defined, and protein altering and/or putative ‘disease causing’ mutations, along with their functional annotation, were identified using ANNOVAR (). Putative pathogenic variants were confirmed by Sanger sequencing using custom-designed primers (http://frodo.wi.mit.edu) (ABI BigDye® v3.1 3130xl Genetic Analyzer, Life Technologies). Comparative genomic hybridization was performed in presumed recessive cases where a single likely pathogenic allele was found in a strong candidate gene. Quantitative pyrosequencing was used to determine the proportion of mutated alleles in given tissues (Pyromark v2.0, Qiagen; Supplementary Table 3). […]

Pipeline specifications

Software tools BWA, Picard, VarScan, Dindel, ANNOVAR
Databases dbSNP
Application WES analysis
Organisms Homo sapiens
Diseases Spinocerebellar Degenerations