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[…] target all exons and flanking 5′ and 3′UTR (untranslated region) sequences (default settings). In total, 909 oligonucleotide probes covering 256,248 bp (base pairs) were included. Genomic DNA was extracted from whole blood using standard techniques; DNA samples were prepared in multiplex according to standard TruSeq Sample Prep and Custom Enrichment protocols (Illumina), and 75 base pairs were sequenced in each direction (paired-end). Sequencing was performed on the Illumina HiScan SQ. Samples from affected and controls were run in two separate runs., Bioinformatic analysis consisted of a standard protocol including image analysis and base calling by Illumina RTA 1.12.4.2, demultiplexing by CASAVA 1.8 (Illumina), and alignment of sequence reads to the reference genome GRCh37/hg19 by BWA []. Picard (http://picard.sourceforge.net/) was used for removing PCR duplicates. The GATK (Genome Analysis Toolkit) was applied for base quality score recalibration, INDEL (insertion and deletion) realignment, and SNP (single nucleotide polymorphism) and INDEL discovery [, ]. Annotation of sequence variants was performed by Annovar []. Variants present in exons ±10 bp intron sequences and 3′- and 5′UTR (untranslated region) were included in further analysis., Variants were classified into five pathogenicity classes (). Variants were classified based on frequency data from 1000 genomes (http://www.1000genomes.org/), dbSNP 135 (http://www.ncbi.nlm.nih.gov/projects/SNP/), 180 in-house normal controls, pathogenicity predictions through the Alamut interface v2.2-0 (Interactive Biosoftware, Rouen, France), and reports in HGMD, IPNMDB, and the literature [, , ]. Variants with prevalence ≥ 0.1% in dbSNP 135 or 1000 genomes and presence in ≥ 2 in-house normal controls were removed unless homozygous or compound heterozyg […]

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