Similar protocols

Protocol publication

[…] enes flanking 50 kb upstream and downstream the DMCpG, distance used in similar studies., , We selected altered genes by Z-score, selecting Z-scores over 2 (P-value <0.05) or 1.5 if two genes were altered in the same region, as recommended in expression analysis., The coding region of five selected genes (ERMN, STX16, SMG7-AS1, PIK3CD and ZCCHC9) was included in a targeted resequencing panel analyzing 279 additional idiopathic ASD cases and 105 controls. Samples were fragmented and processed with the TruSeq DNA Sample Preparation kit (Illumina). The libraries were captured by the NimbleGen SeqCap EZ custom Library (Hofman-La Roche, Basel, Switzerland). Quality control was assessed using FastQC tool, adapter sequences were trimmed using Trim Galore and mapping was performed using BWA. GATK was used for variant calling and Annovar for functional annotation. Rare mutations predicted deleterious (loss of function or missense predicted damaging with the CONDEL program) were selected. We also analyzed exome data of ASD patients available from dbGAP (accession=phs000482.v1.p1 and phs000298.v1.p1; n=931) in order to define the number of deleterious mutations in selected genes. To define whether the burden of deleterious mutations is higher in ASD, we use exome data from controls in the EXAC database, and compared the mutational load in cases and controls (Fisher’s test FDR corrected)., We searched for enriched pathways in DAVIDGo database, and for over-represented functions using CPDB for all the genes associated to the DMCpGs, as well as for the subset of genes with significant association and located in the DMRs., Clustering and principal co […]

Pipeline specifications

Software tools FastQC, Trim Galore!, BWA, GATK, ANNOVAR, Condel
Databases dbGaP
Organisms Homo sapiens