SpliceFinder integrates two functional annotation tools for NGS, ANNOVAR and MutationTaster and two canonical splice site prediction programs for single mutation analysis, SSPNN and NetGene2. To identify novel splicing variants from exome sequencing data, we developed a bioinformatics splice-site prediction procedure to analyze next-generation sequencing (NGS) data (SpliceFinder). Point mutations in intronic regions near mRNA splice junctions can affect the splicing process. Spinelli, Roberta Pirola, Alessandra Redaelli, Sara Sharma, Nitesh Raman, Hima Valletta, Simona Magistroni, Vera Piazza, Rocco Gambacorti-Passerini, Carlo Identification of novel point mutations in splicing sites integrating whole-exome and RNA- seq data in myeloproliferative diseases. Exome Pool- Seq is thus well suited for large-scale, cost-efficient and flexible screening in characterized but heterogeneous entities like NDDs. Compared with other large scale approaches using Molecular Inversion Probes (MIP) or gene panels, it allows flexible re-analysis of data. With a detection rate of 28%, Exome Pool- Seq achieves comparable results to individual exome analyses but reduces costs by >85%. Most of them were confirmed to be de novo, but we also identified X-linked or autosomal-dominantly or autosomal-recessively inherited variants. Twenty five of these were identified in 923 established NDD genes (based on SysID database, status November 2016) (ACTB, AHDC1, ANKRD11, ATP6V1B2, ATRX, CASK, CHD8, GNAS, IFIH1, KCNQ2, KMT2A, KRAS, MAOA, MED12, MED13L, RIT1, SETD5, SIN3A, TCF4, TRAPPC11, TUBA1A, WAC, ZBTB18, ZMYND11), two in 543 (SysID) candidate genes (ZNF292, BPTF), and additionally a de novo loss-of-function variant in LRRC7, not previously implicated in NDDs. In a pilot study with 96 cases we identified 27 variants, likely or possibly affecting function. Sequencing of 96 individuals can be performed in eight pools of 12 samples on less than one Illumina sequencer lane. To address this problem we applied Exome Pool- Seq as an economic and fast screening technology in neurodevelopmental disorders (NDDs). Despite falling costs this is still an expensive and laborious technique, particularly when studying large cohorts. High throughput sequencing has greatly advanced disease gene identification, especially in heterogeneous entities.

Popp, Bernt Ekici, Arif B Thiel, Christian T Hoyer, Juliane Wiesener, Antje Kraus, Cornelia Reis, AndrГѓВ© Zweier, Christiane Exome Pool- Seq in neurodevelopmental disorders.

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