Next Generation Sequencing

Genome Sequencing for 50 Intellectual Disability trios

Genome sequencing was performed in 50 persons with severe Intellectual Disability and their unaffected parents. On the basis of diagnostic interpretation of all de novo variants, a conclusive genetic diagnosis was reached in 20 patients. Together with one compound heterozygous CNV causing disease in a recessive mode, this results in a diagnostic yield of 42% in this extensively studied cohort, and 62% as a cumulative estimate in an unselected cohort. These results suggest that de novo SNVs and CNVs affecting the coding region are a major cause of severe ID.

Dataset: Data included in this manuscript have been deposited at the European Genome-phenome Archive under accession number EGAS00001000769.
Publication: Genome sequencing identifies major causes of severe intellectual disability. Gilissen et al. Nature. 2014 Jul 17;511(7509):344-7.

Exome Sequencing for 100 Intellectual Disability trios

Exome sequencing was performed in 100 persons with severe Intellectual Disabillity and their unaffected partents. This was done in a diagnostic setting to asses the diagnostic yield of Exome sequencing and evaluate the role of de novo mutations.

Dataset: BAM files are available under controlled access at the European Genome-Phenome Archive, EGAS00001000287
Publication: Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability de Ligt J et al. N Engl J Med. (2012)


Genotyping data from 120 trios with unexplained mental retardation

In the study we present a multicenter study in which three European diagnostic centres assessed the use of Affymetrix Mapping 500k SNP arrays for molecular karyotyping in patients with mental retardation Each centre tested DNA from 40 patients with unexplained mental retardation together with their parents. In addition, 38 DNA samples containing known submicroscopic copy number variations (CNVs) were run for validation purposes.

Dataset: GSE13117 record
Publication: Molecular karyotyping of patients with unexplained mental retardation by SNP arrays: a multicenter study. McMullan DJ et al. Hum Mutat. (2009)



MIPVAR (MIP VARiant calling tool) is a fully automated Molecular Inversion Probe (MIP) analysis tool for large-scale MIP experiments. MIPVAR provides support for varying MIP insert sizes and the use of molecular barcodes used in single molecule MIPs (smMIPs). Additionally MIPVAR provides detailed coverage information per MIP.

Publication: MIPVAR: MIP VARiant calling van de Vorst M et al. Submitted to Bioinformatics
Download page: Download MIPVAR at Sourceforge
More information: Maartje van de Vorst


Mobster is a program to detect novel (non-reference) Mobile Element Insertion (MEI) events in Whole Exome and Whole Genome Next Generation Sequencing data with high accuracy. It reads in BAM files and uses both a discordant read pair method and a split-read method to detect these MEI events.

Publication: Mobster: accurate detection of mobile element insertions in next generation sequencing data Thung DT et al. Genome Biol. (2014)
Download page: Download Mobster at Sourceforge
More information: Djie Tjwan Thung


GeCCO (Genomic CNV Classification Objectively) is a bioinformatics tool for classifying copy number variants as either benign or pathogenic.

Publication: Accurate Distinction of Pathogenic from Benign CNVs in Mental Retardation Hehir-Kwa JY et al. PLoS Comput Biol. (2010)
Download page: GeCCO at
More information: Jayne Hehir-Kwa

Screenshot of how the program looks like

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