Computational protocol: A specific mutation in TBL1XR1 causes Pierpont syndrome

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Protocol publication

[…] Targeted enrichment and massive parallel sequencing were performed on genomic DNA extracted from circulating leucocytes of four patients and the parents of one of them. Enrichment of the whole exome was performed using the Nimblegen SeqCap EZ Library V.3.0 (Roche). Each captured library was then loaded on a SOLiD5500xl platform (Applied Biosystems) (patient 20120174 and unaffected parents 20112227 and 20112228, and patients 20112226, 20121069 and 20121072). Paired-end and single-end sequence reads were aligned to hg19 using the Lifescope aligner (V.2.5.1) (Applied Biosystems). Presumed PCR duplicates were discarded using Picard Tools (http://picard.sourceforge.net) in case of single-end reads or Lifescope when dealing with paired-end reads. Local realignment and base-quality-score recalibration were performed with the Genome Analysis Toolkit (GATK2 V.2.2-5-g3bf5e3f).For reads mapping to the human genome reference, mean target region coverage for 20112226 and the trio was 94.5%, with average sequencing depth on target of 92× and for samples 20121069 and 20121072, respectively, 90.5% and 69×. Calls of SNPs and small insertions and deletions (INDELs) were based on 18 unrelated exomes using the GATK Unified Genotyper algorithm, and categorised based on their matching quality, depth of coverage, base quality, the combination of base quality and depth, the position of the alternate allele in the read, and strand bias. Variants were functionally annotated using KGGSeq v0.4 applying available public datasets from the 1000 Genomes Project, NHLBI GO Exome Sequencing Project and dbSNP (V.137), and predictions were made regarding probabilities of being disease causing. Only variants passing all applied GATK filters, predicted to be a de novo mutation within the trio and disease-causing by KGGSeq were retained. […]

Pipeline specifications

Software tools LifeScope, Picard, GATK, KGGSeq
Databases dbSNP
Application WES analysis
Organisms Homo sapiens