Computational protocol: A nonsense mutation in PRNP associated with clinical Alzheimer's disease☆

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Protocol publication

[…] When genetic tests for APP, PSEN1, and PSEN2 revealed no mutations, the patient was included in a whole-exome sequencing study. Genomic DNA was prepared according to Illumina's TruSeq Sample Preparation v3 (Illumina, CA, USA) and capture was performed with Illumina's TruSeq Exome Enrichment according to the manufacturer's instructions. Sequencing was performed in Illumina's HiSeq2000 using 100 bp paired-end reads. Sequence alignment and variant calling were performed against the reference human genome (UCSC hg19) using bwa () and reads processed according with the Genome Analysis Toolkit best practices (). Variants were called using UnifiedGenotyper and recalibrated using VQSR, both tools from the GATK. Finally, variants were annotated using snpEff (). The PRNP mutation was confirmed by Sanger sequencing using standard methodology. […]

Pipeline specifications

Software tools BWA, GATK, SnpEff
Application WES analysis
Organisms Homo sapiens
Diseases Alzheimer Disease