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Pipeline publication

[…] cal entities ()., Here, we describe one more of these cases: a patient clinically diagnosed with AD found by exome sequencing to harbor a nonsense mutation in the PRNP gene., 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., The analysis of the exome sequencing data confirmed the absence of pathogenic mutations in APP, PSEN1, and PSEN2. Additionally, no coding variants were found in the dementia associated genes APP, PSEN2, GRN, TREM2, or PLD3. The patient was found to carry the PSEN1 (NM_000021) p.E318G and the MAPT (NM_001123066) p.Q230R variants., Further inspection of the 9423 coding variants found (445 of which were novel), revealed a nonsense mutation in PRNP (NM_000311, c.C478T; p.Q160*; rs80356711) associated with homozygosity for the V allele at position 129 of the protein., The patient was followed in the Mayo […]

Pipeline specifications

Software tools BWA, GATK, SnpEff