Computational protocol: Overlap between Parkinson disease and Alzheimer disease in ABCA7 functional variants

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Protocol publication

[…] Fragmented DNA was captured using the Agilent SureSelect Human All Exon Kit (Agilent Technologies, Santa Clara, CA), designed to cover 38 Mb or 50 Mb of human genomic sequences. We used the 38 Mb capture kit in the initial 15 individuals (all patients); the remaining samples (N = 603) were processed using the 50 Mb version 3 kit. The libraries were loaded onto an Illumina cBot for cluster generation (Illumina, San Diego, CA). The primer-hybridized flow cells were then transferred to HiSeq2000 sequencers and paired-end sequencing was performed in a 2 × 101b mode (Illumina). The base calling was performed by Illumina CASAVA 1.6 pipeline and aligned to hg19 using Genome Analysis Tool Kit (GATK) v1.1. The Unified Genotyper from GATK performs variant quality score (VQS) recalibration and genotype refinement to make accurate variant calls. In addition, the Unified Genotyper generates normalized Phred-scaled likelihood (PL) scores without priors for each alternate genotype. Variants with VQSLOD <−3, depth <6, and alternate PL scores <99 are excluded from the rest of the analysis presented here. Missing genotypes in reflect low depth of sequencing reads in certain coding regions, not low quality of the called genotypes and are consistent across patient and control data sets. [...] Variants were annotated using SeattleSeq including function within the gene and Combined Annotation Dependent Depletion (CADD) scores. Variants with CADD scores >20 were included in the analysis, as these are among the 1% highest ranked positions genome-wide in terms of potential functionality. […]

Pipeline specifications

Software tools BaseSpace, GATK, CADD
Applications WGS analysis, WES analysis
Organisms Homo sapiens