TY - JOUR T1 - DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation JF - bioRxiv DO - 10.1101/151126 SP - 151126 AU - Elizabeth Nacheva AU - Katya Mokretar AU - Aynur Soenmez AU - Alan M Pittman AU - Colin Grace AU - Roberto Valli AU - Ayesha Ejaz AU - Selina Vattathil AU - Emanuela Maserati AU - Henry Houlden AU - Jan-Willem Taanman AU - Anthony H Schapira AU - Christos Proukakis Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/06/16/151126.abstract N2 - Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol. Droplet digital PCR of two genes also showed protocol-dependent losses. Whole genome sequencing showed GC-dependent variation in coverage with spin column isolation from cerebellum. We also extracted and sequenced DNA from substantia nigra using salting-out and phenol / chloroform. The mtDNA copy number, assessed by reads mapping to the mitochondrial genome, was higher in substantia nigra when using phenol / chloroform. We thus provide evidence for significant method-dependent bias in DNA isolation from human brain, as reported in rat tissues. This may contribute to array “waves”, and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance. ER -