ArticlePloS one2017
DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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Who cites it
17 citing papers in PubMed, 33 citations in OpenAlex.
- A multiplex droplet digital PCR assay for chromosome copy-number determination in Candida albicans.G3 (Bethesda, Md.) · 2026Article
- DNA Isolation Long-Read Genomic Sequencing in Ctenophores.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Insights regarding mitochondrial DNA copy number alterations in human cancer (Review).International journal of molecular medicine · 2022Review
- Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson's disease-associated GBA gene.Communications biology · 2022Article
- Slaying (Yet Again) the Brain-Eating Zombie Called the "Isochore Theory": A Segmentation Algorithm Used to "Confirm" the Existence of Isochores Creates "Isochores" Where None Exist.International journal of molecular sciences · 2022Article
- Method of Microglial DNA-RNA Purification from a Single Brain of an Adult Mouse.Methods and protocols · 2021Article
- Characterization of mitochondrial DNA quantity and quality in the human aged and Alzheimer's disease brain.Molecular neurodegeneration · 2021Article
- Quantification of mtDNA content in cultured cells by direct droplet digital PCR.Mitochondrion · 2021Article
- Thinking outside the nucleus: Mitochondrial DNA copy number in health and disease.Mitochondrion · 2020Review
- Investigation of Somatic Mutations in Human Brains Targeting Genes Associated With Parkinson's Disease.Frontiers in neurology · 2020Article
- Article
- Microarray expression studies on bone marrow of patients with Shwachman-Diamond syndrome in relation to deletion of the long arm of chromosome 20, other chromosome anomalies or normal karyotype.Molecular cytogenetics · 2020Article
- Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing.Acta neuropathologica communications · 2019Article
- Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION.Molecular genetics & genomic medicine · 2019Article
- The role of de novo mutations in adult-onset neurodegenerative disorders.Acta neuropathologica · 2019Review
- Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts.Computational and structural biotechnology journal · 2019Review
- Plasmid-normalized quantification of relative mitochondrial DNA copy number.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 3 countries.
Funding
Abstract
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.
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