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. 2020 May;68(5):240-244.
doi: 10.2144/btn-2019-0172. Epub 2020 Feb 14.

A rapid and simple bead-bashing-based method for genomic DNA extraction from mammalian tissue

Shan Wei  1 , Brynn Levy  2   3 , Nataly Hoffman  3 , Claudia Cujar  2 , Reunet Rodney-Sandy  1 , Ronald Wapner  1 , Mary D'Alton  1 , Zev Williams  1
Affiliations

A rapid and simple bead-bashing-based method for genomic DNA extraction from mammalian tissue

Shan Wei et al. Biotechniques. 2020 May.

Abstract

Conventional genomic DNA (gDNA) extraction methods can take hours to complete, may require fume hoods and represent the most time-consuming step in many gDNA-based molecular assays. We systematically optimized a bead bashing-based (BBB) approach for rapid gDNA extraction without the need for a fume hood. Human tissue specimens (n = 34) subjected to the 12-min BBB method yielded 0.40 ± 0.17 (mean ± SD) μg of gDNA per milligram of tissue, sufficient for many downstream applications, and 3- and 6-min extensions resulted in an additional 0.43 ± 0.23 μg and 0.48 ± 0.43 μg per milligram of tissue, respectively. The BBB method provides a simple and rapid method for gDNA extraction from mammalian tissue that is applicable to time-sensitive clinical applications.

Keywords: genetic testing; rapid clinical diagnostics; rapid tissue gDNA extraction; tissue processing.

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Conflict of interest statement

Financial & competing interests disclosure

S Wei and Z Williams are listed as inventors on patents relating to this technology filed by Columbia University. This research was supported by the National Institutes of Health grants HD068546, HD100013 and U19CA179564, and Columbia BioMedX. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Figures

Figure 1.
Figure 1.. Comparison of workflows between the manufacturer's lysis-based and bead bashing-based, and the rapid bead bashing-based protocol.
Images of each module were adapted from manufacturer's protocols. (A) Workflow illustration remade from manufacturer's protocol in QIAamp DNA mini kit for tissue. (B) Workflow illustration remade from manufacturer's protocol in Quick-DNA Insect/Tissue kit. (C) Workflow illustration of rapid bead-bashing-based gDNA extraction methods reported in this study.
Figure 2.
Figure 2.. Development of rapid bead bashing-based method and extensions.
(A) Comparison of gDNA purified using two β-mercaptoethanol-free protocols by gel electrophoresis. Two tissue samples (A & B) were purified using the Quick-DNA insect/tissue kit protocol (Mfr) and DNA Clean & Concentrator-5 protocol (rapid). (B) Gel image of gDNA extracted from chronic villus tissue samples using the rapid and extended BBB protocols. Tissue samples (samples 1–4) were subjected to the rapid BBB method as well as a 3- and 6-min extension. (C) Evaluation of the impact of the bead-bashing process on the integrity of gDNA. Technical repeats of gDNA were treated for 3, 5 and 10 min bead bashing times. (D) gDNA yields using rapid and extended BBB methods. gDNA yields from each individual sample are shown by dots; the bar graph indicates the mean value ± SD. BBB: Bead bashing-based.
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References

    1. Zhang J, Walsh MF, Wu G. et al. Germline mutations in predisposition genes in pediatric cancer. N. Engl. J. Med. 373(24), 2336–2346 (2015). - PMC - PubMed

    2. • A simple, rapid and robust gDNA extraction method from mammalian tissue can be applied on and can significantly speed up the the listed studies.

    1. Carp H, Guetta E, Dorf H, Soriano D, Barkai G, Schiff E. Embryonic karyotype in recurrent miscarriage with parental karyotypic aberrations. Fertil. Steril. 85(2), 446–450 (2006). - PubMed
    1. Palomaki GE, Deciu C, Kloza EM. et al. DNA sequencing of maternal plasma reliably identifies trisomy 18 and trisomy 13 as well as Down syndrome: an international collaborative study. Genet. Med. 14(3), 296–305 (2012). - PMC - PubMed
    1. De Paoli-Iseppi R, Johansson PA, Menzies AM. et al. Comparison of whole-exome sequencing of matched fresh and formalin fixed paraffin embedded melanoma tumours: implications for clinical decision making. Pathology 48(3), 261–266 (2016). - PubMed
    1. Levy B, Wapner R. Prenatal diagnosis by chromosomal microarray analysis. Fertil. Steril. 109(2), 201–212 (2018). - PMC - PubMed

    2. • A simple, rapid and robust gDNA extraction method from mammalian tissue can be applied on and can significantly speed up the the listed studies.

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