Rescue of Low-Yield DNA Samples for Next-Generation Sequencing Using Vacuum Centrifugal Concentration in a Clinical Workflow

Author:

Vestergaard Lau K.1ORCID,Mikkelsen Nicolai S.1ORCID,Oliveira Douglas V. N. P.1,Poulsen Tim S.1,Hoegdall Estrid V.1ORCID

Affiliation:

1. Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, DK-2730 Herlev, Denmark

Abstract

The implementation of next-generation sequencing (NGS) in clinical oncology has enabled the analysis of multiple cancer-associated genes for diagnostics and treatment purposes. The detection of pathogenic and likely pathogenic mutations is crucial to manage the disease. Obtaining the mutational profile may be challenging in samples with low yields of DNA—reflected by the type of biological material, such as formalin-fixed paraffin-embedded tissue (FFPE), needle biopsies, and circulating free/tumor DNA, as well as a sparse tumor content. Moreover, standardized strict procedures for the extraction of DNA in a clinical setting might contribute to lower amounts of DNA per µL. The detection of variants in low-yield DNA samples remains a challenge in clinical diagnostics, where molecular analyses such as NGS are needed. Here, we performed vacuum centrifugation on DNA extracted from five FFPE tissue blocks, with concentrations below 0.2 ng/µL. Through NGS analysis, we found that low-yield DNA samples could be concentrated to sufficient levels, without compromising the mutational profile.

Publisher

MDPI AG

Subject

General Earth and Planetary Sciences,Water Science and Technology,Geography, Planning and Development

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