Spatially Resolved Genetic Analysis of Tissue Sections Enabled by Microscale Flow Confinement Retrieval and Isotachophoretic Purification.

PMID:31529566

IF: 16.823

Cited by: 10

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Abstract

We have developed a method for spatially resolved genetic analysis of formalin-fixed paraffin-embedded (FFPE) cell block and tissue sections. This method involves local sampling using hydrodynamic flow confinement of a lysis buffer, followed by electrokinetic purification of nucleic acids from the sampled lysate. We characterized the method by locally sampling an array of points with a circa 200 μm diameter footprint, enabling the detection of single KRAS and BRAF point mutations in small populations of RKO and MCF-7 FFPE cell blocks. To illustrate the utility of this approach for genetic analysis, we demonstrate spatially resolved genotyping of FFPE sections of human breast invasive ductal carcinoma.

Keywords

LCM-seq

Spatial Genomics

cancer

gene sequencing

isotachophoresis

tissue sections

tumor heterogeneity

MeSH terms

Breast Neoplasms

DNA, Neoplasm

Female

Formaldehyde

Genotype

Humans

MCF-7 Cells

Microscopy, Confocal

Paraffin Embedding

Point Mutation

Proto-Oncogene Proteins B-raf

Proto-Oncogene Proteins p21(ras)

Real-Time Polymerase Chain Reaction

Sequence Analysis, DNA

Authors

van Kooten, Xander F

Petrini, Lorenzo F T

Kashyap, Aditya

Voith von Voithenberg, Lena

Bercovici, Moran

Kaigala, Govind V

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