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

PMID:31529566

IF: 16.823

Cited by: 11

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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

Spatial Genomics

LCM-seq

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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