Title: Rapid micro fluorescence in situ hybridization in tissue sections,
Abstract: This paper describes a micro fluorescence in situ hybridization
({\mu}FISH)-based rapid detection of cytogenetic biomarkers on formalin-fixed
paraffin embedded (FFPE) tissue sections. We demonstrated this method in the
context of detecting human epidermal growth factor 2 (HER2) in breast tissue
sections. This method uses a non-contact microfluidic scanning probe (MFP),
which localizes FISH probes at the micrometer length-scale to selected cells of
the tissue section. The scanning ability of the MFP allows for a versatile
implementation of FISH on tissue sections. We demonstrated the use of
oligonucleotide FISH probes in ethylene carbonate-based buffer enabling rapid
hybridization within < 1 min for chromosome enumeration and 10-15 min for
assessment of the HER2 status in FFPE sections. We further demonstrated
recycling of FISH probes for multiple sequential tests using a defined volume
of probes by forming hierarchical hydrodynamic flow confinements. This
microscale method is compatible with the standard FISH protocols and with the
Instant Quality (IQ) FISH assay, reduces the FISH probe consumption ~100-fold
and the hybridization time 4-fold, resulting in an assay turnaround time of < 3
h. We believe rapid {\mu}FISH has the potential of being used in pathology
workflows as a standalone method or in combination with other molecular methods
for diagnostic and prognostic analysis of FFPE sections.