Introducing OligoFISSEQ genome mapping technology

CAMBRIDGE, Mass. and BARCELONA, Spain—Researchers from Harvard University, the Centro Nacional de Análisis Genómico (CNAG) and the Centre for Genomic Regulation (CRG) have described, in a paper published today in Nature Methods, a technology which is reportedly the first capable of visualizing hundreds — and potentially thousands — of genomes at the same time under the microscope.

The authors of the study describe OligoFISSEQ, a technology which overcomes the limitations of fluorescence in situ hybridization (FISH) by using new computational methods. OligoFISSEQ is also able to image genomes more cheaply and quickly, as well as increasing range of visibility compared to currently available methods.

“Up to this moment, seeing a large number of different genes at the same time under the microscope was impossible. We combined existing sequencing technologies in a smart way so that we can see hundreds of genes by sequencing their targets under the microscope,” said Marc A. Marti-Renom, co-lead author of the study and ICREA Professor at CNAG-CRG. “Before OligoFISSEQ, reaching this number of genes at the same time was slow and expensive. It is like upgrading from a dial-up phone line to fiber-optic internet and paying 40 times less for it.”

One of the most common ways of studying the genome is by using FISH, which uses fluorescent probes to mark the presence or absence of specific DNA sequences on chromosomes. Scientists have made landmark discoveries with FISH, such as how cells divide, and still use the technology to this day for medical applications, species identification and other applications.

FISH, which was first developed in the 1980s, can only visualize a handful of genes at the same time. New methods have been created that can image genomes at a high resolution, but which can only map a limited number of regions or chromosomes at a time.

For the study, researchers used OligoFISSEQ to create three-dimensional maps of 66 genomic targets across six chromosomes in hundreds of cells. This showcases OligoFISSEQ’s potential to visualize the entire genome at a molecular resolution previously out of reach.

The researchers tested OligoFISSEQ by mapping all of the 46 regions along the length of the human X chromosome. The higher resolution of the technology revealed new patterns in the way the genome organizes itself, including that length of a chromosome’s arm is not correlated with its angle. The researchers hypothesize this may be indicative of cell type, cell state, or cellular health or age.

“In terms of scaling, our capacity to map 46 regions on ChrX at ~1 genomic target per 2.75Mb predicts that OligoFISSEQ could accommodate a thousand or more targets in human nuclei, with the potential to increase that number through a reduction in target size, temporal barcoding to better resolve targets, additional rounds of sequencing and incorporation of expansion microscopy; preliminary studies show that Chr19-9K can support eight rounds of O-LIT and that OligoFISSEQ is feasible in the context of hydrogels,” notes the paper. “Scaling could also be enhanced via microfluidics, which would significantly reduce the time required for each round of sequencing by 15–20%.”

“The resolution offered by OligoFISSEQ has huge potential to shed new light on patterns we could not see before,” continued Marti-Renom. “Because of the coverage it provides to study the genome, it is well suited for spotting what may seem like a minor, seemingly inconsequential change in one part of the nucleus that may have a ‘butterfly effect’ elsewhere. What may have previously have been thought of as random may turn out to be anything but. That is the power of this tool.”