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Chromosome sorting goes “back to the future”

No one can question the advancements represented by DNA sequencing. The contribution made by technological cores specialized in genomics has made possible the first molecular consensus on colorectal cancer. The arrival of a new technique, especially if it is as innovative and revolutionary as this one, always implies the abandonment of other technologies. That is precisely what happened with what is known as chromosome sorting, a method in which flow cytometry is applied to perform genetic studies.

The passage of time has made it possible to recover a technique capable of “very high speeds”, as Dr. Óscar Fornas, head of the Flow cytometry unit of Pompeu Fabra University and the Centre for Genomic Regulation, indicated in remarks to Biocores. Chromosome sorting can reach separation speeds ranging from 100 to 500 chromosomes per second, as compared to the rate achieved with other methodologies, which is around 10-15 chromosomes per day.

Thanks to flow cytometry, it is possible to perform what is known as flow karyotyping, considered by specialists such as Faustina Rubio, Benjamín García and Remedios Romero in their book Técnicas de inmunodiagnóstico as “a complement and an alternative to conventional methods for studying chromosomes in metaphase.” This way, chromosomes can be isolated using preparations in this phase of cell division, and later dyed with fluorochromes to detect any kind of anomaly.

Source: Doc. Dr. rer. nat. Josef Reischig, CSc. (Wikimedia)

“For example, it is possible to map translocations while isolating the translocated chromosome,” states Fornas. This application, and others such as copy number location or deletion mapping, prove that it is not only possible to conduct chromosome sorting, but also to carry out very targeted studies. By doing so, it is possible for researchers to eliminate a high percentage of the genome, in order to analyse only the part they are interested in.

The aberrations that can be detected through chromosome sorting allow us to see, on another note, alterations in the chromosomal size or in the number of basic pairs, as has been concluded at Purdue University. It is also possible to use chromosome sorting to observe trisomy 21, or as shown in the following image, discover the translocation between chromosomes 11 and 12 using a technique derived from flow cytometry.

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Source: Purdue University

Chromosome sorting technology is based on the precept that if a chromosome can be determined through its optical properties (such as light scatter, fluorescence, etc.), it can be resolved with the application of flow cytometry, as discussed in a study published in the journal Functional & Integrative Genomics. In addition to the applications carried out in prenatal detection or plant biology, a field in which protocols have been long in achieving preparations appropriate for chromosome sorting, Fornas also highlights the possibility of combining this type of flow cytometry with other methods.

In fact, chromosome sorting’s going “back to the future” can also be enhanced through its combination with other techniques, such as DNA analysis. For example, using fluorescent in situ hybridization (FISH) it is possible to identify chromosomal alterations with probes to “paint” the chromosomes. This technique enabled the assessment of the telomere dynamics in a population of human lymphocytes, according to a study published in Nature Biotechnology or, more recently, checking the abundance of interstitial telomeric sequences  in chromosomes of Chinese hamsters, to mention just two examples.

As regards targeted genetic studies, chromosomal sorting also opens the possibility of combining these research efforts with the analysis of the previously-isolated genome fraction. The problem, according to Fornas, is that the technique is “difficult to set up”, as it is “complex to prepare the samples and specific, specialized machinery is required.” The UPF-CRG Flow Cytometry Unit is a forerunner in this field, as it has already worked on the sorting of chromosome Y in research related with different species of large primates. The results will enable further advancement in the field of evolutionary biology. Other fields also stand to benefit from the “return” of this technology. “Many studies have already shown its usefulness in pathology and for clinical purposes,” states Fornas, speaking to the wealth of possibilities that flow cytometry brings to R&D.