In recent decades, clinical practice has seen the appearance of molecular analysis technologies that have sophisticated the diagnosis of many diseases, especially hematological cancers. Recently, the debate has been opened about whether the massive sequencing of the genome will render the classic methods for the genetic diagnosis of haematological cancer obsolete, such as karyotype analysis, based on the microscopic observation of chromosomes by highly specialized staff.

Dr. Frances Solé, leader of the Myelodysplastic Syndromes group and coordinator of the Can Ruti Campus of the Josep Carreras Leukaemia Research Institute, Dr. Mar Mallo, leader of the Institute's Microarray Unit, and Dr. Isabel Granada, Head of the Cytogenetics Laboratory of the ICO Badalona Haematology Service, have led an international team to give their vision and offer alternatives. It is published this month in the journal Blood, leader in haematology research.

We speak here with Dr. Solé and Dr. Mallo, so that they can give us some insight on how the debate is progressing (The answers include the impressions of the two researchers, indistinctly).

Is there a scientific debate about which are the most appropriate techniques for diagnosis?

Cytogeneticists have been hearing “you will stop doing karyotypes” for years, and we always reply that there is room for everyone. It is not so much about one technology replacing another, but about how to choose the best one in each situation. For example, in chronic myeloid leukemia, associated with the Philadelphia chromosome (reciprocal translocation between chromosomes 9 and 22), there is no point in sequencing: with a karyotype you have it diagnosed in a very short time and at low cost.

But sequencing can give more information. Wouldn't it be useful to know?

In terms of diagnosis, in the case of chronic myeloid leukemia, once you have the diagnosis you already know what treatment you have to give to the patient. To detect genetic alterations with NGS (next generation sequencing), it takes a long time and a very large bioinformatic effort. Given that, at the present day, the treatment would be the same, the speed in providing it weights a lot more, especially in acute pathologies that cannot wait. In this case, the excess of information is counterproductive, and the trees do not let you see the forest.

So, we could say that massive sequencing is losing large alterations of the genome, the forest, in favor of small details, the trees?

Yes, the structural information of the genome is lost when sequencing, since to do so all the DNA is "shredded", read in small fragments and then reassembled. But it's hard to tell if a fragment has changed places. These alterations, which do not involve loss or gain of genetic information, are very important for cell function because they can activate or deactivate important control elements, initiating a cancerous process. That being said, sequencing is a very useful methodology to see point mutations, alterations that affect one or a few nucleotides, and also to see gains or losses of material. But as of today, it has some limitations at detecting structural changes.

The New England Journal of Medicine article suggests the cytogenetics' days are over in favor of sequencing. Is that why you decided to reply?

We did not want hematologists to get the message that they could forget about cytogenetics, that now it was time to sequence and that was enough. No, sequencing is a good technique, which gives a lot of information, but by the moment it is complementary to cytogenetics, and it will surely be so for many years.

Some of its authors are international references…

Precisely, if this vision became the standard criteria for diagnostic at the international level, many countries where sequencing techniques are not yet implemented, basically due to its high costs, would be unable to adequately diagnose their patients. We say that, by now, cytogenetics continues to be very valid: it is fast, has a low cost, and it can be done in all the hospitals in the world.

Is it so complicated, what do they propose?

Right now, in Spain, there are just a few centers able to sequence in five days. Technically, it is possible, but the subsequent bioinformatic analysis and the elaboration of a diagnostic report for the patients requires more time. In some Asian or Latin American countries, it would be unthinkable.

What reaction has your article, published in the magazine Blood, had?

In general, our cytogenetic colleagues are satisfied and believe that our article will help assess classical techniques such as karyotype analysis, FISH or cytological microscopic assessment. But the article is not just an ode to the technique, it goes further and seeks to contextualize the use of each methodology according to its pros and cons. The goal is always to determine a diagnosis that can initiate an effective treatment. The journal Blood is a reference in the field of hematology and, thanks to this article, hematologists, who are the ones who request the tests to be carried out for a correct diagnosis of patients, will reinforce the concept that cytogenetics is and will continue to be useful in this current moment, where omics technologies are seem to be so trendy.

And which is your proposal in this context?

Today, in most cases, cytogenetics is useful to provide an initial diagnosis that allows treatment to begin. This is very important for any cancer patient. From here, molecular techniques allow us to delve into the particular alterations of the tumor and refine the treatment in a personalized way. The presence of certain mutations, for example, may be indicative of a poor response to treatment.

Is this model feasible?

Much research is still needed to know which are the most important molecular characteristics in each tumor. If we knew them, we could search for them specifically and save time. Here, technology companies have a lot of work to do, because right now you need professionals specialized in bioinformatics to carry out the analysis. If they manage to automate it, we might have the paradigm shift we advocate for.

Time will show, if, at the end, the classic techniques end up being replaced by the new molecular methodologies. Now, it seems that they still have a role to play, but research is advancing by leaps and bounds and the emergence of artificial intelligence can transform everything in a blink. Fortunately, we have good professionals like Dr. Solé and Dr. Mallo who will make sure that, if there is a transition, it will always be for the benefit of the patients.

Reference article:

Yassmine M. N. Akkari, Linda B. Baughn, Adrian M Dubuc, Adam C Smith, Mar Mallo, Paola Dal Cin, María Díez-Campelo, Marta S Gallego, Isabel Granada, Detlef Thomas Haase, Brigitte Schlegelberger, Irma Slavutsky, Cristina Mecucci, Ross L. Levine, Robert P Hasserjian, Francesc Sole, Brynn Levy, Xinjie Xu; “Guiding the Global Evolution of Cytogenetic Testing for Hematologic Malignancies”. Blood 2022; blood.2021014309. doi: https://doi.org/10.1182/blood.2021014309