The genomic revolution: how DNA has transformed the diagnosis of rare diseases

Genetics is a surprisingly recent discipline. As Prof. Seri recalled, 2022 marked the 200th anniversary of the birth of Gregor Mendel — the Augustinian monk who first described the laws of heredity by studying peas in his garden. Considering that many sciences such as physics or chemistry have centuries of history, genetics was practically born yesterday.
The fundamental milestones followed in rapid succession: the karyotype — that is, the description of the correct number of human chromosomes (46) — dates only from 1956. In 1959, Jerome Lejeune described the first chromosomal disorder, Trisomy 21, which causes Down syndrome. The celebrated double helix structure of DNA was discovered by Watson and Crick in 1953. The first point mutation in a gene was identified in 1957 in haemoglobin, explaining the cause of sickle cell anaemia. Decoding of the genetic code dates from 1966, and the first genes were cloned in 1977.
This timeline highlights an important truth: Precision Medicine based on genetics is a recent phenomenon, made possible by discoveries that are barely a few decades old.

The Human Genome Project: a heralded revolution
The great impetus for medical genetics came in the 1980s with the Human Genome Project — a scientific initiative of a scale comparable to the Moon landing. The project was also championed by an Italian Nobel laureate, Renato Dulbecco, and officially launched on 1 October 1990 with a planned duration of 15 years.
History accelerated: in June 2000 — ten years ahead of schedule — at the White House, President Bill Clinton announced alongside scientists Craig Venter and Francis Collins the completion of the mapping of the human genome. As Prof. Seri recalled, showing an original photograph of that historic event, in the front row was Prof. Victor McKusick, considered the father of modern medical genetics.
McKusick was the first to systematically catalogue genetic diseases. In 1966 he published a catalogue with approximately 1,500 entries. This catalogue, today known as OMIM (Online Mendelian Inheritance in Man), is updated weekly and has become the world reference resource for genetic diseases.
The figures from the latest update cited by Prof. Seri (dated 27 February 2025) are impressive: 27,695 total entries, 17,491 known genes, and 7,601 rare genetic diseases caused by mutations in 4,966 genes. The growth has been exponential: from 1,500 known diseases in 1966 to over 7,600 today.

The complexity of the genome: there is no “normal” DNA
One of the most important lessons of the Human Genome Project, emphasised by Prof. Seri, is that there is no “normal DNA” contrasted with a “diseased DNA” in any absolute sense. This is a fundamental conceptual revolution.
All of us carry millions of genetic variants that influence the functioning of proteins, predisposing us to or protecting us from different diseases. The human genome is intrinsically variable: each person has a unique set of variants that makes them different from everyone else.
This complexity also emerges from the relationship between genes and diseases: a single gene can cause multiple distinct diseases. Approximately 1,000 genes are associated with two different phenotypes, 330 with three phenotypes, and 253 with four or more different phenotypes. This is the molecular manifestation of a principle known as pleiotropy: the same genetic defect can produce very different clinical effects.

From the reference genome to the individual genome
The true clinical breakthrough came with the sequencing of the first individual genome. Unlike the reference genome of the Human Genome Project — which was a kind of “mosaic” assembled from multiple people — this involved the complete DNA of a single individual. This raised a crucial question: is it possible to transfer genomic information into everyday clinical practice?
The answer depended primarily on costs. The Human Genome Project cost approximately 2.5 billion dollars and required 10 years. At the time, sequencing every patient’s genome was economically unthinkable. But technology progressed rapidly: today it is possible to sequence a complete human genome in a few days for a few hundred euros.
This reduction in costs of approximately 10,000-fold has made genomic sequencing an accessible diagnostic tool. As Prof. Seri explained, “we have thus abandoned classical (Sanger) sequencing and moved to next generation techniques: gene panels, the exome (the coding part of DNA), and the whole genome.”

The exome: focusing on what matters most
The exome represents only 1–2% of the human genome: it is the part that actually codes for proteins. However, this small segment contains approximately 85% of known pathological mutations. Sequencing the exome rather than the entire genome therefore offers an excellent cost-effectiveness ratio for the diagnosis of many genetic diseases.
But even “just” an exome contains 20–25,000 genetic variants that need to be carefully filtered and analysed. Not all variants are pathological: the majority are normal polymorphisms — harmless variations that contribute to human diversity. Distinguishing pathological variants from benign ones requires expertise, experience and sophisticated bioinformatic tools.
The percentage of cases in which exome sequencing leads to a definitive diagnosis (detection rate) typically ranges between 21% and 35%. However, as Prof. Seri emphasised, this rate can rise to 50% “when the work is shared between geneticists, clinicians and laboratories. Multidisciplinary collaboration is essential.”
This is a crucial point: genomics does not replace clinical medicine, but enhances it. A geneticist alone cannot correctly interpret variants without knowing the clinical details of the patient. A clinician alone cannot assess the pathogenicity of variants without molecular genetics expertise. Only by working together is the probability of reaching a correct diagnosis maximised.

From rare to ultra-rare diseases
Rare diseases, by definition, affect fewer than 5 people in every 10,000. But there are also ultra-rare diseases that affect 1 person in 2 million, or even fewer. Before the genomic era, these patients almost always remained without a diagnosis: how could one identify a genetic defect never previously described, in a patient who might be unique in the world?
Exome sequencing has radically changed this situation. As Prof. Seri explained, “Today, exome sequencing allows us to find genetic defects even in these cases.” His research group has identified 31 new genetic diseases using this approach.
Each newly identified disease represents not only a diagnosis for that patient, but also a research project. After identifying a candidate mutation, functional studies are needed to demonstrate its pathogenicity. It is necessary to understand how that mutation alters the function of the protein and how this leads to the clinical symptoms observed.

A concrete example: intestinal pseudo-obstruction and LIG3 mutations
Prof. Seri presented an emblematic clinical case: three siblings with intestinal pseudo-obstruction (a serious condition in which the intestine does not function correctly) associated with leukoencephalopathy (alterations of the cerebral white matter). None of the known mutations could explain this complex clinical picture.
Exome sequencing revealed two variants in the LIG3 gene, which codes for a mitochondrial ligase — an enzyme essential for the replication and repair of mitochondrial DNA. To confirm that these variants were indeed pathological, functional studies were conducted on zebrafish, an organism widely used as a model in genetics.
Zebrafish with mutations in LIG3 showed defects similar to those observed in human patients, confirming the pathogenicity of the variants. But the story does not end there: based on understanding of the molecular mechanism, an experimental treatment with glutamine was attempted, which led to clinical improvements in the patients.
Today six families worldwide are known to have this condition, and research continues to expand knowledge and potentially develop more effective therapies. This example perfectly illustrates the pathway from genomic discovery to understanding the pathological mechanism, through to the possibility of therapeutic interventions.

When the exome is not enough: whole genome sequencing
Despite the advances, even with exome sequencing approximately 50% of patients with suspected genetic disease remain without a diagnosis. Why? Primarily because the exome covers only the coding regions, but mutations can also be found in regulatory or intronic regions (parts of the gene that do not directly code for proteins) or in other areas of the genome.
This is where whole genome sequencing comes in. As Prof. Seri explained, “Whole genome sequencing offers more uniform coverage and includes regulatory and intronic regions.” Although data analysis is more complex, the genome allows the discovery of mutations that would escape exome analysis.
A study on 55 families with neurodevelopmental defects conducted by Prof. Seri’s group demonstrated the effectiveness of this approach: genomic sequencing led to 21.8% definitive diagnoses and 16.4% potential diagnoses — a total diagnostic yield of 37–38% in patients previously undiagnosed by other methods.

An emblematic case: the deep intronic mutation
Prof. Seri presented a particularly illuminating case: a girl with suspected CHARGE syndrome — a complex genetic disease causing multiple malformations. All genetic tests were negative, including exome sequencing. The diagnosis remained uncertain.
Only whole genome sequencing revealed the cause: a deep intronic mutation in the CHD7 gene — the gene known to cause CHARGE syndrome. This mutation was located in a region not covered by exome sequencing, explaining why it had escaped previous analyses.
With this confirmed diagnosis, the family was finally able to have certainty about their daughter’s condition, access appropriate clinical follow-up, receive genetic counselling on the risk of recurrence in future pregnancies, and benefit from the support of CHARGE syndrome patient associations.

The pangenome: including human diversity
The progress of genomics does not stop. Prof. Seri mentioned the Pangenome project — an initiative creating a reference genome that includes the genetic variability of different ethnicities and populations. The traditional reference genome was built primarily on DNA from individuals of European origin, but genetic variability between populations is significant.
The pangenome aims to create a resource more representative of global human diversity, improving the ability to interpret genetic variants in patients of any ethnic origin. This is particularly important for ensuring equity in Precision Medicine: populations underrepresented in the reference genome have a higher probability of having genetic variants erroneously classified as pathological (false positives) or, conversely, pathological variants that go unrecognised (false negatives).

The multidisciplinary approach: the key to success
A recurring theme in Prof. Seri’s presentation was the importance of the multidisciplinary approach. Genomic sequencing produces data, but data alone are not a diagnosis. What is needed is expert clinicians who accurately assess symptoms and the course of the disease; medical geneticists who interpret genetic variants in the clinical context; molecular biologists who conduct functional studies to confirm pathogenicity; bioinformaticians who develop and apply the tools to analyse genomic data; and genetic counsellors who communicate results to patients and families.
This integration of competencies is exactly what Precision Medicine Centers such as those of HEAL ITALIA aim to achieve: creating environments where all these professional figures work together in a coordinated manner.

From diagnosis to therapy
The ultimate objective of genomic diagnostics is not simply to give a name to the disease, but to open therapeutic possibilities. As demonstrated by the example of LIG3 mutations, understanding the molecular mechanism can suggest rational therapeutic interventions.
In some cases, genetic diagnosis makes it possible to apply therapies already available for other conditions. In others, it can make the patient eligible for clinical trials of new drugs targeting specific molecular defects. In others still, it can suggest nutritional, environmental or supportive interventions that improve quality of life even without “curing” the disease.
Even when effective therapies do not exist, diagnosis has value: it provides certainty to families, allows appropriate clinical management, enables genetic counselling for future pregnancies, and often connects patients with others in the same condition through patient associations.

The future of medical genetics
As Prof. Seri concluded, “the genomic approach, integrated with accurate clinical and multidisciplinary assessment, represents the key to addressing rare diseases, offering diagnoses and, in some cases, concrete therapeutic possibilities.”
The future will likely see genomic sequencing become increasingly routine in clinical practice. Some countries are already experimenting with neonatal genomic sequencing, to identify treatable genetic diseases early. The interpretation of genomic data will continue to improve thanks to the accumulation of knowledge, artificial intelligence and the international sharing of data through databases managed by biobanks and networks such as BBMRI.
But technology alone is not enough. As repeatedly emphasised by Prof. Seri and all the conference speakers, an integrated infrastructure of specialist centres, trained professionals, quality biobanks, shared databases and multidisciplinary collaborations is needed. What is needed, in other words, is exactly what HEAL ITALIA is building: a complete ecosystem for Precision Medicine in rare diseases, in which the power of genomics can be fully exploited for the benefit of patients.