In April 2003, just a couple of decades ago, the first draft sequence of the human genome was published. To achieve this milestone, an intense international collaboration of almost 3,000 researchers worldwide was necessary, which spanned about 15 years and required an investment of close to 3 billion dollars. This initiative culminated in 2000 with the sequencing of the first human genome over 15 months at a cost of 300 million US dollars.

Only 18 years later, genome sequencing is available to almost anyone who wants it. We even have initiatives that provide us with our genome for free, speaking in economic terms (https://www.personalgenomes.org/), although with high intangible, barely noticeable costs, in exchange for our privacy and access to our personal, highly sensitive, and valuable heritage, genomic data. Heritage is unique not only to us as individuals but also to our relatives as it is the genetic currency that is passed on from generation to generation. This data exchange entails important ethical and regulatory dilemmas that will be featured in another story and that Misha Angrist describes perfectly in his book Here Is a Human Being: At the Dawn of Personal Genomics [1].

Scientists are generally not prone to effusiveness, but we can affirm that genomics is one of the areas in science where reality exceeds our dreams and expectations. This impressive genomic revolution in which we are involved allows for the continuous characterization and discovery of genes and molecular causes of many genetic diseases in ever shorter times, increasing the diagnostic yield of many diseases, facilitating the differential diagnosis of complex and genetically heterogeneous diseases to ultimately develop increasingly powerful and sensitive diagnostic methods.

One of the main levers of change has been the development of the technologies for genome sequencing, also known as next-generation sequencing (NGS), with different waves of technology improvements. This technology provides millions of sequences read in only one assay, allowing us to obtain the complete sequence of an individual’s genome in a few days and at an astonishing cost of under 1,000 US dollars. The progressive application of NGS technologies in research has boosted our clinical knowledge, increasing the discovery rate of genes associated with Mendelian disorders [2], allowing the establishment of robust associations between genes and genetic markers in complex diseases to obtain polygenic risk scores, and learning about the intricate molecular basis underlying genetic diseases, as well as the etiology of the transformation of normal cells into malignant cancer cells. All these technological and scientific advances are paving the way towards a precise and personalized medicine.

Whole-exome sequencing (WES) is being used in the clinical setting to obtain a personalized diagnosis of more than 30% of individuals with intellectual disabilities, developmental delay, or congenital abnormalities [3] and allowing for the diagnosis of genetically heterogeneous diseases or those with a complex differential diagnosis that previously represented an unsolvable, diagnostic maze. Currently, NGS technologies provide: i) complete genetic analysis of a newborn admitted to the ICU in a few days to provide the most accurate treatment; ii) analysis of fetal DNA in a few hours from a maternal blood sample without the need for unnecessarily increasing the risk of miscarriage through the use of invasive tests; iii) identification of the genetic profile of a tumor in order to accurately tailor the treatment, providing a precise and personalized treatment for the patient and the disease; iv) identification of mutations and categorization of tumor profiles by liquid biopsy, useful for follow-up and monitoring of the evolution of the disease in a previously treated patient; v) recognition of variants accountable for increased predisposition to common diseases; vi) prediction of individual patient response to certain drugs, avoiding their adverse effects; and vii) the anticipation and prevention of clinical scenarios, one of the great challenges in medicine in developed societies.

Given the impact of the genetic background in the development of rare, common, chronic, and multifactorial diseases, genomic medicine must have the maximum precision to provide the greatest diagnostic yield to direct the treatment. For that, we highlight the importance of incorporating genetic medicine into clinical decisions and treatment algorithms. On the way to personalized medicine, genomic precision medicine can be defined as the centerpiece of the evolution of genomic knowledge. Its main aim is to gather all the information from translational genomic research and direct it towards patient risk stratification of common genetic and biological characteristics, ultimately leading to an accurate diagnosis and, as a byproduct, improving clinical management with personalized treatments and the establishment of accurate prognoses.

This first draft sequence of the human genome provides us with an instructions manual of life, written in a very extensive, complex format with more than 3300 million characters [4]. A reference map on which to base new projects aimed at identifying the genes associated with biological processes to better understand the genetic basis of human health and of the pathology of human diseases. The challenges faced by scientists, researchers, and clinicians are diverse for many reasons, one of them being the ability to read the genomic information necessary to extract conclusions, based on clinical and scientific evidence, in a timely and cost-effective manner. Another challenge is the ability to establish a link between known biological processes and genetic conditions to make a clinical decision that will guide treatment and prognosis of a wide range of diseases with different pathophysiologies on physiologically diverse individuals. As we will see throughout this work, some of these challenges are being addressed in a satisfactory way, whereas most of them are yet to be solved, given that they require important technological, scientific, clinical, and ethical advances.

Although it is an indisputable fact that the emergence of molecular genetic techniques such as NGS has allowed us to standardize pathways to achieve an accurate diagnosis, it has also translated into an number of different genetic tests, where the high level of uncertainty is a challenge to handle and decipher.

WES (whole-exome sequencing) and WGS (whole-genome sequencing) are the most recent technologies based on NGS developed for genomic diagnostic purposes. Undoubtedly, genomic tools, especially WES and WGS, give us a global view of a disease, increasing the knowledge of the underlying mechanisms encoded by the genetic condition. At the same time, such tools also increase the probabilities of finding variants associated with other health conditions, which may or may not be medically actionable, and, being unexpected, are so-called “secondary” or “incidental” findings. The way of reporting and managing these secondary findings, as well as the way of communicating and giving proper clinical recommendations to patients, are some of the main genomic diagnostic challenges. Genomic, high-resolution, high-throughput technologies have opened up new diagnostic pathways, introducing a personalized clinical management but one paired with new challenges as to the use, management, and interpretation of generated databases, needing great bioinformatic support to conduct a final genomic diagnosis.

The diagnostic process comprises a set of steps, rules, and algorithms that aim to identify a candidate variant underlying a genetic condition. For this purpose, a huge number of databases, computational (in silico) predictive programs, and scientific literature must be handled by trained diagnostic personnel in charge, making the final interpretation extremely context dependent (Figure 1.1).

In order to safely progress on this journey through the brave new world of genomics, it is imperative to overcome some challenges, for which it is necessary to be comprehensively trained and to become an expert in the field. It is crucial that the clinical data obtained through this diagnostic process is supervised and approved by a clinician-scientist or physician specialized in genetic diseases to ultimately provide an ethically and clinically appropriate recommendation within the context of the disease and the treatment resources available for that particular disease.

This genomic technology race promises an exciting and challenging future, becoming a reality for research. However, further developments to improve sensitivity, specificity, and clinical validations still need to be established before it becomes a reality in the clinical setting.

Currently, Illumina sequencers are leading this race, given the quality of its sequencing technology, its versatility, and affordable price. Thermo Fisher sequencers follow closely thanks to their integrative solutions and clinical applications, and finally Roche sequencers, which unfortunately could not keep up with their competitors despite starting with the advantage of longer reads.

This amazing competition has allowed a greater accessibility of these diagnostic technologies, expanding the number and quality of their applications. This has led to new approaches and innovative strategies, increasing the accuracy, and reducing the time and costs involved.

Undoubtedly, in the coming years, new players will join this challenging race. Promising new sequencing systems have been developed but have not been able to compete on price or sensitivity, including new fourth-generation sequencing systems. In any case, only those sequencing systems that can provide competitive advantages, such as price or simplicity, without compromising on the quality provided by current sequencing systems, will be able to enter this competitive race of genomics diagnostics.

It is important to highlight that being able to buy the latest generation sequencer does not guarantee better or more accurate diagnosis. Before the acquisition of NGS machines, many issues must be dealt with, and skills must be acquired. The clinical applications of these technologies require extensive technical and molecular biology knowledge to be able to generate genomic data. But we still have a long way to go until this raw data can be converted into clinically useful information.

The days when decisions were based on technical aspects, such as pyrosequencing, sequencing by synthesis or by ligation, hybridization capture or amplicon sequencing gene panels, mean or minimum coverage, vertical (depth) or horizontal coverage, etc., are well over. NGS platforms and technologies are constantly changing and must be adapted and validated before being used in clinical diagnosis. For any NGS platform or enrichment method of regions of interest (ROI), we need to establish the performance and diagnostic yield of our approach in our clinical setting. Currently, any NGS clinical approach does not guarantee a 100% accurate analysis of ROI. This may be due to technical reasons or even intrinsic features of the DNA structure itself. This raises the importance of calculating the analytical sensitivity and specificity and defining the limits of detection, acco...