Genomics in Rare Diseases: An Overview for the Patient, Family and Non-Specialist Healthcare Professional

Keywords::

• genetic disorders
• healthcare
• patient engagement

Genomics & the human genome

Genomics is the study of an organism’s DNA, which is the set of instructions for what a cell does. DNA is comprised of a sequence of four chemical compounds called nucleotides or letters. These are signified by the A,C, G and T ‘letters’, a small proportion of which are grouped into genes, and placed in structures called chromosomes, of which we generally have 23 pairs. These are present in almost all the cells in the human body, apart from mature red blood cells and cornified cells that are found in hair, nails and skin. Genes are units of information that dictate how an organism looks/functions. Accordingly, genetics is the study of the functioning and composition of a single gene.

Genes are responsible for making proteins, which are needed for every living organism. By understanding the function of this sequence of letters, we can understand better how the body grows, develops and works. Genomic sequencing is the process that scientists and clinicians use to ‘read’ the letters in our genome. It can be used to examine specific genes and/or chromosomes which determine specific characteristics of how an organism looks or functions. It can identify changes in genes and/or chromosomes that may cause potentially life-changing conditions. Such conditions can result from a single base pair or ‘letter’ change in an identified gene, as is the case with tuberous sclerosis for example (a rare genetic condition that causes non-cancerous tumors), or because of much larger changes e.g., those seen in Down syndrome, which is caused by an extra copy of a whole chromosome, containing millions of extra letters. Genomic data can also inform on more complex conditions, such as type 2 diabetes, autism and some cancers, which may be caused by a combination of both changes in the genome and environmental factors, such as diet or air pollution [1].

Historically, it has taken many years for patients to receive a genetic test result, most often because the technology available only allowed healthcare professionals to investigate one single gene at a time, or to view the whole genome at a quality too low to make a diagnosis. It is now possible to identify a significant number of potential variations in a person’s genome at once in a matter of days or even hours. Due to innovations in sequencing technology, the cost of DNA sequencing has been decreasing rapidly. This, combined with innovative advances in computational technology, has increased the accessibility of DNA sequencing for use in clinical settings. Large-scale programmes are now looking at using genomics as a standard method in the provision of 21st-century healthcare. An example of this is the UK 100,000 Genomes Project, which began as a research-based programme but has now evolved into the NHS Genomic Medicine Service. This is moving genomics into the mainstream of diagnostics and clinical management of patients, especially those with rare genetic conditions and cancers [2].

Since the Human Genome Project was essentially finished in 2003, it has provided researchers and healthcare professionals with a wealth of data that allows them to understand better how humans experience disease, and how they respond to different types of medication that can result from changes in the roughly 3.1 billion letters that make up the code of the human genome [3]. Precision medicine is a field of medicine that uses information about a person’s individual genome to use new and innovative treatments/care pathways, rather than a ‘one size fits all’ approach that is currently employed. For example, the different ways people respond to drugs can result from the differences we all have in our genomes. Understanding such differences will allow us to select the right drug and correct dosage for each patient. Precision medicine is also bringing about better insights into how biological, environmental, and behavioral influences impact on well-being and disease, for example, how exercise can have a positive impact on health [4].

Its potential to transform healthcare is substantial. Emerging precision treatments can therefore offer enormous benefits to patients, for example, offering cost-effective, efficient, more effective, and targeted care for some of the world’s most prevalent conditions, such as cancers. Such benefits include avoiding unwanted side effects and increasing the chance of success, and financially, by only prescribing drugs to patients where the patient’s genome sequence can show that a drug will be effective. This is already resulting in improved life expectancy and quality of life for many people, as well as changing the way that various diseases are treated. For example, some early onset epilepsies can be treated effectively if the underlying genome cause can be identified [5].

Identifying the genomic changes that result in specific conditions gives opportunities to develop new treatments that are targeted at a specific DNA sequence change. For example, gene therapy for spinal muscular atrophy (SMA) can insert a new working copy of the faulty gene to replace the non-working version in the patient or overcome the way the gene is malfunctioning using antisense oligonucleotides (more commonly known as ASOs), which could, for example, be used to prevent a faulty gene from functioning and therefore prevent disease manifestation [6]. In fact, in some cases, a molecular diagnosis can lead to a management plan that includes simple changes/additions to diet that can prevent or reduce the severity of certain symptoms [7].

Rare diseases

Estimates of the number of rare diseases suggest that around 7000 conditions have been identified, but this is at best an estimate. According to a survey from Rare-X, there are over 10,000 rare diseases, and this number is growing rapidly [8]. Whatever the actual number is, there is a significant level of misdiagnosis and underdiagnosis, even in the most advanced western healthcare systems. While the number of people who have a specific rare disease may be small, when rare diseases are considered collectively, the estimated number of people worldwide who have a rare disease is between 263 and 446 million [9].

A genomic cause accounts for about 80% of rare diseases [10], while examples of non-genomic rare disease include rare infectious diseases and rare cancers [11]. Globally, very few of these are included in newborn screening programmes, which is a broad set of tests carried out on newborn babies to try and identify any rare diseases as quickly as possible. This is a missed opportunity to make an early diagnosis and provide targeted interventions, where these exist. Most rare conditions present in childhood, and around a third of these conditions may, unfortunately, result in a child’s death before their fifth birthday [12]. Many of these conditions are difficult or impossible to diagnose given current scientific understanding. However, progress is rapid, particularly for children with severe genetic neurological conditions. For example Rett syndrome, caused by changes in the gene MECP2, and SYNGAP1-Related Intellectual Disability, caused by changes in the gene SYNGAP1 [13] now have a 40–60% chance of an accurate diagnosis with modern techniques [14].

Different types of genomic testing

Traditional genomic testing has focused on looking at large numbers of nucleotides (letters) changing in a person’s genome. For example, karyotyping, where physical changes such as chromosomal rearrangements can be observed just by looking down a microscope. Array comparative genomic hybridization (aCGH) has superseded karyotyping because it has greater sensitivity at detecting such changes, that is, genomic changes as small as 50,000 nucleotides [15]. Another high-throughput test is single nucleotide polymorphism (SNP) arrays, which can identify thousands of nucleotide differences at specific locations in the genome. SNP arrays can be useful to understanding disease susceptibility and understanding how well suited a drug might be to a patient. Alternatively (or in conjunction with the previously mentioned techniques), sequencing a specific gene or set of genes (referred to as gene panel testing) known to be associated with a suspected condition may also be performed, for example cystic fibrosis. However, this can be a slow and costly process if a cause is not found in the first round of testing.

Whole-exome sequencing (WES) or whole-genome sequencing (WGS) is increasingly being used to investigate all the genes in the genome [10]. WES focuses on the 1–2% of the genome that is responsible for making proteins (coding regions) and there are just under 20,000 protein-coding genes that get produced by the human genome [16]. WGS looks across the entire genome. It is more thorough because it looks at regions within and in between the genes that are referred to as non-coding regions. Such regions are not involved with make proteins but might be involved with turning genes on and off, although the function of much of these regions is still not clearly understood. However, while it is also more costly, WGS can identify regions of large changes (structural variants) in the genome better than WES. Similarly, WES has advantages over gene panel testing by enabling re-analysis of novel genes. Therefore, both WGS and WES allow for reinterpretation of patient genomes in the future. For example, research is progressively identifying novel disease-gene associations, which can then be considered in diagnostic genomic testing. In addition, novel genomic technologies are emerging that offer a more complete look at the human genome, such as long-read sequencing [16]. These techniques can look at a larger variety of genomic variations that can be implicated in disease. This is of particular importance since the overall genetic diagnostic rate is expected to improve over the next decade as a result.

‘Trio’ sequencing examines the genomes of the biological parents as well as the child (the trio) to determine if any changes are inherited, or whether they are ‘new’ (novel) changes that arose in the sperm or the egg. These are fixed in the child at conception and not present in the parents’ blood samples. Scientists estimate that there are around 70 new changes in each person’s genome [17]. Most of these do not cause a problem, but some do and may have significant consequences for the health/wellbeing of the affected child. New changes can only be detected by comparing the sequence of the child with those of the parents, who will not share the change with the child. However, some changes can be recognised as pathogenic without parental sequencing data if healthcare professionals and researchers already know that change is disease-causing from previous studies.

While these techniques may seem complicated, the different tests may be understood better with the explanation that karyotyping and aCGH look for changes of at least 50,000 nucleotide changes within the genome, while exome/genome sequencing is able to identify both large genome changes as well as single nucleotide changes.

Important considerations for healthcare professionals & families undertaking genomic testing

The nature of rare diseases means that unless a healthcare professional specializes in that specific area of medicine, many rare disease patients and families will likely struggle to get a diagnosis and this can be distressing and difficult to come to terms with. The patient may be misdiagnosed, resulting in ineffective or even disease-exacerbating treatment plans. Consequently, patients may be passed from one healthcare professional to another, and potentially useful interventions are missed or delayed. Primary care practitioners are likely to be the first healthcare professionals to encounter patients and families seeking answers for complex undiagnosed diseases. They may have limited knowledge of those disorders and lack access to expert help/decision-making support systems that would enable them to plan an appropriate intervention pathway. It is, therefore, increasingly essential for healthcare professionals to have a working knowledge of genomics and its application in clinical practice. Opportunities for healthcare professionals to gain this knowledge are already being made available, for example, the UK’s NHS Master’s in Genomic Medicine course, and in the USA, through Harvard Medical School’s HMX Fundamentals Courses.

Accurate diagnosis of these complex medical conditions is faster and more affordable with quick access to accurate genome sequencing, and an understanding of what such testing can potentially provide. Without this, people affected by rare diseases often wait months or years to receive a diagnosis and some people never receive a diagnosis at all, although this does not mean the disease is not genetic. When the condition affects children, this delay can be harrowing for the child and their family. This diagnostic odyssey may include visits to multiple specialists for tests and procedures, which are too often invasive, painful, sometimes require a general anesthetic and may be potentially unnecessary.

Misdiagnosis is a challenge for the patient, research and clinical communities focused on efforts to identify treatments and/or interventions for rare diseases. It is challenging for families to present all their concerns about a condition of which they may have no knowledge to a professional, who may also have very limited awareness. It is essential for healthcare professionals to take patients’ concerns seriously, even if they are sometimes imperfectly expressed. Patients live with their disease and may have symptoms that a healthcare professional is not aware of, which can help with diagnosing their condition and when their concerns are not taken seriously this can create tension between the patient and healthcare professional. Healthcare professionals should also give patients enough time to fully present their concerns without interrupting them, particularly during their opening statements, other than to encourage expansion or to gather more details to facilitate the healthcare professional’s understanding of such concerns [18].

Accordingly, there are many areas of impact that families need to consider when genome sequencing is proposed. Healthcare professionals have an ethical obligation to explain the possible risks, benefits and alternatives of a given procedure/intervention to the family. This is a process called informed consent. It is essential that healthcare professionals are given and provide enough time for patients and caregivers to understand what the implications of such decisions might be and to ask questions that might arise. This is particularly important when patients are required to assimilate complex ideas or when the consent forms are written in such a way that is not intuitive.

Due to the limits of our current knowledge, a genome sequence might not reveal a diagnosis, so it is important to manage patient expectations of the likelihood of receiving a genetic diagnosis. If a genome sequence does not find the cause of the patient’s healthcare challenges, it is important to be aware that the cause may still be of a genetic basis. We only know what a fraction of the human genome is responsible for, so the basis for many genetic conditions is still waiting to be discovered. As our understanding of the genome increases over time, it will be important to reanalyse the genomes of those people who have had their genomes sequenced but have previously not had a genetic diagnosis [19].

Some families will receive an ‘uncertain’ result that can bring its own set of challenges. This may include examples where a change in a gene has been found that could explain the disorder, but there is not enough evidence currently to say confidently that it either causes the disorder or does not which can be frustrating for clinicians and families. Such findings are called variants of uncertain significance (VUS). Reanalysis of genomes in the future may establish that the VUS either is or is not disease causing [20].

The consequences of investigation and subsequent lack of diagnosis impacts on the wider family. Understanding the risk of future children developing the same condition is crucial to enable families to cope and plan for a future that may be radically different to that which they had anticipated. Furthermore, a diagnosis can determine other management issues, enabling genetic counselling to help individuals and couples understand more about how their/their child’s condition may impact future children and other relatives. It can help shape overall need for and provision of care, as having a name for a condition facilitates access to services. It also provides a disease label and may relieve parental grief, guilt and self-blame that can result from the absence of a diagnosis [21], while it can be enormously empowering for parents, who often become vocal advocates for their disorder.

Genome sequencing may generate ethical dilemmas. For example, with respect to paternity, sequencing may reveal that the social father of the child is not the biological father. It may also reveal additional findings indicating the presence of hitherto unsuspected health risks that may be mitigated by preventative actions e.g. a patient with risk factors for heart disease or cancer should be monitored for early intervention and swift treatment. Likewise, there is the dilemma of whether to contact at-risk relatives.

Receiving results may take a considerable amount of time, as geneticists look for evidence to enable them to draw conclusions that they can feel confident about. However, testing is much faster than it used to be. While the sequencing of the DNA sample is fast, the interpretation of the resulting genome sequence can be painstaking and is only performed by highly trained clinical scientists. This means there can often be a long delay (months or years) for results to get reported back to patients. It is also important to understand that not all results are certain.

While patients should be aware that currently, very few genetic diagnoses have approved treatments [22], identifying the genetic cause of a condition can, in limited cases, have direct therapeutic implications [23]. Yet, without genome diagnostics many advanced therapy medicinal products (ATMP), such as gene therapy, would not be possible, because we would lack the tools to power research and promote the development of novel therapies for currently difficult to control disorders.

As our knowledge and the number of people receiving a genetic diagnosis increases, the opportunities to utilize the genome to develop precision medicines will develop. Supporting these routes to innovation provides hope for countless patients and families. The challenge for 21st-century medicine is to realise this potential and deliver on the promise it holds [24].

The importance of coordinated healthcare plans & continued patient/family support

As DNA sequencing technology continues to evolve both in accuracy and speed, it is important to highlight to families that genome sequencing results, currently in very limited and the most serious cases, can now be returned in a matter of weeks or days [25]. Although they may positively impact quality of life, any diagnosis can be life changing, and so preparation for results is important on both sides – families and professionals. Suitable family support must also be available in the short- and long-term, i.e., follow-up appointments with a named person in their clinical genetics service, telephone calls, signposting to trusted information and condition-specific support groups – if available. All communication should be accurate, up to date, comprehensible and comprehensive enough to give families an insight into their situation and empower them. For the latter, a high quality, confidential consultation is needed that will allow parents to discuss either positive or negative findings in a supportive and appropriate environment. It is essential to make sure that any prospective multidisciplinary team (MDT) that will be involved in analysing the genomic results are suitably prepared, such that the families do not get the results in a chaotic manner and that the results are explained to them in an accessible way, rather than simply providing a complicated genetic testing report. At present, in the UK, MDTs may be configured to synchronise with the results, as the latter may take 6–12 months to come through; by that time normally there is a team around the child, but with rapid sequencing the situation is very different.

The importance of patient engagement

Patients and families live with their conditions 24 h a day, and this often empowers them to become world-leading authorities on their condition. Consequently, patients are often great champions for their conditions and raise money to fund research, provide information about their condition and support other people who are affected. This is particularly important for rare diseases where there are often only a handful of people identified globally for a given condition. For these ultra-rare conditions there is unlikely to be interest from industry in developing therapies due to the challenges of creating a development programme and the perception of a lack of return on investment unless significant additional incentives such as the Orphan Medicinal Products Regulations are in place.

The patient voice is essential in many aspects of genomics/Biotech and is central in planning research. When patients are not consulted, research and therapeutic initiatives can go awry. One such example is the Spectrum 10K project where the autism spectrum disorder (ASD) community were not sufficiently engaged with before the programme started, and as a result, it was paused for further consultation with patient groups. Concerns about the study included “fears that its data could potentially be misused by other researchers seeking to ‘cure’ or eradicate ASD”, which is an important concept around neurodiversity and perceptions of what is ‘normal’ [26]. Accordingly, large-scale genome initiatives have patient representation that advise on how genomic data should be used [27,28]. Also, it is important for patients and families to be able to let researchers and healthcare professionals know what it is they want from their work. What a healthcare professional and researcher deem to be important can be very different to what a patient wants. Patients can also help bring healthcare professionals and scientists together to have conversations that might not normally be had, as can be seen from disease- and gene-specific support groups, some of whom are already actively involved in therapy development, while they can also encourage other families to participate in research studies when available [29].

The internet and social media have an increasingly important/powerful role for patients and families with rare diseases, as well as healthcare professionals and researchers, by making the latest scientific and medical advances more accessible. For example, support is often provided via social media groups/chats created by parents. Although, families are at risk of accessing information that is worrying and/or inaccurate. Furthermore, the ability to share data with other patients, healthcare professionals and researchers globally is essential for interpreting genome sequencing results, particularly where there may only be a handful of people affected by a specific disorder across the globe. Patients and families are ultimately the most empowered group of people for their conditions, which can be seen from the numerous condition-specific patient-led support groups and charities, both large and small. Broader support groups are available too, such as the UK-based charities Genetic Alliance [30], Gene People [31] and Unique [32]. For those families who do not yet have a diagnosis, syndromes without a name (SWAN) [33] exists. These provide real and virtual communities where patients, parents and family members can come together, network, and exchange ideas such as current news items as well as providing mutual support. The role of patient advocacy and engagement groups in helping to shape and influence policy in the rare diseases, genomics and precision medicine space is illustrated by consortia of patient groups such as the European Organisation for Rare Diseases (EURORDIS), Global Genes and National Organization for Rare Disorders (NORD), and through the input of patient groups to multi-stakeholder consortia such as the International Rare Diseases Research Consortium (IRDiRC).

Conclusion

Genome sequencing is an area of medicine that offers enormous promise for the management of healthcare in the future. However, it is a developing technology and there are many questions as to how and when it can benefit families affected by rare diseases. Because of a lack of knowledge, delayed, slow or even misdiagnosis often occurs, for example, where paediatric epilepsies are sometimes misdiagnosed as gastrointestinal disorders [34]. Too often, this leads to a lack of support, inability to access advocacy groups, therapies/other interventions, and a lost opportunity to participate in clinical research. An incorrect diagnosis may even exacerbate the condition, causing unnecessary pain to the patient, a lost opportunity to intervene with a disease-modifying therapy and a physical/emotional toll on caregivers.

From a family’s perspective, intuition often plays a role in signifying that they or a family member may have a significant healthcare challenge, or that a child may not be developing as expected. Persuading healthcare professionals that their experience and intuition is real may be difficult.

It may also impact on parents’ decisions whether to have further children. This period can be a very challenging time for patients/families, and it can be difficult to remember what they have been told/consented to, either because it was a particularly stressful time, or the consenting happened a long time ago. It is important for the patient/family not to be overloaded with information, but allowed to access the information they need at a rate and literacy level they can contend with, and in the order that they need for it to make sense. Likewise, it is essential for healthcare professionals to provide ongoing support during the patients and families genomic diagnosis journey. In the past, even where a clinical diagnosis for a patient with a rare disease was possible, those affected would often experience isolation and a lack of support. This was often exacerbated if no diagnosis was made.

New advances in genomic medicine, as well as ease of communication enabling patients to find/interact with others on an international scale, means that the future for patients and families with rare diseases grows more promising. As such, patients are increasingly empowered to advocate for their rare disease, raising awareness, funding for research, and driving better healthcare, because ultimately, the patient is the hub around which all healthcare procedures fit.

Acknowledgments

The authors would like to thank Florence Cornish from Genomics England for her comments and suggestions.

Financial disclosure

The authors have no financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Conflict of interests disclosure

A Kent is chair of trustees of Gene People. APJ Parker is a member of the scientific advisory board for UKRET. A Patel is a trustee of Gene People. S Wynn is CEO of Unique and a trustee of Genetic Alliance. CA Steward is a scientific and patient engagement advisor to UKRET as well as several of the participating patient groups. He is a member of IRDiRC’s Diagnostics Scientific Committee. He is employed by Genomics England. The authors have no other competing interests or relevant affiliations with any organization or entity with the subject matter or materials discussed in the manuscript apart from those disclosed.

Writing disclosure

No writing assistance was utilized in the production of this manuscript.