Genetics in Disease

1 Genetics in Disease Sarah Whelan, PhD The human genome contains approximately 20,000 protein-coding genes, which comprise just 1.5–2% of the whole genome. These encoded proteins are the building blocks that keep our cells functional and healthy. However, mutations can affect their function or stop them from working entirely, sometimes driving the pathogenesis of disease. Genetic diseases can be caused by faults in a single gene (monogenic), multiple genes (polygenic) or even whole chromosomes. Some, like sickle cell anemia, are hereditary and present at birth. Others can be caused by spontaneous mutations, either arising from errors in DNA replication or exposure to environmental factors. There are thought to be over 6,000 known genetic disorders; improving our understanding of the genetic basis of disease may help us to improve their diagnosis, treatment and therapy. For example, advances in genetic analysis techniques – such as next-generation sequencing (NGS) – can potentially cut the time to diagnosis and make a huge difference in the lives of patients and their families. This listicle will explore how advances in genetic analysis are helping to develop our knowledge of genetic diseases and improve their diagnosis and treatment. Genetic sequencing aids diagnosis of rare pediatric diseases The field of pediatrics stands to gain hugely from the advances in genetic analysis technologies since rare genetic diseases are often diagnosed in infancy and childhood. Providing NGS analysis at an early age may also bring about worthwhile benefits for the diagnosis and treatment of diseases throughout the rest of an individual’s life. One such project in this field, the Deciphering Developmental Disorders (DDD) study, used genomic techniques such as exome sequencing and single nucleotide polymorphism (SNP) genotyping. Over 13,000 families in the UK and Ireland with children affected by an as-yet undiagnosed severe developmental disorder were involved in the study, in which they underwent in-depth genetic analysis. Using the resulting data, the researchers were able to provide a genetic diagnosis for around 5,500 children involving alterations across approximately 800 different genes. A similar analysis of the children’s parents revealed that approximately 76% of the variants were not inherited from either parent and were a result of spontaneous mutations instead. Listicle GENETICS IN DISEASE 2 Nevertheless, studies of this kind have also highlighted the inequalities in medicine and health equity, as the chances of reaching a diagnosis were lower for families of non-European ancestry. Therefore, more effort and resources should be devoted to improving these results for under-represented groups, helping many more families to get the answers they need. CRISPR-based therapy for sickle cell anemia Researchers Jennifer Doudna and Emmanuelle Charpentier won the 2020 Nobel Prize in Chemistry for their discovery of CRISPR-Cas9 gene editing technology. Since then, the approach has become commonplace in laboratories across the globe and is beginning to lead to amazing discoveries that could revolutionize the treatment of genetic diseases. For example, 2023 brought the FDA’s approval of the first CRISPR-based gene therapy, Casgevy™ (exagamglogene autotemcel), to treat sickle cell anemia. Sickle cell anemia is an inherited condition. It is caused by a mutation in the hemoglobin subunit beta gene (HBB), which results in the production of rigid and abnormally sickle-shaped red blood cells. This sickling limits their oxygen-carrying ability and can even block blood flow during vaso-occlusive crises. These crises cause severe pain that lasts for hours to days, with some patients even experiencing over a dozen crises a year. In these cases, Casgevy is administered as a one-time dose to reduce crisis frequency and severity. This involves collecting the patient’s blood cell-generating hematopoietic stem cells and editing their genome. CRISPR-Cas9 is used to “switch off” a gene whose role is to block the production of a type of hemoglobin produced in fetuses. This gene, called BCL11A, is typically activated after birth to make the body produce “adult” hemoglobin. The edited cells are delivered back to the patient after high-dose chemotherapy to encourage them to engraft in the bone marrow. If successful, the edited cells survive, multiply and give rise to healthy red blood cells that produce fetal hemoglobin, which does not result in sickling. As yet unpublished data from clinical trials suggest that Casgevy was able to prevent severe vaso-occlusive crises for at least 12 consecutive months in 29 of 31 patients (93.5%) with sufficient follow-up, and none experienced graft failure or rejection. Whole-genome sequencing stands to aid cancer treatment The time and cost involved in genome sequencing have reduced significantly since its inception. Completed in 2003, The Human Genome Project took 13 years to finish and cost an estimated $2.7 billion. Now, a genome can be sequenced for around $600 in a single day, and the prospect of the “$100 genome” is on the horizon. With these steps forward in sequencing technology and accessibility, the UK 100,000 Genomes Project in 2018 met its goal of sequencing 100,000 genomes from cancer patients. Now one of the largest sequencing projects of its kind, the project completed whole-genome sequencing (WGS) of over 13,000 solid tumors from 33 different cancer types. WGS provides a more comprehensive examination of a tumor’s genetic profile than other approaches. This could lead to the UK’s National Health Service becoming the first national health system to incorporate WGS into routine cancer care. Listicle GENETICS IN DISEASE 3 Combined with clinical data, WGS may help pave the way for precision oncology, allowing researchers and clinicians to observe patterns of genetic changes tied to treatment responses, which could ultimately inform treatment decisions to improve patient outcomes. AI tool predicts potentially pathogenic mutations The potential impact of advances in genetic analysis is evident; but what can we do with the reams of data produced by these technologies? Could machine learning and artificial intelligence (AI) hold promise in streamlining genetic analysis? Novel genomics technologies have revealed the extent of genetic variation in the human population. Some gene variants do not affect the resulting protein, while so-called missense variants can alter the sequence of amino acids, with varying results depending on the amino acid change. More benign missense variants can have very little effect and are relatively harmless. On the other hand, others can have negative, pathogenic effects by disrupting protein function, possibly leading to disease, such as the mutation responsible for cystic fibrosis. However, only around 2% of the over 4 million missense variants identified in humans are classified as either pathogenic or benign. If the clinical significance of these variants could be determined, new clinical treatments could potentially be developed to target those underpinning genetic diseases. This presents a huge opportunity for machine learning or AI to begin to tackle this problem and provide a foundation for researchers’ investigations. An AI tool called AlphaMissense predicts the effects of genetic variants on the function of the resulting protein. This builds upon AlphaFold, a groundbreaking AI tool that predicts protein structures from genetic information. Researchers used AlphaMissense to predict the effect across the proteome – amounting to 71 million possible missense mutations in over 19,000 human proteins. From this, it was able to predict the effect of 89% of these mutations as either likely benign (57%) or likely pathogenic (32%) – the rest were ambiguous. The same thresholds were found to be 90% accurate using a database of clinical variants. AlphaMissense is described as having “superior performance” compared to previously developed approaches. The database has also been made publicly available to help diagnose rare diseases and potentially identify novel disease-causing genes. Conclusion WGS stands to provide benefits for routine cancer care as well as aiding the diagnosis of rare genetic diseases. As access to sequencing technologies widens as they become cheaper and faster, these benefits will become more widespread. The potential of AI also continues to grow at pace and has huge potential to comb through vast amounts of genomic data to advance the identification of variants responsible for genetic diseases. These advances in our understanding may pave the way to help make a difference in the lives of patients affected by genetic diseases and their families. Sponsored by Listicle