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Missense variants that change the amino acid sequences of proteins cause one-third of human genetic diseases1. Tens of millions of missense variants exist in the current human population, and the vast majority of these have unknown functional consequences. Here we present a large-scale experimental analysis of human missense variants across many different proteins. Using DNA synthesis and cellular selection experiments we quantify the effect of more than 500,000 variants on the abundance of more than 500 human protein domains. This dataset reveals that 60% of pathogenic missense variants reduce protein stability. The contribution of stability to protein fitness varies across proteins and diseases and is particularly important in recessive disorders. We combine stability measurements with protein language models to annotate functional sites across proteins. Mutational effects on stability are largely conserved in homologous domains, enabling accurate stability prediction across entire p

A Stanford researcher told PACCARB that mobile genetic elements, especially an IS element called ISL3, can copy themselves and upregulate genes that give Enterococcus faecium a fitness advantage in transplant patients’ guts; roughly 40% of bloodstream infections in that cohort were traceable to the gut, she said.

Discover how genomics helps prevent chronic diseases through early risk detection, personalized medicine, and targeted lifestyle changes.

Researchers found that ultra-rare genetic variants play a significant role in the heritability of coronary artery disease (CAD), particularly in individuals of European ancestry. These variants, espec...

YouTube video by Oxford Nanopore Technologies

Understanding Breast Cancer Through Its Genomic Architecture Breast cancer, a complex and multifaceted disease, is primarily defined by the intricate structures of its genomes. Recent research conducted at Stanford Medicine has revealed that this genomic architecture can classify breast cancers into distinct subgroups. These classifications could pave the way for groundbreaking therapeutic strategies, especially if interventions are applied at earlier stages of cancer development.

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Prof Lamech M. Mwapagha Africa faces a heavy disease burden of both communicable and non-communicable diseases. Although the continent has generally succeeded over the last 20 years in decreasing the levels of a number of communicable diseases (e.g. cholera and polio), there are some (e.g. malaria and HIV/AIDS) whose prevalence remains quite high. This disease burden has been aggravated with the emergence of drug-resistant strains of various pathogens. Non-communicable diseases such as cardiovascular diseases (e.g. heart attack and stroke), cancer, diabetes and chronic respiratory diseases are also on the rise in Africa, with the number of deaths from these projected to increase over the next decade. The high disease burden in Africa can be significantly reduced through a proactive approach, including a combination of public health strategies to help identify genetic risk factors for diseases, and to tackle the spread of emerging infections and drug resistance. Opportunities There is an increasing body of research which suggests that a better understanding of the genomics of pathogens is likely to play a crucial role in the prevention and treatment of infectious diseases. Knowledge of particular gene expression patterns in pathogens has provided novel targets for drug therapy.  Similarly, genomic analysis has provided important prognostic indicators for breast cancer patients and helped identify the drugs to which such individuals could respond best. This has opened the door to the new era of personalised medicine that aims to tailor therapy according to each person’s genetic makeup and achieve the best outcomes for individual patients, rather than treating all persons with a ‘one size fits all’ approach. A good example was the utilisation of genome sequencing that pointed to a new treatment regimen for Nicholas Volker, who suffered from a gastrointestinal disorder that was cured with a bone marrow transplant. To date, the US Food and Drug Administration has approved 45 human genetic tests, and more than 100 nucleic acid-based tests for microbial pathogens. Although most of this research is being carried out in the developed world, scientists on the African continent are continuously attempting large-scale genome research studies focusing on specific diseases. The international HapMap project and other previous studies have shown that Africans have the greatest amount of genetic variation. Thus, understanding the genetic basis of both communicable and non-communicable diseases in Africans may provide useful insights into devising effective strategies to combat these diseases that have had a large impact on African populations. Challenges Africa still lags behind the rest of the world in the field of genomic research. This is largely attributed to the following challenges:  * Cost of genomic research remains prohibitive for African research centres, due to lack of government funding and support; * A dearth of African scientists with genomic research and computational expertise; * Lack of biomedical research infrastructure; * Lack of collaborative research among African scientists; * A climate of fear about genomic information among the public and health professionals; * Lack of proper engagement with national and regional agencies in the uptake of genomic research; * No proper policies and clear guidelines to inform medical and public health professionals about the level of confidence and the utility of genomic information. Recommendations  African Union member states set a target of 1% of GDP to be invested in research and development, but this has not been realised. So far, only South Africa, Kenya and Senegal are close to this target, at around 0.8% in all three countries. Given the huge potential of genomic research in addressing public health problems, it is crucial that such research is given higher priority in Africa.  Such research should be supported in the context of establishing infrastructure for genomic studies, capacity building and enhancing research collaborations with credible international partners. African genomic scientists should also engage in collaborative research and networks that would enable the exchange of new ideas and knowledge transfer. Such collaborations could indirectly influence policymakers to support investment in genomic research. Already there are programmes that are supporting such initiatives, but there is scope for considerable expansion. Overall, policymakers need to be involved from the outset in all discussions involving genomics research. By engaging community stakeholders, academics and public health professionals in the development of research questions and setting-up of legal regulatory frameworks, the gap between genomics and public health needs can be bridged. This would go a long way towards ensuring the translation of genomic research findings into public health benefits. *Prof Lamech M. Mwapagha is an associate professor of medical biochemistry at the Namibia University of Science and Technology (Nust), specialising in cancer genomics and antimicrobial resistance. He holds a PhD in medical biochemistry from the University of Cape Town and completed postdoctoral training in Cancer Genomics at the International Centre for Genetic Engineering and Biotechnology (ICGEB). The opinions expressed in this piece are his own, and not the views of his employer.