AI and Genetics: AlphaGenome

AlphaGenome is the latest AI model for analyzing vast stretches of DNA, published by Google DeepMind on Jan 28th, 2026. Where its predecessor, Borzoi, created in August 2023, could only analyze 500,000 base pairs, the new version can read more than one million. AlphaGenome can identify points of interest down to a single base pair and shows potential for applications in diagnosing genetic diseases, identifying mutations, and developing therapies. The AI model can also predict the results of single nucleotide polymorphisms, making it a unique tool for understanding gene expression and regulation. 

There are many AI tools being used in the field of genomics with advancements in technology continuing to propel the generation of new versions with increased capabilities. Alternative models are specialized for specific applications such as ChromBPNet, which focuses on predicting the accessibility of chromatin in DNA sequences. Just as AlphaGenome was built upon the foundation provided by Borzoi, the current technology will provide a platform for further development.

Souce:

https://www.sciencenews.org/article/ai-tool-alphagenome-predicts-genetics

Additional Link:

https://pubmed.ncbi.nlm.nih.gov/41606153/

New Study Reveals Shared Genetic Markers Underlying Substance Use Disorders

 

     Scientists have identified genes that are commonly inherited across addiction disorders, regardless of what substance was used. The study was led by researchers at the Washington University in St. Louis. In 2021, more than 46 million people in the U.S., at the age of 12 or older, had at least one substance use disorder, with only 6.3% receiving treatment. About 107,000 people died of drug overdoses in 2021, with 37% of the deaths involving opioid and stimulant drug exposure. Disorders caused by substance use are heritable and influenced by interactions among different genes and environmental factors. The genome-wide association is a method that searches entire genomes for regions of genetic variation, called single-nucleotide polymorphisms, that associate with the same disease or condition among multiple people. In the study, researchers used this method to identify areas in the genome that were associated with general addiction risk and risk of substance specific disorders. A sample of 1,025,550 individuals with genes indicating European ancestry was used and so was a sample of 92,630 people with genes indicating African ancestry. The research team discovered various molecular patterns, including 19 independent SNPs associated with general addiction risk and 47 SNPs associated with substance specific disorders. These identified patterns were among the European ancestry. The strongest gene signals that were consistent across the different disorders were located in areas of the genome responsible for regulation of dopamine signaling, indicating that dopamine signaling regulation is an important part of addiction risk. The genomic pattern associated with general addiction risk predicted higher risk of mental and physical illness, including suicidal behaviors, chronic pain conditions, psychiatric disorders, and respiratory conditions. In children aged 9 to 10 years old, the presence of these genes correlated with parental substance use. Genomic analysis in the African ancestry sample showed one SNP associated with general addiction risk and one SNP associated with alcohol use disorder. 

This research is very intriguing. Firstly, it’s intriguing in that the results between the different ancestries are drastically different. It could also be taken into account the different sample sizes between the two ancestries. However, due to the sample sizes and the limited research done so far, the data cannot be used to categorize genetic risks within certain populations. But, including populations that have historically been underrepresented in biological and biomedical research could lead to a better accuracy in the found results. Hopefully, this research opens a pathway to discovering the factors that protect or predispose a person to a substance use disorder. Through these findings, the hope is that new treatments and preventative measures could be found against multiple substance use disorders

https://nida.nih.gov/news-events/news-releases/2023/03/new-nih-study-reveals-shared-genetic-markers-underlying-substance-use-disorders 

https://www.nimh.nih.gov/health/topics/substance-use-and-mental-health

GWAS Shows Correlation of Cannabis Use Disorder with Lung Cancer

 The Genetic Basis of Cannabis Use Disorder and Lung Cancer

    A recent GWAS from Nature shows a correlation between lung cancer susceptibility and cannabis use disorder. This study was a meta-analysis between nearly 1 million individuals of European, African, mixed American, and East Asian ancestries and it examined single nucleotide polymorphism (SNP) heritability. Using this data, the researchers found that 22 loci were associated with the susceptibility of lung cancer, but in each group, the expression of the SNPs was different. For instance, the East Asian sample group's SNPs were intronic to the semaphorin 6D-encoding gene, whereas the American group was an intergenic region downstream of leucine-rich repeats containing the semaphorin 6D-encoding gene. They used a comparative analysis of psychiatric symptoms and found many overlapping associations between cannabis use disorder and the likelihood of developing lung cancer. This association comes from a likelihood of becoming a smoker and resorting to cigarettes, which would most likely, in turn, result in a greater risk for lung cancer in those populations.

    I found this study to be very interesting and it definitely shines some light on the addictive manner of cannabis and cannabis-containing products. The biological mechanism of cannabis and the cannabinoids involved are still not fully known, which I think is a long-term danger in regards to smoking/consuming cannabis products. Furthermore, those with cannabis use disorder being at a greater likelihood for developing lung cancer is scary to think about and could considerably be an element of medicine/psychiatry to dig deeper to in the meantime. Nevertheless, going forward I think we should be more conscientious of what we are breathing in and consuming, because with lung cancer being the top cause of death, that should be enough to scare us into treating our bodies better. 

Links:

1. https://www.nature.com/articles/s41588-023-01563-z 

2. https://www.news-medical.net/news/20231123/Genome-study-unveils-genetic-ties-between-cannabis-use-disorder-and-lung-cancer-risk.aspx 

Genetic Factors Associated with Increased Longevity Identified

    The article gives new insight into new research claiming that genes actually play a role in determining the life span of people and also influencing the likelihood of age-related diseases. "Aging is a complex process indicated by low energy levels, declined physiological activity, stress induced loss of homeostasis leading to the risk of diseases and mortality." (PMC). In the one study, a specific gene was identified to associate with exceptional longevity, as it was seen to live anywhere from1 to 3 decades more than the average US life span.

    The researchers in order to under genetic components of longevity than took DNA from 800 people that were aged from 95 to 119 years old. The DNA was taken and was then compared with other DNA from random controls. During this study they were able to identify specific genetic variations that are associated with longevity and from there they were able to develop a genetic model that comprised of 150 single-nucleotide polymorphisms. This developed genetic model was able to compute the predisposition of an individual towards exceptional longevity since the model was able to predict exceptional longevity in samples of those that lived to 100 years old and provide a 77% accuracy with this model. 

    With further research, they found 19 subgroups of centenarians which all were associated with different genetics paths and contained a delay onset of age-related diseases. It was also found that 15% of control subjects contained the genetic signature that is associated with longevity. This shows us that there is genetic potential for a longer life span and that further research will need to be done in order to verify the model's utility for genetic testing.

Source: Live Long and Proper: Genetic Factors Associated with Increased Longevity Identified | Scientific American

Other: Genes and Longevity of Lifespan - PMC (nih.gov)

Autism Spectrum Disorder and the Genetic Contributions

     Autism is usually discovered in early childhood by communication dysfunctions and social interactions as well as repetitive and restrictive behaviors and interests.  Autism spectrum disorder is a heterogeneous group of neurodevelopmental conditions set by specific criteria. The main areas affected by this disorder are language level, intellectual functioning, and co-occurring psychiatric and medical difficulties, all of these ranging from very severe to moderate.  The male-to-female ratio of autism is 4:1 in a clinical study.  This sex difference is unknown why but there are a few ideas that were thrown around, one being that there are more underdiagnoses and misdiagnoses in women.  70% of people with autism have other conditions alongside it, the main ones being ADHD, anxiety, depression, epilepsy, sleep problems, and gastrointestinal and immune conditions.  The twin studies suggest that 9-36% of the variance in autism could be from environmental factors, not genetic ones.  From pregnancy-related nutrition factors to heavy-metal exposure, there is a wide range of factors that could be associated with autism outside of the genetic conclusion.  Looking into the genetic world of autism, there are findings from linkage, candidate gene studies, common and rare genetic variation studies, epigenomics, and transcriptomics.  Linkage studies can show the regions of a chromosome that are inherited in affected individuals.  Another example is the SNP-heritability of autism which ranges from 65-12%, showing that variation of a single nucleotide could play a big part in this inheritance.  Looking through this paper there is so much information on different studies down to help prove these theories. There are so many different factors that can contribute to autism and many methods discovered to help investigate the genetic variants that carry out autism and autistic traits.

    The first image, a, explains variance by different classes of variants in autism.  The shades of green show familial recurrence and the purple being the environmental factors that could contribute.  Image b is showing showing the variance change in phenotypic subgroups.  

https://www.sciencedirect.com/science/article/pii/S2001037020303007#:~:text=In%20GWAS%20studies%2C%20SNP%20heritability,measured%20genetic%20variants%20influence%20phenotypes. 

https://www.cambridge.org/core/journals/psychological-medicine/article/genetic-contributions-to-autism-spectrum-disorder/89240047F6928249D9DE91A6A6CFBD52