Category Archives: Human Genetics

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Credit: Rodrigo Muoz

The Patagonian sheepdog (PGOD) originated from the ancestral shepherds of the United Kingdom is nowadays the closest link to a now extinct population of shepherds from which modern herding breeds descend. This was shown by research recently published in the journal named PLOSGenetics.

The research was based on the genomic characterization of the Patagonian sheepdog. For this, it was necessary to take samples of 159 Patagonian sheepdogs from the region of Aysn and Magallanes, in addition to some of them belonging to the Province of Chubut, Argentina. In this route of almost 13.000 kilometers, hair samples and 22 body measurements were extracted, in addition to collecting information on their pastoralist behavior, health status, reproductive status and nutrition, among other data.

For Natasha Barrios, a member of Universidad Austral de Chile and who led the study, this Patagonia dog, unknown in the world, is shown as the missing link between the old shepherds of the United Kingdom and the modern herding breeds. In that line, she said that today we have an idea of what these dogs were and looked like before the official set up of modern breeds. It has been incredibly silent and stealthy working in the extreme of South America for the last 140 years, making it a valuable genetic and cultural reservoir.

DNA sequencing from blood samples was performed by means of a whole-genome genotyping chip. This chip has approximately 170.000 potential markers of polymorphisms within the dog's genome. To identify these variants, the obtained data were compared with data of similar characteristics from 1,514 individuals belonging to 175 recognized dog breeds, considering within this group herding breeds of European origin.

Regarding the advantages of this type of approach, Guillermo Nourdin, Bioinformatics expert at the MELISA Institute, who was responsible for the management and analysis of genomic data, highlighted the global, integrative and massive look at genomic data in the research. In addition, this approach identified common traits that match populations of Patagonian sheepdog together with modern herding dog breeds that have a common ancestor of European origin, he stated.

Finally, Prof. Elard Koch, senior researcher and Chairman at the MELISA Institute, said that they were pleased with the participation of Guillermo Nourdin in this study of Patagonian sheepdogs: "Collaborating with our bioinformatics capabilities in research as relevant as this one, is encouraging for our researchers and a major goal for our institution" Koch remarked.

This research opens the door to the future exploration of different phenotype-genotype association analyzes, which would, for example, the exploration of genetic traits associated with their behavior, resistance and ability to work; additionally, to search for possible diseases prone to some modern herding breeds, where Patagonian sheepdog could be key to understanding how and why they have spread today.

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This work was funded by: National Research and Development Agency, FONDECYT 1181592, Chile. (https://www.anid.cl) to MAG, National Agency for Research and Development, National Doctoral Scholarship 2018, Chile (www.anid.cl) to NB, National Agency for Research and Development, REDI 170062, Chile (www.anid.cl) to CGL, National Agency for Research and Development, PIA/BASAL FB0002, Chile (www.anid.cl) to CGL, The Intramural Program of the National Human Genome Research Institute of the National Institute of Health, Bethesda, Maryland, United States of America to EAO, DLD, HGP, ANH. The sponsors had no role in the design of the study, the collection and analysis of data, the decision to publish or the preparation of the manuscript.

Participating researchers:

Natasha Barrios, Institute of Pharmacology and Morphophysiology, Graduate School, School of Veterinary Sciences, Southern University of Chile; Cesar Gonzalez-Lagos, Department of Sciences, School of Liberal Arts, Adolfo Ibanez University, Santiago, Chile, and Center for Applied Ecology and Sustainability (CAPES), Santiago, Chile; Dayna L. Dreger, Heidi G. Parker, Andrew N. Hogan and Elaine A. Ostrander, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA; Guillermo Nourdin-Galindo, Biotechnology Division, MELISA Institute, Concepcion, Chile; Marcelo A. Gomez, Institute of Pharmacology and Morphophysiology, School of Veterinary Sciences, Universidad Austral de Chile, Valdivia, Chile.

Experimental study

Animals

Patagonian sheepdog: Genomic analyses trace the footprints of extinct UK herding dogs to South America

28-Apr-2022

Competing interests: The authors have declared that no competing interests exist.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

See the original post here:
Discovery of the link between the Patagonian sheepdog and the former shepherds from the UK - EurekAlert

NEW YORK A team from Stanford University and other centers in the US and China have demonstrated that polygenic risk scores (PRS) based on common variants can be bolstered by incorporating clues from rare variants linked to significant gene expression shifts, dubbed expression outliers.

"As individual PRS estimates are comprised of variants across hundreds to thousands of genes, we reasoned that the disease effects of outlier-associated rare variants might have the greatest impact in individuals with a relatively larger burden of outlier-associated rare variant effects mapping to disease-relevant genes," Stanford University researchers Craig Smail and Stephen Montgomery, first and senior authors on a studyappearingin the American Journal of Human Genetics on Wednesday, explained in an email.

Using genotyping data from UK Biobank participants, together with expression quantitative trait locus data from the GTEx project and a computational method known as CrossMap that takes rare variant-related gene expression changes into account, the researchers first flagged rare variants with outsized effects on gene expression.

From nearly 1.8 million rare variants found in the UK Biobank set and in the gnomAD database, they flagged nearly 90,900 rare outlier variants that appeared to impact the expression of 15,871 genes, based on rare variant annotations gleaned from whole-genome and transcriptome sequences in version 8 of the GTEx.

From there, the team used its "independent outlier gene count" (IOGC) score to demonstrate that the expression outlier-related rare variants could improve the performance of body mass index (BMI) PRSs in more than 96,600 of the UK Biobank participants, distinguishing between individuals at higher or lower risk of so-called severe obesity or early bariatric surgery findings that were further validated using data for Million Veteran Program participants.

"We have demonstrated that a high burden of rare variants identified by their association with outlier gene expression can lead to substantial deviations in PRS-predicted phenotype," the authors wrote. "Furthermore, by integrating these rare variants into genetic risk prediction using the IOGC score, we demonstrated improvements in predicting risk for obesity beyond what was achievable with common variant-based PRSs."

In particular, the investigators found that predictions made using expression outlier-linked rare variants outperformed those possible by incorporating insights on protein-truncating rare variants into PRSs. Based on UK Biobank GWAS data spanning more than 1,900 traits or conditions, meanwhile, they saw signs that gene expression outlier-linked variants were somewhat enriched compared to rare variants that did not shift gene expression.

The findings so far suggest that "prediction for multiple complex diseases will benefit from integrating outlier-associated rare variants, including coronary heart disease, type 2 diabetes, and breast cancer," Smail and Montgomery wrote, noting that preliminary work points to improved predictive accuracy in at least two populations, hinting that a similar strategy may boost efforts to apply PRSs in non-European cohorts.

The investigators cautioned that the current approach is reliant on rare variant annotation insights from a relatively small set of GTEx representatives so far, and may be further improved by tapping into growing RNA sequence datasets and resulting variant-gene expression annotations. Likewise, whole-genome sequences from the UK Biobank project are expected to reveal far more rare variants missed with more limited sequence data used in the current analysis.

Consequently, Smail and Montgomery called the current work "a baseline for phenotypic prediction of complex diseases by integrating outlier-associated rare variants."

"Future extensions to our model will include more rare variants as we continue to sequence both transcriptomes and genomes in populations, will look at tissue-specific outlier effects, and incorporate longer-range gene expression impacts such as outlier-associated rare variants in enhancer regions," they noted.

Read the rest here:
Polygenic Risk Score Performance Improved With Expression-Related Rare Variant Insights - GenomeWeb

This kind of first-degree offspring is extraordinary, only having been cited in royal families of the past headed by god-kings such as the Egyptian pharaohs seeking to maintain a pure dynastic bloodline. (It is known, for instance, that Akhenaten married his eldest daughter, Meritaten, and much later, Ptolemy II married his sister, Arsinoe II hence his nickname, "Philadelphus" or "sibling loving.") It has been suggested that this Neolithic elite may have claimed to possess divine powers to ensure the continuity of agricultural cycles by keeping the Sun's movements going.

The findings support the notion that these Neolithic communities were socially stratified and that the massive stone structures were used to bury transgenerational patrilineal members of these clans. Perhaps equally interesting is the fact that in one case relatives were separated by up to 12 generations, pointing to an unusual stability through time of both the funerary tradition and the stratified society where they lived.

We have seen several case studies of past inequality correlating funerary archaeology with genetics that might no longer apply today, where legal regulations (and also the exponential increase of cremations) represent a certain degree of standardisation in funeral practices. Nevertheless, an opposite trend could shape thefuture of the archaeology of death: the trend toward personalised coffins, unconventional funerary memorials, and special grave goods. One way or another, mortuary archaeology will always be an important subfield of this discipline, and one that will need to rely on the hard sciences such as genetics and forensics.

Perhaps one encouraging conclusion is that despite what we have seen on the archaeology of past inequality, societies have been able to evolve and change their social stratifications. One example is Iceland the country has become one of the most egalitarian societies in the world. In 2018, Iceland passed a law that all companies employing more than 25 people will have four years to ensure gender-equal payment because, according to the head of the Equality Unit at Iceland's Welfare Ministry, "equality won't come about by itself, from the bottom up alone".

* This is an edited version of an article thatoriginally appearedinThe MIT Press Reader, and is republished with permission.

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Carles Lalueza-Foxis Research Professor and Director of the Paleogenomics Lab at the Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra) in Barcelona. He participated in the Neanderthal Genome Project and led the first retrieval of the genome of an 8,000-year-old European hunter-gatherer. He is the author of Inequality: A Genetic History, from which this article is adapted (this is an edited version of the original MIT Reader piece).

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Why some ancient societies were more unequal than others - BBC

Recently published research in Nature Genetics featured the most diverse genetic study on type 2 diabetes.

While scientists are aware of certain factors that may increase a persons risk of developing type 2 diabetes, one major question is what role genetics plays.

Researchers from the US and England collaborated to analyze the DNA profiles of thousands of people of varying ancestries. In doing so, they not only identified new genes that contribute to type 2 diabetes, but they also became a step closer to developing a genetic risk score for the disease.

Type 2 diabetes occurs when a persons body does not make enough or use insulin effectively, making it difficult for the body to regulate blood sugar levels. It can be life threatening if someones blood sugar levels get too high or low.

The Centers for Disease Control and Prevention reports that around 37 million Americans have diabetes, and around 90-95% of these people have type 2 diabetes.

According to the American Diabetes Association, a person with type 2 diabetes may experience some of the following symptoms:

If a person suspects they have type 2 diabetes, they can consult with their physician, who can order a blood test to check for the disease.

There is not a cure for type 2 diabetes, but people with the disease can manage their blood sugar levels by taking medications and avoiding foods that spike blood sugar levels.

While there is a lot of research on type 2 diabetes, much of it has primarily targeted people of European ancestry.

Risk scores derived from one ancestry often do not transfer well to others, explained Professor Nathan Tucker in an interview with Medical News Today. Inclusion of diverse ancestries helps us understand the mechanisms of the risk, improving the probability of successful therapeutic development.

Prof. Tucker is an assistant professor and genetics core manager at Masonic Medical Research Institute in Utica, NY.

The authors also noted that genetic risk scores provide unreliable prediction when deployed in other population groups.

The researchers accessed data from other studies to create the Diabetes Meta-Analysis of Trans-Ethnic association studies (DIAMANTE) Consortium. They analyzed the genetic makeup of 180,834 individuals with type 2 diabetes and compared it to 1,159,055 people without diabetes.

The scientists placed people in 1 of 5 groups: European ancestry (51.1%); East Asian ancestry (28.4%); South Asian ancestry (8.3%); African ancestry (6.6%); and Hispanic ancestry (5.6%).

By comparing the DNA of the people with type 2 diabetes to those without, the researchers were able to identify more than 200 loci that were genetically significant in terms of developing the disease.

According to the National Human Genome Research Institute, a locus (or loci in the plural form) is a physical site or location within a genome (such as a gene or another DNA segment of interest.).

This study identifies 237 genomic regions that are associated with altered risk of type 2 diabetes, with nearly 100 evidence-based targets that are prioritized for the next stages of therapeutic development, Prof. Tucker explained.

The researchers also identified genes that may contribute to developing type 2 diabetes.

We have now identified 117 genes that are likely to cause type 2 diabetes, 40 of which have not been reported before. That is why we feel this constitutes a major step forward in understanding the biology of this disease, says Professor Anubha Mahajan.

Dr. Mahajan is a human genetics researcher and professor at the University of Oxford in England.

The sheer magnitude and diversity of this study create enormous potential for being able to one day identify a persons genetic risk for type 2 diabetes.

Inclusion of diverse ancestries helps us understand the mechanisms of the risk, improving the probability of successful therapeutic development, Prof. Tucker commented.

Dr. Brian Fertig, the Founder and President of the Diabetes and Osteoporosis Center in Piscataway, NJ, also spoke with MNT regarding the study.

The findings of this study are not surprising because diagnostic and therapeutic stratifications are too often overly simplified as one size fits all, Dr. Fertig said.

Dr. Fertig also thought the study emphasized the importance of diversity and inclusion in research.

This data underscores the need for a precision, personalized and dynamic scale of medicine, as its rare to see two diabetics with the same clinical and biochemical profile, Dr. Fertig commented. Every individual is unique and as such should have individualized treatment plans.

More:
Type 2 diabetes and genetics: What is the link? - Medical News Today

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Identification of candidate genes associated with bacterial and viral infections in wild boars hunted in Tuscany (Italy) | Scientific Reports -...

You may have heard of the concept of a good hangover. In 2019, for instance, VICE writer Tom Usher tweeted that hangovers are actually quite nice if you're in the right environment. This caused outrage among some and agreement among others, but, as it turns out, the relief of a hangover can sometimes go deeper than being really in bed watching Takeshi's Castle with a Solero or tucking into a tub of Chinese takeaway at 11AM.

Enter: r/hangovereffect, a subreddit which showed up in 2018. The about section reads: A community that feels relief from hangovers and are looking for answers as to why. Most of us are diagnosed with ADHD and exhibit depression, anxiety and fatigue but feel complete remission from all symptoms when hungover from alcohol. If you feel the same way, join us and let's find a cure.

As of today, the subreddit has around 7,700 members who claim that hangovers have been beneficial for their mental health. The posts range from the inspiring to the academic, with people sharing anecdotes and theories about what they call the hangover effect. Often, users are very specific, with posts relating to the pharmacological attributes of alcohol and its effects on the brain. Others are more revelatory. Anyone else noticed not only feeling great but also looking great? wrote one user recently.

One such member is Dylan, 32, from Asheville in North Carolina. Dylan started getting an inkling that he had a peculiar reaction to alcohol in his early twenties. My friends would wake up feeling sick, but Id just feel two steps down from satori [a Japanese Buddhist term for awakening]. Everything was alright it eased my depression, my anxiety, he says.

Alex, 30, lives in New York City. He says he has depression, anxiety and undiagnosed ADHD. His experiences sound similar to Dylans, with a heavy night of drinking making way for a newfound sense of self. I was calm, empathetic, emotional, not anxious, he says.

For Anna, 38, from Toronto, hangovers would make her much happier and more content. The next day my depression would go away. I would feel like a completely different person, she says. For someone who had been on various antidepressants for years, to little effect, being hungover felt like a total relief.

All three are wary of using this particular hack day-to-day and none are frequent drinkers. Drinking every single day would come with its own set of problems, says Alex.

Anna used to drink regularly while working at bars, before stopping completely. It became a bit of a habit for combating anxiety, she says. These days, she drinks socially maybe once a week.

Across the subreddit more generally, there are stories of tactically inducing a hangover without being totally destroyed. One member claims that drinking 200ml of vodka (four double measures) just before bed allows them to feel hungover, but also clear in the head the next day. Alex says that while he doesnt really drink alcohol at home, if I had something important on tomorrow, occasionally Id prompt a social engagement to happen tonight.

Many members also try out different supplements and various experiments in the hope they might find ways to replicate the hangover effect without getting wasted. It's not clear what will work yet, it seems like everyone's got different theories, says Anna, who only discovered the subreddit last week. Shes decided to start experimenting with creatine and glycine two supplements often used by bodybuilders. Some users have claimed these supplements help lift brain fog and help them feel better.

Alex claims that high doses of vitamin C helped a little bit. But then that kind of dissipated.

Dylan, meanwhile, has a whole fucking long list of things hes tried over the years, with varying success. Hes even gone as far to track down some Memantine online a medication usually used to treat Alzheimers disease. Hes been taking the medication, unprescribed, for over a year.

My life has been incredibly improved. I have no complaints. Every day my PTSD, depression and anxiety are getting better, he says. He believes the Memantine works because it inhibits NMDA receptors essentially, it decreases abnormal activity in the brain. Through what he calls extensive self-research, Dylan believes that those who experience the hangover effect might have hyperactive NMDA receptors, which is why the medication helps.Memantine is like a diet ketamine, almost, in that you can function on it, he says.

The amount of casual theorising and DIY experimenting away from medical supervision and regulation is concerning for obvious reasons. One rule of the subreddit is that all theories about the hangover effect must be backed up by scientific sources where possible, and that people should try to write in a critical and scientific way. However, this can be tricky when you consider that most of the members are presumably not scientists, nor medical experts. For many, though, this subreddit has become a last resort. You cant exactly go to your GP and say, I feel better when Im hungover!

Melissa Herman, Ph.D, is an Assistant Professor at the Bowles Center for Alcohol Studies. While she agrees that unregulated experiments should be avoided, she says that there could be some truth to the hangover effect, for some people. Its an area that clearly needs further research.

My guess is that the positive symptom relief that they're feeling is because the alcohol is acting on different circuits that are dysregulated in their specific condition, she explains. By circuits, Herman is referring to the groups of neurons inside our brains. Without getting too scientific, neurons are what send messagesto our nervous systems, and one persons messaging system might be quite different to the nexts.

Targeting those circuits is a huge field in neuroscience right now, and there are clinical trials underway, looking at human genetics. So I think there will be positive movement in this area. If not immediately, then one day.

That said, Herman warns against using alcohol to achieve the hangover effect and expresses concern about people cherry picking and that not looking holistically means the brain could be harmed in other ways by some of these experiments.

Alcohol is a really potent pharmacological compound and it affects many parts of the brain, she adds. In other words, sure, alcohol might make some people less anxious the next day. But it can also cause brain cells to die and brain tissue to shrink. In fact, its associated with 2.8 million deaths each year worldwide and is also more generally known for causing anxiety the morning after hence the term hanxiety. One study found around 22.6 percent of participants reported anxiety during a hangover.

Still, for a lot of people, the hangover effect is clearly a very real and confusing conundrum. Hopefully, in the near future, the thousands of people in this subreddit wont have to choose between being hungover or miserable and anxious. Until then, *clinks glasses*.

@_rhysthomas_

More:
Can a Hangover Improve Your Mental Health? These People Think So - VICE UK

Evan Eichler

Professor, University of Washington

It has been more than 20 years since scientists announced the completion of the Human Genome Project even though the $3 billion effort to sequence the 3 billion bases of human DNA was not, in fact, complete. Technological limitations meant that roughly 8 percent of the genome remained a mystery.

In April, the Telomere-to-Telomere Consortium closed nearly all the gaps, adding roughly 200 million bases of genetic information that codes for more than 1,900 genes.

This new treasure trove of data, detailed in six papers in Science, stands to advance autism research, says Evan Eichler, professor of genome sciences at the University of Washington in Seattle.

Spectrum spoke with Eichler, who was part of the Human Genome Project and the Telomere-to-Telomere Consortium, about what secrets may emerge from once-murky regions of the genome.

This interview has been edited for length and clarity.

Spectrum: How will having a more complete human genome affect autism research?

Evan Eichler: Because our reference genome was incomplete, some gene sequences were not correctly mapped to their place in the genome. So when we would find a variant in an autism genome that was missing from the reference genome, we didnt always know where it was or which gene or genes it affected. This new telomere-to-telomere draft improves mapping across the board. The sequences we gather from people with autism are now more likely to be mapped to the right place.

One phenomenon often associated with autism is the deletion or duplication of DNA, known as copy number variation (CNV). In our recent paper in Science, we analyzed the new telomere-to-telomere data and found that it was a better predictor of true copy number 9 times out of 10 when compared with the old reference. That means were in a much better position to assess CNVs, which we know to contribute to autism, than with the old reference that was full of holes.

S: How was this updated human genome sequence produced differently from previous ones?

EE: We typically sequence autism genomes with short reads, which are just a few hundred bases long. When we do this, were missing genetic variation that occur over long stretches of DNA, particularly structural variation such as large deletions, duplications and rearrangements of DNA. We have previously shown that about 75 percent of all structural variation in the human genome goes undetected if we rely only on short-read data. Roughly 10 percent of autism cases stem from known structural variation in DNA. If we can sequence the genomes of autism families with long reads, many thousands of bases long, we can explore the 75 percent of structural variation that was previously undetected and potentially find more genetic causes of autism.

S: Are there potentially new autism-linked genes in the more complete genome?

EE: About 500 genes have been mapped to complex regions of the new reference genome that were previously excluded from sequencing studies because our techniques didnt reliably map there. Among those genes are ones important for brain function, such as SRGAP2C. The number of copies of this gene influences where, how and when dendrites form during development, which influences the density and strength of synaptic connections. Its a gene incredibly important to brain function, whose duplicate copies we couldnt reliably detect with short reads.

Another gene, ARHGAP11B on chromosome 15, was previously found to be deleted in two people with autism and intellectual disability. Its known to increase neuronal stem cell division during development. That gene is typically not studied in autistic people because it was mapped to very repetitive regions of the genome that previous genome-sequencing techniques skipped over entirely.

S: What could we learn about autism from the dark regions of the human genome that do not code for proteins?

EE: DNA that makes up the short arms of human chromosomes, called acrocentric DNA, may be important in autism. Those stretches were only sequenced in the last year or so of the Telomere-to-Telomere project.

There are gene families in acrocentric DNA that encode rDNA, which helps form the ribosomes that produce proteins in cells. We know autism is often linked with having too many or too few copies of genes; acrocentric DNA is another category of DNA we can now analyze for the same problem. If we can compare the rDNA of people with autism with that of neurotypical individuals, any differences we see may help us understand the chances of developing autism.

S: Now that we have a new reference genome, will some autism studies need to be repeated?

EE: Yes, well need to run all autism genomes against this new, more complete reference genome. Im particularly interested in looking for variations in genes on the X chromosome, which is linked with sex. There are significant sex differences in boys versus girls when it comes to autism, with boys four times more likely to be autistic than girls. Now, with the new reference genome, we can detect copy number variations and other genetic variation better than before, including on the X chromosome.

We would also like to look at unsolved cases of autism those not linked to any known rare genetic variants and those without high polygenic risk scores, which reflect common genetic variants associated with the condition. These unsolved cases account for a very large fraction of kids with autism. Maybe in the dark regions of the genome, or in genes not characterized before, we can find answers especially with long-read sequences of Mom, Dad and unaffected siblings to shed light on how these unsolved cases are genetically distinct or similar to their family members.

S: What about methylated DNA DNA with chemical tags called methyl groups on top. There is evidence that these epigenetic tags, which influence gene activity, play a role in autism.

EE: With new long-read sequencing techniques such as nanopore sequencing, we can distinguish methylated sequences without having to amplify or convert the DNA beforehand, as was necessary with prior techniques. There might be differences in epigenetic modifications of DNA between people with and without autism that we missed before, which could help address some of the unsolved cases of autism.

S: How feasible is it for researchers to conduct long-read sequencing, or for families to access it?

EE: The major limitation is the cost. Sequencing and assembling a genome well with long reads costs about $10,000, compared with about $1,000 with short reads. Most insurance companies are not going to pay for long-read sequencing. Theres also the issue of throughput. Since it started in 2016, the SPARK project has aimed to look at 50,000 families using exome sequences, which capture only the protein-coding regions of the genome. In that same time, we could look at just 50 families with long-read whole-genome sequencing. [SPARK is funded by the Simons Foundation,Spectrumsparent organization.]

But costs always come down with time. I think that long reads will replace short reads in 10 years. I think every family deserves to have their genomes fully sequenced and characterized, to help them make decisions such as what the best care for their children should be. We just have to get the technology to a cost-effective point.

S: The newly sequenced parts of the genome often contain highly repetitive DNA. Autism has been linked to the presence of such repetitive regions. What might these new regions tell us about autism?

EE: The short answer is we dont know yet. But there is evidence that those regions are very relevant to autism. Two common genetic causes of autism include duplications on chromosome 15q, which account for about 1.5 percent of autism cases, and deletions on 16p11.2, which account for just under 1 percent of autism cases. We know that repetitive regions are hotspots for chromosomal damage that can lead to deletions and duplications, but they werent precisely mapped. Now we can precisely map these regions of genomic instability and gain insights on how breaks occur there and potentially lead to autism.

S: Does anything else come to mind with this new work?

EE: One thing thats still a puzzle is that the same genetic variation strongly linked with autism can have very different outcomes in one kid versus another. Some children may be mildly affected, whereas others may be severely affected. I dont think the odyssey of this work ends with finding the primary genetic causes of autism. We need to understand the background in which these variations lie the way they interact with other genetic variation to understand their true outcome.

Another thing I have reflected on more recently is how most of the innovations we see with this new project were driven by scientists a full generation younger than me. I think that bodes well for the future, to have so many young people interested in solving these difficult problems. The future of human genetics research is in good hands.

Cite this article: https://doi.org/10.53053/GPXL5356

Read more:
Autism and the complete human genome: Q&A with Evan Eichler | Spectrum - Spectrum

ByAnnika Weder

A nearly 40-year-old study is the basis for new groundbreaking collaborative research identifying the relationship between genetics, proteins, and disease risk, while shedding light on racial health disparities in the process.

The new study, the results of which have been published in a paper in Nature Genetics, has provided a wealth of information that will allow the research community to test the ways in which proteins affect health outcomes, such as the risk for developing various types of cancer or heart disease or contracting COVID-19. The work could also lead to the development or repurposing of therapeutic drugs to treat human disease. The researchers hope the study will increase the understanding of the genetic basis of disease, in particular because the diversity of study participants will unlock new information about the links between proteins and disease.

The makings of this comprehensive study date back to the mid-1980s, when the Atherosclerosis Risk in Communities study was launched with Josef Coresh from the Department of Epidemiology in the Bloomberg School of Public Health as a principal investigator. ARIC, for which Johns Hopkins is a key field center, investigated causes of atherosclerosisa disease characterized by the build-up of fats, cholesterol, and other substances in the walls of arteriesand measured how cardiovascular risk factors, medical care, and outcomes vary by race, sex, place, and time.

The study was notable in two critical ways: it followed individuals for decades, collecting biological samples at regular intervals; and it included Americans of European ancestry as well as Americans of African ancestry. Beginning in 1987, more than 10,000 participants regularly received physical examinations and follow-up phone calls to maintain contact and to assess the health status of the cohort. Data collected include participants' medical history, demographics, health behaviors, and genetic information. The ARIC study has become a valuable resource, resulting in over 2,500 publications to date. Many independent research projects have used ARIC data for a range of topics including the study of heart disease, kidney disease, diabetes, and cognitive decline.

When Nilanjan Chatterjee, Bloomberg Distinguished Professor of biostatistics and genetic epidemiology, learned through graduate students he was co-advising with Coresh that ARIC also collected participants' proteomic datainformation about the proteins present in organismshe realized the immense untapped potential this resource held.

Image caption: Nilanjan Chatterjee

Image credit: CHRIS HARTLOVE

Proteins have a central role in many biological functions, supporting the structure, function, regulation, and repair of organs, tissues, and cells. Proteins support muscle contraction and movement, for example. They transmit signals to coordinate processes between different organs and move essential molecules around the body. Antibodies that support immune function, hormones that help coordinate bodily function, and enzymes that carry out chemical reactions such as digestion are all proteins. Because proteins control many of the mechanisms critical to an organism's health, diseases can often trace their origins to mutations in proteins.

Proteomics, the systemic analysis of proteins, gathers information about the proteome, the complete set of proteins produced by a given cell, organ, or organism. It falls under a class of disciplines collectively referred to as omics, which aim to collectively characterize the groups of biological molecules that translate into the structure, function, and dynamics of an organism. Other examples of omics studies include genomics, the study of an organism's full genetic information; epigenomics, the study of the supporting structure of the genome; and transcriptomics, the study of the set of all RNA molecules.

"ARIC is an incredibly unique data source, both because of the amount of genetic, proteomic, and other omic data they have on such a large number of study individuals, and because of its inclusion of individuals from European and African ancestries," says Chatterjee. "Diverse ancestry data is completely lacking in many omics studies. ARIC had a wealth of proteomic data that had not been analyzed, so we were very happy to take advantage of this incredible resource available to us right here at Johns Hopkins."

For their study, the researchers first analyzed genetic variants that correlate with protein levels in individuals to identify protein quantitative trait loci, or pQTL, portion of DNA. They then developed machine learning-based models that can predict information about an individual's proteinsinformation that is not always collectedbased on genetic information, which is often more accessible in large-scale studies.

Nilanjan Chatterjee

Bloomberg Distinguished Professor of biostatistics and genetic epidemiology

This model in turn will allow scientists to identify links between the levels of certain proteins in an organism and its corresponding disease risk. Knowing which proteins to target in order to prevent development of a disease is crucial for developing new drug therapies or repurposing existing drug therapies, as many drugs work by targeting the body's proteins.

To demonstrate how the model works, the team applied it to proteome-wide association studies for two related traits: gout, a common form of arthritis, and its closely related biomarker, uric acid. The results showed that an existing drug could be repurposed to combat gout.

"'Omics' innovations have made multi-disciplinary collaborations necessary, exciting, and productive," says Coresh. "The lived experience of over 10,000 participants in the ARIC cohort, combined with data on nearly 5,000 protein levels in their blood, allowed for the development of tools that are broadly applicable to human health and disease. We have already seen more than a half a dozen new investigations using the tools and the methods will be even more broadly applicable."

For Chatterjee, the study's powerful models and insightful findings underlined the importance of using diverse populations in genetic and omics studies.

"African populations in particular have a lot more genetic variation because the population is older," Chatterjee says. "Excluding people of African ancestry means we miss out on a large fraction of genetic variations and how it impacts health outcomes. Taking results from a genome-wide association study done with only individuals of European ancestry and trying to apply the results to other populations does not work as well for understanding disease risk, which is not surprising. To best serve all patients, diversity in omics studies is imperative."

Josef Coresh

Epidemiologist and principal investigator on the ARIC study

In addition, the team found that information garnered from populations of African ancestry added incredible value for interpreting results from study participants overall.

"Because European populations are newer, their genes are more confoundedmany variants always come together, and it is difficult to determine which genetic variant is causally related to a trait," Chatterjee explains. "African populations are older, and over more generations, the tight linkage among variants have broken down and it becomes possible to identify which variants are most likely to be the causal variant for a trait."

Looking forward, for Chatterjee, an exciting aspect of this project was the immense potential for impact these models have. Chatterjee hopes that a multi-omics approach in a multi-ancestry study will unlock a more comprehensive understanding of the genetic basis of complex disease and how that genetic basis arises. Next steps may include developing and improving statistical and machine learning models to combine data from populations of multiple ancestries, data from other types of -omics studies, and extending analysis to rare variants.

The authors emphasize that the study would not be possible without the strong partnerships and collaborations across Johns Hopkins and beyond, including the sophisticated data analysis led by Department of Biostatistics PhD student Jingning Zhang and post-doctoral fellow Diptavo Dutta.

Given the collaborative nature of the undertaking, it was important to the team to make the resources and models they developed available to others. They have made the models available online.

"Anyone can download these models for use in their own study to test for the effect of proteins on whichever traits they are investigating," Chatterjee explains. "Our work has already generated ideas for many follow-up studies using proteomic data, and it has been exciting to see that, in fact, people have already started using the models in their own protein association studies."

Read this article:
Study probes the relationship between genetics, proteins, and disease risk - The Hub at Johns Hopkins

Singular Genomics Systems, Inc.

LA JOLLA, Calif., May 10, 2022 (GLOBE NEWSWIRE) -- Singular Genomics Systems, Inc. (Nasdaq: OMIC), a company leveraging novel next-generation sequencing (NGS) and multiomics technologies to empower researchers and clinicians, today announced the formation of its scientific advisory board (SAB). The SAB comprises a distinguished group of academic and industry experts who will advise on the companys product and service offerings and research and development pipeline.

We are pleased to announce the launch of our scientific advisory board and are privileged to work with such accomplished leaders in science and medicine, said Eli Glezer, Ph.D., Founder and Chief Scientific Officer of Singular Genomics and newly appointed Chair of the SAB. This groups expertise in DNA sequencing, human genetics, oncology and immunology will be an invaluable resource as we expand the applications of our G4 sequencing system and develop the PX platform as a powerful tool for spatial biology.

The members of Singulars SAB include:

David L. Barker, Ph.D., Board Member of Singular Genomics, AmideBio, and Aspen Neuroscience, Scientific Advisor to Luna DNA, and Board Member and Chairman at Bionano Genomics. Dr. Barker previously served as Vice President and Chief Scientific Officer of Illumina, while also sitting on their Scientific Advisory Board. In his academic career, Dr. Barker conducted interdisciplinary research in neurobiology as a Postdoctoral Fellow at Harvard Medical School, Assistant Professor at the University of Oregon, and Associate Professor at Oregon State University. Dr. Barker holds a BS with honors in Chemistry from the California Institute of Technology and a Ph.D. in Biochemistry from Brandeis University.

Lawrence Fong, M.D., Efim Guzik Distinguished Professor in Cancer Biology at the Helen Diller Family Comprehensive Cancer Center at the University of California, San Francisco (UCSF); Co-Director of the Parker Institute of Cancer Immunotherapy at UCSF; Co-Lead of the Cancer Immunity and Immunotherapy Program in the UCSF Cancer Center. Dr. Fong is also a physician-scientist in the Department of Medicine, Division of Hematology/Oncology at UCSF, where he directs both a translational research program and an NIH-funded research lab. Dr. Fongs research examines the mechanisms that underlie clinical response and resistance to immunotherapies. This work includes tracking antigen-specific T cell responses in treated cancer patients and developing biomarkers that are associated with clinical outcomes. Dr. Fong has received multiple awards including the NIH Outstanding Investigator Award. Dr. Fong received his BA from Columbia and M.D. from Stanford, and completed internal medicine training at the University of Washington, as well as an oncology fellowship and post-doctoral training at Stanford in 2002.

David H. Ledbetter, Ph.D., FACMG, DABMGG, Chief Clinical & Research Officer at Unified Patient Network, Inc. Dr. Ledbetter also served as Executive Vice President and Founding Chief Scientific Officer at Geisinger, where he helped lead their MyCode biobank/genomics project one of the largest in the world. Dr. Ledbetters current research focuses on leveraging longitudinal electronic health information with large-scale DNA sequencing to determine the clinical utility and cost-effectiveness of precision medicine approaches in real-world health system settings. Dr. Ledbetter is internationally recognized for his research on the genetic basis of childhood neurodevelopmental disorders, having discovered the genetic cause of Prader-Willi syndrome and Miller-Dieker syndrome early in his career. Dr. Ledbetter is a graduate of Tulane University and earned his Ph.D. at the University of Texas-Austin.

Elaine Mardis, Ph.D., Board Member of Singular Genomics; Co-Executive Director of the Institute of Genomic Medicine at Nationwide Childrens Hospital and holds the Steve and Cindy Rasmussen Endowed Chair in Genomic Medicine. Dr. Mardis is also Professor of Pediatrics at The Ohio State University College of Medicine. Additionally, Dr. Mardis serves on the Supervisory Board, Science and Technology Committee, and the Compensation and Human Resources Committee at Qiagen. Dr. Mardis is a pioneering researcher internationally recognized in cancer genomics with a focus on the application of genomic technologies to improve the understanding of human disease and the precision of medical diagnosis, prognosis and treatment. Dr. Mardis received her BS in zoology and her Ph.D. in chemistry and biochemistry, both from the University of Oklahoma. She has authored more than 380 articles in peer-reviewed journals, has contributed chapters for several medical textbooks, and is an elected member of the U.S. National Academy of Medicine.

Daniel Shoemaker, Ph.D., former Chief Scientific Officer of Fate Therapeutics. Dr. Shoemaker has worked in the industry for over 25 years, helping to build several successful organizations ranging from startups to public companies. Most recently at Fate, he led the companys innovation efforts to bring multiple iPSC-derived cell therapies to the clinic. Previously, Dr. Shoemaker served as Chief Scientific Officer of ICx Biosystems, a biotechnology firm that developed advanced detection technologies for use in biodefense, cancer and prenatal diagnostics. He was also a founding scientist at Rosetta Inpharmatics. Dr. Shoemaker received his BS in biochemistry from the University of California, Santa Barbara and his Ph.D. in biochemistry from Stanford University.

Story continues

About Singular Genomics Systems, Inc. Singular Genomics is a life science technology company that is leveraging novel NGS and multiomics technologies to build products that empower researchers and clinicians. Our mission is to accelerate genomics for the advancement of science and medicine. Our Singular Sequencing Engine is the foundational platform technology that forms the basis of our products as well as our core product tenets: power, speed, flexibility and accuracy. We are currently developing two products that are purpose-built to target applications in which these core product tenets matter most. Our first product, the G4, targets the NGS market. Our second product in development, the PX, combines single-cell analysis, spatial analysis, genomics and proteomics in one integrated instrument to offer a versatile multiomics solution.

Forward-Looking Statements Certain statements contained in this press release, other than historical information, may constitute forward-looking statements within the meaning of the Federal securities laws. Any such forward-looking statements are based on our managements current expectations and are subject to a number of risks and uncertainties that could cause our actual future results to differ materially from our managements current expectations or those implied by the forward-looking statements. These and other risk factors that may affect our future results of operations are identified and described in more detail in our most recent filings on Forms 10-K and 10-Q and in other filings that we make with the SEC from time to time, including our Quarterly Report on Form 10-Q for period ended March 31, 2022, filed with the SEC on May 10, 2022. Accordingly, you should not rely upon forward-looking statements as predictions of future events or our future performance. Except as required by applicable law, we undertake no obligation to update publicly or revise any forward-looking statements contained herein, whether as a result of any new information, future events, changed circumstances or otherwise.

Investor ContactMatt Clawson949-370-8500ir@singulargenomics.com

Media ContactDan Budwick, 1AB973-271-6085dan@1abmedia.com

Read more from the original source:
Singular Genomics Announces Formation of Scientific Advisory Board - Yahoo Finance

Swedens Olink Holding (Nasdaq: OLK) has announced that Oxford Genomics at the University of Oxford is adopting its technology, becoming the UKs first Olink lab.

It is hoped that the partnership will enable new techniques to unravel mechanisms of disease using the Olink Explore platform.

"We are trying to make the drug development process more precise by understanding the heterogeneity in the patients instead of one drug fits all"According

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