Category Archives: Human Genetics

SUNNYVALE, Calif., Nov. 9, 2021 /PRNewswire/ -- 23andMe Holding Co. (Nasdaq: ME) ("23andMe"), a leading consumer genetics and research company, today announced the appointment of Dr. Sandra Hernndez, President & CEO of the California Health Care Foundation ("CHCF"), to its Board of Directors.

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"Dr. Hernndez is a passionate advocate for improving today's healthcare system by enabling anyone, including those in underserved communities, to get access to the care they need," said Anne Wojcicki, CEO, and Co-Founder of 23andMe. "Leveraging her incredible expertise, Dr. Hernndez will play an important role as 23andMe rolls out a new digital primary care experience that delivers personalized, preventative care to individuals in an affordable and accessible way."

As the President & CEO of CHCF, an independent, nonprofit philanthropy dedicated to improving California's healthcare system, particularly for those with low incomes, Dr. Hernndez has been a leading figure in improving access to coverage and advocating for better care. Prior to joining CHCF, Dr. Hernndez was CEO of The San Francisco Foundation, one of the nation's largest community foundations, which she led for 16 years. She previously served for nearly a decade in the San Francisco Department of Public Health, including several years as Director of Public Health for the City and County of San Francisco.

"As a mission-driven company focused on empowering individuals with direct access to their genetic health information, 23andMe has the potential to help create a truly personalized approach to healthcare," said Dr. Sandra Hernndez, President & CEO of CHCF. "I look forward to joining the 23andMe Board as the company works to make a new individualized primary care experience more accessible to everyone."

Dr. Hernndez served as an assistant clinical professor at the University of California, San Francisco, School of Medicine and currently serves as a leadership council member of the UCSF Institute for Global Health Sciences. She practiced at San Francisco General Hospital in the AIDS clinic from 1984 to 2016. She is a graduate of Yale University, the Tufts School of Medicine, and the certificate program for senior executives in state and local government at Harvard University's John F. Kennedy School of Government.

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About 23andMe23andMe, headquartered in Sunnyvale, CA, is a leading consumer genetics and research company. Founded in 2006, the company's mission is to help people access, understand, and benefit from the human genome. 23andMe has pioneered direct access to genetic information as the only company with multiple FDA authorizations for genetic health risk reports. The company has created the world's largest crowdsourced platform for genetic research, with 80 percent of its customers electing to participate. The 23andMe research platform has generated more than 180 publications on the genetic underpinnings of a wide range of diseases, conditions, and traits. The platform also powers the 23andMe Therapeutics group, currently pursuing drug discovery programs rooted in human genetics across a spectrum of disease areas, including oncology, respiratory, and cardiovascular diseases, in addition to other therapeutic areas. More information is available at http://www.23andMe.com

Forward-Looking StatementsThis press release contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended, including statements regarding the future performance of 23andMe's businesses in consumer genetics and therapeutics and the growth and potential of its proprietary research platform. All statements, other than statements of historical fact, included or incorporated in this press release, including statements regarding 23andMe's strategy, financial position, funding for continued operations, cash reserves, projected costs, plans, and objectives of management, are forward-looking statements. The words "believes," "anticipates," "estimates," "plans," "expects," "intends," "may," "could," "should," "potential," "likely," "projects," "continue," "will," "schedule," and "would" or, in each case, their negative or other variations or comparable terminology, are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. These forward-looking statements are predictions based on 23andMe's current expectations and projections about future events and various assumptions. 23andMe cannot guarantee that it will actually achieve the plans, intentions, or expectations disclosed in its forward-looking statements and you should not place undue reliance on 23andMe's forward-looking statements. These forward-looking statements involve a number of risks, uncertainties (many of which are beyond the control of 23andMe), or other assumptions that may cause actual results or performance to be materially different from those expressed or implied by these forward-looking statements. The forward-looking statements contained herein are also 8-K filed with the Securities and Exchange Commission ("SEC") on June 21, 2021 and in 23andMe's Current Report on Form 10-Q filed with the SEC on August 13, 2021, as well as other filings made by 23andMe with the SEC from time to time. Investors are cautioned not to place undue reliance on any such forward-looking statements, which speak only as of the date they are made. Except as required by law, 23andMe does not undertake any obligation to update or revise any forward-looking statements whether as a result of new information, future events, or otherwise.

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23andMe Announces Appointment of Dr. Sandra Hernndez to Board of Directors - Yahoo Finance

Penn Medicine: $9.5 Million Grant from Warren Alpert Foundation to Increase Diversity in Genetic Counseling Programs

Penn Medicine has been awarded a $9.5 million grant from the Warren Alpert Foundation to continue its efforts to increase diversity in genetic counseling, a field that, despite impressive leaps forward in genetic knowledge, lacks a diverse workforce. The Alliance to Increase Diversity in Genetic Counseling grant will support 40 underrepresented students in five genetic counseling programs in the northeastern U.S. over five years to expand all dimensions of diversity. The Perelman School of Medicine at the University of Pennsylvanias master of science in genetic counseling program will lead this effort, joined by participating genetic counseling masters degree programs at Boston University School of Medicine; Rutgers University, the State University of New Jersey; Sarah Lawrence College; and the University of Maryland School of Medicine. Ten students will be selected yearly to receive full tuition support and a cost of living stipend.

The University of Pennsylvanias master of science in genetic counseling program (MSGC) and the collaborative programs are committed to increasing diversity and inclusion in the genetic counseling field and encouraging post-graduate training and career advancement opportunities for genetic counselors. Previous philanthropic gifts to the MSGC program have supported a robust summer internship for undergraduates who are underrepresented in genetic counseling, which, in its first year, led to several rising juniors and seniors learning about the field and considering applying to the program. The Class of 2023 is Penn MSGCs most diverse ever, with 35% of students from underrepresented backgrounds.

We are honored to receive this grant from the Warren Alpert Foundation to continue to expand diversity and inclusion in genetic counseling while growing the overall genetic counseling workforce, said Daniel J. Rader, chair of the department of genetics in the Perelman School of Medicine and chief of the divisions of human genetics at Penn and Childrens Hospital of Philadelphia. The foundation is extraordinarily forward-thinking in making this generous funding available to address a critical need as the implementation of genomic medicine continues to rapidly expand.

On the 50th anniversary of genetic counseling being established as a field, we celebrate the first time an alliance of genetic counseling programs has collaborated to increase diversity and inclusion with scholarships, post-graduate training, and career advancements for genetic counselors, said Kathleen Valverde, program director of the Penn MSGC.

A key rationale for increasing diversity in the genetic counseling workforce is to improve support for patients from underrepresented backgrounds. The field is currently comprised of 95 percent white women. Therefore, underrepresentation of genetic counselors from diverse backgrounds can strain critical dialogue between genetic counselors and patients, whose health outcomes are often improved through interaction with medical professionals they can relate to more personally. Unless genetic counseling becomes more accessible, existing disparities will be exacerbated. Addressing this issue will require integrated strategies, including expanding genetic research, improving genetic literacy, and enhancing access to genetic technologies and genetic counseling among underrepresented populations in a way that avoids stigmatization and other harms.

Supporting innovative organizations dedicated to understanding and curing disease through groundbreaking research, scholarship, and service is why we are delighted to award Penn with this generous grant from the Warren Alpert Foundation, said August Schiesser, executive director of the Warren Alpert Foundation. Recruiting and training underrepresented individuals in genetic counseling will increase the numbers of professionals in the field, leading to an increase in access to community-based genetic education and genetic counseling services delivered by individuals who reflect different populations.

The Penn MSGC program leadership brings extensive experience in genetic counseling education and, with this grant, it will expand its reach to diverse students preparing them to be successful professionals who will advance the field of genetic counseling, said Emma Meagher, a professor of medicine and pharmacology, chief clinical research officer and associate dean of master and certificate programs in the Perelman School of Medicine.

Interested applicants for Penn can visit https://www.med.upenn.edu/geneticcounseling for more information. Penns application deadline is January 5, 2022, with deadlines for Boston University School of Medicine, Rutgers University, Sarah Lawrence College, and the University of Maryland School of Medicine ranging across December 2021 and January 2022. Ten students will be selected yearly to receive full tuition support and a cost of living stipend.

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Penn Medicine: $9.5 Million Grant from Warren Alpert Foundation to Increase Diversity in Genetic Counseling Programs - UPENN Almanac

Newswise By comparing genetic data from European and African population groups, scientists atUChicago Medicine Comprehensive Cancer Centerhave identified seven new regions of the human genome that are associated with increased breast cancer risk.

In addition to laying a foundation for better risk modeling and more accurate genetic screening for cancer, the study highlights the importance of studying diverse patient populations, researchers said. The findings would not have been possible without incorporating data from African-American, Afro-Carribean and African women, saidDezheng Huo, PhD, Professor of Public Health Sciences and Medicine at UChicago Medicine.

Previous studies mainly looked at European populations, and they missed this, said Huo. We just added a relatively small sample size of African-ancestry populations, and we found the locations.

Although including women of African ancestry led to the discovery, the findings apply to women of both backgrounds, he noted.

The findings were published in July 2021 inNature Communications.

For the new study, researchers analyzed genome-wide association studies (GWAS) of both European-ancestry and African-ancestry women. Each study compared genome scans of women with breast cancer and women who were healthy, with a goal of identifying genetic variants or mutations that may play a role in cancer.

The European study was large, with genetic data from more than 220,000 women. However, it was not until researchers compared it with a smaller data set of around 19,000 women of African ancestry that they identified seven regions on the genome that had previously been overlooked for cancer risk.

Previous studies missed the variants because they have weaker effects in women of European ancestry, Huo said.

Once the variants were identified in the African-ancestry population, researchers were also able to find them in the European-ancestry group and show that they were associated with breast cancer risk in that population as well.

There are some variants that you can easily pick up in one population and not in other populations where the signal is weaker, Huo said. But once you pick it up, you find it doesnt just apply to that group.

Previous studies have identified genes associated with increased breast cancer risk, includingBRCA1andBRCA2. However, these two genes only account for a small proportion of cancers, and research is ongoing to identify more genetic risk factors. Most cancers, including breast cancer, are complex diseases driven by a combination of many gene mutations.

The seven regions identified by the study give scientists a map to narrow down the search for more genes that are part of the puzzle, Huo said.

As a next step, Huo and his team are working to use the newly discovered genetic markers to develop polygenic risk score models, research that could help make cancer risk assessments more accurate.

They also want to work with colleagues conducting laboratory studies to look closer at the genetic regions they found and try to identify the specific genes or mutations associated with cancer risk, as well as to better understand how they contribute to the development of cancer.

In addition to potential clinical applications, the study also points to the importance of diversity in genetic research, Huo said. For better data, future cancer research should include a variety of racial groups, including people of African, Asian, Hispanic and Native American ancestry, he added.

People of European ancestry are over-represented in medical research, Huo noted. Thats partly because they make up a larger share of the United States population, and may also be related to lower levels of trust for the healthcare system among some groups, he said.

Without their inclusion in studies, we cannot discover this new knowledge, he said.

The study, Cross-ancestry GWAS meta-analysis identifies six breast cancer loci in African and European ancestry women, was published inNature Communications. Additional study authors include Babatunde Adedokun, Guimin Gao, Peter N. Fiorica and Olufunmilayo Olopade of the University of Chicago; Zhaohui Du, Sue A. Ingles, David V. Conti, Michael F. Press and Christopher A. Haiman of the University of Southern California; Thomas U. Ahearn, Regina G. Ziegler, Stephen J. Chanock, Montserrat Garcia-Closas, Cari M. Kitahara and Stefan Ambs of the National Cancer Institute; Kathryn L. Lunetta, Gary Zirpoli and Julie R. Palmer of Boston University; Jonine Figueroa of the University of Edinburgh; Esther M. John of Stanford University; Leslie Bernstein of City of Hope Comprehensive Cancer Center; Wei Zheng, Sandra L. Deming-Halverson and William Blot of Vanderbilt-Ingram Cancer Center; Jennifer J. Hu of the University of Miami; Sarah Nyante, Melissa A. Troester, Jeannette T. Bensen and Andrew F. Olshan of the University of North Carolina; Elisa V. Bandera of Rutgers Cancer Institute of New Jersey; Jorge L. Rodriguez-Gil of the National Human Genome Research Institute; Song Yao and Christine B. Ambrosone of Roswell Park Comprehensive Cancer Center; Temidayo O. Ogundiran, Oladosu Ojengbede, Adeyinka G. Falusi and Chinedum Babalola of the University of Ibadan, Nigeria; Katherine L. Nathanson of the University of Pennsylvania; Anselm Hennis of the University of the West Indies, Bridgetown, Barbados; Barbara Nemesure of Stony Brook University; Lara E. Sucheston-Campbell of The Ohio State University; Lawrence H. Kushi of Kaiser Permanente Northern California; Gabriela Torres-Mejia of Instituto Nacional de Salud Publica, Cuernavaca, Mexico; Donglei Hu, Laura Fejerman and Elad Zivof the University of California San Francisco; Manjeet K. Bolla, Joe Dennis, Alison M. Dunning, Douglas F. Easton, Paul D. P. Pharoah and Qin Wang of the University of Cambridge; Kyriaki Michailidou of The Cyprus Institute of Neurology & Genetics; Dale P. Sandler, Jack A. Taylor and Katie M. OBrien of the National Institute of Environmental Health Sciences; Joel Yarney of the Korle Bu Teaching Hospital, Accra, Ghana; Baffour Awuah of the Komfo Anokye Teaching Hospital, Kumasi, Ghana; and Beatrice Addai-Wiafe of the Peace and Love Hospital, Kumasi, Ghana.

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Comparing African and European populations leads to breast cancer risk discovery - Newswise

Famine exposure during early fetal development has been associated with higher rates of mortality, obesity, diabetes and schizophrenia. This can be seen, for example, in survivors of the Dutch famine caused by the Nazi blockade of the Netherlands in World War II. This famine ended over 70 years ago, but for survivors who were conceived during the famine, the health effects persist. Experiments in animal models have shown that diet in pregnancy can switch genes on or off and lead to major changes in body weight and other health-related effects.

Researchers atBaylor College of Medicineand theLondon School of Hygiene and Tropical Medicine(LSHTM) recently published a study on the developmental origins of health and disease (DOHaD) hypothesis that nutrition and other environmental exposures in early life have important consequences for lifelong health. Their findings were published inScience Advances.

Over thelast 10 years, researchers in The Gambia have employed an experiment of nature to investigate mechanisms underlying DOHaD phenomena. In subsistence farming communities, individuals conceived at different times of the year experience wide variation in nutrition during early development. The researchers investigated links between this seasonality and DNA methylation a molecular marking system of DNA that can turn genes on or off.

Using this approach, we have identified many genes in children in which the DNA methylation state appears to be influenced by their mothers diet in early pregnancy around the time of conception. But a major question has been: So what? said Dr. Toby Candler, lead author with the MRC Unit The Gambia atLSHTM.

To address this question, the researchers focused on just one gene they previously proved to be sensitive to nutrition around the time of conception:PAX8. This gene plays a key role in thyroid development, suggesting a straightforward hypothesis: nutrition-related methylation differences atPAX8influence thyroid development and function.

To test it, they measuredPAX8methylation in hundreds of Gambian children at 2 years of age to identify those with the highest and lowestPAX8methylation (within the top or bottom 10 percent). They then studied these same children again when they were 5 to 8 years old. This approach showed that lowPAX8methylation predicts increased thyroid volume (21 percent larger) and increased free T4, a key thyroid hormone. Even though the free T4 changes are considered be within the normal range, increased free T4 was associated with a decrease in body fat and bone mineral density.

PAX8methylation in the children also was associated with their mother's nutrition around the time of conception, specifically with circulating levels of vitamins B6, B12, homocysteine and cysteine.

Taken together,these results indicate a link between early environmental exposures,PAX8gene methylation and thyroid gland development and function, suggestinga molecular pathway linking maternal nutrition around the time of conception to epigenetic changes in the early embryo that persist for years, with consequences for postnatal health.

PAX8is the very first candidate gene we studied to ask whether low versus high methylation at these nutritionally-sensitive genes has any consequence for later health and metabolism, so these findings are really exciting, said Dr. Matt Silver, senior author and associate professor atthe MRC Unit The Gambia atLSHTM.

Weve identified thousands of genes with individual-level methylation differences that are established in the early human embryo. Many of these are associated with maternal nutrition around conception, so these results suggest enormous potential to better understand the epigenetic origins of human variation in health outcomes, said Dr. Robert Waterland, professor of pediatrics nutrition at the USDA/ARS Childrens Nutrition Research Center at Baylor and Texas Childrens Hospital.

Further work is required to confirm the direct causal connections between specific nutrients and DNA methylation marks established in the early embryo that persist into childhood, and likely beyond. The long-term goal is to provide future public health interventions aimed at optimizing the mothers nutrition before conception to improve health outcomes for their children.

Toby Candler is funded by an MRC Clinical Research Training Fellowship (MR/S006516/1). The British Society of Paediatric Endocrinology and Diabetes provided funding for this work to Toby Candler through its Research and Innovation Award 2018. The Gambian studies are supported by core funding from the U.K. Medical Research Council (MRC) MC-A760-5QX00 and by MRC grant MR/ M01424X/1. Programme funding for Andrew Prentice supported data acquisition and analysis of the whole-body DXA scans (U105960371 and U123261351).

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Beyond genetics: Early nutrition and epigenetic prediction of future health outcomes in humans - Baylor College of Medicine News

Several studies conducted over the years have found that South Asians have a higher burden of Coronary Artery Disease (PCAD) compared to other ethnicities.

A 2004 INTERHEART study first found that the mean age of the first presentation of heart attack was 53 years, a full10 years ahead of patients from Western Europe, China, Central and Eastern Europe.

Similarly, studies comparing the health of South Asian immigrants show that compared to local populations, they demonstrated a higher burden of CAD.

The INTERHEART study also indicated that South Asians who suffered a heart attack have low HDL-C (good cholesterol) levels, higher triglyceride levels, and a higher particle burden for LDL-C (bad cholesterol) levels.

Also Read |What's wrong with young Indians' hearts?

South Asians also have other risk factors, like dysfunctional HDL levels (where HDL particles lose their antioxidant and anti-inflammatory properties) and Lipoprotein (a) levels.

When asked about the roles of genes in Heart Disease, particularly among the Indian population, Dr Swathi Shetty, Assistant Professor at the Centre for Human Genetics, says the answer is not straightforward.

"If you have a history of heart disease in the family, that could indicate a higher genetic risk than the average population. But because there are so many variables causing heart disease, to pinpoint particular genes is difficult," Dr Swathi says.

CAD, like Cancer, is a multifactorial disease where genetics, environment and lifestyle play a major role. This is in stark contrast to single-gene disorders like Beta Thalassemia, Huntingtons disease or Cystic Fibrosis, where we know the gene associated with the disease.

Also Read |Genetic factors may have led to Puneeth Rajkumars death

"Compared to cancer we are still way behind. We know much more about cancer genes. Cancer is basically the proliferation of cells. It is easier to look at those because we know there are genes which control the division. In Cardiovascular disease (CVD), there are many other factors involved, including the Nitric oxide in your vessels, coagulation factors, and many more,"Dr Swathi says.

For instance, in 2011, 58 genomic regions associated with CAD were discovered, but most of the heritability cannot be explained.

"They have done studies among people with CVDs and looked for areas of DNA that they have in common. And we have found regions that are not even an expressed gene. That is another layer of difficulty. It [gene] doesn't code for a protein. Is it really increasing the risk? For these, we need huge numbers of patients to try and correlate," Dr Swathi adds.

Another 2018 paper studying Premature Coronary Heart Disease burden in South Asians identified six variants of the CX3CR1 gene which were unique to South Asians and "not found in large (mostly European) cohorts".

But the study concluded that findings "do not allow definite conclusions, especially with regard to how these could impact therapy."

While CAD does seem to have a genetic component involved, we also know that lifestyle factors like smoking, exercise, stress management etc also impact development of the disorder, which is something that people can still control and moderate, Dr Swathi adds.

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Is there a genetic component to heart disease? - Deccan Herald

NatureScot is one of several organisations joining a pioneering initiative to sequence the genomes of all species found in Britain and Ireland in an effort better understand our biodiversity and how it will cope with climate change. By Andrew Collier.

We are in a race against time to save not just the planet, but many of the things living on it. Climate change is causing a massive threat to biodiversity, and we know that it is going to mean species will disappear.

As we face this threat, we need to find ways to preserve the natural ecosystems that we have. An answer to these challenges is likely to be found in sequencing genomes the sets of DNA present in all organisms.

An internationally important project to carry out this work is currently being undertaken in Scotland and across Britain and Ireland by a pioneering initiative known as the Darwin Tree of Life project.

Part of this game-changing science is being conducted at the Beinn Eighe National Nature Reserve in Wester Ross, managed by NatureScot, Scotlands nature agency.

The hugely ambitious project will run until 2029 and aims to sequence, assemble and openly publish the genomes of all species found in Britain and Ireland, beginning with 2000 species representing every family of plant, animal and fungus.

It also aims to develop the tools and techniques that will be needed to complete the cataloguing of tens of thousands of remaining species before the end of the decade.

As well as NatureScot, a number of other highly respected organisations are involved in the project. They include the Royal Botanic Garden Edinburgh, the University of Edinburgh, the Natural History Museum in London and the Wellcome Sanger Institutes Tree of Life programme.

In addition, experts from National Museums Scotland and the Highlands Biological Recording Group, a citizen science organisation which has been surveying Highland wildlife since the 1980s, have played an important role in the research in Scotland.

Professor Mark Blaxter is the Project Lead at the Wellcome Sanger Institute near Cambridge, one of the worlds leading genome research organisations. He said: One of the goals of the project is that we will really start to understand the processes that generate biodiversity the processes of evolution. It might let us predict what is going to happen in the future.

David OBrien, NatureScots Biodiversity Evidence and Reporting Manager says the scope and ambition of the project was a major draw for the agency: When we first heard about this, we thought that this was potentially a game changer for genetic research in the UK and Ireland, but specifically so in Scotland.

Its an extremely ambitious project, but it has so many potential benefits when it comes to nature conservation. We tend to think of nature as either a habitat or a species a woodland, for instance, or a Scots pine tree within that woodland.

We dont normally think about the genes within that tree, or within the woodpecker thats banging on it. But genes are the building blocks for all of it. You cant have species without these.

Sample collecting from Beinn Eighe has already started. A recent trip in September focused on invertebrates, particularly wasps and moths, while earlier ones have concentrated on flora.

Techniques used in the field include sweeping, which involves catching flying insects in nets, and beating in other words, knocking bugs, larvae and similar species out of the trees and onto canvas.

Another method is suction sampling, sometimes called bug hoovering. This involves the use of a machine that resembles a reverse leaf blower to suck invertebrates out of the undergrowth.

Other technologies used include a pooter two rubber tubes attached to each other at either end of a sample container. By sucking on one end of the device, the collector can get specimens into a container with a high degree of accuracy. A gauze filter stops the specimen becoming an unwanted snack for the collector.

In addition, bright lamps are placed inside cylindrical traps. These attract moths overnight which are also then collected.

Once they have been gathered in, a small sample is identified by expert taxonomists before being flash frozen to preserve their DNA, which degrades very quickly after death. They are then transported to the Natural History Museum for DNA barcoding an essential part of the process which looks at unique segments of each species' genome, which is a helpful way to then quickly identify them in their environments. Finally, samples are taken to Sanger for whole genome sequencing.

We are seeing signs of biodiversity decline all around us, says David OBrien. Obviously, we are worried. Those genetic building blocks hold the key to resilience and how animals, plants and fungi will adapt. So when the idea of this project was floated past me, I thought we just had to be part of it.

NatureScot is deeply and actively involved in the study, helping to fund the laboratory work and having an input into the key species that will be sequenced first. It has also made its managed sites available Beinn Eighe is the focal point, but lichens have been collected from its other reserves.

We are making sure that everything goes smoothly by ensuring that everything is coordinated and that the various nature-related bodies can understand why we are doing this and what we hope to get from it. We will also get to use some of the information in the later stages of the project.

There are a number of things that can be done with this data, Dr OBrien says. One use comes from collecting Environmental DNA (eDNA) through a technique that works best in ponds and rivers. We are already doing this in Scotland we take water samples and put them through a filter in a lab.

You then look at the DNA that is in the water, shed from skin or from the faeces, and that will indicate the species present. Its really useful for knowing where they can be found and it reduces disturbance of them compared to other survey methods. Thats helpful when it comes to conservation.

Climate change, he adds, means that new diseases and pathogens are arriving in Scotland. Having genetic diversity will give the animals and plants more scope when it comes to having resistance, and sequencing will help us to understand this.

Also, as climate change starts to affect our wildlife, we expect that some species will be better able to adapt, and within those species there will be individual examples that have the genes to help them cope a bit better with the new regime.

If we are serious about protecting nature for its own sake as well as for the benefits we get from it, then making sure that we have the full toolbox is key. To have that, we need to understand what is there at a genetic level.

Yet another benefit of the project is that genome sequencing can reveal that two species that look the same are in fact completely different. This means that it is possible that we discover species we do not currently know exist.

There is a tendency in Scotland, David OBrien says, to believe that none have been lost here since the great auk became extinct in the 1840s. But we could be losing some tiny creatures without even knowing they were ever there.

However, if I was a betting man, Id be happy to put a small wager on us discovering some new species through this project. In Scotland, we already have an international reputation for genetics in relation to wild species, and thats something we can build on and share with other countries.

Beinn Eighe is a treasure trove for harvesters of genomic data

Choosing a main survey area for the groundbreaking Darwin Tree of Life project proved to be a major challenge for the team involved not because there were too few potential locations in Scotland, but because there were so many.

When it came to choosing a focal site, we were faced with a tremendous task, says David OBrien. So many are internationally recognised.

In the end, Beinn Eighe in Wester Ross was thought to be particularly well qualified. It was the first national nature reserve to be established 70 years ago and is home to a wide variety of animals, fungi and plants.

These include the northern prongwort, a liverwort found nowhere else in the world apart from on a neighbouring mountain. Beinn Eighe was also the first Gene Conservation Unit to be registered in the UK in recognition of its work to protect the locally adapted Scots pine.

However, other sites in Scotland will also be surveyed. So far more than 150 specimens from over 100 different species have been collected. A highlight has been a moth, Griposia aprilina, also known as the merveille du jour or marvel of the day. It is perfectly adapted to camouflage itself against lichen.

The data gathered from the project are likely to prove hugely useful. Genomic data will help us to gain a fuller understanding of how species have evolved and responded to changes in climate.

This in turn will help humankind to address some of the fundamental problems it faces when it comes to land use, food production and decarbonisation.

The reference genome data will also prove to be a treasure trove for biotechnologists and pharmaceutical scientists looking for novel biomaterials substances that have been engineered to interact with biological systems for a medical purpose.

The data will also be massively useful to medical researchers and benefit human health for example, by helping to develop new antibiotics to overcome antimicrobial resistance or treatments, or for fighting emergent pathogens leading to illnesses such as Covid-19.

Biomaterials will also have an important role to play in creating a sustainable future and a post-carbon economy. They could prove to be key to scientific and technological development in a number of areas, including micro systems operating via sensory inputs and post-oil rubber and plastics.

Genetic diversity underpins the adaptive potential of species and so the resilience of ecosystems, says David OBrien. We became involved in this project because we recognise that if we are to safeguard this, we first need to understand it.

We see it as a great opportunity to ensure the genetic diversity of Scotlands wildlife is recorded and made available to all.

IT IS GOING TO BE TRANSFORMATIVE

Understanding and conserving biodiversity is fundamental to human survival and the Darwin Tree of Life project will advance our knowledge in this area, according to one of the leading figures working on the initiative.

Professor Mark Blaxter is the Project Lead at the Wellcome Sanger Institute near Cambridge, one of the worlds leading genome research organisations. Genomics allows us to understand the DNA that is in every species, he says, and this should help us to tackle the current biodiversity crisis.

One of the goals of the project is that we will really start to understand the processes that generate biodiversity the processes of evolution. It might let us predict what is going to happen in the future. We really hope to provide an amazing foundation for people to conserve, promote and expand biodiversity. Genetic monitoring is really important in conservation.

Those on the project also believe that they will provide the raw materials necessary to generate a new sort of economy, he adds. There are many natural materials out there that are untapped.

Our hope is that by finding the genetic materials for all these species, we will enable new pharmaceuticals to be found to treat old diseases and new ones. We will make it possible to transition from the carbon-based economies we have at the moment to ones based on natural products.

Professor Blaxter and his colleagues on the project also believe that it will capture the public imagination. If every species has its genome sequenced, we are going to change the way people do biology forever.

It will be an amazing transformation to how we understand the natural world. If you think about it, the human genome was completed about 20 years ago, and that has changed the way we look at human medicine and how we understand human society.

It will be the same for these genomes. If we have that sort of information for every species, it is going to be transformative.

Link:
NatureScot: Race is on to track down the tree of life - HeraldScotland

image:Dr. Stephen J. O'Brien (back row, second from left) with orphans in Botswana view more

Credit: Dr. Stephen J. O'Brien

Research Take-a-Ways:

FORT LAUDERDALE/DAVIE, Fla. HIV emerged from African chimpanzee transmission to humans in the first decades of the 20th century. The deadly AIDS disease was first detected among American gay men, hemophiliacs, transfusion blood recipients, and IV drug users sharing needles in the early 1980s. Since then, the rapid world-wide spread of HIV has claimed 37.2 million lives leaving some 38 million people living with HIV infection today.

Today, African AIDS comprises 65-70% of all HIV cases worldwide. In Africa, the HIV-1C strain, which has been suggested as more easily transmitted in heterosexual contact, is predominant. Although AIDS spread and transmission have been reduced by widespread dissemination of anti-retroviral therapies, the horror of AIDS continues, particularly in sub-Saharan Africa.

This study was led by Nova Southeastern University (NSU)Halmos College of Arts and Sciences professor and research scientist Stephen J. OBrien, Ph.D., in collaboration with researchers at the Laboratory of Genomic Diversity at ITMO University, St Petersburg, Russia, Botswana-Harvard AIDS Institute, Gaborone Botswana, T. H. Chan School of Public Health, Harvard University, Boston, and Yale University, New Haven, and St. Petersburg State University.

Epidemiological variation in HIV acquisition, AIDS progression and therapy effectiveness has been attributed, in part, to endemic gene determinates. Studies in the past decades have discovered more than 50 human gene variants that confer relative sensitivity or resistance to AIDS. Nearly all these important studies involved American and European Caucasian patients in spite of the fact that sub-Saharan Africa is the epicenter of AIDS.

In 1996, author Max Essex and the President of Botswana established the Botswana Harvard AIDS Institute Partnership (BHP) in Gaborone Botswana to carry out training , surveillance and treatment of HIV-AIDS patients implementing research Virology, Molecular biology, immunology, genetics and epidemiology

In one of the largest studies to date of African people at risk for HIV infection, a group of 1,173 patients recruited by BHP were sequenced, genotyped, and analyzed to reveal three new common genetic DNA variants that influence whether one becomes infected and in American replication cohort studies the rate and AIDS defining disease by which infected individuals progressed to AIDS.

OBrien and his team have pioneered the field of AIDS Restriction Gene discovery for 25 years, beginning when he led a Research Laboratory at the National Institutes of Health (1986-2012).

The research, published today in the Proceedings of the National Academy of Sciences, revealed three new human genes (AP3B1- Chr-5; PTPRA-chr-20; NEO1-Chr-15) with a marked influence on HIV acquisition. Each gene variant was statistically significant in a Genome Wide Association Study -GWAS of 1.3-8.6 million single nucleotide polymorphism-SNPs.

The new study provides valuable insights into the genetic variants associated with HIV-1C infection and AIDS progression in sub-Saharan Africa, potentially paving the way for new therapies.

Each associated gene has been previously implicated functionally in one or more stages of AIDS pathogenesis and their association was replicated using independent American AIDS cohorts.

A provocative aspect of the AP3B1 variant is that it encodes two alleles G and T, predicting TT, GT and GG genotypes. The Botswana population has a relatively high allele frequency of the G variant (MAF=0.38) relative to other world populations, yet no homozygous GG individuals were detected in Botswana. The GG genotype is also completely absent among 2500 people of all races studied to date, raising the prospect that the AP3B1 -GG genotype may be lethal genotype which does not survive embryogenesis. Further there are several described variants in the in the AP3B1 gene that cause Hermansky-Pudlak syndrome, a rare genetic disease affecting pigmentation and platelets that is sometimes fatal.

The study further describes the replication of 13 previously described AIDS resistance genes using the Botswana population cohort, increasing the confidence in the influence of each. The replication studies were facilitated by the GWATCH ( Genome Wide Association Tracks Chromosome Highway) cyber suite of programs that enhance GWAS data analyses, replication, and release.

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About Nova Southeastern University (NSU):At NSU, students dont just get an education, they get the competitive edge they need for real careers, real contributions and real life.A dynamic, private research university, NSU is providing high-quality educational and research programs at the undergraduate, graduate, and professional degree levels. Established in 1964, the university includes 15 colleges, the 215,000-square-foot Center for Collaborative Research, the private JK-12 grade University School, the world-classNSU Art Museum Fort Lauderdale, and theAlvin Sherman Library, Research and Information Technology Center, one of Floridas largest public libraries. NSU students learn at our campuses in Fort Lauderdale, Fort Myers, Jacksonville, Miami, Miramar, Orlando, Palm Beach, and Tampa, Florida, as well as San Juan, Puerto Rico, and online globally.With nearly 200,000 alumni across the globe, the reach of the NSU community is worldwide.Classified as having high research activity by the Carnegie Foundation for the Advancement of Teaching, NSU is one of only 59 universities nationwide to also be awarded Carnegies Community Engagement Classification, and is also the largest private institution in the United States that meets the U.S. Department of Educations criteria as a Hispanic-serving Institution.Please visitwww.nova.edufor more information.

Proceedings of the National Academy of Sciences

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1-Nov-2021

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NSU research scientist leads group that discovered gene variants that delimit HIV-1 infection - EurekAlert

New cutting edge technology recently installed at the Cummings School of Veterinary Medicine at Tufts University reminds Cheryl London, the associate dean for research and graduate education, of the 1966 sci-fi film Fantastic Voyage.

In the movie, an intrepid submarine crew shrinks down small enough to float through an injured scientists bloodstream to save his life.

The new technology, called spatial profiling, allows scientists to see so deep into tissue samples that London, an oncologist, said it feels like youre actually there on the surface of the cell.

Its like taking a birds-eye look inside the cell itself, London said.

The Cummings School won a $2 million grant from the Waltham-based Massachusetts Life Sciences Center for the new equipment this spring, and it was installed over the summer.

London and her team submitted their grant proposal to the MLSC, an organization that pools state and private money to invest in science research across the state, through the agencys Research Infrastructure Program in the fall of 2020.

At the end of February of this year, an email informed London that Tufts had won the competitive grant.

When you get the notification that youve been funded its one of those woo-hoo moments, London said. You do a little dance, and youre pretty excited.

The equipment was installed last June and July in the newly renovated Peabody Pavilion lab space, and by September it was available for use.

The new lab equipment also includes advanced genetic sequencing and NanoString technology, which is able to sequence the DNA of a single cell.

London said the technology is a product of the latest in a series of major scientific leaps in the fields of genomics and pathology and has advanced rapidly.

Spatial profiling technology was only developed in the last five years. Next generation sequencing is slightly older, having been developed in the years following the conclusion of the Human Genome Project in 2003.

This is the first time that either technology will be available on Tufts campus, and the new lab will function as a shared resource, London said. While the technology is currently only available to those who have been trained extensively on how to use the expensive equipment, students and faculty from any of the universitys campuses will be able to submit proposals to use the equipment. London is talking with researchers at Tufts University School of Medicine who intend to apply for funding for experiments that use the technology.

Some research is already underway with the new technology. One of the few researchers who has been using the technology for her research is Heather Gardner (GBS20), a Cummings School assistant research professor specializing in veterinary oncology and genetics.

Gardner studies the impact of losing subsets of genes when DNA is transcribed into RNA in the context of bone cancer. The next generation sequencing has enabled her to examine that process in individual cells, she wrote in an email to the Daily.

The spatial-profiling technology is helping Gardner too. It allows her to zoom in on canine bone cancer micro-environments to examine how the tumors change gene expression.

This equipment really compliments and adds a new dimension to the research already being done, Gardner said.

Frequently, Cummings School researchers like Gardner are doing experiments on nonhuman animal cells not only to develop therapies for the animals themselves, but to use them as models for treatments in humans as well.

For that to work, though, scientists have to ensure the animal models accurately mimic the human body.

Sometimes models look like theyre the real deal on the outside, London said. But when you look at the genetic level its really not the same.

The new technology will help Cummings School researchers do just that.

Joseph Sullivan, vice president of marketing, communications, and community relations at the MLSC, said the organization was very proud to have funded Tufts new equipment.

Sullivan wrote in an email to the Daily that the organization hopes the new shared resources will catalyze scientific collaboration, research and innovation in Worcester and the rest of central Massachusetts with the Cummings School as an anchor institution.

For now, London said the team is still getting [its] feet wet but quickly warming up to the new lab.

Walking in and seeing all of this is super cool, London said. Its like a car enthusiast seeing 10 Lamborghinis in a garage. Its amazing to see the power of the equipment you have around you.

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New technology sends Tufts veterinary scientists on journey to center of the cell - Tufts Daily

Technological advances have been pivotal in expanding scientific research and contributing to an exponential increase in data output. A primary factor contributing to the rise in data output has been the shift from manual bench work to high-throughput technologies. In addition, the generation of such enormous volumes of data has led to breakthroughs in microprocessing, data management and AI used to interpret the data. These advances have further spurred the development of high-throughput laboratory technologies to keep pace with data processing speeds.1 As such, high-throughput technologies have become crucial to research areas, including drug discovery, genomics, and molecular biology.

High-throughput technologies have enabled researchers to take on ambitious projects that are expected to transform medicine. For example, Prof. Michael Snyder, chair of the department of genetics and directors of the Center for Genomics and Personalized Medicine at Stanford Medicine, is currently running the Integrated Personal Omics Profiling (iPOP) study. iPOP involves undertaking unprecedented deep biochemical profiling of approximately 100 individuals generally classed as healthy. In doing so, the study hopes to determine what normal biochemical and physiological profiles look like at an individual level. This information will enable researchers to understand what processes are affected in various disease states and ultimately improve diagnoses, disease monitoring, and the success of targeted therapies. When asked about the role of high-throughput technologies in this study, Snyder said, nearly all assays are high throughput, including genomics approaches, many other omics assays and wearables. We believe that genome sequencing and other omics technologies, as well as wearables, will be routinely employed by the healthcare sector. Most importantly, we hope to transform what is presently sick care into healthcare where we focus on keeping people healthy rather than treating people when they are ill.

High-throughput systems are well established in drug discovery, where hundreds of thousands of potential drug candidates need to be screened.1 In addition, high-throughput sequencing technologies have transformed genetics and genomics, with over one million human genomes sequenced by 2020.2 This sequence data has provided the pharmaceutical industry with many potential drug targets that warrant further exploration, fueling the need for greater throughput.3One of the main mechanisms of increasing throughput is miniaturization, as smaller experimental platforms and the need for reduced reagent volumes will allow more experiments to be conducted with fewer resources, thereby lowering costs.4,5 The push to miniaturize experiments has given rise to microfluidics, which investigates and manipulates fluids at the submillimeter scale. Working with smaller sample and reagent volumes is also advantageous when working with precious samples. In addition, microfluidics also leverages the microscale fluid phenomena, giving researchers far greater control over the spatiotemporal dynamics that impact the experiment.6Other technologies that enable high-throughput include automation, robotics, and liquid-handling robotics. This article will explore how high-throughput technologies are continuing to advance research in the life sciences. It will also and highlight various areas directly benefiting, including drug discovery, genomics and molecular biology.

Continued here:
High-Throughput Technologies: Exploring Advances and Key Applications - Technology Networks

Joo Pedro de Magalhes scours the human genome for clues that might help us understand why people age and what we might do to stop that. Without fail, each time hes done one of these studies, nearly every gene ends up having some kind of link to cancer.

Always, he said. You always have some cancer-related genes in there.

The University of Liverpool researcher started to wonder just how many human genes are associated with cancer, and set about doing an analysis of genetic papers on the online medical archive PubMed. Of the 17,371 human genes studied at one point or another in papers in the archive, the vast majority have some connection to cancer.

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I think for nearly 90% of genes for which there are publications, they mention cancer in at least one of those publications, de Magalhes said. That surprised me a bit. I think what it means is that people really study cancer more than anything else.

On the one hand, his findings published in a commentary Wednesday in Trends in Geneticsare a bit of an academic oddity. But on the other, de Magalhes believes the results might indicate a trend that is complicating sciences ability to tease out which genes are underpinning true drivers of cancer and which are just passengers.

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STAT spoke with de Magalhes about the trend and what it means for the future of genetic analyses in cancer. This interview has been lightly edited for length and clarity.

What were some of your first reactions to the analysis results?

I was surprised by how strong the effects are. Nearly 90% of genes are associated with cancer. Its like a tongue-in-cheek observation, you know? Like, hey, if you work on cancer, any gene is likely to be associated with cancer.

But there have also been people pointing out that when you analyze genetic networks, you need to control for the number of publications associated with any gene in order to gather therapeutic insights. So, if you do this type of analysis, youll have this bias that the vast majority of genes have already been associated with cancer.

Why does that make it more difficult to study cancer genetics?

The main challenge is that if youre trying to interpret results or trying to identify new drug targets in the context of cancer, you have too many genes associated with it. If every gene can be associated with cancer, then figuring out which cancer-related genes are driving different types of cancer and identifying the best biomarkers becomes challenging. It becomes a problem of how we prioritize and study the genetics of cancer.

Finding a simple association is enough to have a publication. Thats the problem. By and large, many associations with cancer are quite I dont know if weak is the right word. Theyre just correlations.

Funnily enough, I was talking about this work with a colleague and she said that something similar is happening for Covid now. A lot of people just finding associations because theres such a huge research effort on Covid-19.

How can scientists avoid some of the pitfalls you describe and improve the study of genetics then?

It means you have to be careful. Unless you have direct genetic evidence, you have to be careful of cancer associations, and I dont think most people do that. I would say Im guilty of that as well. Also, if you want to associate a gene with cancer, if you study it hard enough then you probably will. A lot of the associations can be spurious, I think, but people can take the opportunity to say, Hey, I found this gene. Its associated with cancer. We need money to study it.

That kind of sounds like a bad thing, but is it so bad? If everyone can wave this big flag and say, Hey, my gene is also associated with cancer, and it might be important, maybe that would help more people get funded to do basic science on random genes. Then who knows, maybe you actually do find something really important?

Thats a good question. I dont know! In an ideal world, wed have a lot more investment in research, and wed be able to study all sorts of associations. I guess my take is that funds are limited, so we have to prioritize the funding allocation in some way because you cannot study every gene, right? Some are more important than others.

So, how do we pick the right genes to study?

Its a gray area. Causal associations would be best. When theres mutations in patients that are predisposed to cancer, that would be evidence of a causal role not just some association. One thing weve done is look at the number of publications associating a particular gene with longevity, but you can do the same with cancer. Theres a bit of a subjective element here, too, though.

Do you think that the vast majority of genes have been linked to cancer reveals something about cancer? Like its reinforcing this idea that our genetic machinery gets old, makes mistakes, and then its cancer?

Yes, thats right. If you look at genome instability, it increases with age. You can see it has more predispositions and the number of mutations increases with age in human tissues as well. So, I see this as a factor predisposing you to cancer development.

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The vast majority of genes have been tied to cancer, complicating research - STAT