Category Archives: Human Genetics

Among the topics discussed at this years annual meeting of the American Association for Cancer Research (AACR) was disparities in cancer care. Several MSK researchers presented research that directly addresses these problems.

In a prerecorded presentation, MSK physician-scientist Sana Raoof explained how clinical trials of liquid biopsies a type of blood test for cancer can include concrete measures to reduce disparities related to access and inclusion.

Dr. Raoof said such trials should aim to include at least 25% of participants who are non-white a figure that more accurately represents the percentage of non-white individuals in the U.S. population. Previous liquid biopsy trials have included 4% to 13% non-white participants.

The lack of representation of minorities is a huge problem in cancer clinical trials, Dr. Raoof says. Its not just a problem because its unfair and inequitable; its also a problem because it affects scientific conclusions.

To improve access to liquid biopsy trials, academic medical centers should seek to partner with community hospitals that see a more diverse patient population, she says.

Liquid biopsies may aid in early detection because they could potentially be administered in a primary care physicians office, rather than at a cancer center, where most imaging scans and other tests are performed.

In the context of the COVID, were seeing later and later stages at diagnosis across multiple types of cancer, Dr. Raoof says. People are missing their cancer screening tests and are therefore being diagnosed when they have symptoms at later stages, when its harder to cure the disease. That is particularly affecting minorities who, at baseline, have worse access to healthcare.

The lack of representation of minorities is a huge problem in cancer clinical trials.

Sana Raoof, MD, PhD physician-scientist

It would be very useful, Dr. Raoof continues, if we had a point-of-care test that was convenient, quick, and cheap that could be used by everyone but might be of particular benefit to minorities to supplement cancer screening.

Dr. Raoof wrote an editorial about the potential of liquid biopsies to address disparities in access in the Boston Globe last year.

MSK computational oncologist Francisco Sanchez-Vega is part of a team that has for a number of years been studying the genomics of colorectal cancer, trying to identify genomic features that correlate with worse outcomes. They are mining the wealth of genomic data obtained from MSK-IMPACT, a gene-sequencing panel that looks for cancer-associated mutations in 500+ genes.

While doing this work, Dr. Sanchez-Vega noticed that, on average, African American patients in the MSK-IMPACT cohort had worse outcomes compared with other patients. The question that he and others want to understand is why.

The general belief is that this disparity is probably driven by socioeconomic factors, differences in risk factors, differences in access to healthcare, maybe differences in environmental exposure, lifestyle, diet, etc., Dr. Sanchez-Vega says. But we had a very good opportunity to try to understand if there were any genomic features that could at least partially explain these differences or give some insight into these differences.

In his presentation at AACR, Dr. Sanchez-Vega discussed the various genomic factors that they measured, including tumor mutation burden, location of the tumor, and frequency of various oncogenes. The study population included 3,963 patients with colorectal cancer treated at Memorial Sloan Kettering Cancer Center (MSK), including 336 (8%) self-reported Black patients and 3,627 (92%) self-reported white patients.

They found some differences. For example, right-sided colon tumors were more common among Black patients (37% versus 25% in white patients). Hypermutated tumors, including tumors with a condition called microsatellite instability, were more frequent among white patients (12% versus 8% in Black patients).

Tumors in Black patients were enriched in KRAS mutations (60% versus 45% in white patients), but high-risk KRAS-G12C mutations accounted only for 3% of all driver KRAS mutations in Black patients versus 8% of all driver mutations in white patients.

When the investigators factored in all these genomic and clinical differences, however, they still did not explain the difference in outcomes between the two groups namely, that Black patients had shorter overall survival from the time of sequencing (median 28months versus 50months for white patients). This was true even though all patients were treated at the same single institution (MSK) during the study.

Dr. Sanchez-Vega cautions that these results may not apply behind the specific cohort of people who came to MSK, since this population may not be fully representative of the wider community. Nevertheless, the results would seem to point to other factors beyond genomic ones to explain these disparities in outcomes.

For certain types of cancer, knowing ones precise genetic ancestry can be important for properly assessing genetic risk factors for the disease and weighing possible treatments. Perhaps the best example of this phenomenon is people with Ashkenazi Jewish European ancestry, who have a much higher risk of carrying a high-risk BRCA1 or BRCA2 mutation than the general population. These mutations put one at risk for hereditary breast, ovarian, prostate, and pancreatic cancers.

Traditionally, establishing someones genetic ancestry required looking at genetic markers from across the entire genome. At AACR, computational biologists Kanika Arora, Michael Berger, and their colleagues in the Marie-Jose and Henry R. Kravis Center for Molecular Oncology presented their work showing that data from MSK-IMPACT which sequences only a subset of genes in the human genome can be used to reliably establish someones genetic ancestry.

The finding raises the possibility that genetic ancestry testing could be incorporated into routine clinical care whenever a test such as MSK-IMPACT is administered. The potential benefits include a more accurate genetic risk assessment than self-reported race.

A lot of times in medicine, self-reported race is used as a substitute for genetic ancestry, but its not always a good indication of someones actual genetics, explains Arora. For example, someone who identifies as Black could have close to 100% African ancestry, or they could have 50% or less African ancestry. So, while both are Black, self-reported race does not always capture the genetic component well, which is why for certain questions about risk factors, its important to look in detail at measures of ancestry.

A lot of times in medicine, self-reported race is used as a substitute for genetic ancestry, but it's not always a good indication of someone's actual genetics.

Kanika Arora computational biologist

According to the investigators, one particularly noteworthy finding to emerge from their analysis is a discrepancy in the rates of clinically actionable alterations in patients of African ancestry versus patients of European ancestry as determined by MSKs OncoKB database. While the overall proportion of biologically relevant driver mutations was similar between the two groups, patients of African ancestry had, on average, fewer options for drugs matching those mutations.

There are likely several reasons for that, Dr. Berger says, including the fact that genomic-sequencing panels themselves are skewed toward the genomic data collected from largely European populations.

Regardless of the reason, the data would seem to call for more equitable drug development programs, he notes. Patients with African ancestry are not as well served as people with European ancestry by our current precision oncology therapies, Dr. Berger says.

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At AACR, MSK Researchers Spotlight Health Disparities and Propose Solutions - On Cancer - Memorial Sloan Kettering

Archaeologists and members of the Muwekma Ohlone Tribe worked together on the project, which revealed the longstanding genetic roots of the region's Native peoples. Courtesy of Far Western Anthropological Research Group

For decades, a misperception that the San Francisco Bay Areas Muwekma Ohlone Tribe was extinct barred its living members from receiving federal recognition.

Soon, however, that might change. As Celina Tebor reports for USA Today, a new DNA analysis shows a genetic through line between 2,000-year-old skeletons found in California and modern-day Muwekma Ohlone people.

The research, published in Proceedings of the National Academy of Sciences, flies in the face of more than a century of misconceptions about the tribe and its peoples long history.

The study reaffirms the Muwekma Ohlones deep-time ties to the area, providing evidence that disagrees with linguistic and archaeological reconstructions positing that the Ohlone are late migrants to the region, write the authors in the paper.

Members of the tribe, scholars and the public are hailing the work as a chance to correct the recordand perhaps open up opportunities for the tribe to regain federal recognition, which allows tribes to qualify for federal funds and grants and be acknowledged as independent and sovereign. In the early 20th century, the tribe was on a federal list of recognized tribes, but was removed in 1927.

The tribes history mirrors that of other Native Californians. After more than 10,000 years in the area, Native people were forced to submit to colonization and Christian indoctrinationfirst by the Spaniards, who arrived in 1776, and then, beginning in the 19th century, by settlers from the growing United States.

As a result, the Ohlone and other Native groups lost significant numbers to disease and forced labor. Before European contact, at least 300,000 Native people who spoke 135 distinct dialects lived in what is now California, per the Library of Congress. By 1848, that number had been halved. Just 25 years later, in 1873, only 30,000 remained. Now, USA Today reports, there are just 500 members of the Muwekma Ohlone Tribe.

The Ohlone people once lived on about 4.3 million acres in the Bay Area. But federal negligence and anthropologist A.L. Kroebers 1925 assessment that Native Californians were extinct for all practical purposes caused the federal government to first strip the Muwekma Ohlone of their land, then deny them federal recognition, writes Les W. Field, a cultural anthropologist who collaborates with the Muwekma Ohlone, in the Wicazo Sa Review.

Even though Kroeber recanted his erroneous statement in the 1950s, the lasting damage from his diagnosis meant the very much not-extinct members of the Muwekma Ohlone Tribe never regained federal recognition, according to the New York Times Sabrina Imbler.

The new research could change that. It arose after the 2014 selection of a site for a San Francisco Public Utilities Commission educational facility. The area likely contained human remains, triggering a California policy that requires developers to contact the most likely descendants of people buried in Native American sites before digging or building. When officials contacted the Muwekma Ohlone Tribe, its members requested a study of two settlement areasSi Tupentak (Place of the Water Round House Site) and Rummey Ta Kuuwi Tiprectak (Place of the Stream of the Lagoon Site).

Experts from Stanford University, the University of Illinois Urbana-Champaign, cultural resources consulting firm Far Western Anthropological Research Group and other institutions led the research.

But members of the Muwekma Ohlone Tribe were involved in every aspect of the study, from the initiative to pursue the project to the selection of research questions, in archaeological excavation and ancient genomics involving sites in their historical lands, and in present-day genomic analysis with current tribal members, according to the study. Tribal members even helped exhume the bodies.

Researchers and tribe members alike commented on the unique nature of the collaboration.

When youre a student doing the work, its not common to have this kind of direct connection to the people who are the data that youre working with, says lead author Alissa Severson, a doctoral student at Stanford University at the time of the research, in a statement. We got to have that dialogue, where we could discuss what were doing and what we found, and how that makes sense with their history. I felt very lucky to be working on this project. It felt like what we should be doing.

Jennifer A. Raff, a paleogeneticist at the University of Kansas who was not involved in the study, describes the work as fascinating.

If other tribes are interested in using genetics to investigate histories, they may be encouraged by the fact that some researchers are doing this work in a careful way, Raff tells Science magazines Andrew Curry.

The team analyzed the DNA of 12 individuals buried between 300 and 1,900 years ago, then compared the genomes to those of a variety of Indigenous Americans. They found genetic continuity between all 12 individuals studied and eight modern-day Muwekma Ohlone Tribe members.

It was surprising to find this level of continuity given the many disruptions the Ohlone people experienced during Spanish occupation, such as forced relocations and admixture with other tribes forcibly displaced by the Spanish, co-author Noah Rosenberg, a population geneticist at Stanford, tells the New York Times.

Tribe members hope the new evidence of the Muwekma Ohlone Tribes longstanding connection to the landand their ancestorswill spur politicians to finally recognize the tribe. According to an official tribal website, Muwekma Ohlone families started the reapplication process in the early 1980s and officially petitioned the U.S. government for recognition in 1995. Despite filing a lawsuit against the Bureau of Indian Affairs, the tribe is still not recognized by the U.S. government.

Co-author Alan Leventhal, a tribal ethnohistorian and archaeologist who works with the Muwekma Ohlone Tribe, tells USA Today hes hopeful this new research will help cut through some of the bureaucratic red tape thats been delaying the tribes petition.

Privately, this further validates the tribe, he says. Now, as politicians are reading, they're noticing. And now we'll be lending support for the tribe's reaffirmation.

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This Native American Tribe Wants Federal Recognition. A New DNA Analysis Could Bolster Its Case - Smithsonian Magazine

Just like human beings, pets can suffer from blindness, too, and only a few pet parents are aware of the causes, symptoms and prevention methods of blindness. Dr Dilip Sonune, the director of veterinary services at Wiggles.in says your pet may become blind due to several reasons, from poor nutrition to old age, injuries or even accidents.

Here are some common causes:

GlaucomaThis condition is caused by increased pressure in the eye. Glaucoma can occur due to genetics and sometimes other conditions like uveitis, eye tumor and lens luxation.

CataractThis condition causes painless cloudiness in the eye that can lead to partial or complete blindness. Uveitis in cats and factors like genetics and diabetes in dogs are common causes of cataract in pets.

Old ageLike humans, old age can cause blindness in pets, too.

Suddenly Acquired Retinal Degeneration Syndrome (SARDS)This is a condition in dogs that causes sudden blindness. It can occur in completely healthy dogs and the causes are unknown.

Progressive Retinal Atrophy (PRA)PRA is mostly an inherited disease that occurs commonly in dogs and rarely in cats.

Injury or traumaAn injury or trauma to the brain or the eye and eye area can also cause blindness.

Health conditions that can cause blindness in pets are diabetes, heart disease, kidney disease, liver disease and systemic diseases, says Dr Sonune.

Symptoms of blindness in pets

Early detection of symptoms can sometimes prevent complete blindness. If you notice any of the following in your pet, visit your veterinarian.

Afraid to move around. Bumping into furniture or other objects. Excessive anxiety/jumpy behaviour. Unable to find their food, water or toys. Puffy, cloudy, swollen, watery or red eyes. Irritation near the eye area. Hesitant and unwilling to explore new places. Depression

How can blindness be prevented in pets?

According to the doctor, here are some ways in which you can prevent blindness in pets:

1. Add foods to the diet that are good for their vision: Foods like broccoli, eggs (without yolk), fish, blueberries and carrots are great for your pets vision. Carrots especially, rich in beta carotene, make for an excellent food that maintains good vision. You can pick a few of the ingredients and blend them together with some water. Add the blend as a top-up to their food. Do check with your veterinarian before changing your pets diet.

2. Clean their eyes regularly: Use pet wipes, baby wipes or a small piece of wet cloth to clean their eyes on a regular basis. This maintains good eye hygiene and prevents infections.

3. Get the hair around the eyes trimmed: Sometimes, eye infections can be caused due to irritation caused by the hair around the eyes. Visit a professional grooming service to get it trimmed.

4. Do not let them put their head out of the car window: Many pet parents do this and although it can be fun, it can hurt them. Small pebbles or tiny insects can cause an injury; the dust can cause infections.

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Expert explains causes of blindness in pets and ways to prevent it - The Indian Express

New research has identified 75 regions of the human genome involved in Alzheimer's development. File photo by BillionPhotos.com/Shutterstock

April 4 (UPI) -- An international team of researchers has identified 75 regions of the human genome associated with the development of Alzheimer's disease, including 42 never before linked with the common form of dementia, they said Monday.

After analyzing the genomes, or complete genetic data, for thousands of people, the researchers found 75 loci, or regions, of DNA involved in Alzheimer's, they reported in an article published Monday by the journal Nature Genetics.

Several of the identified regions of the genome are involved in the accumulation of amyloid-beta in the brain, which is known to cause Alzheimer's, according to the researchers.

In addition, they identified genes that affect production of a protein called tau that is found in brain cells. Changes in tau production also have been linked with Alzheimer's disease, the researchers said.

Based on their findings, the researchers have developed a genetic "risk score" for Alzheimer's, though it is still in the draft stage and is not yet ready for use in clinical practice, they said.

"Our knowledge of the genetics of AD common forms cannot allow it to be used as an individual diagnostic tool yet," study co-author Jean-Charles Lambert told UPI in an email.

"On the other hand, we show in our paper that this knowledge makes it possible in populations to define groups of individuals more or less at risk of developing the [disease]," said Lambert, research director at Inserm in Lille, France.

On Thursday, researchers working with the National Human Genome Research Institute announced that they had mapped a complete human genome for the first time.

This map could serve as a "reference," or guide, for researchers seeking to identify the genetic component of various diseases and traits, they said.

Amyloid-beta and tau have both been linked with Alzheimer's, the most common form of dementia in the United States, affecting some 6 million people, most of whom are age 65 years and older, according to the Alzheimer's Association.

However, it is not yet fully understood why some people have higher levels of amyloid-beta in their brains than others, placing them at higher risk for cognitive, or brain function, decline, Lambert said.

Most cases of Alzheimer's are thought to be caused by the interaction of different genetic and environmental factors, the latter of which include air pollution, research suggests.

In addition to identifying the genome regions behind amyloid-beta and tau development, Lambert and his colleagues also noted that many people with Alzheimer's also have modifications, or changes, in the genome that impact immune response, they said.

These changes affect the function of microglia, or the immune cells in the central nervous system that play a "trash collector" role by eliminating toxic substances, the researchers said.

The analysis also revealed that the tumor necrosis factor alpha-dependent signaling pathway, which plays a role in cell development, according to researchers.

The findings suggest that future clinical trials of therapies designed to treat Alzheimer's should focus on targeting amyloid-beta, microglial cells and the tumor necrosis factor alpha signaling pathway, they said.

They plan to validate the accuracy of their genetic risk score in future studies.

"This genetic knowledge will be the basis of personalized medicine" for Alzheimer's patients, Lambert said.

"This research is important today for the development of therapeutic approaches but in the not-so-distant future, for the clinical management of patients at the earliest stage," he said.

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Researchers identify regions of genome involved in Alzheimer's - UPI News

Researchers have finally deciphered a complete human genetic instruction book from cover to cover.

The completion of the human genome has been announced a couple of times in the past, but those were actually incomplete drafts. We really mean it this time, says Evan Eichler, a human geneticist and Howard Hughes Medical Institute investigator at the University of Washington in Seattle.

The completed genome is presented in a series of papers published online March 31 in Science and Nature Methods.

An international team of researchers, including Eichler, used new DNA sequencing technology to untangle repetitive stretches of DNA that were redacted from an earlier version of the genome, widely used as a reference for guiding biomedical research.

Deciphering those tricky stretches adds about 200 million DNA bases, about 8 percent of the genome, to the instruction book, researchers report in Science. Thats essentially an entire chapter. And its a juicy one, containing the first-ever looks at the short arms of some chromosomes, long-lost genes and important parts of chromosomes called centromeres where machinery responsible for divvying up DNA grips the chromosome.

Some of the regions that were missing actually turn out to be the most interesting, says Rajiv McCoy, a human geneticist at Johns Hopkins University, who was part of the team known as the Telomere-to-Telomere (T2T) Consortium assembling the complete genome. Its exciting because we get to take the first look inside these regions and see what we can find. Telomeres are repetitive stretches of DNA found at the ends of chromosomes. Like aglets on shoelaces, they may help keep chromosomes from unraveling.

Data from the effort are already available for other researchers to explore. And some, like geneticist Ting Wang of Washington University School of Medicine in St. Louis, have already delved in. Having a complete genome reference definitely improves biomedical studies. Its an extremely useful resource, he says. Theres no question that this is an important achievement.

But, Wang says, the human genome isnt quite complete yet.

To understand why and what this new volume of the human genetic encyclopedia tells us, heres a closer look at the milestone.

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Eichler is careful to point out that this is the completion of a human genome. There is no such thing as the human genome. Any two people will have large portions of their genomes that range from very similar to virtually identical and smaller portions that are wildly different. A reference genome can help researchers see where people differ, which can point to genes that may be involved in diseases. Having a view of the entire genome, with no gaps or hidden DNA, may give scientists a better understanding of human health, disease and evolution.

The newly complete genome doesnt have gaps like the previous human reference genome. But it still has limitations, Wang says. The old reference genome is a conglomerate of more than 60 peoples DNA (SN: 3/4/21). Not a single individual, or single cell on this planet, has that genome. That goes for the new, complete genome, too. Its a quote-unquote fake genome, says Wang, who was not involved with the project.

The new genome doesnt come from a person either. Its the genome of a complete hydatidiform mole, a sort of tumor that arises when a sperm fertilizes an empty egg and the fathers chromosomes are duplicated. The researchers chose to decipher the complete genome from a cell line called CHM13 made from one of these unusual tumors.

That decision was made for a technical reason, says geneticist Karen Miga of the University of California, Santa Cruz. Usually, people get one set of chromosomes from their mother and another set from their father. So we all have two genomes in every cell.

If putting together a genome is like assembling a puzzle, you essentially have two puzzles in the same box that look very similar to each other, says Miga, borrowing an analogy from a colleague. Researchers would have to sort the two puzzles before piecing them together. Genomes from hydatidiform moles dont present that same challenge. Its just one puzzle in the box.

The researchers did have to add the Y chromosome from another person, because the sperm that created the hydatidiform mole carried an X chromosome.

Even putting one puzzle together is a Herculean task. But new technologies that allow researchers to put DNA bases represented by the letters A, T, C and G in order, can spit out stretches up to more than 100,000 bases long. Just as childrens puzzles are easier to solve because of larger and fewer pieces, these long reads made assembling the bits of the genome easier, especially in repetitive parts where just a few bases might distinguish one copy from another. The bigger pieces also allowed researchers to correct some mistakes in the old reference genome.

For starters, the newly deciphered DNA contains the short arms of chromosomes 13, 14, 15, 21 and 22. These acrocentric chromosomes dont resemble nice, neat Xs the way the rest of the chromosomes do. Instead, they have a set of long arms and one of nubby short arms.

The length of the short arms belies their importance. These arms are home to rDNA genes, which encode rRNAs, which are key components of complex molecular machines called ribosomes. Ribosomes read genetic instructions and build all the proteins needed to make cells and bodies work. There are hundreds of copies of these rDNA regions in every persons genome, an average of 315, but some people have more and some fewer. Theyre important for making sure cells have protein-building factories at the ready.

We didnt know what to expect in these regions, Miga says. We found that every acrocentric chromosome, and every rDNA on that acrocentric chromosome, had variants, changes to the repeat unit that was private to that particular chromosome.

By using fluorescent tags, Eichler and colleagues discovered that repetitive DNA next to the rDNA regions and perhaps the rDNA too sometimes switches places to land on another chromosome, the team reports in Science. Its like musical chairs, he says. Why and how that happens is still a mystery.

The complete genome also contains 3,604 genes, including 140 that encode proteins, that werent present in the old, incomplete genome. Many of those genes are slightly different copies of previously known genes, including some that have been implicated in brain evolution and development, autism, immune responses, cancer and cardiovascular disease. Having a map of where all these genes lie may lead to a better understanding of what they do, and perhaps even of what makes humans human.

One of the biggest finds may be the structure of all of the human centromeres. Centromeres, the pinched portions which give most chromosomes their characteristic X shape, are the assembly points for kinetochores, the cellular machinery that divvies up DNA during cell division. Thats one of the most important jobs in a cell. When it goes wrong, birth defects, cancer or death can result. Researchers had already deciphered the centromeres of fruit flies and the human 8, X and Y chromosomes (SN: 5/17/19), but this is the first time that researchers got a glimpse of the rest of the human centromeres.

The structures are mostly head-to-tail repeats of about 171 base pairs of DNA known as alpha satellites. But those repeats are nestled within other repeats, creating complex patterns that distinguish each chromosomes individual centromere, Miga and colleagues describe in Science. Knowing the structures will help researchers learn more about how chromosomes are divvied up and what sometimes throws off the process.

Researchers also now have a more complete map of epigenetic marks chemical tags on DNA or associated proteins that may change how genes are regulated. One type of epigenetic mark, known as DNA methylation, is fairly abundant across the centromeres, except for one spot in each chromosome called the centromeric dip region, Winston Timp, a biomedical engineer at Johns Hopkins University and colleagues report in Science.

Those dips are where kinetochores grab the DNA, the researchers discovered. But its not yet clear whether the dip in methylation causes the cellular machinery to assemble in that spot or if assembly of the machinery leads to lower levels of methylation.

Examining DNA methylation patterns in multiple peoples DNA and comparing them with the new reference revealed that the dips occur at different spots in each persons centromeres, though the consequences of that arent known.

About half of genes implicated in the evolution of humans large, wrinkly brains are found in multiple copies in the newly uncovered repetitive parts of the genome (SN: 2/26/15). Overlaying the epigenetic maps on the reference allowed researchers to figure out which of many copies of those genes were turned on and off, says Ariel Gershman, a geneticist at Johns Hopkins University School of Medicine.

That gives us a little bit more insight into which of them are actually important and playing a functional role in the development of the human brain, Gershman says. That was exciting for us, because theres never been a reference that was accurate enough in these [repetitive] regions to tell which gene was which, and which ones are turned on or off.

One criticism of genetics research is that it has relied too heavily on DNA from people of European descent. CHM13 also has European heritage. But researchers have used the new reference to discover new patterns of genetic diversity. Using DNA data collected from thousands of people of diverse backgrounds who participated in earlier research projects compared with the T2T reference, researchers more easily and accurately found places where people differ, McCoy and colleagues report in Science.

The Telomere-to-Telomere Consortium has now teamed up with Wang and his colleagues to make complete genomes of 350 people from diverse backgrounds (SN: 2/22/21). That effort, known as the pangenome project, is poised to reveal some of its first findings later this year, Wang says.

McCoy and Timp say that it may take some time, but eventually, researchers may switch from using the old reference genome to the more complete and accurate T2T reference. Its like upgrading to a new version of software, Timp says. Not everyone is going to want to do it right away.

The completed human genome will also be useful for researchers studying other organisms, says Amanda Larracuente, an evolutionary geneticist at the University of Rochester in New York who was not involved in the project. What Im excited about is the techniques and tools this team has developed, and being able to apply those to study other species.

Eichler and others already have plans to make complete genomes of chimpanzees, bonobos and other great apes to learn more about how humans evolved differently than apes did. No one should see this as the end, Eichler says, but a transformation, not only for genomic research but for clinical medicine, though that will take years to achieve.

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We finally have a fully complete human genome - Science News Magazine

"People ask me, 'Why is it so expensive?' and I tell them because there are so many complicated steps involved in the whole process," says Rodriguez. "It's definitely an emotional reason for pet clients. They want to be able to carry on that strong emotional bond that they have with the pet."

The industry has since expanded elsewhere in the globe. Sooam Biotech in South Korea offer dog cloning services, as well as Sinogene in China.

However, many scientists remain uncomfortable about the whole premise. Lovell-Badge argues that there is "no justification" for pet cloning as while the resulting animals will be genetically identical, they will not have the same behavioural characteristics and personalities as all creatures are a product of both genes and their environment.

"People really want their pet that knows them and knows certain tricks and so forth," says George Church, professor of genetics at Harvard Medical School. "In that sense, it's a little bit taking advantage of people's grief."

Reviving extinct species

In the years that followed Dolly's cloning, the central question was whether scientists would ever extend the technology to humans, and the many moral and ethical issues that would invoke.

But while a human embryo was successfully cloned in 2013, the process of creating an entire human being has never been attempted because of the likely public outcry. Chinese scientists did clone the first primates in January 2018, long-tailed macques Zhong Zhong and Hua Hua, but there are currently no suggestions that this work will continue into further primate species.

Instead, most funding is being devoted to using cloning to resurrect animals on the verge of extinction. Efforts are underway to clone both the giant panda and the northern white rhino a species for which there are just two animals left on the planet while in the last two years, ViaGen have cloned the black footed ferret and Przewalski's horse, both of which are endangered.

Church is leading the most ambitious project, a quest to revive the woolly mammoth, a species that last lived some 4,000 years ago. His de-extinction company Colossal has already raised 11m ($14.5m) in funding to support the idea, which will involve creating an elephant-mammoth hybrid through taking skin cells from Asian elephants and using cloning technology to reprogram them with mammoth DNA.

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The people cloning their pets - BBC.com

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Credit: MD Anderson Cancer Center

HOUSTON Neal G. Copeland, Ph.D., and Nancy A. Jenkins, Ph.D., both professors of Genetics atThe University of Texas MD Anderson Cancer Center, have been elected to the 2022 class of Fellows of the American Association for Cancer Research (AACR) Academy.

The husband-and-wife geneticists, who co-led a joint laboratory for nearly 40 years, are recognized for their contributions to cancer genetics and for innovations to create mouse models of cancer and a variety of other human diseases.

The mission of the AACR Academy is to honor distinguished scientists whose contributions have propelled significant innovation and progress against cancer. This years class of 33 inductees joins 256 existing fellows in working collectively to advance the mission of the AACR.

Copeland and Jenkins join 10 additional MD Anderson fellows, including current members James P. Allison, Ph.D., Ronald A. DePinho, M.D., V. Craig Jordan, Ph.D., Margaret L. Kripke, Ph.D., Guillermina (Gigi) Lozano, Ph.D., and Louise C. Strong, M.D. Former members, now deceased, include Isaiah J. Fidler, D.V.M., Ph.D., Emil J Freireich, M.D., Waun Ki Hong, M.D., and John Mendelsohn, M.D.

We are so pleased to see Neal and Nancy recognized for their lasting impacts in the field of cancer research and human health, said Peter WT Pisters, M.D., president of MDAnderson. These remarkable scientists pioneered many of the approaches still used in cancer biology today, and we applaud their selection as part of this group of exceptional fellows.

Copeland and Jenkins together developed many of the earliest techniques to model human cancer in mice using insertional mutations. They were among the first to show that the Sleeping Beauty transposon could be mobilized within cells to insert itself within other genes and drive cancer formation. This technique enabled researchers to identify many of the genes and signaling pathways that we now know drive cancer development.

Using the Sleeping Beauty system, they modeled 16 different types of cancer affecting 10 organ systems and validated many of the cancer-related genes discovered through this work. They continue to collaborate in defining genes involved in the progression and metastasis of pancreatic cancer using laser-capture microdissection to isolate specific cancerous lesions followed by whole genome amplification and DNA sequencing.

They also developed a liquid-phase, capture-based sequencing and bioinformatics pipeline to facilitate the sequencing of transposon insertion sites from single tumor cells, making it possible to study tumor evolution at the single-cell level and to unambiguously identify cooperating cancer genes.

Neal and Nancy helped to establish foundational approaches to cancer research that continue to yield new insights, said Giulio F. Draetta, M.D., Ph.D., chief scientific officer. Their work epitomizes our efforts to pursue impactful discovery research to drive cancer breakthroughs, and we are proud to have them as a part of our MD Anderson research community.

Copeland received his bachelors degree in biology and a doctoral degree in biochemistry from the University of Utah.

Jenkins received her bachelors degree in chemistry from Sweet Briar College. She earned a masters degree in microbiology and a doctoral degree in molecular and cellular biology from Indiana University.

The couple met during their postdoctoral fellowship at Dana-Farber Cancer Institute, after which they started a laboratory together at the University of Cincinnati. They spent 21 years together leading research at the National Cancer Institute, followed by five years at the Institute of Molecular and Cell Biology in Singapore. They joined the Houston Methodist Research Institute in 2011 and MD Anderson in 2017.

Copeland and Jenkins each are members of the National Academy of Sciences and The Academy of Medicine, Engineering and Science of Texas. Among numerous honors, they were awarded the 2020 Prince Hitachi Prize for Comparative Oncology. They have co-authored more than 800 peer-reviewed scientific publications.

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Neal Copeland and Nancy Jenkins elected Fellows of the AACR Academy - EurekAlert

Dr Miriam Stoppard reports on a discovery which could help us to understand the ageing process and how key proteins could help us to live longer, healthier lives

Image: Getty Images)

For years, Ive followed the research on ageing that seeks to slow down the process. So are we any closer to achieving what could be the Holy Grail of medicine?

Studies from Edinburgh University investigating which proteins could influence how we grow old hint that we might be.

In the largest genetic study of ageing, scientists have uncovered two blood proteins that influence how long and healthy a life well live.

Their ambition is to develop drugs that target these proteins as a way of slowing down the whole process.

From adulthood onwards our bodies are in inevitable decline, which results in age-related diseases and eventually death.

The rate at which we age and die depends on genetics, lifestyle, environment and chance. This study reveals the part played by the proteins (the genetics) in this process.

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Our levels of these are determined by the DNA we inherit from our parents and they, in turn, affect our health.

Scientists combined the results of six large genetic studies into ageing totalling hundreds of thousands of people. They studied 857 proteins and identified two that had powerful negative effects on growing older.

For instance, people who inherited DNA that causes raised levels of these proteins were frailer, had poorer self-rated health, and were less likely to live an exceptionally long life than those who didnt.

So, what do these proteins do? The first, LPA, is made in the liver and thought to play a role in blood clotting.

High levels of LPA can increase the risk of hardening of arteries which leads to heart disease and stroke.

The second protein, VCAM1, resides on the lining of blood vessels and controls their expansion and contraction in blood clotting and the immune response.

Levels of VCAM1 increase when we have an infection and this gingers up the immune system.

The researchers say with drugs that lower levels of LPA and VCAM1, we might improve the quality and length of our lives.

Theres already a clinical trial testing a drug to lower LPA as a way of diminishing the risk of heart disease, and VCAM1 in early animal studies improved cognition during old age.

The identification of these two key proteins could help extend the healthy years of life, says Dr Paul Timmers, lead researcher at the MRC Human Genetics Unit at Edinburgh University.

Drugs that lower these protein levels in our blood could allow the average person to live as healthy and as long as individuals whove won the genetic lottery and are born with genetically low LPA and VCAM1 levels.

Brave new world!

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'There are two blood proteins that could hold the key to a long, healthy life' - The Mirror

TUESDAY, March 22, 2022 (HealthDay News) -- Antibodies from a COVID-19 infection linger in most children for up to seven months, even if they had no symptoms, a new study finds.

To come to that reassuring conclusion, researchers analyzed data from 218 children in Texas, ages 5 to 19, who were enrolled in an ongoing survey launched in October 2020 to track COVID-19 antibody status in children and adults over time.

Blood samples were collected from participants before vaccines became available and during the surges of the Delta and Omicron variants.

While 96% of children who were infected with COVID-19 still had antibodies at least six months later, 58% did not have infection-triggered antibodies at their third and final blood test.

The report, published March 18 in the journal Pediatrics, did not assess the impact of vaccination.

"This is the first study from the Texas CARES survey that includes data from all three time points in the survey," said corresponding author Sarah Messiah. She is a professor of epidemiology, human genetics and environmental sciences at the University of Texas Health Science Center at Houston.

"These findings are important because the information we collected from children infected with COVID-19 didn't differ at all by whether a child was asymptomatic, severity of symptoms, when they had the virus, were at a healthy weight or had obesity, or by gender," she added in a university news release. "It was the same for everyone."

To date, 14 million children in the United States have tested positive for the virus, and these findings help improve understanding of how it affects children, according to Messiah.

"Adult literature shows us that natural infection, plus the vaccine-induced protection, gives you the best defense against COVID-19. There has been a misunderstanding from some parents who think just because their child has had COVID-19, they are now protected and don't need to get the vaccine," Messiah said.

"While our study is encouraging in that some amount [of] natural antibodies last at least six months in children, we still don't know the absolute protection threshold," she added. "We have a great tool available to give children additional protection by getting their vaccine, so if your child is eligible, take advantage of it."

More information

For more on children and COVID-19, go to the American Academy of Pediatrics.

SOURCE: University of Texas Health Science Center at Houston, news release, March 18, 2022

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Antibodies From COVID Infection Shield Kids for Up to 7 Months - HealthDay News

SAN DIEGO, Dec. 23, 2021 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (BNGO), pioneer of optical genome mapping (OGM) solutions on the Saphyr system and provider of the leading software solutions for visualization, interpretation and reporting of genomic data, today announced that University Hospitals Leuven in Belgium, after previously receiving its accreditation from the Belgian Accreditation Body (BELAC) for using OGM in analysis of acute lymphoblastic leukemia (ALL), is expanding its BELAC-accredited menu to include acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL) and facioscapulohumeral muscular dystrophy (FSHD).

With the flexibility we now have as an accredited laboratory by BELAC, our teams can develop OGM-based assays addressing hematological malignancies without the need for a new audit, said Barbara Dewaele, PhD, supervisor of the Laboratory for Genetics of Malignant Disorders at University Hospitals Leuven. We are excited to move forward using this valuable tool to analyze the genomes of patients with cancer and rare diseases.

At the European Cytogenomics Conference in July 2021, Dr. Dewaele shared the results of implementing an OGM-based assay for ALL patients that her team developed with Bionanos Saphyr system. As presented by Dr. Dewaele and her team, compared to their existing workflow, the new workflow including OGM as a primary analysis method reduced the number of fluorescence in-situ hybridization probes used by 90% and eliminated the need for multiplexed ligation polymorphism assays. In their new workflow including OGM, it is complemented with karyotyping to detect ploidy changes and the presence of small subclones. This transformation resulted in a turnaround time that was 14 days faster, a cost savings of approximately 50% and higher overall success rates in finding pathogenic variants in samples.

In parallel, as part of their menu expansion efforts, and under the direction of Dr. Valrie Race, Center for Human Genetics at University Hospitals Leuven, a validation of Bionanos EnFocus FSHD tool will be conducted on a prospective cohort of FSHD samples to confirm OGMs capability to accurately measure the length of D4Z4 repeat arrays and assess reproducibility and repeatability of the workflow. Preliminary results were presented at the European Society of Human Genetics conference in August 2021, and reported that OGM can be a powerful and robust technique for FSHD testing in genetic diagnostic laboratories by providing results that are concordant with the current gold standard, Southern blot analysis in a substantially simpler workflow that does not use radioactivity.

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Dr. Dewaele reported that she and her colleagues have doubled their weekly sample volume relative to when they first started using their Saphyr system and believe they are on track to reach their goal of 500 samples per year with this instrument. The teams at University Hospitals Leuven believe that the time and cost savings from using OGM-based assays could be a competitive advantage relative to traditional techniques. OGM is also complementary to many of the tools used in typical molecular pathology and cytogenomics labs and, as a result, it can be helpful to interpretation of results from assays such as karyotyping, which can be used to confirm OGM findings.

Erik Holmlin, PhD, President and CEO of Bionano Genomics, commented, We are impressed at the drive and persistence of Dr. Dewaele and all of the teams at Leuven, which has enabled the hospital to expand its lab testing portfolio. We are thrilled that University Hospitals Leuven has determined its plans for menu expansion, which are facilitated by the accreditation and formal confirmation letter received from BELAC. We believe that the path followed by Dr. Dewaele is indicative of what other labs can follow along the way to making OGM an essential and widely used method in clinical genomics research, said Dr. Holmlin. OGM can allow new workflows that are faster and provide answers to questions quickly, which may allow for treatment decisions to be taken sooner. Since OGM has been shown to find clinically relevant variants that other techniques may miss, it may also provide answers to questions researchers may not know they had about these specific cancers and genetic diseases.

Dr. Barbara Dewaele will be presenting at Bionanos Symposium on January 11, 2022. At the Symposium, more than 25 esteemed speakers from around the world will present their latest scientific findings using Bionanos Saphyr system for OGM in constitutional cytogenomics, hematologic malignancies, solid tumors, and in combination with next-generation sequencing. A link to register for the Bionano Genomics 2022 Symposium is available at https://www.labroots.com/ms/virtual-event/bngo2022

About Bionano Genomics

Bionano is a provider of genome analysis solutions that can enable researchers and clinicians to reveal answers to challenging questions in biology and medicine. The Companys mission is to transform the way the world sees the genome through OGM solutions, diagnostic services and software. The Company offers OGM solutions for applications across basic, translational and clinical research. Through its Lineagen business, the Company also provides diagnostic testing for patients with clinical presentations consistent with autism spectrum disorder and other neurodevelopmental disabilities. Through its BioDiscovery business, the Company also offers an industry-leading, platform-agnostic software solution, which integrates next-generation sequencing and microarray data designed to provide analysis, visualization, interpretation and reporting of copy number variants, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view. For more information, visit http://www.bionanogenomics.com, http://www.lineagen.com or http://www.biodiscovery.com.

Forward-Looking Statements of Bionano Genomics

This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as may, will, expect, plan, anticipate, estimate, intend and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) convey uncertainty of future events or outcomes and are intended to identify these forward-looking statements. Forward-looking statements include statements regarding our intentions, beliefs, projections, outlook, analyses or current expectations concerning, among other things: the inability or delays in the University Hospitals Leuven to expand its menu; the inability for other labs to utilize the steps taken by University Hospitals Leuven to make OGM a widely used method; the ability for University Hospitals Leuven to continue processing the increased volume of samples; OGMs ability to provide new, faster workflows; OGMs ability to find clinically relevant variants that other techniques miss and to provide answers to questions not yet asked; Dr. Dewaeles ability to present at Bionanos Symposium; and the impact of the expansion of our commercial leadership team, including our expectations regarding the growth of Saphyr and our ability to bolster customer support and experience globally. Each of these forward-looking statements involves risks and uncertainties. Actual results or developments may differ materially from those projected or implied in these forward-looking statements. Factors that may cause such a difference include the risks and uncertainties associated with: the impact of the COVID-19 pandemic on our business and the global economy; general market conditions; changes in the competitive landscape and the introduction of competitive products, technologies or improvements in existing technologies; failure of OGM to accurately and consistently perform as observed by University Hospitals Leuven or others; subsequent results could negate the results observed by University Hospitals Leuven or others; changes in our strategic and commercial plans; our ability to obtain sufficient financing to fund our strategic plans and commercialization efforts; the ability of medical and research institutions to obtain funding to support adoption or continued use of our technologies; and the risks and uncertainties associated with our business and financial condition in general, including the risks and uncertainties described in our filings with the Securities and Exchange Commission, including, without limitation, our Annual Report on Form 10-K for the year ended December 31, 2020 and in other filings subsequently made by us with the Securities and Exchange Commission. All forward-looking statements contained in this press release speak only as of the date on which they were made and are based on managements assumptions and estimates as of such date. We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of the receipt of new information, the occurrence of future events or otherwise.

CONTACTSCompany Contact:Erik Holmlin, CEOBionano Genomics, Inc.+1 (858) 888-7610eholmlin@bionanogenomics.com

Investor Relations:Amy ConradJuniper Point+1 (858) 366-3243amy@juniper-point.com

Media Relations:Michael SullivanSeismic+1 (503) 799-7520michael@teamseismic.com

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University Hospitals Leuven in Belgium Outlines their Menu Expansion Plans for Optical Genome Mapping as One of their Primary Analyses in Leukemias...