Category Archives: Genetics

Genetics

Epigenetics The spirituality of genetics – The Financial Express

SHAERI NAWAR | Published: June 30, 2021 12:56:05

Imagine a twin - Rahim and Karim. One day they visited a festival where Karim got lost and had ever since lived on the roadside. Rahim grew up in a stable normal family household while Karim grew up with less stability, less access to nutritious food and education but more laborious activity.

Forty years later, Rahim unexpectedly found his long lost sibling. More than the reunion with his brother, what shocked Rahim was the fact that his twin brother was not like him. Karim was shorter than him, had a deeper voice and no longer suffered from any genetically inherited disease that they both had in childhood.

As the traits are genetically inherited, Rahim decided to consult a genetic scientist. The scientist studied their genetic code and found that their DNA is exactly the same as it used to be when they were born. However, it turns out that they dont just look different but they actually have become genetically different just by living in different conditions despite having the same genetic codes. This is where epigenetics comes in the picture.

Epigenetics is the study of how the environment influences our genetic makeup. According to the national public health agency of the United States, The United States Centers for Disease Control and Prevention (CDC,) it is the study of how your behaviours and environment can cause changes that affect the way your genes work. Unlike genetic changes, epigenetic changes are reversible and do not change your DNA sequence, but they can change how your body reads a DNA sequence.

An example can help to understand it better. Say, our genome is a paragraph and all of the letters and punctuations would be in the exact same order and give the paragraph a meaning. Now keeping the letters in the same order while shuffling the punctuations would potentially change the message of the paragraph for a reader. Similarly, no cell of the body will be able to read and follow the instructions in the DNA sequence as it results in epigenetic changes. Epigenetics literally means above genetics where a change is evident without a physical change in the DNA sequence.

What causes epigenetic changes?

Diet, physical activity, smoking, environmental pollutants, family relationships, psychological stress, working on night shifts, financial status and many more are the core causes of epigenetic changes.

How epigenetics works

The genetic mechanism of epigenetics is quite complex following a cascade of biological reactions. Nonetheless, a simplified explanation for the curious minds has been presented.

Genes act as the switch that controls everything our body does. Specific genes are there to do specific functions and show specific traits. This genetic switch needs to be turned on or off in order for a gene to work. This turning on/off phenomenon is controlled by a chemical (a methyl group) being added or removed from that gene. This phenomenon is called DNA methylation. For example, a gene that is normally supposed to remain off and if a methyl group is added to turn the gene on, then that could result in epigenetic changes.

The placebo effects

Placebo is a substance or treatment, based on the idea that our brain can convince our body into accepting a fake treatment and thus having a cure somewhat. But have you ever pondered about the mechanism behind it? How does a supposedly fake treatment magically improve health like real ones? Many would answer it happens because we are conditioned to think that we are getting treated which is partially correct.

Our thoughts influence the level of our hormones which run some of the brain functions. The brain sends signals to the cell to function in a certain way. The cell signals to switch a gene on or off to carry the cellular function. As a result, it all comes down to the regulation of the genetic switch. The bottom line is that our mind-body connection is reinforced by epigenetics.

For instance, the genome is the actual hardware of the computer (your body), then epigenome is more like the software which tells the hardware what to do even though the genome is going to do all the work. The fact is that you can influence your genetic expression.

Interestingly, epigenetic characteristics are passed on to children from parents as well. If somebody is a chain smoker, thats bad for the individual but it is thought that he wouldnt necessarily be harming his unborn child in any measurable way. However, this idea is changing pretty rapidly because some of the epigenetic information get stuck on the genomes and are passed from generation to generation. So, if you are a chain smoker, chances are your kids would have more affinity towards smoking than a non-smokers kid.

Epigenetic anomalies

Over the last few decades, numerous scientific studies have been conducted to decode the science behind male infertility. As a matter of fact, the valid cause behind the mechanism of more than 50 per cent of male infertility cases is unknown. Owing to this concern, a number of studies have been conducted, which have inferred that the abnormal methylation of the sperm is highly correlated with male infertility.

Also, epigenetic changes are now considered as one of the hallmarks of many cancers. Disruption of epigenetic processes can lead to altered gene function and transform cells causing malignancies and cancer.

However, as the old saying goes, the cure lies in the problem. Epigenetics both causes and cures cancer. In a study published in the Japanese Journal of Clinical Oncology, it has been found that methylation that takes place in tissues and that is non-cancerous acts as a signal to identify the risk of tumour formation. So, this is emerging as a target for cancer prevention.

Epigenetic drugs

The U.S. Food and Drug Administration has approved seven epigenetic drugs for the treatment of haematological malignancies or cancer. Some of these drugs have been acquired from the enzymes that function during epigenetic occurrences.

All in all, from being the cause of some potential diseases and cure of some, epigenetics has enormous advantages. It gives one the power to shape oneself and as a matter of fact, soon epigenetics would be the personalised healthcare tool for individuals.

Shaeri Nawar is a life science researcher. He is currently a research fellow at Asian Network for Research on Antidiabetic Plants (ANRAP). E-mail: [emailprotected]

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Epigenetics The spirituality of genetics - The Financial Express

Genetics

Study shows genetic link to age of first sex, childbirth – New Zealand Herald

Lifestyle

1 Jul, 2021 11:24 PM2 minutes to read

You might think that your first time was linked to a number of factors, such as love, lust, morality or social mores.

But new research has revealed that the age we lose our virginity may actually be tied to our unique genetic code.

An international team of scientists, led by Oxford University and including input from New Zealand, found 371 regions of our DNA that influence milestones such as when we first have sex and have our first baby, both for women and men.

"This is one of these studies where you wonder, did my genes make me do it?" Andrew Shelling, head of the University of Auckland's Medical Genetics Research Group, told The AM Show.

Shelling also revealed that environmental factors do play a bigger part, saying: "Just because they found a correlation with a gene doesn't mean to say that's going to cause us to have sex at an earlier age than anyone else."

The study's leader, Professor Melinda Mills at the Leverhulme Centre for Demographic Science at the University of Oxford, said that the research could have wide-ranging implications.

"Age at first sexual intercourse and age at first birth have implications for health and evolutionary fitness. We anticipate that our results will address important interventions in infertility, teenage sexual and mental health," she said.

Professor Mills told the Daily Mail that the study shows an "interaction of both nature and nurture".

According to a 2016 survey by condom makers Durex, New Zealand had one of the youngest average ages of first sex in the countries surveyed.

Kiwis had an average age of 17.5, compared to 18.4 in the US and 21.2 in China.

30 Jun, 2021 09:46 PMQuick Read

1 Jul, 2021 03:32 AMQuick Read

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Brazil 17.3 New Zealand 17.5 Germany 17.8 UK 18.3 US 18.4 Canada 18.5 France 18.7 Ireland 18.7 Mexico 19.1 Spain 19.5 Japan 20.4 China 21.2 India 22.5 Malaysia 23.7

However, an earlier study from a Kiwi sex toy retailer showed that our sexual confidence doesn't peak until our late 20s, spiking again in our early 50s.

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Study shows genetic link to age of first sex, childbirth - New Zealand Herald

Genetics

Men: Know Your Genetics to Lower Your Cancer Risk and That of Your Family – Baptist Health South Florida

A gene mutation that could put you at higher risk for cancer is just as likely to come from your father as your mother. Unfortunately, only 4 percent of those undergoing hereditary cancer gene testing are male, leaving a huge gap in the knowledge that could help you avoid cancer altogether or inform treatment decisions, according to a study published in the journal JAMA Oncology.

Louise Morrell, M.D., a genetics specialist and medical director of Lynn Cancer Institute at Boca Raton Regional Hospital, part of Baptist Health.

Men do not often seek testing and many times do not understand the importance of the information, saysLouise Morrell, M.D., a genetics specialist and medical director of Lynn Cancer Institute at Boca Raton Regional Hospital, part of Baptist Health. The more accurate our information, the better our guidance on prevention. In genetics, unlike other areas, the benefit extends to family members and perhaps for generations to come.

Inherited Cancers

Today, up to 15 percent of cancers are tied to a hereditary link. Knowing about those links may help you and other members of your family prevent or reduce the risk of cancer.

Scientists have identified many mutations that increase the risk for breast and gynecologic cancers, some prostate cancers, colon cancer, gastro-intestinal cancers, kidney cancer and more. For example, a man with prostate cancer tied to aBRCA2mutation, could pass that mutation to his son or daughter, increasing the risk of breast cancer in both children and of prostate cancer in the son.

Raising awareness of the value ofgenetic assessmentandtesting, particularly among men, is important to the experts atLynn Cancer InstituteandMiami Cancer Institute. Because the field of genetics moves at a rapid pace, discoveries may impact everything from guidelines for cancer screenings to treatment options for those who have cancer.

Although researchers have worked for decades on uncovering the links between genetic mutations and cancer, public knowledge grew when actress Angelina Jolie had her breasts removed in 2013, and then her ovaries in 2015, because she carried theBRCA1 gene mutation that is linked to a higher risk of breast and ovarian cancer. Ms. Jolies mother, grandmother and aunt had died from cancer, and her decision to prophylactically remove her breasts, ovaries and fallopian tubes to lower her cancer risk came after multiple tests and conversations with experts. The sameBRCA1andBRCA2mutations that raise the risk of breast cancer in women, also raise the odds of breast cancer in men by eight times, according to the American Cancer Society.

Ask Questions

Arelis Mrtir-Negrn, M.D., medical geneticist and head of the Clinical Genetics program at Miami Cancer Institute, part of Baptist Health.

Whether you are a man or a woman, your familys health history may be the key to your future, saysArelis Mrtir-Negrn, M.D., medical geneticist and head of the Clinical Genetics program at Miami Cancer Institute. Because as many men pass down mutations as women, you should be as aware of your fathers familys cancer history as your mothers. Know your family history. Ask questions. In general, the earlier cancer is caught, the better the chance of survival.

Like Ms. Jolie, when Matthew Knowles, the father of artists Beyonc and Solange, announced he had breast cancer in 2019, he put the spotlight on genetics. His mother, aunt and great aunt had died from breast cancer and he learned his rare male breast cancer was caused by aBRCA2 gene mutation. He understood that his daughters had a 50 percent chance of inheriting his mutation.

Genetic testing among Blacks is much lower than other races. Physicians would like that to change, particularly since some breast cancers that have a poorer prognosis also have a higher incidence in Black women. Fortunately, subsequent testing showed neither daughter had the mutation. Mr. Knowles underwent a mastectomy.

Thinking of genetics as a recipe may help some people better understand, genetic counselors say. All people inherit two copies of each gene: one from their mother and one from their father. Variations in genes are normal and are what give us our diversity. A slight change in the recipe may not make much of a difference but the wrong ingredient or too much or too little of something may cause the recipe to change drastically. In addition, not all mutations carry the same risk.

ABRCAmutation might lead to an 80 percent risk of breast cancer but anATMmutation might have a 20 percent lifetime risk, Dr. Morrell says. These are very different, which is why having this information is so valuable.

Its important to note that just because you carry a mutation doesnt mean you will get cancer. There are many things we take into account when we assess risk, Dr. Mrtir-Negrn says. We can suggest lifestyle modifications that could lower their chances of getting cancer. There are times when we might also suggest medications or present the idea of preventive surgery.

The genetic teams at Lynn Cancer Institute and Miami Cancer Institute offer multidisciplinary care to patients and often their family members who may also be affected to better understand their risks, help them determine if genetic testing would be beneficial, and assist them with understanding the results, whether they are positive, negative or inconclusive. The team also develops personalized cancer prevention for previvors, the term used for those with a predisposition to cancer.

Fortunately, technological advances continue to make it possible to test for more genes. In recent years, improvements have sped up testing and made it less expensive. In addition, in someone already diagnosed with cancer, the answers from genetic testing can help drive treatment and surgery decisions.

Who Should Consider Cancer Genetic Assessment?

Men should consider assessment if they:

Couples who have a family history of cancer and are considering pregnancy also frequently take advantage of genetic assessment. If you really want to be able to tell your children they are not at risk to have a particular mutation, you need to test both parents, Dr. Morrell says. The offspring can only inherit a mutation that the parents have. Mutations do not skip generations. The parent has to also inherit it.

For more information on genetic assessment, testing and counseling at the Morgan Pressel Center for Cancer Genetics at Lynn Cancer Institute, clickhere; for information on Miami Cancer Institutes Clinical Genetics program, clickhere.

Tags: genetic testing, Lynn Cancer Institute, Miami Cancer Institute

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Men: Know Your Genetics to Lower Your Cancer Risk and That of Your Family - Baptist Health South Florida

Genetics

Free genetic testing offered to propel medical research, All of Us program building most diverse database – KLAS – 8 News Now

LAS VEGAS (KLAS) The National Institutes of Health (NIH) All of Us Research Program is offering no-cost genetic testing, just in time for Fathers Day.

The free genetic testing kit offers a unique opportunity to discover your ancestral past and learn more about your own health.

By participating in the NIH program, researchers will be able to study your results in hopes of better understanding how certain genetic traits affect underrepresented communities, which could greatly affect the future of customized healthcare.

Matthew Thombs, Senior Project Manager of Digital Health Technology at Scripps Research walked 8NewsNow through what participants would experience when they sign up for the study. He also explained why he is proud to be a part of the All of Us Research Program:

I joined the All of Us Research Program a little over a year ago and have fallen in love with its mission of creating the largest and most diverse health resource ever. I lost a close family member a few years ago to a condition I believe could have been managed with changes to their lifestyle. What we are building will empower researchers with the information needed to make such conclusions and forever alter how diseases are treated. I hope that what we are doing here will help my son grow up in a world where health care is more of a priority and many of the ailments we seetodayare things of the past.

You can sign up for the program online or by downloading the All of Us mobile application from the iOS or Android app store. Once you open the application, you would create a personal profile, sign the necessary consent forms and decide if you would also like to receive a salivary kit. The test kit would be mailed to you free of charge, and include a pre-paid mailing label to return your sample.

MOVING AWAY FROM ONE-SIZE-FITS ALL HEALTH CARE

Thombs says a fun aspect of TheAll of UsResearch Program is learning more about traits that may have been passed down to you. Can you roll your tongue like your father? Does caffeine sensitivity run in your family?

You may even discover that you need to modify or remove something from your diet to improve your health or help you feel better. Your test kit results provide you with information on what makes you you.

The information collected is also shared anonymously with more than 800 researchers in search of medical discoveries for COVID-19, Alzheimers, Cancer, and other conditions.

INVITATION JOIN THE RESEARCH PROGRAM

Thombs says The All of Us Research Program is working to build a diverse community of one million or more participants across the country to help researchers learn more about how genetics, environment and lifestyle affect individuals health, especially those in communities who have largely been left out of these kinds of research programs.

We want to be able to propel research forward, said Thombs.

Perhaps your genetic makeup allows you to recover from certain ailments and return to excellent health. That data is valuable and can help someone whose body struggles with the same illness. To understand how humans function and what makes us sick, all human beings need to be included in research studies.

According to Thombs, participants can provide as much or as little information as they like, every single data point matters.

Feel free to visit the All of US website at http://www.joinallofus.org/health for more information.

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Free genetic testing offered to propel medical research, All of Us program building most diverse database - KLAS - 8 News Now

Genetics

Giles Yeo: Lets consider the type of food we eat, not fixate on calories – The Guardian

Since the dawn of the 20th century, almost all weight loss guidelines have used calories as a simple measure of how much energy were consuming from our food. But according to Giles Yeo, a Cambridge University research scientist who studies the genetics of obesity, theres one problem: not all calories are created equal. In his new book, Why Calories Dont Count, Yeo explains that what really matters is not how many calories a particular food contains, but how that food is digested and absorbed by your body.

Can you explain why you feel calorie-counting is a flawed approach to weight loss?There was an American chemist in the 19th century called Wilbur Olin Atwater who calculated the calorie numbers for different foods, by working out the total energy intake you get from them. But his calculations never took into account the energy it takes our cells to metabolise food in order to use it. This is important. Its why for example a calorie of protein makes you feel fuller than a calorie of fat, because protein is more complex to metabolise. For every 100 calories of protein you eat, you only ever absorb 70.

So we need to consider the type of food were eating, rather than fixating purely on the calorie content. You could be aiming to eat 800 calories a day, but how much energy your body actually absorbs will depend on whether youre eating sugar, celery, or steak.

How could people use this information practically when trying to manage their weight?What really annoys me is when weight loss gurus say things like: Oh, just replace the chocolate bar with a banana. Now thats a dumb thing to say, because sometimes life demands a banana, and sometimes life demands a chocolate bar.

But you can make a better practical choice in those situations by considering how the body processes food. It takes a lot longer to digest food elements like protein and fibre, so you absorb less of those calories, so if you choose a chocolate bar thats higher in nuts or dry fruits, that will make it a better chocolate bar.

Speaking of more nuanced approaches to managing weight, recently, body mass index has come under fire as being an inherently flawed measure of obesity. Is it still appropriate for doctors to use BMI?I would define an obese person as someone who is carrying too much fat, so that it begins to influence their health. But then the question is, how much is too much fat? Your fat cells are like balloons, they get bigger when you gain weight, they shrink when you lose weight. But everyones fat cells expand and contract to different amounts, so everybody has a different safe, fat-carrying capacity. Famously, us east Asians cannot get too big BMI-wise before we increase our risk of diseases such as type 2 diabetes, because we have a lower safe fat-carrying capacity.

BMI is very useful for looking at population trends, because its free to measure, and you only need your height and weight. But at an individual level, this is not useful to predict health because it doesnt take into account genetic and ethnic differences in fat capacity. You could be a rugby player, or the same size as a rugby player, and be all fat, and yet have the same BMI. So I think healthcare professionals need to consider the whole, rather than simply BMI itself.

The FDAs approval of semaglutide the first new drug to be approved for obesity since 2014 has made a lot of headlines this year. Is obesity something we should be treating with drugs?I see it as being part of the toolkit. A lot of people consider obesity as a lifestyle disease; they perceive that being larger than someone else comes down to choice, when this is not the case. For many people, its more difficult to say no to food purely because of their genetics.

Semaglutide makes your brain think youre slightly fuller than you are, so you eat less, and if someone is finding it difficult to lose weight, why not use it? Im not countenancing drugging the entire population, but I think semaglutide should be one of the tools we use, alongside lifestyle intervention, exercise, all of those things.

You research genetic factors that control susceptibility to obesity. What do these genes do?We now know that more than 1,000 genes are linked to obesity, and the vast majority of them influence pathways in three different parts of the brain that ultimately influence your feeding behaviour. One is the brains fuel sensor called the hypothalamus, then theres the part of the brain that senses how full you get, and then theres the hedonic part of the brain that makes eating feel good. All of these regions speak to one another, and some of these 1,000 genes influence these pathways. A mutation that causes a slight insensitivity in your brain to how full you are could influence how much you want to eat, making it more difficult to say no to temptations.

For example, we know that one in 330 people in the UK have mutations in a particular pathway called the leptin-melanocortin pathway, which renders your brain slightly less sensitive to how much fat youre carrying.

Will we be able to use our genetic knowledge of obesity to develop new treatments that regulate appetite?Yes, theres now a drug called setmelanotide, which targets the leptin-melanocortin pathway. It has just been approved in the US for rare genetic causes of obesity, and the European Medicines Agency should be approving it within weeks. Eventually it will be trialled in the larger population, much like semaglutide was, to see whether you can fool your brain into thinking that youre carrying more fat, and so you end up eating less. This is an example of how understanding the basic biology of obesity, the wiring, the genes involved, can result in cogent and hopefully sustainable ways of tackling it.

In your book, you touch on how obesity isnt solely genetic, and factors such as socioeconomic status play a key role in determining how those genes are expressed, and how much they matter.The heritability of body weight the percentage of the trait that is down to your genes is a range, which lies somewhere between 40 and 70%.

A colleague of mine, Professor Clare Llewellyn at UCL, has a twin cohort called the Gemini study, where shes looked at the role of socioeconomic status on body weight. Shes shown that if you take middle-class families, the heritability of their body weight is roughly around the 40% mark. But you go to households with the lowest socioeconomic class, and the highest levels of food insecurity, suddenly it jumps to 70%.

Genetically, theres no difference between people who are poorer and those who are richer its an accident of birth. But because of your socioeconomic situation, your risk of obesity can jump from 40% to 70%. It shows that if we manage to cure poverty, childhood poverty in particular, we can drop the heritable risk of obesity from 70% to 40% without even touching the biology of the system.

Exercise has been getting a bad rep for its weight loss powers. Is that really deserved? You run a lot: are you doing that to keep trim or for other reasons?In and of itself, exercise is not effective for weight loss. It is in principle possible to lose weight through exercise Tour de France cyclists eat at least 5,000 calories a day and still lose weight during the three-week race. The problem is most of us mere mortals dont exercise anywhere near enough for this to be effective. It is, however, useful for weight maintenance after you have achieved weight loss. So I stay active on my bike and running, to stay fit, but also to maintain my weight.

Why Calories Dont Count by Giles Yeo is published by Orion (14.99). To support the Guardian and Observer order your copy at guardianbookshop.com. Delivery charges may apply

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Giles Yeo: Lets consider the type of food we eat, not fixate on calories - The Guardian

Genetics

The sequencing of genetic material is a powerful conservation tool – The Economist

Jun 15th 2021

IN SEPTEMBER AND October 2000, the carcasses of several northern hairy-nosed wombats and some fragments of intestine were discovered in Australias Epping Forest National Park, apparently left behind by a mystery predator. Cattle farming has shrunk the wombats natural habitat and consequently their population, which reached a low of just 20-30 animals in the 1970s before land-management policies helped push numbers back up to roughly 100 in the early 2000s. By sequencing DNA extracted from the Epping Forest remains, researchers identified six males and one female. But what had slain 6% of the known wombat population?

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Suspicion fell on either dingoes or wild dogs, and the final answer came packaged inside faeces collected in the park. Some yielded the same genetic sequences as the carcasses. They had been left by dingoes. The team had identified their killers, and in 2002 a 20km protective fence was put up around the forest.

Environmental DNA, or eDNA, has emerged as an increasingly popular tool among conservation biologists and land managers, as DNA-sequencing tools have become progressively smaller, faster and cheaper. The field began in the late 1980s, when microbiologists started using it to look for bacteria in rivers and sediment. This had previously involved smearing water or dirt on Petri dishes to grow colonies of the resident microbes and then identifying them under the microscope, based on the shape of the colonies or how they responded to being stained with dye. It was lengthy and error-prone. Extracting DNA from samples instead, and comparing their genetic sequence to reference libraries, was quicker and more reliable.

The same approach was adopted and built upon in the early 2000s by ecologists, who were aware that the animals they studied were constantly shedding DNA in faeces, saliva, blood, scales and sloughed tissue. Gathering and sequencing this material provided valuable information without needing to interact with the animals themselves. The approach found particular favour early on with researchers studying freshwater systems. By simply dipping a test tube into a stream, they could find out if a target species was present and even how abundant it was.

Because trace amounts of DNA can be amplified before sequencing using a method called polymerase chain reaction (PCR, the same method used to detect SARS-CoV-2 in coronavirus testing), eDNA studies can detect species present in low numbersa useful tool for tracking down rare species, or spotting invasive ones before they wreak havoc on a fishery. Other studies have sought evidence that escapees from fish farms were mating with wild populations, potentially eroding them.

DNA from scat, as wild animal droppings are known, can map out food chains without having to capture and kill animals in order to examine the contents of their guts. Killing large or rare species like whales, even for conservation purposes, poses ethical and practical challenges. But whale scat has the great advantage of buoyancy. Finding a turd floating in the middle of the ocean is made easier with the help of dogs that are trained to sniff out the signature smells of excrement belonging to a range of endangered species. DNA in the netted excrement can be analysed to determine what the animal ate, or what bacteria live in its gut.

On land, researchers can use eDNA from faeces, urine or hair to see how populations are interacting. In Malaysia, an ongoing project is focused on whether sub-populations of the Malayan tiger are still connected when deforestation has fragmented their habitat. In Britain eDNA is used to monitor a protected newt. Other projects have begun to show that cells left in footprints in snow can yield enough DNA to identify species and possibly sex.

Several groups are attempting to identify all the individuals belonging to a population from footprint DNA, which would transform monitoring of populations, help with the tracking of animals as they roam across wide areas without the need for radiotags, and setting sustainable hunting quotas. Researchers at the US Forest Service are trying this with wolves.

So-called metagenomic studies use e DNA to map the genetic make-up of entire communities, such as coral reefs, or the vast, largely unexplored bacterial community that lives deep inside the Earths crust and whose biomass is an order of magnitude greater than that of all animals combined. Such studies can offer a genetic snapshot that might take years of field studies to establish.

The field is booming, but there are challenges. It can be difficult to tell when eDNA was deposited. DNA sampled at one point in a river could have come from anywhere upstream. And species identification is only as good as the species-specific genetic barcodes and reference genomes that serve as points of comparison. This has spurred a rush of projects to either identify a unique genetic signature for every species, such as the International Barcode of Life, or sequence the whole genomes of as many species as possible (see chart). The $4.7bn Earth Biogenome Project aims to sequence 1.5m species in ten years. As well as collecting and preserving genomes, such genetic databases can be mined for information on susceptibility to disease, or for potential medicines.

But even though genetic sequencing has become much cheaper since the late 20th century, it remains prohibitively expensive for most researchers outside America, Europe and China. Sequencing technologies are improving rapidly, however. In particular, Oxford Nanopore, a British company, has developed portable technology that allows sequencing to be done in the field, not just in the lab. It relies on nanopore sequencing, a technique in which strands of DNA are drawn through a nanometre-sized pore in a biological membrane. Each of the four letters of the DNA alphabet produces a distinct electrical signal as it passes through the pore, allowing the sequence to be read in real time.

Oxford Nanopores Min ION, a USB-powered, pocket-sized device, allows every part of the sequencing process to be done in the field. Sequences are produced within an hour. The devices are relatively affordable: prices start at around $1,000, though subsequent recharges are needed to run more samples. They have been used to sequence viruses in Brazil, amphibian DNA in Tanzania and bacteria on the International Space Station.

The technology also opens up new possibilities for investigation and enforcement. Genetic sequencing in the field can be used to identify the nature and origin of illegal bushmeat, fish or smuggled ivory. A paper published in Forensic Science International: Genetics in March 2021 compared results obtained by the Min ION with the standard sequencing methods used in wildlife forensics. It found the results to be comparable, potentially paving the way for handheld devices to be used in wildlife-crime prosecutions.

Full contents of this Technology QuarterlyThe other environmental emergency: Loss of biodiversity poses as great a risk to humanity as climate changeSensors and sensibility: All kinds of new technology are being used to monitor the natural world* Cracking the code: The sequencing of genetic material is a powerful conservation toolCrowdsourced science: How volunteer observers can help protect biodiversitySimulating everything: Compared with climate, modelling of ecosystems is at an early stageBack from the dead: Reviving extinct species may soon be possibleBridging the gap: Technology can help conserve biodiversity

This article appeared in the Technology Quarterly section of the print edition under the headline "Cracking the code"

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The sequencing of genetic material is a powerful conservation tool - The Economist

Genetics

The global animal genetics market is projected to reach USD 7.7 billion by 2026 from USD – GlobeNewswire

New York, June 14, 2021 (GLOBE NEWSWIRE) -- Reportlinker.com announces the release of the report "Animal Genetics Market by Products Genetic Testing ) - Global Forecast to 2026" - https://www.reportlinker.com/p06094510/?utm_source=GNW On the other hand, the shortage of skilled professionals in veterinary research, and emergence of alternatives like lab-based meat are some factors restraining market growth.

The live animals accounted for the largest share of the animal genetics market in 2020.Based on products and services, the animal genetics market has been segmented into live animals, genetics materials, and animal genetic testing services.The factors attributing to the large revenue of the live animals segment include the high demand for live animals for breeding purposes.

The introduction of disease-resistant animals has further boosted the demand for live animals, as they are economically viable for owners and increase their profitability.

The market in Asia Pacific is projected to witness the highest growth rate during the forecast period (20212026).Europe accounted for the largest share of the animal genetics market in 2020. Better accessibility to technologies and well-established distribution channels, the growing demand for livestock food products, high intake of animal-derived proteins, and increasing animal welfare activities in the developed countries of Europe and North America account for their larger market shares.

A breakdown of the primary participants referred to for this report is provided below: By Company Type (Supply-side): Tier 1: 25%, Tier 2: 35%, and Tier 3: 40% By Designation: C-level: 20%, Director-level: 55%, and Managers: 25% By Region: North America: 40%, Europe: 25%, Asia-Pacific: 20%, Latin America: 10% and Middle East & Africa: 5%The major players in the animal genetics market include Neogen Corporation (US), Genus (UK), URUS (US), EW Group (Germany), Groupe Grimaud (France), CRV Holding (Netherlands), Topigs Norsvin (Netherlands), Zoetis (US), Envigo (US), Hendix Genetics (Netherlands), Animal Genetics (US), VetGen (US), DanBred (Denmark), Tropical Bovine Genetics (India), Trans Ova Genetics (US), Inguran LLC dba ST Genetics (US), Semex Alliance (Canada), Genetic Veterinary Sciences (US), Cobb-Vantress (US), Milk Source (US), Eurogene AI Services (Ireland).

Research Coverage:The report analyzes the animal genetics market and aims at estimating the market size and future growth potential of this market based on various segments such as product and services, and region. The report also includes competitive analysis of the key players in this market along with their company profiles, product and service offerings, recent developments, and key market strategies.

Reasons to Buy the ReportThe report can help established firms as well as new entrants/smaller firms to gauge the pulse of the market, which, in turn, would help them garner a greater share. Firms purchasing the report could use one, or a combination of the below mentioned five strategies.

This report provides insights into the following pointers: Market Penetration: Comprehensive information on the product portfolios of the top players in the animal genetics market. The report analyzes the market based on the products and services, and region. Product Development/Innovation: Detailed insights on upcoming technologies, research and development activities, and product launches in the animal genetics market. Market Development: Comprehensive information about lucrative emerging markets. The report analyzes the markets for various types of animal genetics solutions across regions. Market Diversification: Exhaustive information about products, untapped regions, recent developments, and investments in the animal genetics market. Competitive Assessment: In-depth assessment of market shares, strategies, products, distribution networks, and manufacturing capabilities of the leading players in the animal genetics markets.Read the full report: https://www.reportlinker.com/p06094510/?utm_source=GNW

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The global animal genetics market is projected to reach USD 7.7 billion by 2026 from USD - GlobeNewswire

Genetics

Rapid Genetic Testing May Have Spared This Baby From Death – MedPage Today

For an infant with seizures, every passing hour risks more harm to the newborn's brain.

That's why this story from Rady Children's Hospital in San Diego is so inspiring, not just for parents and their children, but for doctors and geneticists.

It shows the huge progress since the start of the Human Genome Project 30 years ago, not only in faster sequencing of 3.2 billion base pairs, but the ability to convert that information into a diagnosis. This case, which was published in the New England Journal of Medicine, is one that was easy and inexpensive to treat.

The ordeal began one Sunday night in October 2020 when a frightened couple took their 41-day-old child to Rady's emergency department (ED) because he wouldn't stop crying. The same thing happened to their newborn daughter 10 years earlier, before genetic testing was as advanced. The sister deteriorated rapidly and died before her first birthday. Would her brother have the same dire course?

'This Is Why I Chose Genetics'

"This [baby] is exactly the reason I chose biogenetics," said Anna-Kaisa Niemi, MD, who is both a Rady neonatologist and metabolic geneticist. "You always try to find the defect and the diagnosis and if you do, you're able to start treatment fast. But it's never happened this fast before."

Late that October night, a head CT showed worrisome changes and an MRI revealed concerning white patterns in the infant's basal ganglia. The ED team transferred the baby to the hospital's NICU. When Niemi arrived Monday morning, the child was still crying.

"It wasn't a hungry cry, or 'my diapers are dirty' cry, or even 'I have a broken bone' cry. It was non-stop, inconsolable crying, like something is very wrong in the brain," Niemi told MedPage Today. "I don't want to say scary, but it was very alarming to me. I knew we needed to figure it out right away."

A physical exam revealed downward eye deviation, and the parents disclosed they are first cousins, more hints for a possible genetic abnormality. An electroencephalogram identified brain seizures.

Mallory Owen, MBChB, a pediatric neurologist who then was working with the affiliated Rady Children's Institute for Genomic Medicine (RCIGM), described what happened next.

"We got a call from the [hospital] medical director who said we have a baby in the NICU who I think might really benefit from having this research protocol, 'ultra-ultra' rapid whole genome sequencing," said Owen.

There are some 1,500 genetic diseases associated with epileptic encephalopathy with similar or identical symptoms but very different treatments, Owen said.

To attempt to figure out which one it could be, a blood sample was drawn by 4 p.m. Monday and sequencing began at 7:23 p.m. It was completed by 6:30 a.m. Tuesday, according to a timeline prepared by Owen, lead author of the case report.

By 7:24 a.m. Tuesday, the in-house sequencing process was aided by Rady's partners, Illumina, which has developed DNA PCR-Free Prep, and Alexion Pharmaceuticals, whose scientists helped narrow the list of variants to match the infant's symptoms.

One in a Million

The result, 10 minutes later, revealed the boy had autosomal recessive thiamine metabolism dysfunction, syndrome 2, (THMD2) a defect in the mechanism responsible for transporting thiamine from the blood to the brain. But lucky for him, oral supplements of two over-the-counter vitamins, thiamine and biotin, resolved the problem.

THMD2 is extremely rare, occurring in an estimated one-in-a-million babies, according to the institute's medical director, David Dimmock, MD. It's a two base-pair frameshift, which Owen described as like a line of text in which the last two letters of one word are shifted into the next word, "and suddenly all the words don't make sense because the spaces between the words are in the wrong places."

It is likely that because the mutation is homozygous, the child inherited one copy from his mom and one from his dad, who each had the same mutation because they are related, she said.

By 12:13 p.m. Tuesday, vitamin tablets were crushed, added to liquid in appropriate dosage and administered to the infant through a feeding tube. Six hours later, his crying, seizures and irritability had resolved and as of June 14, have not returned. "The baby looked completely different," said Niemi. "It's unbelievable how fast (the vitamins) worked."

Time will tell if the baby, now 9 months old, will have permanent damage from his first 5 weeks of life. Owen acknowledged some signs of delayed development that could resolve in time, though it's too soon to tell. "No baby with this particular disease has been treated this early," she said.

But without this diagnosis, Owen is confident the boy would follow the path of his sister, who had the same seizures and "basically made no developmental progress from 2 months of age to the time of her death."

RCIGM had been working on developing a way to sequence the entire genome faster for 6 years. At commercial labs nationally, standard whole-genome sequencing can take weeks to identify a culprit sequence variant.

'Ultra-Ultra-Rapid' Sequencing

Like several other genetic projects around the globe, the institute has developed faster techniques: a "rapid" method that takes less than a week and an "ultra-rapid" protocol that averages between 30 and 50 hours. Still experimental, however, is this 13.5-hour process, nicknamed "ultra-ultra-rapid" by the team.

Time is of the essence in newborns, and a week or two delay can be fatal. During that time, the clinician has already administered ineffective treatments that may even have caused harm. "There could already be permanent brain damage, and when that happens, it's irreversible," Owen said.

Marc Williams, MD, president of the American College of Medical Genetics and Genomics, who heard about the case on social media, called Rady's latest sequencing speed "transformative," potentially saving many children from conditions such as intellectual disability or cerebral palsy.

For most hospitals today, if a clinician orders a sequence for a child with a suspected abnormality, it would be sent to an outside laboratory and take anywhere from 1 to 3 weeks to get back, and even then, may not give enough specific information.

"One could argue the difference between 50 hours or 30 hours or 13 hours isn't all that big of a deal," he told MedPage Today. But the bigger deal, he said, is now we have "a child who has a chance at a normal outcome, as opposed to either death or severe disability if we did things the way we've always done them."

Asked if there is a kind of race going on among geneticists to see who can beat the clock, Williams said Rady's team keeps trying to beat itself. "They're pushing the limit to show how fast we can do this, in some ways, like a sprinter who sets a world record, but now says I think I can go faster."

The institute now does sequencing for a network of 60 other children's hospitals in the U.S. and Canada. Since last October, it has performed ultra-ultra-rapid sequencing on two other babies and got a diagnosis for one of them, a rare mitochondrial disease. That case is being written up for publication.

Does Rady see itself as the go-to institute for hospitals with patients suspected of having treatable genetic conditions?

Mallory said that becoming a "center of excellence" for whole genome sequencing is one of its aims, especially for NICU babies. But, she said, "rapid sequencing needs to be something that is not led by a single center. It's a huge project, with huge massive data requirements, and really should be pushed forward by a large assortment of institutions, of which Rady is one."

Rady's ultra-ultra-rapid sequencing is still in the research phase. It was funded by numerous federal grants to its president/CEO, Stephen Kingsmore, MBChB, DSc, and did not cost the family.

Currently, the Rady institute's cost is around $10,000 for standard sequencing, although this varies case by case. When it's ready and has received required approvals, the ultra-ultra-rapid will cost much more.

That's why bills were recently introduced in the U.S. Senate and in the California legislature to cover the cost.

Sen. Susan Collins (R-Maine), introduced S. 2022, the Ending the Diagnostic Odyssey Act, which would give states the option of providing federal matching funds for whole genome sequencing for Medicaid-eligible children with conditions that are suspected of having a genetic cause.

In California, state Assemblymember Brian Maienschein, whose district includes Rady Children's, has introduced AB 114, the Rare Disease Sequencing for Critically Ill Infants Act, which would improve access to rapid whole genome sequencing for Medi-Cal beneficiaries.

Cheryl Clark has been a medical & science journalist for more than three decades.

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Rapid Genetic Testing May Have Spared This Baby From Death - MedPage Today

Genetics

Woman finds her biological father through DNA kit, after decades of searching – wtkr.com

SEAFORD, Va. - This Fathers Day is one to remember for a father-daughter duo who recently met her biological dad, thanks to a 23andMe DNA kit after several years of searching for him.

Adopted at 5-years-old, 43-year-old Julie Lane had always wondered who her biological father was. After more than ten years of searching for her father, she had almost given up.

I always wanted to know. You feel like youre missing a part of who you are, she said.

Julie had tried several things from researching to several genetics companies. She says her dads common name made it hard to track him.

"The information I had, his name, his ex-wifes name, the fact that he was military. I thought surely I can find him. After about ten years, I had kind of given up.

Then her family encouraged her to try something new.

"My husband and best friend pushed me and said why dont you try one more genetic tests before you give up."

Thats when she brought a 23andMe DNA kit as a last resort. To her surprise, she matched with a cousin that led her to what she always wanted, her biological father.

I just didnt expect that when the results came, it to go like it did. It's 8 o clock at night and theyre calling around and saying hey there's this girl on 23andMe and she comes up as a DNA match and she thinks youre her dad, could it be."

Julie's father had been looking for her too.

"I started trying to find her in the mid-80s. It still is overwhelming," Jeff Williams said.

In March, her father drove up from Texas to meet her. She also met her brother JP, whos ten years younger than her. Her dad left her a briefcase full of pictures during the visit.

She says the first time she saw a picture of her brother she recently met, he looked almost identical to her son.

News 3 reached out to 23andMe and they released this statement:

With genetic testing readily available to consumers, we are increasingly hearing stories of families discovering and reuniting with newfound relatives, and of customers finding unexpected results in their reports. Although 23andMe was not designed specifically to help people confirm parentage or find biological parents, our DNA Relatives tool does help people find and connect with participating genetic relatives. This feature is completely optional, meaning customers must actively choose to participate and are informed up front that by using the tool, they may discover unexpected relationships.

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Woman finds her biological father through DNA kit, after decades of searching - wtkr.com

Genetics

Genetic Mutation Reveals Surprising Role of Bioelectricity in Early Brain Formation – SciTechDaily

In polymicrogyria, the cortex of the brain has many irregular, small folds (gyria) and disorganization of its layers, caused by mutations in one of several genes. Many affected children have severe developmental delay, intellectual disabilities, and epilepsy, Credit: Richard Smith/Sebastian Stankiewicz, Boston Childrens Hospital

A mutation in four children with polymicrogyria illuminates the role of bioelectricity in early brain development.

In polymicrogyria, the cortex of the brain has many irregular, small folds (gyria) and disorganization of its layers. Many affected children have severe developmental delay, intellectual disabilities, and epilepsy, and many need to use a wheelchair. Mutations in several different genes can cause this overfolding of the brain condition.

Studying four patients with polymicrogyria, Richard Smith, PhD, identified mutations in a gene that caused him to do a double-take. His curiosity drove him to investigate the role of this gene, called ATP1A3, in the developing brain.

ATP1A3 is critical to many cell biological processes, says Smith, an investigator theDivision of Genetics and GenomicsatBoston Childrens Hospital. Its one of the most important genes we have in our brains.

ATP1A3 encodes a protein that makes up part of a cellular pump. It moves sodium and potassium ions across the cell membrane, allowing our cells to maintain differing concentrations of charged ions on either side, similar to a battery. This difference enables electrical currents to flow into or out of cells, drivingaction potentialsin neurons and other essential cell functions.

For me it was very compelling to understand how these pump proteins, and the flow of ions, contribute to core mechanisms in brain development, says Smith, an electrophysiologist by training. We got a lot of great biological insights by studying these four patients.

When and where in the typical developing brain is ATP1A3 turned on? To answer this question, Smith, with senior investigatorChristopher Walsh, MD, PhDand colleagues at multiple other sites, obtained donated human tissues from several hospital tissue banks and the NIH NeuroBiobank. The investigators analyzed samples from two times in early brain development: at around 20 weeks gestation, when the fetal cortex, initially smooth, starts to fold, and in infants soon after birth.

Using single-cell RNA sequencing (DropSeq) in collaboration withMarta Florio, PhD, at Harvard Medical School, they looked for expression (turning on) of ATP1A3 in about 125,000 individual neurons from 11 areas of the prenatal cortex. They also profiled about 52,000 neurons from the infants, sampling four areas of the cortex.

Overall, ATP1A3 expression levels were highest in the prefrontal cortex at both time points, and highest in the most active, frequently-firing neurons in the cortex. In the fetal cortex, ATP1A3 expression was particularly high in the subplate, a layer that disappears later in development. Electrical activity in the subplate is thought to be a hub of signaling driving synapse formation, neuron migration, and other brain developmental processes.

In the infants, we found increased expression of the gene in interneurons, which are inhibitory, says Smith. We think that ATP1A3 mutations may disrupt the balance of excitation and inhibition in the brain, which could contribute to epilepsy in other ATP1A3-related conditions.

The work, published inPNAS, underscores how research in rare diseases can yield fundamental insights in biology in this case, how the brain develops its contours and organizational pattern. It provides a map for future studies of how mutations in ATP1A3 cause the brain to form abnormally.

When we first published this as a preprint, we had a lot of people reach out to us with patients with overlapping phenotypes, so it is very exciting to better understand this disease, says Smith.

The findings may also inform scientists understanding of other known ATP1A3-related disorders. While the patients with polymicrogyria had severe mutations causing loss of function of the gene, milder mutations cause a spectrum of later-onset neurologic diseases including alternating hemiplegia of childhood, which causes bouts of temporary paralysis; amovement disorderknown as rapid onset dystonia parkinsonism; and childhood-onset schizophrenia. These later-onset disorders may be more amenable to therapeutic intervention.

Polymicrogyria is at the extreme end of severity, but we think that ATP1A3-related disorders in the middle of this spectrum could have early pathogenic roots that could possibly be treated before they become more severe, says Smith.

He adds that ifnewborn DNA sequencingbecomes common, it could offer a window of opportunity for treating ATP1A3 related disorders before they manifest clinically.

As for polymicrogyria, a structural malformation is trickier to reverse, but infant brains are amazingly plastic and capable of reorganizing, says Smith. So if you could lessen the epilepsy-related damage from the earliest point, you might be able to improve quality of life.

Reference: Early role for a Na+,K+-ATPase (ATP1A3) in brain development by Richard S. Smith, Marta Florio, Shyam K. Akula, Jennifer E. Neil, Yidi Wang, R. Sean Hill, Melissa Goldman, Christopher D. Mullally, Nora Reed, Luis Bello-Espinosa, Laura Flores-Sarnat, Fabiola Paoli Monteiro, Casella B. Erasmo, Filippo Pinto e Vairo, Eva Morava, A. James Barkovich, Joseph Gonzalez-Heydrich, Catherine A. Brownstein, Steven A. McCarroll and Christopher A. Walsh, 14 June 2021, Proceedings of the National Academy of Sciences.DOI: 10.1073/pnas.2023333118

Smith is supported by the NIH National Institute of Neurological Disorders and Stroke and the Tommy Fuss Foundation. Walsh is a HHMI Investigator, and receives funding from the Paul Allen Discovery Foundation and the NIH.

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Genetic Mutation Reveals Surprising Role of Bioelectricity in Early Brain Formation - SciTechDaily