What will the $100 genome mean?
In May 2022, Californian biotech Ultima Genomics announced that its UG 100 platform was capable of sequencing an entire human genome for just $100, a landmark moment in the history of the field. The announcement was particularly remarkable because few had previously heard of the company, a relative unknown in an industry long dominated by global giant Illumina which controls about 80 percent of the world’s sequencing market.
Ultima’s secret was to completely revamp many technical aspects of the way Illumina have traditionally deciphered DNA. The process usually involves first splitting the double helix DNA structure into single strands, then breaking these strands into short fragments which are laid out on a glass surface called a flow cell. When this flow cell is loaded into the sequencing machine, color-coded tags are attached to each individual base letter. A laser scans the bases individually while a camera simultaneously records the color associated with them, a process which is repeated until every single fragment has been sequenced.
Instead, Ultima has found a series of shortcuts to slash the cost and boost efficiency. “Ultima Genomics has developed a fundamentally new sequencing architecture designed to scale beyond conventional approaches,” says Josh Lauer, Ultima’s chief commercial officer.
This ‘new architecture’ is a series of subtle but highly impactful tweaks to the sequencing process ranging from replacing the costly flow cell with a silicon wafer which is both cheaper and allows more DNA to be read at once, to utilizing machine learning to convert optical data into usable information.
To put $100 genome in perspective, back in 2012 the cost of sequencing a single genome was around $10,000, a price tag which dropped to $1,000 a few years later. Before Ultima’s announcement, the cost of sequencing an individual genome was around $600.
Several studies have found that nearly 12 percent of healthy people who have their genome sequenced, then discover they have a variant pointing to a heightened risk of developing a disease that can be monitored, treated or prevented.
While Ultima’s new machine is not widely available yet, Illumina’s response has been rapid. In September 2022, the company unveiled the NovaSeq X series, which it describes as its fastest most cost-efficient sequencing platform yet, capable of sequencing genomes at $200, with further price cuts likely to follow.
But what will the rapidly tumbling cost of sequencing actually mean for medicine? “Well to start with, obviously it’s going to mean more people getting their genome sequenced,” says Michael Snyder, professor of genetics at Stanford University. “It'll be a lot more accessible to people.”
At the moment sequencing is mainly limited to certain cancer patients where it is used to inform treatment options, and individuals with undiagnosed illnesses. In the past, initiatives such as SeqFirst have attempted further widen access to genome sequencing based on growing amounts of research illustrating the potential benefits of the technology in healthcare. Several studies have found that nearly 12 percent of healthy people who have their genome sequenced, then discover they have a variant pointing to a heightened risk of developing a disease that can be monitored, treated or prevented.
“While whole genome sequencing is not yet widely used in the U.S., it has started to come into pediatric critical care settings such as newborn intensive care units,” says Professor Michael Bamshad, who heads the genetic medicine division in the University of Washington’s pediatrics department. “It is also being used more often in outpatient clinical genetics services, particularly when conventional testing fails to identify explanatory variants.”
But the cost of sequencing itself is only one part of the price tag. The subsequent clinical interpretation and genetic counselling services often come to several thousand dollars, a cost which insurers are not always willing to pay.
As a result, while Bamshad and others hope that the arrival of the $100 genome will create new opportunities to use genetic testing in innovative ways, the most immediate benefits are likely to come in the realm of research.
Bigger Data
There are numerous ways in which cheaper sequencing is likely to advance scientific research, for example the ability to collect data on much larger patient groups. This will be a major boon to scientists working on complex heterogeneous diseases such as schizophrenia or depression where there are many genes involved which all exert subtle effects, as well as substantial variance across the patient population. Bigger studies could help scientists identify subgroups of patients where the disease appears to be driven by similar gene variants, who can then be more precisely targeted with specific drugs.
If insurers can figure out the economics, Snyder even foresees a future where at a certain age, all of us can qualify for annual sequencing of our blood cells to search for early signs of cancer or the potential onset of other diseases like type 2 diabetes.
David Curtis, a genetics professor at University College London, says that scientists studying these illnesses have previously been forced to rely on genome-wide association studies which are limited because they only identify common gene variants. “We might see a significant increase in the number of large association studies using sequence data,” he says. “It would be far preferable to use this because it provides information about rare, potentially functional variants.”
Cheaper sequencing will also aid researchers working on diseases which have traditionally been underfunded. Bamshad cites cystic fibrosis, a condition which affects around 40,000 children and adults in the U.S., as one particularly pertinent example.
“Funds for gene discovery for rare diseases are very limited,” he says. “We’re one of three sites that did whole genome sequencing on 5,500 people with cystic fibrosis, but our statistical power is limited. A $100 genome would make it much more feasible to sequence everyone in the U.S. with cystic fibrosis and make it more likely that we discover novel risk factors and pathways influencing clinical outcomes.”
For progressive diseases that are more common like cancer and type 2 diabetes, as well as neurodegenerative conditions like multiple sclerosis and ALS, geneticists will be able to go even further and afford to sequence individual tumor cells or neurons at different time points. This will enable them to analyze how individual DNA modifications like methylation, change as the disease develops.
In the case of cancer, this could help scientists understand how tumors evolve to evade treatments. Within in a clinical setting, the ability to sequence not just one, but many different cells across a patient’s tumor could point to the combination of treatments which offer the best chance of eradicating the entire cancer.
“What happens at the moment with a solid tumor is you treat with one drug, and maybe 80 percent of that tumor is susceptible to that drug,” says Neil Ward, vice president and general manager in the EMEA region for genomics company PacBio. “But the other 20 percent of the tumor has already got mutations that make it resistant, which is probably why a lot of modern therapies extend life for sadly only a matter of months rather than curing, because they treat a big percentage of the tumor, but not the whole thing. So going forwards, I think that we will see genomics play a huge role in cancer treatments, through using multiple modalities to treat someone's cancer.”
If insurers can figure out the economics, Snyder even foresees a future where at a certain age, all of us can qualify for annual sequencing of our blood cells to search for early signs of cancer or the potential onset of other diseases like type 2 diabetes.
“There are companies already working on looking for cancer signatures in methylated DNA,” he says. “If it was determined that you had early stage cancer, pre-symptomatically, that could then be validated with targeted MRI, followed by surgery or chemotherapy. It makes a big difference catching cancer early. If there were signs of type 2 diabetes, you could start taking steps to mitigate your glucose rise, and possibly prevent it or at least delay the onset.”
This would already revolutionize the way we seek to prevent a whole range of illnesses, but others feel that the $100 genome could also usher in even more powerful and controversial preventative medicine schemes.
Newborn screening
In the eyes of Kári Stefánsson, the Icelandic neurologist who been a visionary for so many advances in the field of human genetics over the last 25 years, the falling cost of sequencing means it will be feasible to sequence the genomes of every baby born.
“We have recently done an analysis of genomes in Iceland and the UK Biobank, and in 4 percent of people you find mutations that lead to serious disease, that can be prevented or dealt with,” says Stefansson, CEO of deCODE genetics, a subsidiary of the pharmaceutical company Amgen. “This could transform our healthcare systems.”
As well as identifying newborns with rare diseases, this kind of genomic information could be used to compute a person’s risk score for developing chronic illnesses later in life. If for example, they have a higher than average risk of colon or breast cancer, they could be pre-emptively scheduled for annual colonoscopies or mammograms as soon as they hit adulthood.
To a limited extent, this is already happening. In the UK, Genomics England has launched the Newborn Genomes Programme, which plans to undertake whole-genome sequencing of up to 200,000 newborn babies, with the aim of enabling the early identification of rare genetic diseases.
"I have not had my own genome sequenced and I would not have wanted my parents to have agreed to this," Curtis says. "I don’t see that sequencing children for the sake of some vague, ill-defined benefits could ever be justifiable.”
However, some scientists feel that it is tricky to justify sequencing the genomes of apparently healthy babies, given the data privacy issues involved. They point out that we still know too little about the links which can be drawn between genetic information at birth, and risk of chronic illness later in life.
“I think there are very difficult ethical issues involved in sequencing children if there are no clear and immediate clinical benefits,” says Curtis. “They cannot consent to this process. I have not had my own genome sequenced and I would not have wanted my parents to have agreed to this. I don’t see that sequencing children for the sake of some vague, ill-defined benefits could ever be justifiable.”
Curtis points out that there are many inherent risks about this data being available. It may fall into the hands of insurance companies, and it could even be used by governments for surveillance purposes.
“Genetic sequence data is very useful indeed for forensic purposes. Its full potential has yet to be realized but identifying rare variants could provide a quick and easy way to find relatives of a perpetrator,” he says. “If large numbers of people had been sequenced in a healthcare system then it could be difficult for a future government to resist the temptation to use this as a resource to investigate serious crimes.”
While sequencing becoming more widely available will present difficult ethical and moral challenges, it will offer many benefits for society as a whole. Cheaper sequencing will help boost the diversity of genomic datasets which have traditionally been skewed towards individuals of white, European descent, meaning that much of the actionable medical information which has come out of these studies is not relevant to people of other ethnicities.
Ward predicts that in the coming years, the growing amount of genetic information will ultimately change the outcomes for many with rare, previously incurable illnesses.
“If you're the parent of a child that has a susceptible or a suspected rare genetic disease, their genome will get sequenced, and while sadly that doesn’t always lead to treatments, it’s building up a knowledge base so companies can spring up and target that niche of a disease,” he says. “As a result there’s a whole tidal wave of new therapies that are going to come to market over the next five years, as the genetic tools we have, mature and evolve.”
This article was first published by Leaps.org in October 2022.
The Friday Five: An mRNA vaccine works against cancer, new research suggests
The Friday Five covers five stories in research that you may have missed this week. There are plenty of controversies and troubling ethical issues in science – and we get into many of them in our online magazine – but this news roundup focuses on scientific creativity and progress to give you a therapeutic dose of inspiration headed into the weekend.
Listen on Apple | Listen on Spotify | Listen on Stitcher | Listen on Amazon | Listen on Google
Here are the promising studies covered in this week's Friday Five:
- An mRNA vaccine that works against cancer
- These cameras inside the body have an unusual source of power
- A new theory for what causes aging
- Can bacteria make you excited to work out?
- Why women get Alzheimer's more often than men
Last minute holiday gifts for the bio-inspired
“Merry Christmas! Isn’t it fun to say Merry Christmas to everyone? Time for a party and presents and things that make children happy and give their hearts wings!” go the lyrics of the popular Christmas poem. But adults (of various religions) need their gifts this time of year, too. For the biologically inspired big children, the process of finding the right fit can be daunting. To inform your choices in both conventional and unconventional ways, Leaps.org is presenting a roundup of the coolest bio-products related to health, nutrition, gaming, lifestyle and more.
AYO Circadian Light Therapy Wearable
We don’t hear it tick, but we have our own clock inside our body–more precisely, circadian clocks. Our cells contain tiny molecular clocks that keep track of our circadian rhythms, or our sleep and metabolism pattern and activity levels, on a daily basis. Chronic circadian disruptions can lead to sleep disorders, poor energy levels, weight gain, lousy mood, and sped-up aging, as well as increased risk for every “modern” disease out there, from diabetes to cancer.
Now, high-tech glasses have been developed that attempt to mimic the benefits of sunlight. In the morning and afternoon, these glasses shed blue light into your eyes to stimulate the master clock at the base of your brain for less drowsiness. The technology's design draws from an area of research, chronobiology, that received a Nobel Prize in 2017 and has become increasingly active in recent years.
“We have been developing and testing the AYO Circadian Health solution for the past five years in collaboration with some of the world's leading experts and researchers in chronobiology, light therapy and health,” said Alexander Dimitrov, co-creator of AYO. “We have done studies with over 25,000 participants, and over one million light sessions,” Dimotrov continued, partnering with institutions such as Mount Sinai Hospital, City of Hope and the U.S. Department of Defense.
The technology could fundamentally reshape the way we view sleep, health and our daily calendars. And, when connecting to a mobile app, the glasses could minimize circadian disruptions for travelers between conflicting time zones.
($269)
myDNAge Test
It's not easy for many people to break free of their attachment to the concept of chronological age, which counts years by how many times we’ve circled the sun since the day we were born. Society lumps us all into one age bracket according to our date of birth but, lately, research is suggesting that we should do some serious deconditioning. According to these studies, the more accurate measure is your biological age, a measurement based on various biomarkers of the body’s overall health and resilience, regardless of your calendar age.
If you want to find out your “true” biological age, myDNAge is a test that focuses on epigenetics, or patterns of changes in DNA methylation, with some initial research pointing to its accuracy. It offers a snapshot of your epigenetic age as well as key biomarkers related to your metabolism, risk of Alzheimer's and more, according to Xiaojing Yang, group leader of epigenetics at myDNAge. “You can perform tests six to 12 months [apart] to track the impact of lifestyle changes,” Yang said. The kit could be a useful tool both for citizen scientists and biohacking veterans.
($299 for one kit–Use code NEWYEARNEWME to receive 50% off a second kit)
Prairie Sky Yak Cheese
Do you love cheese? Do you love exotic cheese? Do you have an interest in preserving biological and genetic diversity? If you answered yes to all three questions, yak cheese was made for you. This type of cheese typically comes from a free-range yak living 13,000 feet above surface level in the Tibetan Himalayas, a relative of the endangered Wild yak. (North America is home to at least 5,000 registered yaks.)
“When I learned that we had a piece of rare biodiversity to be preserved for future generations, I realized that the yak in North America needed a job,” said Nicole Geijer Porter, president of World Heritage Yak Conservancy (WHYC), an organization formed to protect heritage yak “If an animal cannot be beneficial to the rancher in some way, exclusively as pets and lawn ornaments, they will go extinct. Raised for meat they are often hybridized with cattle to grow bigger and faster, so they will also go extinct,” said Porter, an epigeneticist turned yak herder.
Each slice of cheese and piece of butter supports the genetic testing and tracking of Tibetan yak. (You can become a member of WHYC through the Adopt-A-Yak program). “This project is also of biological importance because of the low methane emission research on yak, and the high nutritional content of the milk and cheese,” said Porter.
As for flavor, the Prairie Sky Yak Gruyere is a semi-hard cheese with a nutty taste sometimes compared to chocolate; Tomme de Savoie is a semi-soft Alpine cheese reminiscent of a washed rind muenster; and the Yak Cheddar is made with yak milk following the classic English recipe from Wells Cathedral, with earthly and pungent flavors.
(Various prices; $59.95 for the Three Yak Cheese Flight Gift Box, $139.95 for the Regional Himalayan Yak Cheddar Gift Basket and more)
Bite Toothpaste Bits
The price of a healthy smile is steep. Each year over one billion plastic toothpaste tubes are thrown out, over 50 Empire State Buildings worth of these tubes end up in landfills or oceans, and many animals suffer and die each year in cruel tests for improving oral care in people.
Sustainable oral care is both an act of self-love and giving back to the environment. Bite is a toothpaste that boasts about its green practices for a reason: it uses recyclable glass bottles with aluminum lids that break down into sand after they’ve been used. For shipping, Bite uses kraft envelopes padded with recycled and compostable newspapers, and its boxes are made of fully recycled, corrugated cardboard and sealed with paper tape. Bite refills come in 100% home compostable pouches every four months (still no plastic).
Sustainability aside, there may be an element of fun to Bite – as you brush, a mint foam forms “like magic,” the company claims.
Fractional Laser Treatment for Skin
The environment is hard on our skin: from ultraviolet rays to pollution, a constant oxidative war is waged upon it, leading to loss of collagen and damage to the barrier function of the skin. A fractional laser treatment is a type of laser skin resurfacing procedure that essentially traumatizes the skin – in a good way - through subjecting a small area of it to tiny amounts of laser energy. The laser penetrates the second layer of skin, the dermis, leading to skin exfoliation, which stimulates collagen and elastin production.
The treatment may help with soothing acne scarring, correcting uneven skin tone and texture, and reducing wrinkles and fine lines, sun damage and age spots. Recent research suggests the fractional laser can help with improving skin elasticity and reducing the amount and depth of wrinkles, though there’s little to no evidence for any benefits for eyebags, dark circles, discolorations within the eye area and water retention.
(Typically, a single fractional laser treatment costs $750 for a small area, $1500 for a full facial treatment, and $2000 for full face.)
Gadgets and Apps to Measure Your Heart Rate Variability
Heart rate variability may sound like a condition that requires immediate medical treatment, but the more you have of it, the better for your health. Although you may think of the heart as a steadily beating metronome, there are actually small differences in the amount of time between each beat. These differences are called HRV, and having more HRV has been linked to better fitness and fewer diseases.
HRV is easy to measure with a range of gadgets on the market, including Fitbits and Oura Rings. Which product floats your boat is a matter of personal preference, but the Polar H10 chest strap offers some advantages. For example, you can measure your HRV with the Polar H10 while walking around, unlike some devices that require you to stay still while taking a reading.
Plus, the Polar sensor pairs with free apps such as Elite HRV that are great for tracking how your HRV changes over time. "HRV really helps you gauge if you're moving in a positive or negative direction" with your health, says Jason Moore, the CEO and founder of Elite HRV and Spren. Have fun experimenting over the holidays with different lifestyle habits that are associated with higher HRV, some studies show, such as intermittent fasting, regular exercise and just getting more sleep.
($89 for the Polar H10, $0 for the Elite HRV app)
FoodMarble AIRE2
Its predecessor, FOODMarble AIRE1 was a pocket-size breath-testing device that measured hydrogen on the breath. More hydrogen means less digestion, and the AIRE1 used advanced breathalyzer technology to figure out what exactly is going on with the gut. Now, the company has launched FoodMarble AIRE2, which also measures methane alongside with hydrogen. High levels of methane in the body may cause abdominal pain, bloating and constipation, cirrhosis of the liver and chronic pancreatitis. The AIRE2 also comes with haptic feedback to make it easier to use.
Research suggests that these breath tests are valid as at-home diagnostic tools for many digestive conditions. To get the most accurate results, though, it’s important to closely follow the recommended protocol - for example, you can’t eat or drink anything for 10 to 12 hours before the test.
($229)
Adventurist Backpack’s Classic Backpack
The Classic backpack is a perfect option for life science aficionados who enjoy getting outside and exploring in nature. Padding in the front and back provides extra protection for camera gear, laptop, and other electronics, and it's completely water-resistant so you can get outside in winter weather.
Nobility points: Adventurist Backpack Co. is partnered with national non-profit Feeding America, and every backpack sold helps provide 25 meals to families in need across the U.S.
($65)
This Saves Lives
Speaking of nobility points, you could load your new backpack with a food choice that helps feed others as well. In 2013, actors Kristin Bell, Ryan Devlin, Ravi Patel and Todd Grinnell teamed up to start This Saves Lives, which makes power bars full of vitamins and nutrients, and the company has a unique business model: for every bar you buy, a packet of food is sent to a child in need. In addition to offering essential nutrients, the bars are non-GMO, kosher and gluten-free. Note: This Saves Lives is owned by the same company, GOOD Worldwide, that owns Leaps.org.
(Wild Blueberry & Pistachio bars, $23.99)
NADI X Pants
Even if you’re a yoga zealot enjoying the benefits to your strength, balance and flexibility, chances are you're performing the movements sort of askew. Wearable technology wants to improve your yoga posture and these sleek yoga pants called NADI X have subtle electronic sensors that track how you place your hands, rotate your hips, and align your back. The leggings use haptic feedback (or vibrations on your skin) to slowly guide you into correct alignment. You can also combine the wearable with an app that contains 40 poses and fitting music. Even if you aren't into yoga, you could use the pants for a perfect stretching session. If you do use it for yoga poses, the pants will “speak” to you, letting out a soothing "om" sound once everything is perfect.
Meta Quest Pro VR headset
When it comes to perfecting virtual reality (VR), the Meta Quest Pro VR headset is one step ahead the rest. In a vibrant 3D virtual space, your Meta avatar has the ability to translate your real-life facial expressions into the virtual realm so the experience can feel more personal, while controllers track your movement and use haptic feedback to translate your hand gestures and finger actions into VR as well. Unlike its Quest 2 headset, Meta markets this Quest Pro headset, which was just released in October, as a great tool for work and business meetings, but you can also use it to play games, watch movies, or download fitness apps or mental-health related apps – some of which are designed to help you get boxing workouts with long-distance friends, fight your fear of heights or meditate in outer space.
Rouge Sur Mesure Custom Lip Color Creator
Beauty and artificial intelligence (AI) complement each other well in the new Yves Saint Laurent lip personalized color – which wants to put the final nail on the coffin of generic lipsticks. This is a lipstick printer at its core. You pair a device to your smartphone and then insert three lipstick cartridges into the base, each of which comes with a color palette (all four could create up to 4,000 lipstick shades). Particularly charming is the fact that you can take a photo of your outfit, and the app will suggest shades that match or clash it.
($299, cartridges $89 each)
Dairy-Free Cream Cheese and Meatless Breakfast Patties
On the environmental front again, meatless patties and dairy-free cream cheese constitute conscientious and delicious choices for vegans, vegetarians and pretty much anyone else. Chicago-based Nature's Fynd is worth checking out. It uses a microbe named Fusarium strain flavolapis, which has origins in an acidic hot spring at Yellowstone National Park.
“We use this remarkable microbe to grow Fy — a nutritional fungi protein that’s made into a wide variety of delicious and sustainable foods,” says Karuna Rawal, Nature’s Fynd CMO. Fy is grown via a breakthrough fermentation process using a fraction of the water, land, and energy compared to traditional protein sources.
It’s a sustainable way to grow food for Earth’s population,” but Nature’s Fynd isn’t just concentrating on Earth. The company recently partnered with NASA to send Fy to space. “As long as there’s an appropriately controlled environment, we can grow Fy anytime, anywhere. It could be a nutritious food source for astronauts on deep space missions," said Rawal.
CBD Oil
Biologically curious people may be especially interested in trying cannabinoid (CBD) oil. CBD is a natural and safe substance found in cannabis, which has been found to tackle anxiety and depression, reduce symptoms of post-traumatic stress disorder, help manage chronic pain and migraines, improve sleep patterns, and keep panic attacks at bay. Kanibi’s Isolate CBD Oil Tincture is a good choice as it is cinnamon-flavored and made in an FDA-inspected facility.
($109--25% off on your first order)
Govee RGBIC Floor Lamp
Another winner for anyone who's been hearing about the health benefits of obeying your circadian rhythms: "RGB" lights, or red-green-blue lights that can be operated by remote control to shine bright blue light during the day and then, with a few touches of your phone, bathe you in warmer, red light to get you ready for bed. Look for RGB bulbs to stick into the light fixtures you already have, or you could opt for the Govee floor lamp that syncs with an app on your phone (or Alexa) for circadian color changing. You can also put it on party mode and watch it shift across 16 million color shades in response to the rhythms and beats of Cuddle Up, Cozy Down Christmas and Hanukkah Oh Hanukkah.
($99)
PackPoint
If you suffer from packing anxiety (or incompetence), an app may take away the pain. PackPoint is an app that builds your packing list according to trip type, activities and weather. You add your trip details, select activities (fancy dinner, business meeting, or even workout are some examples), and PackPoint tells you what you need to bring to your destination. The app is free, but upgrading to Premium for a small fee lets you add your own activities and packing list items.
(Free, Premium Package $2.99)
Eternity Rose
Roses symbolize love, passion, innocence, friendship, and the disarming power of natural beauty. They wilt fast, though, and their spectacle is an unsettling reminder of the fragility of beauty and existence. Unless you dip the rose in 24 karat gold.
The Eternity Rose is put through an intricate three-month process of electroplating, or coating the rose with copper and then with other metals in micro-thin layers. You won’t have to see your flowers sag after a few days because these roses never die. The glitter of gold atop the natural rose (or platinum or silver–whatever you prefer) will fit right in with the Christmas Eve ambiance.
($169 for the gold rose)