Read Your DNA Story
“After 19 years of not knowing anything, and then just from spitting in a tube, I have a pile of information all about me.” “I am so grateful for the opportunity to finally have confirmation of my history.” “I have never had anyone look like me…It’s just great to find out who I am.” Well, as thrilling and amazing as these testimonies sound, understanding and decoding DNAs is the most exciting scientific discovery of all time. People have spent decades together trying to track down their lost genetic ancestry or loved ones for many years. Thanks to the “secret code” in all of us! Individuals can today get easy and affordable access to their genetic information and this is made possible by 23andMe. With an aim to help people access, understand, and benefit from the human genome, they generate the data that not only reveals ancestry insights but also enables groundbreaking research and innovative products.
“For a little bit of spit and a few hundred dollars, we can check out genetic predictions for traits we already know we have—perhaps blonde hair or blue eyes—as well as susceptibilities for diseases we may have yet to develop, such as cancer or diabetes,” notes Anne Wojcicki, the pioneer woman renowned for bringing genome mapping to the common man for tracking linage as well as medical treatment. Through her company, Anne has built one of the world’s largest databases of individual genetic information. Its novel, web-based research approach allows for the rapid recruitment of participants to many genome-wide association studies at once, reducing the time and money needed to make new discoveries, and the company has created a proven and standardized resource for finding new genetic association and confirming genetic loci discovered by others. “In a world where health is poorly understood, we use data to better understand wellness and disease. We bring science to our customers and help them use it in meaningful ways.”
As Simple As Spitting
Primarily, the company offers two Personal Genetic Services: Health + Ancestry and Ancestry. Both services require submitting a saliva sample using 23andMe’s saliva collection kit that is then sent to the lab for analysis. The Health + Ancestry Service provides insights on one’s health predispositions, carrier status, traits, wellness, and ancestry. This is done through analyzing, compiling, and distilling the information extracted from one’s DNA into 125+ reports that customers can access online and share with family and friends. This Ancestry Service helps to understand who one is, where his/her DNA comes from and his/her family story. This DNA information is then entered into the reports of 23andMe services: Ancestry Composition, Ancestry Detail Reports, Maternal & Paternal Haplogroups, Neanderthal Ancestry, DNA Family, and DNA Relatives to retrieve results. Upon receiving the sample, the company’s CLIA-certified lab extracts DNA from cells in the saliva sample and processes the DNA on a genotyping chip that reads hundreds of thousands of locations in the genome. Eventually, the genetic data is analyzed, and personalized reports are generated based on well-established scientific and medical research.
Betty’s Birthday Wish
Betty Jeannotte’s only wish when she turned 100 was to learn about her ancestry. “Years and years ago, I’d done a little research, but I never got very far,” she said. “And I was curious.” She got a 23andMe kit and a chance to work with a genealogist to find out a little bit more about her ancestry. He found 7 generations of her maternal family. The information added another layer to what she already knew. Her 23andMe Ancestry Composition showed she’s about 80 percent English and Irish with a little bit of German in the mix. That reflects accurately with what she knows about her parents’ family histories. Her mom was “of Yankee stock,” while her dad, who had been a vaudeville magician, was a Bostonian whose family originally came from Ireland.
For 23andMe, the mission is about transforming lives. They are keen to provide more regions, more connections and more ways to help people like Betty know their DNA story. Some ancestry services are records-based, which means that the data can be retrieved from historical records such as birth, death and marriage certificates, to trace a lineage. 23andMe offers genetics-based ancestry reports and tools, which means that they analyze a DNA to trace one’s lineage and learn about his/her ancestral origin through 23andMe Ancestry Composition.
Trace. Discover. Connect
Furthermore, 23andMe’s unique service, Haplogroups provides reports on one’s maternal and paternal lineage by identifying their haplogroups. A haplogroup can trace part of his/her ancestry back to a specific group of individuals in the distant past. This helps in understanding how the migration of one’s DNA tells the story of their ancestors. Alongside, one can explore genetic similarities and differences between themselves and their relatives using Share and Compare service.
“We can even point to specific Neanderthal DNA that is associated with traits that you might have, like height and back hair,” points out Anne. Even though Neanderthals vanished about 40,000 years ago, their DNA lives on. Research tells us that they interbred with humans around 60,000 years ago. 23andMe can tell how much of one’s DNA is derived from Neanderthals and how that compares to others. Moreover, 23andMe’s DNA Relative Finder helps in connecting with people who share DNA with you and message them. This enables them to meet relatives—maybe even hear new family stories, share photos and get a better understanding of their family’s’ history.
Making an Impact
Over the years, Anne’s determination and power has shocked the scientific world. As a part of her mission to change healthcare through empowering their consumers, her company also conducts its own research to try to identify new therapies for both common and rare diseases. “I am obsessed with bringing the consumer voice to healthcare.” To further this effort, 23andMe’s genetic research gives everyday people the opportunity to make a difference by participating in a new kind of research—online, from anywhere. Once participants answer online survey questions, researchers link their genetic data to study topics from ancestry, to traits, to disease. These contributions help drive scientific discoveries. On average, a customer who chooses to opt into research contributes to over 230 studies on topics that range from Parkinson’s disease to lupus to asthma and more. “With the help of our 23andMe community, we believe we can accelerate research and make an impact with our genetic data.” Alongside, all researches are governed by an Institutional Review Board (IRB). The IRB is an independent ethics panel that ensures all research is conducted in accordance with government and ethical guidelines.
For 23andMe, genetics is personal! This has in fact impacted many lives, over the years, by giving people a chance to “find family and answers”, “reveal ancestry”, “strengthen family bonds”, and “get a stronger sense of their self.” Anne calls this, “democratizing personal genetics and making it more accessible,” as she is considers each life story a pathway to connect to humanity and improve the world.
Viruses: Biological versus Computer
By Mark Webb-Johnson, Chief Technology Officer of Network Box
During this time of the COVID-19 pandemic, those of us working with computer viruses continue to be amazed at the similarities between the techniques used by the medical community to fight SARS-CoV-2 (the virus that causes the COVID-19 disease) and the processes involved in our electronic anti-virus systems. Let’s look at some of these similarities, and see how computer anti-virus researchers help protect.
By Mark Webb-Johnson, Chief Technology Officer of Network Box
What is the Virus?
SARS-CoV-2 is an RNA virus. Essentially, a strand of information wrapped up in a protective shell and a mechanism to infect cells – information, envelope, infection mechanism.
By comparison, a computer virus consists of the payload, a carrier, and an exploit mechanism. For example, the payload would be the malicious code, the carrier an email message, and the exploit mechanism something to take advantage of a vulnerability in a particular mail client. Another example would be script downloaded from a web page, taking advantage of a web browser exploit.
The virus’s primary purpose is to replicate – to make copies of itself. SARS-CoV-2 does this by infecting cells (in the lungs, stomach, and other areas of the human body), then using the cell’s own mechanisms to make copies of its RNA and make new virus particles.
Computer viruses have the same primary purpose of replication. They want to infect as many hosts as possible. Once in a computer system, they make multiple copies of themselves and transmit out to new hosts. It is this self-replication capability that defines this as a virus.
Identification and Testing
The gold standard for identifying viruses is the whole genome sequence. This maps the full sequence of the chemical components of the RNA (made up adenine, uracil, guanine, and cytosine; abbreviated as A, U, G, and C), and results in a very long string of these four letters. That is excellent for precise identification, but not so good for testing. Due to mutations, what we know of as SARS-CoV-2 is actually a collection of hundreds of different strains of the same fundamental virus, each with their own slightly different sequences (more on this later).
To test for the virus, researchers instead concentrate on relatively small portions of the full sequence. This way, they can extract samples from a potentially infected human, amplify the RNA in the sample to obtain enough to test with, and then compare that against the portion of the full sequence. That is the RT-PCR test.
Computer virus researchers work similarly. The payload of the virus itself is a sequence of computer code that can be expressed in binary, or more commonly in hexadecimal notation. Computer viruses are often intentionally self-encrypted and randomized (we call these polymorphic viruses) to avoid whole sequence detection. Nowadays, these are by far the most common form of computer virus seen.
Researchers extract portions of the sequence that don’t change and use pattern matching techniques to detect those partial sequences in suspicious samples. We call these ‘signatures,’ and they can be effectively used to detect known viruses in suspicious samples.
Immune Response and Vaccination
The human immune system has a component known as the ‘adaptive’ immune system. The system works by identifying portions of viruses already in the body, and creating antigen-specific cells designed to identify, remember, and attack that specific antigen. These cells protect against future infections of the same virus and can survive in the body for some time (months, or years, typically). This is why after you’ve had the measles once, for example, you usually don’t get it again. Vaccinations work by purposely injecting the body with antigens that will generate such an adaptive immune response, to protect you from future specific infections.
Computer anti-virus systems store databases of signatures of known viruses. When your computer receives a new file, it can scan it, look for a match against those signatures, and take action if a match is found (quarantine, etc.). Such signature-based systems are the computer equivalent to the body’s adaptive immune system.
Innate Immune Response
Another component in the human immune system is known as ‘innate.’ This system can detect what is not ‘you’ (what is ‘foreign’) and attack the invader. It relies on the antigen’s chemical properties and doesn’t need to have previously seen that specific antigen.
For computer anti-virus, this is extremely hard to achieve well. The capability to detect and block previously unknown viruses is what differentiates good anti-virus systems from the poor. Various techniques are used, but mostly revolve around a) decoding the virus code to the rawest form, b) detecting suspicious encoding or exploit behavior, and c) using emulation or sandboxing techniques to see what the virus does when executed. Looking at behavior, rather than code sequences.
Mutations and the Future
RNA viruses such as SARS-CoV-2 are very poor at accurate replication, and sometimes the copies made are not perfect. Base pairs get flipped. Portions of the sequence are lost. Parts of other viruses are incorporated. Before long, you are dealing with bad copies of bad copies of a bad copy. It is like the story of a million monkeys with a million typewriters, eventually producing the works of William Shakespeare. Sometimes these viral mutations are beneficial to the virus, but most often not. Whatever the outcome, these mutations are the way the virus adapts to further its goal of replication.
Thankfully, we do not see the same with computer viruses. A computer virus can and does make perfect copies of itself, 100% of the time. Sure, we have self-encrypting polymorphic computer viruses, and randomizing fragments are often introduced, but the core code of the virus is not changed, and certainly not randomly. Perhaps in time, we will see this, but with today’s non-forgiving computer CPU architectures, it is unlikely to be a successful approach.
Of course, given enough monkeys and enough typewriters, anything is possible. Perhaps they can even improve on Shakespeare. Before that day comes, however, make sure you are prepared. Subscribe to a Managed Security Services Provider (MSSP) that can adapt, and protect you from cyber threats.
AI to help kids struggling with ADHD, PDD-NOS
Stephane Bourles, CIO, Brain Balance
AI to help kids struggling with ADHD, Autism, Asperger Syndrome , PDD-NOS and other ASD’s
Left Brain or Right Brain?
In a properly functioning brain, both hemispheres communicate equally and at lightning speed, millions of times per minute. In a poorly functioning brain, the left and right sides of the brain only impart partial information, causing frequent miscommunication. This is called Functional Disconnection and is the root of many types of learning, behavioral and social problems found in children. The Brain Balance program puts the left and right brains back in sync using sensory motor exercises, academic skill building, and nutrition guidelines.
How does the Assessment Work?
The assessment consists of sensory, motor, and academic testing of more than 900 functions. The outcome of this assessment is a highly customized report providing parents with a complete understanding of their child’s behavioral, social, and academic skill levels.
We use AI to determine which brain hemisphere we believe to be stronger or weaker. The Machine Learning algorithm used for the assessment is not always accurate, which we know based on the feedback from our staff—yes we let them disagree with the system, which is intended as a tool to help them support their own assessment, but not to necessarily force them into a decision they don’t agree with.
But as valuable as an individual observation based on years of experience is, it still remains just the view of one individual. That is why we look at Artificial Intelligence as a new solution combining neural network architectures with massive computing power to enable our solution to learn a pattern from large datasets and make statistical predictions based on test results and feedback we already have for tens of thousands of students.
What is next?
Thanks to many product releases with different Machine Learning models we tested, we were able to improve our assessment accuracy and achieve precision, recall and F1 scores over 0.95. The limitation of this AI model is it is not 100% accurate and you don’t know for sure the source of truth. Since AI is a “black box” which can’t explain its prediction for most models, you have to trust your staff first.
Similar to clinical decision support systems helping healthcare practitioners, we believe this fast growing dataset about children, combined with new Artificial Intelligence models such as Explainable AI, will help our staff improve a child’s initial assessment, which will then improve our overall program’s results.
The importance of information to empower health-app users
Liz Ashall-Payne, CEO, ORCHA
Shining a light between the rock and the hard place: The importance of information to empower health-app users
Apps, and their use for the promotion of health and wellbeing, are the subject of increasing interest and enquiry; particularly in light of the NHS’ Long Term Plan, and ever-increasing pressures on scarce NHS resources. But finding and downloading effective, engaging, and most importantly, safe health-apps, is a significant challenge. While many have suggested that health-apps could be a ‘silver-bullet’, aimed at quashing the woes that stem from decreasing funding and increasing demand for incumbent NHS services, it is important to tread with caution.
Unlike pharmaceuticals, over the counter remedies, talking therapies, physiotherapy or surgery, health-apps can not only be sought, but readily obtained in absence of gatekeeping and safeguarding. The result is that you or I can download upwards of 200,000 health-apps today, with as little as a click of a button on the app-store. While this can be argued as the unique value-proposition of app-based health technologies, a lack of guarantees regarding the quality and content of such apps, means that this open-access feature of apps also represents the chief concern; and is likely limiting the enthusiasm with which healthcare professionals engage and promote their use.
The number of apps labelled as ‘pranks’ or for ‘illustration purposes only’ has been subject to year-on-year growth. But for those looking for convenient, easily accessible, and often cost-free support; or for those who are either vulnerable or impressionable; such technologies can pose significant health risks, beyond those that are apparent and conveyed (if at all) in the short description within the app store. An app that misleadingly claims to monitor blood pressure or blood sugar for example, may result in either (1) misleading information, (2) modifications to disease management not representative of true disease status (including the use of insulin or warfarin), or (3) serious adverse events including hypoglycaemia or stroke. One such app for monitoring blood pressure has been downloaded upwards of 1,000,000 times on the Android Google Play app store, while boasting a review rating of 4.3/5.
This raises questions regarding the utility of both the subjective user review score (which is inherently limited in only capturing both very positive or very negative views) and the number of prior downloads of an app, as potential surrogates for app quality. Recent research into apps targeted at chronic insomnia disorder conducted by the Organisation for the Review of Care and Health Applications (ORCHA) confirmed this. In this analysis, which is now available in the journal BMJ: Evidence-Based Mental Health, it was demonstrated that both user review scores, and the number of prior downloads of a health-app, were not only unreliable as proxies for quality, but in fact were inversely related; and as these metrics increased, the objectively measured quality of apps decreased (as assessed by presence of clinical evidence, data privacy policies etc.) This has left a considerable void regarding where reliable indicators of the safety and quality of app-based health technologies can be found, something which at least in part, has been tackled by the National Health Service (NHS).
Courtesy of the NHS’s digital assessment questionnaire (DAQ), and the NHS apps library (beta version), the number of ‘accredited’ and NHS-approved health-apps is increasing, albeit at a leisurely pace, with approximately 50 apps accredited so far. While a step in the right direction, the rigour with which such reviews are conducted comes at the expense of speed, and an estimated review time of 6-8 weeks, limits the possibility of such initiatives being conducted at scale. As such, the difference between the total number of health-apps available (~300,000), and those which have been quality-tested and approved by regulators or accreditation bodies (~50); is if anything, increasing; leaving little or no information regarding the validity, efficacy, and most importantly the safety, of 99.99% of health-apps available today; which to date have been downloaded by potential users upwards of 50million times.
This is where the Organisation for the Review of Care and Health Applications (ORCHA) aim to transform the process of health-app research and information provision. Positioned as an open-access, free of charge and publicly facing repository regarding the user experience, clinical efficacy, and data privacy of thousands of health-apps, ORCHA’s aim is simple; to empower and inform potential users of health-apps regarding potential risks and benefits, prior to committing to use. Through a structured, objective and peer-reviewed assessment, consisting of 160 question areas, answered on a ‘yes’ or ‘no’ basis, ORCHA provides information to the 99% of users of health-apps, which are yet to be formally assessed by health technology assessment bodies, and in doing so, ORCHA removes the information asymmetry that is currently clouding the health-app market in, distrust, disbelief, and uncertainty. Publishing a new review of a health-app every 30minutes on average, ORCHA pull in information for all 300,000+ apps available on both iOS and Android Google Play, organise these into medically approved sub-categories (including diabetes, mental health and diet and exercise), and then order these apps from the most to the least downloaded.