The Dawn of Personal Genomics

That sure was a fun party this weekend, seeing all your friends after the pandemic. Everyone was vaccinated, gleefully sharing their laminated cards, high-fiving each other after a year apart. You were all up late, laughing, catching up, sharing appetizers, hugging, getting back in the swing of things. We felt so normal, excited to be with humans again!

It's Monday. You feel this scratchy feeling at the back of your throat. Your "allergic sneezing" has progressed into a light cough, and the celebration headache hasn't faded away. You've got a big presentation on Wednesday and having a cold is the last thing you need. What if it's a new variant of Covid-19? Oh God. Not now!

Without breaking a sweat, you pull out your smartphone. A few taps later you're connected directly to your physician. She asks a few questions. "You do look a little under the weather. The phone is telling me your heart rate is elevated, and it does seem like you have a slight temperature. Let's see what's going on inside. Would you like to stop by the office, or do you feel up to a PG?"

"I can do a PG. No problem."

"Ok, I see you have one of our Bento devices. I'll keep an eye out for your data. We'll get to the bottom of this! Feel better."

PG - Personal Genomics. It'll soon be as common as the PC. You walk over to the kitchen, move the coffee maker aside, and plug in the PG. It looks something like this older, but colorful unit from Bento Laboratories in 2020. These devices are about the size of a briefcase today.

First, wash your hands thoroughly. Then there's the part nobody likes, but it sure beats taking off a half day, spending time driving in traffic, waiting in a room full of sick patients. You pull out The Mosquito, a sampler device, and take a finger prick of blood.

You eject a small capsule from the Mosquito, a tiny, fresh vial of blood the size a large multivitamin. This clear capsule neatly fits into the PG, which you insert, press down, hear a faint click, then press "Start." You're reminded of making coffee this morning in your Keurig, where you inserted pods to make a fresh cup of coffee.

The PG timer starts at 30 minutes. The PG is busy cooking those few drops of blood into a brew of DNA, amplified and replicated for testing on your phone. The chemical process was invented in 1983, while a chemist was driving to his weekend home on the California coast, eventually earning him a Nobel prize in 1993. This is the "wet lab" part of the new biotech world, encased in a simple machine that fits on a kitchen counter.

While that's happening, you get distracted. You swipe left on your phone, pulling up Instagram. After a few minutes catching up with friends, you swipe again and enter an endless scroll of Tik Tok videos. Before you know it a soft ringing occurs on the phone.

"Please authorize release of genomic data."

Your phone is asking for digital confirmation, then a signature. You tap YES, sign the release. A nanopore sensor inside the PG sends raw signals to the cloud. You feel assured that your data is secure and standardized, available to share with future doctors, hospitals and pharmacies in two clicks. You're intrigued by the new transparency of your genomic makeup, and how it impacts your personal healthcare.

You settle back into the couch, watching some TV. Just as your show begins to get interesting, you hear your phone ringing again. This time it's your doctor, smiling in her office.

"Thanks for doing the PG! Would you like to discuss the results in figure 1?"

"Sure." [Note to self: You love the transparency!]

Every bacteria and virus contains a genetic signature. By applying deep learning algorithms to the PG data, then matching the results against a large database of genes, the cloud can identify concentrations of organisms. These can be visualized in mobile apps today, such as a hypothetical "Figure 1" below. It shows various concentrations of genetic material on the right (this time, in a mushroom, but you get the idea):

Figure 1

"Well, the good news? You don't have Covid-19... or any of its variants. This looks like an upper respiratory infection. I'll prescribe antibiotics and have it delivered to your apartment within the hour, ok?"

"That's a relief. Sure... thanks Doc."

"Ok, your prescription is on the way. According to the data, there are no adverse reactions associated with this or other medications and supplements you're taking. Further, the data show that this treatment is effective with 98.2% of people with your DNA demographics and medical conditions. I've sent the prescribing information to your Google Assistant, who will help you follow the therapeutic regimen. Is there anything else I can help you with?"

"Nah, I'm good. Thanks."

The phone alerts you. Since your diagnosis and recommended treatments are consistent with 99.1% other patients with the same condition, and your genome shows the chances of complications are low, your insurance company has pre-approved payment. An hour later, your medicine shows up. You're on way to recovery, ready for that big meeting on Wednesday.

Sound far-fetched? Not really. The building blocks of this future are forming today... just not widely available.

• Do It Yourself kits for genomic hobbyists are available for about twice the mass-produced price of Bento Labs ($7000). Harvard teaches genomic sequencing in a freshman Biology class. Cold Spring Harbor published a series of YouTube videos a decade ago, describing how to do these techniques by hand.
• A mass-produced, personal sequencer from Bento Labs in the UK applies chemical processes to turn samples of saliva, blood and more into a small vial of liquid. This liquid extracts and amplifies the internal DNA and RNA for analysis. All for $1999.
• Oxford Nanaopore Technologies (ONT) sells a handheld DNA and RNA sequencer for $1000, while compiling a waiting list for a cell-phone sized version. The ONT device drags microscopic DNA sequences through tiny "nano-holes" in a transistor, sending a signal across the hole, then measuring the interference caused by DNA. Each of the elements of DNA - A, T, C and G - create unique patterns, detectable by the same math used for human speech recognition. These can be integrated into cell phones and personal sequencers.
• Free open source software turns the raw nanopore signals into genetic sequences of A, T, C, and G. These are the biological versions of 1's and 0's. Other free software searches online gene databases in seconds, matching these sequence with known bacteria, viruses and genetic conditions. The list grows daily, just as the web does today.
• Telemedicine is enjoying a resurgence after FDA eased regulation and insurers recognized video calls as legitimate healthcare treatment.
• In the last few months, researchers substantiated the ability to test blood, saliva, and other biological samples within minutes on nanopore devices. These results challenge the massive, multi-billion dollar incumbents who rely on slower, multi-day approaches that grow bacteria in petri dishes in remote labs.

I'm excited about a future of PG -- personal genomics -- where AI and data can diagnose common illnesses in minutes. The devices may sit on our kitchen counters, or perhaps housed in vending machines at the corner drug store. Personal genomics accelerate precision medicine, as well as advanced techniques including the gut microbiome.

Yet, despite all these amazing advances, we're just getting started. To put this in perspective, these recent developments remind me of my first encounter with computers. Back in the 70's we'd assemble computer kits with 4k of memory from mail-order houses for $700 plus. That's equivalent to $3500 today, roughly the same price as an early PG. Back then, Dr. Jack Baur wondered if these new devices could assist in health care. Here's his setup... remind you of anything?

Dr. Baur progressed from building an oxygen monitor for infants, to building a company to record health records in a digital format. The company he spun off evolved into EPIC, one of the top electronic health record companies today.

This is going to be an inspiring decade in health assurance as genomic machines proliferate, dropping in cost, approaching the ease of a smartphone. The PG revolution has begun!