Genome Sequencing: There’ll Be an App for That

GeekMom Health Science
Conference Notes–photo credit Andrea Schwalm

Ten years ago, in spring 2001,  I learned how to administer intravenous antibiotics.

My younger son, a toddler at the time, was recovering from a protracted infection and emergency surgery. We’d spent two of the previous four months as residents in different hospitals already, but he still needed six more weeks of  IV antibiotics. If I was willing to commit to taking over as nurse, we could finish this last leg of recovery at home.

My first reaction to the suggestion was disbelief.  “But…my degree…is in English. Writing. Making stuff up. I  cry when I have to pull the neck packet out of a roasting chicken! How will I do this???”

“We’ll send a nurse to the house. She’ll show you what to do, she’ll order the equipment and medicine, and she’ll check in on your son every couple of days.”

Oh, well that sounded reasonable…people did this all of the time?

In June 1999 I’d given birth to my second son and the ride had been bumpy from the get-go. In his first year, my son had suffered through three different “transient” skin disorders, a dozen double-ear infections (with ruptured ear drums), a three-day hospitalization for the croup, a couple of respiratory infections, and a case each of thrush, fifth disease and hand, foot and mouth virus. No single illness had been particularly noteworthy, but cumulatively we’d racked up an extraordinary amount of time in the pediatrician’s office.

Three-quarters of the way through this first year, my husband completed his military commitment and we moved back home to Long Island. The plan had been: put all of the non-essential belongings in storage and move in with the in-laws in order to  save for a house. The day after we arrived back home, I was on the phone looking for a pediatrician and an internist — this time, we were both sick (ear infections, sinus infections, and pink eye).

At 12 months my son developed a fourth rash: clear bubbles on his scalp and face that would weep, then scab thickly. Some of the boils would be tiny but some got as big as crusty dimes. At 14 months he developed a fungal infection in the scalp (probably a result of the itchy boils) and started losing patches of baby hair in loose tufts. At 16 months he developed impetigo. Seventeen months: another double ear infection. Eighteen months: the flu…

About a week into his second January, my son and I woke together from a nap and the best I can put it looked as if his face and neck had turned to jelly. When his pediatrician came later that day to the hospital, he told me, “I would never have recognized him if he hadn’t been lying in your arms.” At that point, my son was treated for acute, bacterial cervical lymphadinitis. Kind of unusual, but not completely unheard of.

However, this swelling didn’t go away. Over the ensuing five weeks in-hospital and two months out-patient, this jelly swelling morphed into a softball-sized growth ballooning out from my son’s neck. Ultimately, we ruled out cancer, thyroid disease, tuberculosis, Kawasaki Disease, viral infection, and fistula while weathering CAT scans, x-rays, sonograms, an echo cardiogram, weekly blood sticks and a test where I was asked to physically pin my son down while barium slush was squirted in his mouth. In an ideal world, he would have swallowed the slush and allowed the technicians to track its path through his throat and down his esophagus. In our world, an entire roomful of doctors and technicians wound up annoyed and heavily-spattered in barium, no closer to a diagnosis.

We stumped three hospitals. By March, however, the swelling had grown large enough that my son had to hold his head perched to the side (which affected his depth perception and ability to navigate space). At that point, the pediatric neck and throat surgeon we’d been consulting with watched him silently for a few minutes and finally said, “Yeah, I think we’re ready for surgery.”

I’d believed that “surgery” would equal “fixed.” Instead, “surgery” turned into “diagnosis.” The surgeons found three abscesses full of pus in my son’s neck (we’d find two more abscesses in his lung nine months later, after it collapsed). The pus was cultured and found to be full of staph aureas. My son’s blood counts and illnesses were entered into a National Institute of Health database and we were given a diagnosis for a primary autoimmune disorder.

“Is this…bad?” I’d immediately asked the doctor, expecting him to assure me that I was over-reacting.

“I can’t honestly answer that question,” the infectious disease doctor had replied. “No one really knows that much about Hyper Ige. If you want to use the hospital computer to look it up, you’re welcome to. There’s not a lot out there, though.”

My son hasn’t had to be hospitalized since his pneumothorax (which occurred at the end of 2001). After that event, he started taking daily oral antibiotics prophylactically. This medicine has allowed my son to lead a relatively “normal” life — in the last eight years we’ve had two cases of pneumonia that have lasted more than a month. Otherwise, my younger son hasn’t been any sicker than his  “healthy” older brother. We do quarterly blood checks to make sure that the antibiotic doesn’t affect his liver. We get flu shots. We avoid contact sports because he has a predisposition to long-bone breakage. We spend a lot of time at the dentist’s and orthodontist’s because another facet of his syndrome is that his baby teeth have collectively refused to fall out and have all had to be pulled. We bow out of social engagements if anyone on the other end seems too sick. We alter our lives in small ways and generally feel very lucky to have the option.

Invariably, when I explain to people that my son takes daily antibiotics, they ask at least one of these questions:

  1. Is this anything like AIDS? Answer: No. My son’s primary autoimmune disorder is genetic and is not contagious. Should you choose it, however, refraining from fully inoculating your child is potentially life-threatening to my immune-impaired son.
  2. Have you considered using (pick one: ginger, garlic, echinacea, mallow, coltsfoot, aromatherapy, animal therapy) in place of the antibiotic? Short answer: no. Slightly longer answer: According to the advice of our team of doctors, antibiotic therapy offers the best outcomes with the least risk. I’m siding with the roomful of PhDs and MDs on this one.
  3. Will he always have to take antibiotics? Answer: We don’t know.

That last question is tricky. In my heart of hearts I’ve always wanted to answer no, one day he’ll be cured. There are only about 200 people in the world with my son’s disorder, though. For a long time, his diagnosis was relegated to “orphan disease” status–too insignificant to fully research.

A great deal has changed in this last decade, however. I recently was fortunate enough to receive a scholarship in order to attend a Genetic Diseases of Children conference in Manhattan as an affected parent and as a family support worker. One of the most interesting sessions for me was a “whole genome sequence analysis-101” plenary session entitled “Whole Genome/Exome Sequencing For Diagnosis: Are We There Yet?” given by Eric Schadt, Chief Scientific Officer at Pacific Biosciences.

Schadt started out with the history: the first genome took 13 years and three billion dollars to sequence. By 2014, however, he expects labs to be able to sequence “hundreds of genomes in less than an hour for less than $100 apiece.” As another scientist stated later, genome sequencing will “be more like a blood test…cost less than an x-ray.”

“Ten years out?” Scheidt conjectured, “you’ll have a real-time ‘disease weather map’ app–it’ll come with your iPhone, for free, and you’ll get 50 free genome sequences to get you started. You’ll be able to sequence whatever you’re exposed to in real time, assess your genetic risk, and personalize your treatment.”

That’s the intriguing news.

We’re still a long way from taking our understanding of the genome and turning it into personalized cures for genetic disorders, though. The prevailing belief now is that geneticists must do more than identify quirks in linear gene sequences in order to develop cures, they must additionally understand the algorhythmic interplay taking place between DNA, RNA, protein metabolites, behavior, and environment. That depth of knowledge is going to require an incredible amount of data from affected patients–which in turn is going to require infrastructure and privacy protection that haven’t yet been fully developed, either ethically or physically.

The human creature, as it turns out, is a complicated beast. Unlocking the mystery of how its systems operate will come down to more than mere sequencing.  I suppose to expect anything less complex would be to teeter toward hubris — which any English major could tell you is synonymous with arrogance and almost always results in tragedy…

One concrete improvement that has taken place just in my son’s life as a result of the human genome project, though, is that rare and “ultra rare” diseases are being perceived by researchers in a new light: they are no longer financial albatrosses around the unwilling necks of researchers and pharmaceutical companies, but instead are genetic Rosetta stones providing rare insight into the responsibilities of specific molecular strands.

In 2001, if you Googled my son’s diagnosis, very little would come up in response. Today, there are illustrated fact sheets that I can print out to educate his teachers and hundreds of references to papers and studies about Hyper IgE  in Google Scholar.

I have to believe those changes are the first steps toward our cure.


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7 thoughts on “Genome Sequencing: There’ll Be an App for That

  1. Wow. How scary for your family those first few years. I am sure it is hard not knowing all the answers. I’m so happy your son has been able to lead a relatively normal life. Science is amazing!

  2. Very compelling story. I can’t even begin to imagine how much strength you need to get through something like that. Thanks for telling it.

    Just this morning I heard of this other excellent program to help families with rare genetic conditions that I thought was terrific–I hope it helps families like yours:

    ” @sangerinstitute: New project to improve diagnosis and care of UK children who fail to develop normally due to changes in genetic makeup

  3. Coincidentally, I received a letter today from the CDC (Centers for Disease Control and Prevention) about participating a a survey about vaccination. I hope the trend to avoid vaccinations, which is largely based on disinformation, can be reversed.
    Vaccination protects everyone, especially the vulnerable.
    We had a little girl in preschool who couldn’t receive vaccinations due to multiple allergies. I remember how worried her mom was that she might be exposed to some of those nasty childhood diseases. You guys have had a hard road and I wish you the very best

  4. Andrea, I find this endlessly fascinating on the one hand and also have deep sympathy for you and your family on the other. I work in epidemiology research these days (a long way from my art degree) and due to my job I’m introduced to new areas of research constantly. I am enthusiastic in agreeing with Mr. Schadt; even now with projects like 23 & Me where a detailed genetic profile is available for about $100, it brings genomic sequencing ever closer to the every day consumer.

    On the personal side, I have undifferentiated connective tissue disease, which is a fancy way of saying, “we have no idea why your immune system is attacking your body”, and prior to my current pregnancy I’d been on a weekly chemotherapy dose for three years and still continue to take a medication that was originally designed to be an anti-malarial. But knowledge and research is bringing us closer to an understanding of these immune disorders. Why is inflammation on the rise and what’s the connection between auto-immune and allergies? I think we’re closer to finding an answer to these types of questions than we could have imagined just a few short years ago.

    Long ramble, sorry, but thank you for sharing your story with us.

  5. Mary: Thank you for the information about the Sanger Institute–it is now on my list of things to research 🙂

    Mindy: Your question “Why is inflammation on the rise and what’s the connection between auto-immune and allergies?” is something that interests me, too. Also: is there a connection between those issues and the rise in autism spectrum diagnoses? Feel free to forward any worthwhile articles my way 🙂

    Thank you for your comments, everyone. *laugh* I can say this now, but I was in a horrible mood the week I worked on this piece. It was tough to have to revisit that time…but I feel so lucky to have what I do today.

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