Discovery of cost/availabity of high end sequencing/analysis technologies

Pat Tagert here. As a handful of you may know, my son died last summer, just 18 days after Steven Keating. He was diagnosed with sporadic ALS at the age of 33, and lived another seven years, the last 18 months on a ventilator. He was the most prolific user of TOBII eye gaze technology in Canada at the time of his passing, controlling his electronic environment with few limitations with the help of the eye gaze technology.

As some may know, amyotrophic lateral sclerosis (aka motor neuron disease, aka Lou Gehrig’s Disease) is typically a disease of late onset. The most prevalent age at onset is in the 7th decade. A small fraction of ALS is of familial Mendelian origin, estimates of 5%-12% of all ALS, probably nearer the lower %. Researchers have learned most of what they know about ALS by sequencing and analysis of those with familial ALS. Familial ALS, depending on the variants involved, can occur at almost any age, from very early childhood to late adult onset. Sporadic ALS mostly occurs between the ages of 50-75, with the incidence dropping off after that. I had always imagined that ALS was a very rare disease, the proverbial “one in a million”, but certainly not so, per the latest statistics. Researchers last year at Trinity University of Dublin, targeting only persons of native Irish ancestry, who published after an approximately 10 year study in Ireland, discovered that native Irish have an approximately 1 in 340 probability of ALS (I averaged between male and female statistics). Satistics are similar for Britain, and Finland is another hotspot.

More than 5 years ago (after it became apparent that no institution/researchers were interested) I tried to do an “ad hoc” trio research for my son, using my PGP whole genome, and whole exomes I bought for my son and his mom. My goal was simply to discover any causal variants. I failed miserably of course, and worse, it became a distraction while my son’s disease progressed. Near the end I discovered a potential causal variant (but with low confidence), and by then I had come to realize how completely inadequate all my efforts had been.

The most obvious first thought for most observers might be “okay, but why so much emphasis on discovery of causal variants?”, and of course the answer is that there is zero probability of a cure without knowing the cause. It’s the first step.

So, there are people every day somewhere discovering that they are going to die from this disease, but most of them have already lived a full life. My son was in his prime when he received the diagnosis, with a young son of his own. I had no idea where to turn for information, so I learned as best I could and blundered along, and mostly what I have learned is just how far I was from access to the technologies that might have made a difference.

So, that’s my project. What kind of technologies are available, at what cost, and how can people suffering from sporadic ALS (and especially young people) gain access to these technologies, so that every tiny facet of their genomes is thoroughly explored, no stone left unturned? Of course, the obvious problem is how to pay for it, but that can’t be determined without first knowing the cost.

The next time a young family man starts feeling fasciculations and starts to lose his strength, where can he turn to find out what’s causing his disease, if all the “usual” options are out of reach?? I want to know what it costs to get a de novo assembly whole genome sequence, with every remote niche of the genome explored in it’s entirety, no loose ends,and all related technologies, including methylome testing for epigenetic modifications. That’s the only hope for discovering what’s causing this dreadful disease, and in fact, there are obviously many causes for ALS, as there are for all complex neurodegenerative diseases, and it may be that most patients need a 100% genome sequence to discover the cause, while some fraction can discover causal variants with less expensive and more widely available technologies. How then should testing progress in an orderly logical fashion?? Is that ultimately an unreachable goal? I just want to put a $ figure on it, and find out what’s available.

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So sorry about your son. One thing you may want to consider is the country you’re talking about. Private insurance vs. NHS (and what NHS or equivalent would fund) will make a huge difference in both cost and care.

Hi Pat, I’m very interested in your quest, and though it is different in scope and complexity from the simple self-tracking projects we’re typically exploring here, it reminds me of some work by Hugh Reinhoff in exploring the causal root of his daugher’s rare genetic disease. ( Is there something in his story that could be useful?


Hello, Frances. Thanks for your reply. Sorry for the delay, just very busy over the past few days.
I’m not yet convinced that private insurance versus NHS makes much difference for terminal diseases with no known cure and no available treatments that will increase lifespan or impair the progress of the disease. My son got very generous support for very basic nursing care, considering that there are no effective treatments for sporadic ALS. NHS and private insurance both defer to “research” for any condition that has no established treatments. I suppose that they make a reasonable case that they can’t pay for research, but when research is the only option that offers the slightest shred of hope, that’s not easy for a terminal patient to hear and accept.

But my son is gone now, so this is no longer about what happened, but rather the possibilities for people like him in the future. When research is your only hope, and nobody is beating down your door to include you in research, what are your best options, and especially considering that it’s not even about finding a cure, but just discovering what is the cause of the disease that it is slowly destroying you. Anyone newly diagnosed with sporadic ALS is still facing the same dilemma my son faced, no cures on the horizon, and worse, no definitive way to get a molecular diagnosis. There are already at least two dozen genes with variants associated with familial ALS, and I think in the long run, there will be many, many variants and epigenetic regulatory modifications discovered to be pathogenic. I think that ALS, as well as many, many other neurodegenerative diseases will be known to be highly polygenic. That is already the case, and it lends weight to the idea that for each individual, a molecular diagnosis is warranted, whatever that takes. I also understand that budget constraints are still the deciding factor in most cases, so my objective is to gain clear insight into what a molecular diagnosis might cost in the real world if it were considered as an option, and not only what it’s ultimate market price might be, but the actual real world operating expenses for producing those results, the lab costs, if you will, versus market price.

Hello, Gary. Thanks for responding and sorry for the delay, just a busy week for me.

There was much in Dr. Reinhoff’s story that is familiar at a personal level, and I greatly appreciate the link. I thought about quoting some of it, but it would be too much to quote, and anyone interested should read the whole story.

I’ll respond to the story with a few observations. First as he said, he is “a physician trained in medical genetics”. My highest academic achievement was an associate degree in nursing from a rural community college, graduating when I was almost 40 years old, and a father of four. Zero training in genetics, not even biochemistry 101. So I had nowhere near the insider connections. Worse, my career was in surgery. Surgeons aren’t reknowned for their interest in genetics, and especially not molecular genetics. I occasionally encountered an anesthesiologist or pediatric surgeon with a bit of interest in genetics, but certainly no one with any training or expertise in molecular genetics.

So as the years passed, I asked my questions poorly, and often found myself tongue tied when I first spoke to anyone with the ability to help, as in my first phone conversation with a board certified molecular geneticist.

The parallel to the story was that shortly before my son’s death, I finally identified a novel de novo missense variant in his whole exome in dynactin 1 (DCTN1) V715F, not published in any public database, and with a SIFT score of 0 and PolyPhen score of 0.926 - 0.997, per Broad Institute’s Variant Effect Predictor. Tragically, in the past few weeks, I discovered an old screen shot from almost 5 years ago, of a page of query results using Qiagen’s Ingenuity Variant Analysis that showed this same variant clearly. Five years ago, I had no idea what I was looking at, and just tucked away the screen shot in a dark corner of my computer. Also more than five years ago, a computer whiz did a realignment of the whole exomes I had, for the purpose of producing a trio comparison using different data sources, the end result being a VCF file of novel variants. Again I had no idea of the value of what had been done, and I recently found this DCTN1 variant in that VCF file as well. The variant in question has not been investigated by anyone but me, as far as I know, and I certainly don’t have any means of doing followup to determine what kind of downstream transcription impact it might have. Similar coding variants are listed in OMIM as potentially pathogenic for ALS, but who knows. Also, the original alignment provided a low confidence call score for the variant, and I have no other data to confirm it or rule it out.

A couple of months ago, I discovered a cluster of novel and extremely rare de novo 3’ UTR variants in his HOXA3 gene, which is implicated in fetal neurodevelopmental regulation, so that’s another question now. All in all, I’m seeing far, far more de novo and novel variants in his whole exome than is par for the course, which suggests that 1) the data is unreliable or 2) for whatever reason, he has a multitude of somatic novel variants of presumably developmental impact or 3) a multitude of novel de novo variants are present and contributed to his disease or 4) he actually has a lot of germline novel variants (makes not sense) or 5) no idea, but maybe someone else could make sense of it.

And last, my son has siblings, and a son of his own, and nieces and nephews, and a new grand nephew. They are my family. There are far too many unknowns. Unlike Bea’s story, my son’s story did not end well. He died at the age of 40 after suffering for years. I’m the only one in my family that has the remotest chance of finding answers. We are all pretty bright, but this is the razor’s edge, and I’m certainly nowhere near capable of finding the answers we need. My only consolation is an Einstein quote - " I have no special talent. I am only passionately curious." All I can do is keep trying. It’s not over until it’s over.

I’m happy to have you here Pat, and appreciate the importance of understanding the monster – even if that doesn’t provide a cure.

I’ve known that ALS isn’t primarily a genetic disease, and I took some time to read about it (on the Wikipedia page, nothing fancy).

From everything I’ve read, ALS is as random as most cancers: a random event that, in rare cases, can be triggered by genetic predisposition – and maybe likelihood is also affected by environment (e.g. lung cancers and smoking) – but in most cases, what happened is essentially… random. Exploring all that genetic and epigenetic data might yield nothing at all related to what happened.

(One thing that stood out to me was a theory of ALS having a prion-like mechanism. That means a misfolded protein triggers propagation of misfolding – “good” versions of the protein become misfolded when they come into contact with misfolded versions – and like cancer, a random event turns into a cascade.)

You seem to place strong belief on genome data holding answers. But I think it may genuinely be the case that genomic data holds little more than mild modulation of risk, and that information does little to help prevent or treat the disease.

Cancer genomics has had successes: but it is characterizing cancer genomes. Not the genome someone inherited, it’s characterizing the cancer itself. By doing that, it enables targeted therapies known to be effective against a particular cancer type.

But what does it mean to characterize a case of ALS, potentially for targeted therapy? As with cancer, it won’t mean the personal genome. And it seems there isn’t any “ALS genome” to characterize (e.g. if it’s a propagation of proteins rather than metastatic cells).

I think this sort of endeavor to better generally understand a disease or condition isn’t what is intended for our self research effort in the Keating Memorial activity, but I want to support your quest for understanding – and I hope some of my thoughts above are helpful.