

In Treatment for Leukemia, Glimpses of the Future - thecoffman
http://www.nytimes.com/2012/07/08/health/in-gene-sequencing-treatment-for-leukemia-glimpses-of-the-future.html?_r=2&hp

======
tokenadult
Here's some good commentary on this case in a blog post "The future of cancer
therapy?" from a cancer physician in today's Science-Based Medicine blog:

[http://www.sciencebasedmedicine.org/index.php/the-future-
of-...](http://www.sciencebasedmedicine.org/index.php/the-future-of-cancer-
therapy/)

"While the story is basically one long anecdote that shows what can be done
when new genomic technologies are applied to cancer, it also shows why we are
a very long way from the true 'individualization' of cancer care.

. . . .

"Taking the results of the sequencing of the entire genome and RNAseq data and
analyzing them allows scientists to probe the genome and transcriptome of
cancers in a way that was never before possible. It produces an enormous
amount of data, too, terabytes from a single experiment. At cancer meetings
I’ve been to, investigators frequently refer to a 'firehose' of data,
petabytes in magnitude. Indeed, the sheer quantity of data from these
experiments challenges the bandwidth of universities doing them, and, in fact,
it’s not at all uncommon for the preferred means of sending experimental data
to be to load up a hard drive with the data and send it by the quaint but
effective method of overnight mail to other investigators because it’s faster
and more reliable that way. Not surprisingly, serious computing power and
major advancements in computer algorithms have been necessary to develop the
methods of analyzing data from these experiments.

"What I’m trying to convey is that what WUSTL did for Dr. Wartman was not a
little deal. It was a big deal that took a lot of resources and effort and
likely cost well over $100,000. Apparently it was paid for through research
grants, and Dr. Ley claims that no patients were neglected while all that
sequencing and computing firepower were transferred to sequencing Dr.
Wartman’s cancer genome and transcriptome, having done the same thing for a
previous patient."

In other words, the glimpse of the future that we may be able to derive from
this case shows that the future is still far off, and the steps to reach the
future are enormously expensive. More details are available in other
paragraphs of the linked Science-Based Medicine post.

~~~
fghh45sdfhr3
I don't know. $100,000 to find a great treatment for one cancer, which
previously had no treatment, seems cheap!

And I think a truck full of hard drives hurdling down the highway has had
greater bandwidth than most of the world's networking for a while now.

As the future of medicine is clearly personalized I think the costs associates
with genome sequencing and other analysis will come down. Or, at least, I hope
they do.

~~~
bedris
Just to be clear, this $100,000 was spent to possibly identify a potential
treatment for one _person's_ cancer, not one type of cancer in general.

In other words, this was a $100,000 diagnostic test with no guarantee that an
actionable diagnosis would result. By that, I mean that the results of the
sequencing analysis either (a) might not pinpoint a driver mutation or (b)
might pinpoint a driver mutation that does not have an efficacious drug
available to act on that mutation. Also, all caveats about tumor heterogeneity
and evolution, etc., apply.

An integrating sequencing approach involving the analysis of normal and
cancerous cells to identify actionable mutations is the best we have for now,
but it is still a hugely expensive, time-consuming, and technically-
challenging process with an enormous failure rate associated with it.
Nonetheless, I think it's terrific that, in this instance, it yielded valuable
and actionable information that resulted in a meaningful clinical result. One
step at a time!

------
jostmey
I wonder if he was somehow unknowingly, inadvertently exposed to the trigger
in lab that caused the cascade of events leading to runaway cell division. He
was, after all, working in a lab studying Leukemia, and he probably worked
with Leukemia cell lines a lot. Of course, there is no way to really know how
he contracted the cancer, but it is intriguing to wonder about such things.

~~~
balsam
This paper's title says he studied mouse leukemia, but does anybody have a
link to the human leukemia paper?

<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3069786/>

~~~
chrisamiller
To the best of my knowledge, this hasn't been published.

------
tuxguy
This article was part 1 of an NYT series called 'Genetic Gamble : New
approaches to fighting cancer'

Part 2 : A New Treatment’s Tantalizing Promise Brings Heartbreaking Ups and
Downs

[http://www.nytimes.com/2012/07/09/health/new-frontiers-of-
ca...](http://www.nytimes.com/2012/07/09/health/new-frontiers-of-cancer-
treatment-bring-breathtaking-swings.html?pagewanted=all)

Part3 : A new genetic test of ocular melanomas offers uncanny accuracy, but do
you want to know ?

[http://www.nytimes.com/2012/07/10/health/genetic-test-
change...](http://www.nytimes.com/2012/07/10/health/genetic-test-changes-game-
in-cancer-prognosis.html?pagewanted=all) ( HN :
<http://news.ycombinator.com/item?id=4220123> )

------
msie
I am not surprised that the guy didn't get any help from his insurer or the
drug company.

~~~
mangala
Yea what more proof do you need that insurers will screw anyone out of money
than an expert in his disease's field being denied a promising attempt to save
his own life.

------
aantix
What are the major differences between the type of sequencing that was
performed in the article and the type that is provided by companies such as
23andMe?

~~~
chrisamiller
Most of 23andMe's customers don't really get sequencing. They get genotyped on
a SNP chip, which only tells you about a million or so positions (out of ~3.2
billion).

The other product that 23andMe is starting to offer is exome sequencing, where
they analyze just the coding regions of the genome (around 1% of the total
content). This sort of analysis can be enormously useful and can provide much
information, but will miss variations in non-coding regions. It also has
limited ability to detect structural variations, where a chunk of DNA gets
moved around, deleted, or duplicated.

What they did here was whole genome analysis, coupled with sequencing the RNA
products of gene expression. This turned out to be enormously important,
because the main driver of his cancer turned out to be over-expression of a
gene.

------
Squazic
I find the lack of accessibility to the poor for such treatment troubling. Dr.
Wartman was lucky enough to work in a cancer research lab that covered the
costs of the genome and RNA sequencing AND he had rich doctor friends who
helped chip in to buy enough drug for him. While the costs of sequencing are
dropping quickly, medical drugs don't fall in price at the same rate. And
there's always the chance that a drug to cure that particular mutation doesn't
exist. What then? Spend millions on years of research to make the drug?

~~~
chrisamiller
_And there's always the chance that a drug to cure that particular mutation
doesn't exist. What then? Spend millions on years of research to make the
drug?_

This is indeed the case for most mutations that we're finding in cancer
genomes. (That's the bad news).

The good news is that many cancers do have "druggable" genes that are altered,
and even though the cells have many mutations, attacking just the druggable
gene is often enough to prolong life and improve outcomes.

The other good news is that even though many different genes can be mutated,
there are a much smaller number of pathways that are altered. (those for cell
cycle control, apoptosis, etc). By targeting key points in those pathways, one
drug may be effective against dozens of different mutations.

