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[cancer] Update on the Science Fiction Author on Trial fundraiser

Science Fiction Author on Trial (NIH trial, that is!)


Thank you very much to everyone who has donated to my fundraiser in support of my costs for the NIH study I am now enrolled in. Thank you as well to everyone who has provided promotion, cross-promotion and signal boost. And finally, thank you so much to those who have donated premiums to the fundraising process.

As of my writing this post on Monday morning, we are at almost two-thirds of goal. I cannot express my gratitude enough. These days, my life erodes in so many ways, growing smaller and smaller. At times like this, I am reminded how good my life still is, how large each of you help make it be.

The fundraising site was updated over the weekend with some terrific premiums. Kevin J. Anderson, Prime Books, and Clarkesworld Magazine have made generous donations for contributions at given levels. I’ve put a dozen copies of my private printing of The January Machine, to be awarded by random drawing. I also have something cool forthcoming for all donors at any level, though we’re not quite ready to announce it, and there’s a couple of more really neat things in the pipe as well.

Give a nod to Shlom Ster for pulling this together. And think of me this week, as I literally dedicate myself to science. I’m in for some difficult and painful times in the very near future.

See my original post here for a bit more background on the fundraiser, if you are interested.

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[cancer] Fundraiser: Science Fiction Author on Trial

It must be the season or something. I’m back off to NIH on Tuesday for surgery followed by some extensive and fairly brutal immunotherapy. As recently discussed, this is a very expensive process for me and my family. Not the treatments themselves, which are covered by NIH at no cost to me, but the expense of having my caregivers in Maryland for five weeks while I am being treated. Not to mention the expense already incurred during our two-week visit for enrollment.

I’ve discussed the costs in general here, and in more detail here. I’ve discussed what we’re doing, clinically and scientifically, here.

Shlom Ster has been kind enough to put together a fundraiser on Youcaring.com, where we held last year’s Sequence a Science Fiction Writer fund raiser. This year, we’re calling it Science Fiction Author on Trial (NIH trial, that is!).

Premiums are still being organized. There has been some excellent generosity from various donors, and I’ve put a dozen copies of The January Machine in myself. Hopefully by Monday that will all be up on the fundraising site.

I have very mixed feelings about tapping the generosity of my friends and fans again, but this is where we are. Still fighting for my life, slowly losing, but trying everything we can.

Thank you to everyone who gave last year, to everyone who’s already given this year (there has been some startling and heart warming generosity), and to everyone who’s helping pass the word.

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[writing|help] The Clayton Memorial Medical Fund is doing a fundraiser

So, the Clayton Memorial Medical Fund has been a big presence in my life these past few years, helping me financially at times of great need. (I did not need them this year, as it happens, thanks to all your generosity with the Sequence a Science Fiction Writer fundraiser back at the beginning of the year.) Their reserve funds are running low, and they have asked me to try to boost the signal on a much-needed year-end fundraiser.

Here’s what my friends at the Clayton fund have to say about themselves:


The Clayton Memorial Medical Fund helps professional science fiction, fantasy, horror, and mystery writers living in the Pacific Northwest deal with the financial burden of medical emergencies. Even with insurance, co-pays can quickly add up to thousands of dollars, and over the past few years, we have faced a heavy draw on our money. The Fund is now down to a few thousand dollars.

The Clayton Fund was founded seventeen years ago by Oregon Science Fiction Conventions, Inc. (OSFCI) in response to the illness of Portland writer Jo Clayton. Our initial money came from a national campaign by writers and fans of science fiction and fantasy to help Jo and other writers. The Fund has since assisted many writers in the region deal with medical and dental emergencies.

As part of OSFCI, the Fund is a 501(c)(3) non-profit organization. Donations to the fund are tax deductible and often qualify for matching donations from employers.

Donations can be made using PayPal through the Fund’s Web site (http://www.osfci.org/clayton) or mailed to:

Clayton Memorial Medical Fund
c/o OSFCI
P.O. Box 5703
Portland, Oregon 97228

Please be sure to include full contact information so we can mail you a letter acknowledging your donation.

I’ll be donating from my surplusage from this year’s fund raising for my benefit. If you’ve got a few extra bucks this season looking for a tax deduction, why not join me? It’s an excellent cause helping writers who often have run out of financial lifelines. It’s an organization that has been of great help to me personally. That’s two fantastic reasons right there.

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[links] Link salad gets ready to leave the madness

Bill Lindblad auctions off a rare, signed edition of GRAILS to benefit me. Check it out. Facebook announcement or eBay auction page.

British Weather Terms — Ah, the queen’s English. (Via Daily Idioms, Annotated.)

Major disruptions expected after severe quake in New Zealand — I hope all my friends there are safe and well.

US jets dropped bombs on Great Barrier Reef — Because reasons! Oh, well. At least they were inactive.

Eight-Corner Store: 1904 — A cool photo from historic Cuba.

Overweight? Maybe You Really Can Blame Your Genes

Candidate for Roanoke County Board of Supervisors: Religious Freedom Only Applies to Christians — Ah, the patriotism of conservatives. Now 100% Constitution-free, except for the Second Amendment no doubt. (Snurched from Slacktivist Fred Clark.)

Satanic Temple Sees Westboro Baptist’s Funeral Protests, Raises Them Gay Wedding On Top Of Fred Phelps’ Mom’s Grave — Hmm. (Via [info]danjite.)

The Wealth of Nations: The U.S. is No. 1 in Inequality — we’re number one! We’re number one! Go USA!

QotD?: How many people did you spend your weekend with?


7/21/2013
Writing time yesterday: 0.0 hours (chemo brain)
Hours slept: 6.25 hours (solid)
Body movement: 0.0 hours (away from home)
Weight: n/a (away from home)
Number of FEMA troops on my block conducting Department of Justice investigations of white patriots: 0
Currently reading: Real Happiness: The Power of Meditation: A 28-Day Program by Sharon Salzberg; Leviathan Wakes by James S.A. Corey

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[cancer|movies] Filming the Roadtrip to Mordor

From an announcement by Waterloo Productions:

Roadtrip to MordorAuthor Jay Lake has been given 3-6 months to live. Before he dies, he’s going to take his daughter to New Zealand. We want to make a documentary of their trip.

This is an effort parallel to the Lakeside documentary, also from Waterloo Productions. Producer Donnie Reynolds wants to follow me, [info]the_child and Lisa Costello to New Zealand. We’ll be touring both the South and North Islands in the company of the redoubtable team of [info]danjite and [info]khaybee. Donnie wants to fold this into the larger effort of documenting my life and death.

Note this fundraiser isn’t to pay for our trip. I did that out of the overage of funds from the Acts of Whimsy fundraiser last spring. That’s already down to all of you who supported and contributed with such incredible generosity. This effort is to get Donnie, his second cameraman and all his equipment from Texas to New Zealand and back. The whole project is off budget from Lakeside.

This is important to me because the trajectory of my illness means I’ll never make it to Antarctica like I’d hope. New Zealand will by my last great adventure shared with my daughter and with Lisa. I hope you’ll consider helping Donnie out, because we can tell more of my story, and [info]the_child‘s through this process.

I live every day in spectacle here in the decline of my life. Let us make of it a grand spectacle. If you so desire, you can help Donnie out here.

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[travel|events] Forthcoming appearances

This year, I have been on what I’m privately calling my ‘farewell tour’. Given my life expectancy and declining health, this is not unreasonable. Even if I live much more than another year, I do not expect to be in adequate shape to travel past about the end of this summer. If I am wrong, well, it shall be delightful to have a ‘reunion tour’. But for now, I have no travel plans past LoneStarCon 3, a/k/a Worldcon.

June 26th, 2013 (that would be today), 7:00 pm: the suburbs of Portland, OR
Milwaukie Ledding Library Book Club — We will be discussing my multiple award nominated novella, “The Stars Do Not Lie“, as well as my novel Green.

June 28th and 29th, 2013: Seattle,WA
Lisa Costello and I shall be at The Locus Awards Weekend in Seattle, as well as the associated Clarion party.

July 5th, 2013: Seattle,WA
I shall be at that week’s Clarion party in Seattle, along with Lisa Costello.

July 17th to July 21st, 2013: San Diego, CA
[info]the_child and I shall be at San Diego Comic Con. I’ll be signing at the Tor table Friday morning. I do expect to be mobility impaired, and so will likely be using a scooter, which means I will be harder to spot, and spend less time out in public than I’d prefer.

July 27th, 2013: Portland, OR
JayWake here in Portland, Oregon. Surrounded by friends and family, and hopefully you.

July 30th to August 14th, 2013: New Zealand, various cities
[info]the_child, Lisa Costello and I are going to New Zealand. Since I’ll never make my planned trip to Antarctica, this is the next best thing. We used some of the overage from the Acts of Whimsy fund raiser to make this, my final grand act of whimsy, possible. We’ll be traveling around the islands with [info]danjite and [info]khaybee, and possibly with Waterloo Productions. I will publish an itinerary, and there will be Open Dinners in Wellington and probably Auckland. If you’re going to be in Kiwistan those dates and wish to see me, do get in touch with me or [info]danjite.

August 29th to September 2nd, 2013: San Antonio, TX
Lisa Costello and I will be attending LoneStarCon 3. [info]the_child and Mother of the Child will be there as well, along with various other members of my family. If I’m able to walk on the stage, I’ll be in the Hugo Awards ceremony as part of the Campbell Award presentation. Otherwise, Lisa Costello and [info]the_child will stand in for me.

The only plan I have after WorldCon is to attend OryCon if I am able to leave my house. If my health holds better than expected, I may pop up at a few other Pacific Northwest or Bay Area events in the fall and over the winter, but that doesn’t seem terribly likely.

It’s been a lot of fun rattling around this circuit the past fourteen years. My profound thanks to everyone who has helped make my convention-going life as much fun as it has been. All of you party on and party loud.

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[cancer] Talking cancer and genomics with a computational biologist

Yesterday, Dad, Lisa Costello and I had the opportunity to meet with Rich Mazzarella, Ph.D., the Chief Computational Biologist for Appistry, the company that is doing the clinical analysis of my genome sequencing. That was a fascinating ninety minutes. There was no particular agenda to the meeting, though Dad and I had prepared a few questions which were eventually covered in the process of the discussion.

Summary

Rich discussed my personal DNA sequencing and Appistry’s analysis of it, including reference to some issues they had loading the data. We reviewed the value of RNA sequencing, what we can expect to see from it, and how we might accomplish that. Rich promised to call a colleague at one of the few labs doing RNA sequencing to seek a possible second source for that procedure since our primary source is requiring a multi month Institutional Review Board (IRB) process before they can proceed. He also talked quite a bit about the DNA and RNA sequencing process, how it’s being used now and where it’s going clinically. This strayed into some overview of animal genomics and how human and animal genomics work.

In addition to that, we discussed some elements of my diagnosis, treatment plans and the conversation with the oncologist here at M.D. Anderson in Houston. Rich offered some specific opinions on some of the outcomes there.

My Personal DNA Sequencing and Appistry’s Analysis Thereof

Rich said that the data they’d received from the sequencing lab presented some problems at loading. He didn’t believe that the sequencing process was bad, but he felt they’d made some odd choices encoding the data and with their choice of software and protocol for the first-tier analysis. Appistry backed out of that analysis to the raw data and re-encoded with a different software package more to their liking. There is currently a problem with the end portion of genome, which reflects a much larger base pair count than expected. Rich believes this is likely a trivial artifact of data processing, and plans to review my files in the next few days. He feels it may be two to three weeks before a final report is available, but he can provide an interim report sometime next week.

What we can expect to see in the report is a summary of overly activated gene complexes which may have clinical significance for me and my cancer. To that end, we also talked about the process of cross-referencing those identified gene complexes with pharmaceutical databases that list drug-gene interactions and provide suggestions for drugs targeting the identified gene complexes. Rich mentioned that Appistry will shortly have access to a database at M.D. Anderson which he feels is superior to their current data sources. This is one reason for the delay in getting us a final report on the gene sequencing; he wants to use that database to run the cross-reference.

The Value of DNA and RNA Sequencing, and What We Can Expect From It

We talked about the value of the sequencing process, especially in light of an observation made by my M.D. Anderson oncologist that the science was too far in advance of clinical practice to be useful. Rich clearly didn’t agree with that, though he conceded that this was an issue. Up until this point, and for the next few years, DNA and RNA sequencing are going to be personal medicine. There aren’t yet best practices or regulatory guidelines for how apply these technologies, and many doctors are either resistant to or indifferent because of this. In my experience thus far, the team at at my home hospital is interested in learning more from this process, and applying whatever we can learn to my clinical benefit.

Rich indicated that identifying the active gene complexes via DNA sequencing was only half the battle. He felt that RNA sequencing was if anything perhaps more important, as that will indicate which genetic instructions are being most widely executed at the cellular level. This in turn would point to the most likely treatment targets. The challenge is that RNA sequencing resources are even more scarce than DNA sequencing resources. We have a request into a major university with which Appistry has affiliations for RNA sequencing, which they are willing to do, but right now that request is pending a multi-month IRB process. This is another area where the lack of consistent regulatory guidance and the absence of best practices causes problems. Rich knows a scientist at another institution who may be able to do the work for us on a faster turnaround basis, and will be following up.

He confirmed my feeling that fundamentally we are still shooting in the dark here. Rich’s point was that if we do reveal treatment targets through DNA or RNA sequencing, we can have a much higher degree of confidence that those treatments will be effective. Instead of working from statistical medicine as oncology normally does (i.e., out of every 100 patients with my cancer history, X% will respond to treatment A, while Y% will respond to treatment B, etc.), we are aiming for personalized medicine based on my precise genetic factors (the DNA sequencing) and a close look at what’s actually going on inside me at the cellular level (the RNA sequencing).

The DNA and RNA Sequencing Process, Including Use Notes and Comments on Animal and Human Genomics

We talked about the current state of play in DNA and RNA sequencing. Rich has been working in this field since the early 1990s, including about 10 years with the Human Genome Project. The throughput on these processes is still very minimal, vastly below the levels required to be clinically useful. Even now, with the current generation of sequencing equipment and analysis software, it can take multiple calendar weeks and many person-days and computing-hours of effort to process one DNA sequencing from start to finish.

To date, perhaps several dozen people have made clinical use of DNA sequencing, and almost none have made clinical use of RNA sequencing. All the uses that Rich is aware of thus far have been one-offs, much like my own. The first early phase clinical trials seeking to develop repeatable data and best practices in application to specific diseases are only just getting started.

Essentially, this is still a boutique or craft service with no commercial availability yet. The effort around me is near the leading edge of the science and well beyond the leading edge of clinical practice. Even on a case-by-case basis, it can be difficult to get work done, especially work with clinical applications.

We talked about the variation in human genomes. This amounts to rather less than 1% of the total human genome. We share 60% or more of our genome with mice, for example (and presumably other mammals). Rich discussed the value of conservation in genetics, and copy density, specifically how a high copy density (i.e., number of repetitions of a gene within a total genome) can reflect both the importance of that gene through redundancy and the opportunities for evolutionary change through plasticity. One of the things they look for in the DNA sequencing is that copy density, as cancer (as well as other disease) can switch off or delete gene copies that might be effective in fighting them — this is called reduction in heterozygosity.

My Diagnosis and Treatment Plans

Rich agreed with the M.D. Anderson oncologist’s negative view of prescribing Vectibix for me at this time, given my recent metastatic history. Also, after reviewing my genetic test report from my home hospital, he questioned the use of EFGR inhibitors against a tumor with an EFGR resistant mutation. I told him I’d asked this same question and been told that the evidence of EFGR resistance was literally a handful of cases, and wasn’t considered statistically significant.

He also looked up the drugs cited in the experimental study I’ve been referred to here at M.D. Anderson. Rich did not feel they’d be particularly effective for me, and considered going forward with the Regorafenib to be the best option by far for now, pending new ideas emerging from the DNA sequencing and analysis or the proposed RNA sequencing and analysis.

Rich emphasized the value of multidrug treatments with respect to cancer treatment. This has to do with the mutation rate in response to selection pressure from the drugs being administered. A single drug treatment requires only a small mutation for the cancer to become resistant. A multidrug treatment requires two, independent mutations, which squares the odds in my favor. This suggests to me that even if we do go forward on Regorafenib, we should consider a second drug at the same time.

Dad asked about the citation of Celebrex as an off-label cancer fighting drug due to its role as a COX-2 inhibitor. Rich pointed out that if I were taking daily aspirin (which I am), I was already taking a COX-2 inhibitor, so the role of Celebrex for me would be relatively minimal. I want to discuss this with my medical oncologist at my home hospital, however. I do know they are supportive of the sequencing information and potential new directions in prescribing. Rich felt like I really needed an oncologist who was a Ph.D./M.D. with some specific expertise in this area.

Miscellaneous Details

We learned a few other things. For one, Appistry writes the software that manages all of FedEx’s air express dispatching. Dad asked how they had gotten from there into genomics. Rich said that from an IT point of view, it was all Big Data. We talked about how the Appistry server arrays were configured to be highly fault-tolerant without central controllers to provide a single point of failure, and how analysis of sequencing data was parceled out among those servers.

I wouldn’t have been having this conversation yesterday if not for the Acts of Whimsy fundraiser; all the hard work by Mary Robinette Kowal, Catherine Shaffer, and so many others who contributed their time and effort; and most especially the generosity and support of all of you who supported this process.

You guys brought me to this meeting, and to the testing and clinical effort behind it. If we find a path forward to extend my life or possibly cure me, it will be because of you.

Thank you.

Meanwhile, today, I take my leave of Texas once again and fly back to Oregon. Lots to think about.

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[cancer] The fundraiser in retrospect

Wow.

That’s all I can say.

Wow.

Yesterday, the Acts of Whimsy fundraiser closed. $48,665 was raised from 1,331 supporters. Donations ranged from $1 to $500. (More on this below.) The unlock levels were multitudinous and hilarious, and too many to list here, but my thanks to everyone who threw themselves into this, both formally up front and informally along the way. My most special thanks to Mary Robinette Kowal and Catherine Shaffer for organizing and managing this thing. They are amazing human beings and dear friends.

As you probably are aware, the point of this fundraiser was to meet my expenses for genomic testing of my tumor tissue. I’ve had colon cancer for almost five years, and been through four (or five, depending on how you count them) generations of metastasis since then. These are increasingly frequent and increasingly aggressive events for me. In the time since the fundraiser was launched, I’ve been diagnosed as incurable — not terminal yet, but that’s the next step. Genomic testing gives us opportunities for both life extension and the slim but not vanished possibility of a cure.

What the genomic testing and subsequent clinical analysis do, specifically, is identify genes or gene sequences that are overly active, and may be associated with tumor formation and tumor growth. An example of this is the PTGS2 gene responsible for COX-2. The clinical analysis then involves a second step of identifying pharmaceuticals that engage those suspect genes as therapeutic targets, much as with COX-2 inhibitors. That can suggest lines of treatment to my oncologist that may lie outside the normal clinical guidelines for my type of cancer. As I’ve essentially outlived those guidelines already — most people in my cancer cohort are either cured or dead after five year — this is important. My cancer is obvious refractory to chemotherapy (meaning it laughs at the drugs and carries on), and based on the genetic information we extract, may not even be colon cancer at all, but something else masquerading as colon cancer. So we’ll reach into both the oncological pharmacopeia as well as the wider world of pharmaceuticals looking for potential life extenders and life savers.

It’s a new technology, built on some pretty new science, so my going through the process is also part of the validation of this testing as a clinical best practice. In other words, your funds, spent through me, are benefiting SCIENCE!, as well as future cancer patients. My life might be spared, or at least eased before my passing, but this will also help millions of others.

I commented on this yesterday, but just to give an update on how the money is being spent:

  • 5%, or roughly $2,400, will go to charities or other fundraisers. I’ve already regifted $850 of that amount.
  • $13,000 has already gone to the primary sequencing effort now nearing completion in the lab.
  • Up to another $1,000 for fulfillment expenses associated with shipping the 100s of GB of data generated by this testing.
  • $7,000 budgeted for RNA sequencing, which is a separate type of testing that may yield additional pharmaceutical options.
  • $2,500 to meet the direct out of pocket costs for my third liver resecting, last month’s surgery.
  • About $1,000 more to meet co-pays which are exempted from my insurance carrier’s out of pocket limitations.
  • $5,000 set aside to make up income shortfalls from future rounds of Short Term Disability which I will likely take this year.
  • The balance of the funds will be held in reserve pending identification of additional extraordinary expenses not covered by health insurance, and to provide me with the opportunity to take some time off with my loved ones as possible.

One final note I wanted to make was about the donations. I am grateful to everyone who gave, at any level (or in some cases, frequency). But in a sense, I’m most impressed by what the political types call the “small dollar donors”. Anyone who clicked to send me $1 or $3 or $5 is someone who probably needed those dollars more than I do. For hundreds of people to engage at that tells me something about how much love and generosity there is in our genre community.

Thank you all. From the bottom of my heart.


If you missed the fundraiser, but still want to chip in, there is a Tip Jar link on the top left corner of my home page.

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[links] Link salad spares you your life from this monstrosity

Richard & Shela West Housing Fund — A cancer survivor with much larger issue than I have. I’ve donated.

Klingon Act of Whimsy — Five Klingon pickup lines, as part of the Acts of Whimsy fundraiser. Heh.

Joker’s next move will shock Bat-fans — I can only remind you of this.

Alexander Graham Bell and a tetrahedral kite — Wow…

Sheep Marks and Identification — Department of things you never knew you never knew. Including smit marks and lug marks. You’re welcome. (Via Daily Idioms, Annotated.)

Moshers, Heavy Metal and Emergent BehaviourThe collective behaviour of moshers at heavy metal concerts is mathematically similar to a disordered 2D gas, say physicists.

‘Young’ black hole is nearby, NASA says; doorway to a new universe?

Shifting Cultural Sensibilities and Valentine’s Pleas — Wow. Just wow.

100 Abandoned Houses — Detroit real estate. Wow… Also, this: 30+ of the most beautiful abandoned places and modern ruins I’ve ever seen. (Thanks to Lisa Costello.)

The USPS Media #FAIL — This is an important story that almost no one seems to understand. (Via David Goldman.)

To the Pope-o-Mat!Scenes From a Multiverse on the pope’s resignation.

Massive Police Shootout in Cleveland Despite Lack of Criminals — I definitely feel safer now. (Via David Goldman.)

Majority of Republicans want to impeach Obama because they hate AmericaFor some reason, when people go and get an education, they start to disagree with a lot of Republican positions (this is related to the GOP’s judge, journalist and scientist problem). So, rather than conclude that maybe people with educations don’t like Republicans because, you know, they’re now better informed about the world – Republicans have concluded that college “brainwashes” kids to become liberals, and thus education is bad.

QotD?: Does Beelzebub have a devil set aside for thee?


2/14/2013
Writing time yesterday: 1.0 hours (2,400 words on novella in progress, to 11,100 words)
Hours slept: 6.75 hours (solid)
Body movement: 0.5 hours (stationary bike)
Weight: 230.8
Number of FEMA troops on my block helping illegal immigrants infiltrate America: 0
Currently reading: Mort by Terry Pratchett

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[cancer|personal] The final hours of the fundraiser, pushing for a strong close for SCIENCE!!!

I was going to post a concluding summary about the Acts of Whimsy fundraiser this morning, but I see the effort is still open in its final hours. We’re pushing for a final $50,000 stretch goal, and we’re pretty close.

The original goal was $20,000, but I’ve already exceeded that amount in funds spent or committed to medical needs. The overage is very much to the point, and going to good use. Trying to keep me alive a few more years seems pretty worthy to me, but of course I’d think that. Also, SCIENCE!

Among other things, I appear to be one of the first patients to ever commission the genomic testing and analysis on a private basis. Possibly literally the first. Up until no, it’s been an experimental process. And it’s still expensive. Tests that will be less than a thousand dollars in a couple of years are still five or ten thousand or more. We paid $13,000 for the primary genomic sequencing. We’ll pay about another $7,000 for the RNA sequencing that the analysis group recommended. Plus there’s exome sequencing, though I think we’ll get that data from the original run.

But in me doing this, and in all of you funding this, we’re making it easier and more useful for the next patients who need it. I’m already a statistical outlier in a number of ways, from some of my unusual drug side effect responses, to my notable longevity with my type of cancer — the vast majority of my cancer cohort are either cured or dead at this point, while I’ve expressed between three and five generations of metastasis, depending on how you count them.

Whether or not we ever find s cure, this fundraiser and the efforts it is paying for are helping others survive. We are blazing a path and even teaching doctors as we go.

So for that, I think we should all be thankfully proud.

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