Ten days ago I got an email from Anthropic. My project got into their AI for Science program, with $30,000 in Claude credits. Thank you to everyone in the program for supporting this 🫶
The project is my own tumor 🥹
I'm 35 and I have stage 4 breast cancer. I'm a software engineer, and since March I've been building tools to understand my cancer. Today I can write the name of a gene and see it in thousands of cells of my tumor.
My liver metastasis, cell by cell. Each dot is one cell, and the color shows how much of one gene (ESR1) it has.
I also need someone who can manufacture a personalized vaccine for me, and a hospital that can give it. More on that at the end.
How it started
For a long time the doctors said my pain was sciatica. It kept getting worse, so in the end I paid for an MRI myself. The result came by email in January 2024, and I read it alone. I was sure it was a mistake.
In March this year my cancer progressed, and I decided to learn everything I could about my tumor.
Where things stand
My cancer is in my liver and my bones. My tumor is a rare type. There is no specific guideline for a case like mine, and every answer takes weeks.
My liver in 3D, built from my own CT scan. The yellow spots are lesions. Some were found by AI and a radiologist hasn't confirmed them yet.
The goal is a personalized vaccine, made from my own tumor, so my immune system learns what to attack.
When I started I didn't really know what a neoantigen was. Now I can read a sequencing report and talk with researchers, and I don't get lost so often.
How it's built
I build it with Claude Code. It's a team of more than 30 agents, and each one has one job. One reads papers and looks for trials in other countries. Another only checks every number against its source. When a question is hard, two or three agents answer on their own, and if they disagree I see it. Reports and files come to my phone on Telegram, and nothing goes out until I say yes.
My doctors make every medical decision. The agents help me get to each appointment with better questions, and the experts check them. Sometimes they change them a lot.
The biopsy protocol
I needed a new biopsy, in Zürich. You can't repeat a biopsy easily. If a sample is not taken, or is not stored the right way, it's lost.
So I wrote the protocol with my system: which samples, and how to keep each one depending on what we want to analyze later. Then the team at Dr. Paloma Cejas's lab at Dana-Farber, who would analyze the samples, reviewed it and made it better.
My tumor, cell by cell
This one still gives me goosebumps.
Dr. Cejas's lab sequenced my liver and bone metastases cell by cell, with a technology called 10x Flex that works on stored tissue. I have the data on my laptop.
No conclusions yet. We're going through it slowly with the team.
A 3D map of my disease
I had two PET scans and a lot of reports, and I couldn't see the whole picture.
Left: every bone lesion from my two PET scans, colored by tracer. Right: one of my vertebrae in 3D, seen with each PET and with CT.
So I built a 3D map of my metastases from those two scans. We used it with my medical team to talk about which lesion to biopsy. They made the call. It helped that we were all looking at the same map.
When my port stopped working, I rebuilt it in 3D from three CT scans taken months apart, to see if the catheter had moved.
My port and its catheter in 3D, rebuilt from three CT scans. The purple device is an illustration.
Two years of blood tests in one screen
Every blood test comes as a PDF. After some months you have dozens, and nobody reads all of them.
I put them in one panel: more than 1,800 values from over 70 blood draws since December 2023. A doctor can see quickly how each value changed over time.
I need a vaccine manufacturer and a hospital
The next step is the whole exome of my tumor compared with my healthy DNA. After that, AI can't help me much.
Thank you to everyone who donated or wrote to me. If you can make the vaccine or give it, or you know who can, write me. My DMs are open, and everything is on helpmiriam.com 💜
