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Vibe coding my way to a healthy family: Introducing Gamow Labs

ddmckinnon.com

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Re: Vibe coding my way to a healthy family: Introducing Gamow Labs

#121

Post by dmckinno »

maaaaattttt wrote: post #116

I would be curious to know if the WGS was done using short read or long read. There is a lot of hope that long read is "just" what is needed to catch these type of cases nowadays (not sure about this particular one).

This was short read.

I'm in the process of getting my first batch of long reads, but I am skeptical that this is the "just" what's needed. There is little doubt that long read > short read, but I think that computational techniques for both need to be improved significantly.

There is already some clinical evidence to support my hypothesis. The first clinical long read trial at Kansas City Mercy showed a 10% bump in diagnostic rate, which is great but not fully solving the problem: https://news.childrensmercy.org/unlocking-answers-faster-chi...

Re: Vibe coding my way to a healthy family: Introducing Gamow Labs

#122

Post by mixdup »

picofarad wrote: post #109
mixdup wrote: post #104

Earlier quoted context omitted.

>The question is where that ends. Terminating due to a susceptibility to aggressive cancer? Maybe. Due to lower intelligence? Perhaps. Lower physical strength? Probability of autism? Unsymmetrical facial features (e.g. 'ugliness')? Why/how a pregnancy started (consensually or not for example) or the motivation behind making that choice (just don't want a kid, some genetic diagnosis, etc) are irrelevant. If abortion i…

I am pro-choice, but really I'm hoping there is enough advancement in medicine to "fix" genetic issues and the sorts of things people would terminate after a positive test result. If that is actually possible someday, legitimately, I am switching to pro-life. With only rape/incest or mother's certain death as reasons for termination. I realise this is a weird and nuanced take, but I was adopted and it was back when t…

If you feel that abortion is killing an otherwise viable human being, then you should be pro-life now. Especially if you're anti-death penalty and feel that no one should die for any reason. On the other hand if there are any reasons why abortion would be ok, why aren't all reasons ok? Either it's wrong or it's not, and if you are on the pro-life side why should a child be punished because of how it was conceived? On the other hand, if you believe that a non-viable fetus is not a live human being, the decision to stop before it gets to that point is independent of any reasoning

Having conditions on abortion are completely nonsensical and irrational. I don't get it

Re: Vibe coding my way to a healthy family: Introducing Gamow Labs

#123

Post by arjie »

dmckinno wrote: post #100
arjie wrote: post #28

Huh, this is fascinating. My wife and I did IVF with WGS in order to find a much less catastrophic shared genetic condition[0]. We have the FASTQs for my parents, and brother, and my wife and me, and our daughter (and our other embryos) and I've run it through the standard Opus[1] (since 4.5) and none have contradicted our genetic counselors or IVF doctors. This is an interesting, and devastating, condition far more…

Opus-4.8/GPT-5.5 coupled with their respective harnesses will do a good job for more vanilla cases, I realized a custom harness and set of skills and MCP servers became essential as complexity increased (mostly hard SVs). I'll get an eval and more technical post out in a few weeks. If you are open to chatting about your experience, I'd love to hear from you. I spend a lot of time learning from and supporting other ra…

Certainly. If there’s something I can do for you that will assist I’m happy to do so. Email on profile and I don’t mind chatting in person in SF should you so desire.

Re: Vibe coding my way to a healthy family: Introducing Gamow Labs

#124

Post by grvdrm »

brayhite wrote: post #114
grvdrm wrote: post #91

Earlier quoted context omitted.

Dad of 2 girls. 8 and 4. Not saying that life couldn’t have been equally great without them, but they are amazing. Rewired me in best way possible: to appreciate non-work life as much as anything else (perhaps more). None of us really know what to do!

Becoming another individual’s whole world changes your own, for better or worse. I was a “such is life” type of person when experiencing tragedy, and fairly ho-hum during joyous moments. With kids, something changed, or “rewired”. I tear up at Bluey episodes and lose sleep due to irrational fears of an early death and not witnessing moments in my kids’ lives. Having and raising kids is a trip.

Right there with you on unexpected tear-stream moments, fears, but also all those happy moments you can't anticipate.

In past year I've watched my older (8) start competing on a cheerleading team. Immense tear-streaming joy watching her light up in front of a crowd and build confidence. I was immediately overcome the first time and always feel a strong swell of emotion.

Re: Vibe coding my way to a healthy family: Introducing Gamow Labs

#125

Post by MattGrommes »

darkwater wrote: post #110
w0m wrote: post #106

Earlier quoted context omitted.

I had no idea I would turn into a helicopter. it's kind of crazy how it rewires you.

Being an helicopter has a specific (and negative) meaning; caring and worrying for your kids seems just how many humans are wired.

The real difficulty is deciding what caring means. Some people decide caring means getting onto your adult child's job interview call because you think they need help. For others, caring means giving them a safety net but letting them learn and possibly fail on their own.

Re: Vibe coding my way to a healthy family: Introducing Gamow Labs

#126

Post by salubrioustoxin »

ACD is devastating and insidious. Every baby admitted to the NICU, even for minor breathing issues, should get a rapid genome.

That said, it’s notoriously difficult to call these types of causal microdeletions, outside of a few known ones. Any insights you make on those efforts would advance the field quite a bit.

Re: Vibe coding my way to a healthy family: Introducing Gamow Labs

#127

Post by abirch »

331c8c71 wrote: post #112
abirch wrote: post #98

Earlier quoted context omitted.

There can be plenty of prior art; however, AI can democratize that knowledge. There are many things it's helped me accomplish which are trivial to people who are far more knowledgeable than me.

I am not sure what specifically you mean by "AI" here but it's a bit naive (no offence) to think the field is so dumb that it haven't been looking at "AI" for a few years already. See https://www.biorxiv.org/content/10.1101/2023.10.02.560464v1 for instance nostos/limbus, genoox, engenome, congenica are a few companies/products that I have heard about and have been around for years (the last one was defunct from what…

I thought that the author had used AI to vibe code the software to help him look through the genomic data

"Like all of the others, this WGS came back non-diagnostic. Unlike the others, my heartbreak had passed the point of hopelessness and I was ready to do something. I contacted every lab we had worked with and requested access to all genomics files. I was going to figure this out myself.

"After a few days, my initial results shocked me. The prototype I built not only accomplished my original goal of confirming that Warren seemed healthy (spoiler: everything is fine), but it found the genetic mutation that took our first son Owen’s life. How could something I built so quickly outperform the top sequencing lab in the country?"

Re: Vibe coding my way to a healthy family: Introducing Gamow Labs

#129

Post by fabbbbb »

Silamoth wrote: post #113
fabbbbb wrote: post #37

Earlier quoted context omitted.

How will this lead to saving lives? The only possible consequence is abortion?

If a couple gives birth to a baby with a debilitating condition and dies after 6 weeks, that’s an additional baby death. If instead of having that baby, a couple gives birth to a healthy baby, it will likely survive into adulthood, meaning there’s one less baby death. It sounds like you just take issue with abortion. That’s more of a you problem than a problem with quantifying baby deaths.

This is an anecdotal example, isn’t it? What do people today abort for, after genetic diagnosis? Down-Syndrome and other markers with highly random and non-fatal outcomes.

I have no problem with abortion itself.

Re: Vibe coding my way to a healthy family: Introducing Gamow Labs

#130

Post by fabbbbb »

nkrisc wrote: post #36
fabbbbb wrote: post #16

It reads like a specific genome would lead to deterministic outcomes. It does not. Life is messy. Most Down Syndrome people have happy lives, some can even live alone and have an independent daily live. Life expectancy is up to 60 years. Yet in Iceland „Democratization“ of genetic diagnosis lead to basically 0% Down Syndrome kids (births). Where does this stop? What with someone of a genetic indication of aggressive…

People born with Down syndrome deserve all the respect and dignity any other person does. I have two kids. If I could have chosen whether or not they would be born with Down syndrome I would choose would “without” every single time. If either of them were born with it I would love them the same but I would never choose it, if I had the choice to make.

Is there such choice? Today parents are not doing that choice but choosing to stop the life of the kid with Down-Syndrome. So I’m not sure they are receiving „all the respect“ today - are they?
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