I watched the announcement and gave it a spin as I'm a heavy user of cowork/code. So far I'm super impressed. I used it to analyze my whole genome sequencing data I have as my son has a rare genetic condition. I used it to answer a question I'd asked a few bioinformaticians to help me with but never got a satisfactory answer, it solved it in about a minute - whether his n-of-1 de novo, heterozygous single nucleotide mutation was likely passed down from mom or dad. It performed a read-backed phasing analysis on the data, identified a nearby SNP with overlapping coverage where mom was homozygous and dad was heterozygous. Identified my variant on his mutated allele so looks like it came from me..
It also crosschecked my data against AMCG Secondary Finding genes and ClinVar likely pathogenic/pathogenic variants and came back with identical results to my Natera Horizon carrier screening results.
I'd previously tried and failed to do this all with some ChatGPT guidance and subsequently hired a couple of bioinformatician post-docs at top tier universities via Upwork who had failed to give me satisfactory results.
Not sure how to feel about this. I think its super cool that you can dive into this, but it sucks that its your son that has this condition for which you have to do this analysis. I hope it all turns out well.
Quick question: where did you get your genome read and get the raw files? As far as I know, as service like 23andme does not give you back the raw files.
Thanks for the kind words. Actually we got the trio whole genome sequencing through our neurologist/geneticist a couple of years ago. It was performed by a company called GeneDx. They interpreted the data at the time which is how we got to a diagnosis but knowing I'd want to dive in to it later I asked for the raw data. They provided it as the raw CRAM files and also the VCF (variant call files) which are a bit smaller. But each company has its own pipeline and for example uses different versions of the reference human genome which made working with the data quite hard for me and the people I enlisted. Claude Science seemed to make very easy work of it. Also to be clear, the question I was trying to answer was whether his mutation was likely passed down through my sperm or mom's egg - neither of us have the mutation in our own genomes. Turns out spontaneous (de novo) mutations are much more common in sperm because Spermatogonial stem cells have undergone many more cell divisions over their lives. Everyone has de novo mutations (70+), one of his just happens to be in an unlucky location.
GeneDx aren't direct to consumer so you'd need to get it ordered through a physician but there are some DTC options for example, Dante Labs, Nebula Genomics, Sequencing.com but I can't speak to the quality of their testing.
23andMe doesn't do whole genome or whole exome sequencing. They use a microarray technology that tests for about 650,000 single nucleotide polymorphisms. You can actually download the your raw data on 23andMe and do your own analysis or use a tool like promethease.
I'm an MD so I'm quite comfortable exploring this data and whatever it uncovers. Tools like Claude Science are going to put a lot of power in the hands of every day people, potentially outside the guidance of genetic counseling/docs, which many organizations in the past (including the FDA) have been hesitant to allow.
I can vouch for Nebula. Just follow their recommendation to not get the 1x service if you want to use the data for medical reasons. The more passes they make, the more accurate the result.
Downside: those files are HUUUUUGE. Have a good reason to do it before pulling one down and trying to work with it.
Files are huge for sure (mine are like 25Gb x 3 of us) but Claude Science / Macbook Pro M5 Max knocked out my analyses in minutes using command line tools like bcftools and scripting. Honestly think this opens up WGS data to much easier analysis and refreshing those analyses in minutes as new discoveries are made.
I'm working on a website that lists veterinary practices owned by private equity or large corporations to help people make more informed decisions about where they take their pets. It started as a small passion project after our dog (who was sideswiped by a car) died at the hands of a vet practice recently acquired by private equity. We were billed over $13k for 2 days of care where his diagnosis and the opportunity to treat it was missed, there was zero continuity of care, no medical leadership and predatory billing practices.
That’s a great idea and I wonder if you’d consider including the UK. My vet got taken over and now they keep spamming me with “offers” - so I no longer know if my dog really needs a checkup or not.
Thanks! Actually I did add the UK very recently but this is a good reminder to improve the UI to make it more obvious, if you go to https://www.privateequityvet.org/vet-list/map.html you can toggle between US and UK. I have over 2000 practices listed in the UK.
It's been a painstaking process of combing consolidator websites (eg. PetVet Care Centers, NVA) for practice names, verifying and adding them to a list over the course of over a year. I now get many people writing in to report practices that aren't on the list - admittedly it's not complete list as practices are still being acquired (although independents are now in the minority) and often the old practice branding is kept and the fact it's PE owned is hidden.
If anyone wants to see how private equity has transformed the veterinary industry check out www.privateequityvet.org/vet-list - over 7000 practices mapped across the US so far. Our dog died at the hands of a recently acquired PE practice :(
It makes rules harder to break? It inspires kids to be knowledgeable because it can be cool? It teaches thinking outside the box? It makes you question your surroundings and not blindly following the rules?
Auricle is developing a next-generation neurostimulation implant to restore hearing and the ability to understand speech in the millions of people who no longer benefit from acoustic amplification with hearing aids but who aren't prepared to take on the risks of a cochlear implant.
We're searching for a full-time engineer to join our founding team. Our device and prototypes are partly mechanical, electrical and software so we'll need someone who can wear multiple hats but is comfortable primarily in the mechanical domain as we execute on early clinical and pre-clinical studies.
Experience with rapid prototyping using 3D printing, CAD and bench models is a must. Experience of medical device development within a quality management system and developing pre-clinical models is highly valued. Bonus points for electrical engineering experience, programming experience (Python/Matlab) and a passion for auditory science. More than anything, we're looking for someone who will be highly motivated to help bring a complex but life changing device to patients.
We're a small team formed out of Stanford and backed by YC (W21), based out of Fogarty Innovation in Mountain View. The role is primarily in-person with very occasional travel to study sites and with some flexibility for hybrid work from time to time.
We're excited to hear from you! francis@auricle.com
Congratulations on the launch, this looks like a super useful product and I'll give it a try. I've been responsible for conducting hundreds of qualitative interviews over zoom in the past and while the insights were very useful, it took me months to execute. Scheduling and no shows were a massive pain and this has the potential to make it almost hands-off.
Auricle is a medical device company developing a breakthrough minimally-invasive neurostimulation implant to restore hearing in patients who no longer benefit from hearing aids but aren't prepared to make the jump to a cochlear implant. The company is a spin-out from Stanford and YC-backed. We're looking to fill two roles:
1) Our first full-time mechanical engineer to lead electrode design and surgical implantation. Experience with small-scale medical devices ideal, bonus points for experience with implantable devices. Role will be in-person in the Bay Area.
2) A simulation modeling engineer for a summer internship with potential for full-time role, will consider full-time to start for the right candidate. Experience with 3D modeling and Finite Element Analysis required, bonus points for experience with Sim4Life and/or NEURON. Role can be remote or in-person.
You'll be joining an early team working on a very exciting real-world application with a huge market opportunity ahead. Interested? Please contact Francis, Co-founder & CEO email: francis@auricle.com
That's exactly why Tesla are so good at what they do! I've had VW , BMW and Ford rental cars in the last year and they are literally stuck in the dark ages when it comes to on car entertainment and the things that just work and are very responsive in a Tesla.
It also crosschecked my data against AMCG Secondary Finding genes and ClinVar likely pathogenic/pathogenic variants and came back with identical results to my Natera Horizon carrier screening results.
I'd previously tried and failed to do this all with some ChatGPT guidance and subsequently hired a couple of bioinformatician post-docs at top tier universities via Upwork who had failed to give me satisfactory results.
And this is just getting started!