packeted · HackerTrans

10 days agodiscuss

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.

packeted

10 days agodiscuss

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.

packeted

10 days agodiscuss

Marginally but the data manipulation is actually being done locally as the genome CRAM files are like 24Gb each.

packeted

11 days agodiscuss

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.

And this is just getting started!

packeted

5 months agodiscuss

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.

packeted

5 months agodiscuss

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.

packeted

5 months agodiscuss

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.

The site has become quite a hit and gets thousands of unique visitors each day. https://www.privateequityvet.org/vet-list

packeted

6 months agodiscuss

I'm looking forward to reading your book! Part of my expose of PE in the veterinary business can be found at https://www.privateequityvet.org

packeted

6 months agodiscuss

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 :(

packeted

10 months agodiscuss

Wow, great work. This is the kind of citizen hackery we need in society :)

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