hlatyping
gnomad-browser
hlatyping | gnomad-browser | |
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1 | 15 | |
52 | 78 | |
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0.0 | 9.7 | |
about 1 month ago | 2 days ago | |
Nextflow | TypeScript | |
MIT License | MIT License |
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hlatyping
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Ask HN: How to be my own genetic disease researcher for my partner?
Here's a post I made on reddit about how to do exactly this:
https://www.reddit.com/r/Nebulagenomics/comments/nhjfpa/how_...
You use the VCF and a java project called the Exomiser, and it will give you output files with all the pathogenic variants marked
In my case and is the case with a lot of rare diseases you could have unique pathology and mutations in a certain gene but that don't show up as pathogenic in clin var. For example my family has a lot of autoimmune diseases and as expected my HLA genes are totally trashed. However none of these mutations have ever been seen and flagged before especially was WGS is so new.
If you only have a list of genes and the genomizer will give you a list of the genes that are the most heaviy affected, you can put them into this app to get some further data and idea about what kind of tissue expression or rare disease spectrums you may be dealing with: https://maayanlab.cloud/Enrichr/
sadly the reality is though you can have all that and it almost puts you at a disadvatnage with doctors because you look crazy and sus claiming you have some HLA mutation or whatever. Who told you that? Oh well I data mined it...uh huh sure....honestly to get it back into the medical system and to be taken seriously you'd probably have to get a doctor to retest it, for example I can can spin this up to get my HLA alleles from my fastq https://github.com/nf-core/hlatyping
But no doctor is going to put that in my medical record until I convince them to run a blood test for the same damn thing.
if anyone wants to help me with my own genetic search woes and help me out or know solutions please let me know. if you want to help me publish or add to that guide somewhere let me know - i asked nebula if they wanted to print it on the blog and they said the'd be interested but I just never cleaned it up
gnomad-browser
- All identified polymorphisms in a given gene, how to find?
- AskScience AMA Series: We're human genetics researchers here to discuss connections between people in different geographical regions. Ask us anything!
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Converting 23&Me raw data into a format usable by Admixtools 2
try one of these: GnomAD (https://gnomad.broadinstitute.org/) 1000 Genomes (http://browser.1000genomes.org) dbSNP (http://www.ncbi.nlm.nih.gov/snp)
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What is the maximum number of human?
Maybe you can ask the opposite question; what are the bounds of of a functional human being. https://gnomad.broadinstitute.org/ GnomAD is a aggregation of healthy human genetic sequences which was primarily built on the aggregated control groups of many genetic sequencing studies. There are studies of this data analysing the co-occurrence of variants in gnomAD which may help.
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Insights from personal sequencing data I can explore.
Maybe something like this? https://promethease.com/ Clinvar for variants that might be of clinical relevance. https://gnomad.broadinstitute.org/ for allele frequencies & some info about variants.
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What are some non-pathogenic alleles of the SNCA gene, or how do I find them?
You could look at aggregation databases such as gnomad https://gnomad.broadinstitute.org/ anything with a frequency incompatible with the disease is likely non pathogenic
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Ask HN: Who is hiring? (March 2022)
Broad Institute of MIT and Harvard | Cambridge, MA | Frontend Software Engineer | REMOTE or HYBRID (New England area)
We are hiring a frontend developer to help lead the next phase of the gnomAD browser, a web application for displaying the world's largest collection of human genome/exome sequences. https://gnomad.broadinstitute.org. Looking for applicants who are excited about data visualization and designing complex interfaces for scientific research.
Apply here: http://broad.io/cq7dw8
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Ask HN: Who is hiring? (February 2022)
Broad Institute of MIT and Harvard | New England | Software Engineer | REMOTE/HYBRID
Our team is focused on building the tools necessary to visualize and interpret massive data sets of human genetic variation and functional genomic information. We have developed gnomAD (https://gnomad.broadinstitute.org), the world’s largest public reference dataset of human exomes and genomes. gnomAD has become one of the most widely used resources in the field, and is now the default reference database for virtually all clinical interpretation pipelines, as well as a standard analysis resource for a wide variety of genetic and biological studies. We estimate gnomAD has contributed to the clinical diagnosis of over 2 million patients with genetic disorders.
Your role will be to maintain the gnomAD browser, our open source web application for exploring gnomAD and related datasets, and develop new scientific functionality as we continue to grow to over 1 million human samples. You will work with a team of software engineers, computational biologists and clinical and research users to develop new features and visualizations that incorporate user feedback. Software engineering skills and an interest in user interface design and data visualization are key. Basic familiarity with genomics and DNA sequencing data is preferred, but not required. Most importantly, the ideal candidate will have enthusiasm for playing a critical role in a team-oriented project and learning new domains.
Minimum Requirements
- Ask HN: How to be my own genetic disease researcher for my partner?
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How to check if a discovered mutation is novel or was discovered before ?
If you're talking about humans, start with gnomAD: https://gnomad.broadinstitute.org/