#genotyping — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #genotyping, aggregated by home.social.
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T-DNA insertions: more surprises than you think 🌱🧬.
PCR can miss extra T-DNAs & complex rearrangements. Long-read sequencing captures the full picture. Still super relevant for plant genomics!
🔗 https://doi.org/10.1186/s12864-021-07877-8
#PlantScience #Genotyping #LongReadSequencing #Arabidopsis @PuckerLab -
#23andMe Sale Shows Your #Genetic Data Is Worth $17
23andMe sold genetic data of 15M people for $256M to a #pharmaceutical #Regeneron. 23andMe does not perform full genome sequences. It instead does #DNA #genotyping, which look at parts of #genome that vary from person to person.
Sale to Regeneron means #gene data collected by 23andMe will be used for development of new #drugs, which felt like the most likely and perhaps best-case scenario for the company’s bankruptcy.
https://www.404media.co/23andme-sale-shows-your-genetic-data-is-worth-17/ -
Beyond #Poliomyelitis: A 21-Year Study of Non-Polio #Enterovirus #Genotyping and Its Relevance in #AFP in São Paulo, #Brazil
Source: Viruses, AbstractIn the context of the near-global eradication of wild poliovirus, the significance of non-polio enteroviruses (NPEVs) in causing acute flaccid paralysis (AFP) and their impact on public health has gained increased attention. This research, conducted from 2001 to 2021, examined stool samples from 1597 children under 15…
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Hands up ✋ who's working on #polyploid #genotyping and imputation?
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With phased/haplotype-aware genomes becoming more frequent I'm Curious 🤔 to hear from others how you have been handling SNP/variant calling against them 🧬 Are you sacrificing heterozygous calls and aligning to all haplotypes, or only using one of the haplotypes as the reference, or do you have a pipeline tool that compares and combines the haplotypes during variant calling? #bioinformatics #genomics #genotyping
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And it’s finally here 🥳 {resurface} my #rstats package for imputing missing genotype allele frequencies, such as those from pooled samples or populations. Stems from some scripts I wrote nearly 10 years ago, which I can now finally say is open. I hope to progressively add more imputation options.
#imputation #genomics #genotyping #bioinformatics
https://github.com/lpembleton/resurface -
Interested in how the #HBV population is structured? What genetic signatures differentiate genotypes? We used a computational approach to identify which amino acids (aa) in #HBV are key in #genotyping and found several key aa in #polymerase spacer domain. Draft available online in Virus Evolution but final PDF should be available soon. This was a partnership between the Universities of Lisbon, Tel Aviv, Oxford and Cambridge.
https://academic.oup.com/ve/advance-article/doi/10.1093/ve/veac116/6887177?login=false
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Exploring SSAfrica plasmodium genetic diversity using microsatellite variants & SNPs in resistance genes
@malariagenomics
@epiverse
#Malaria #genomic #microsatellite #genotyping #amplicon
https://www.nature.com/articles/s41598-022-26625-w -
CW: boring #bioinformatics
We have been looking for a simple and fast way of #genotyping a #bam file at known sites that we get from a reference #vcf.
We ended up using #freebayes with -@ -l --report-monomorphic options.
BUT I was quite surprised by the lack of information and clear documentation for performing this seemingly trivial task without going through the whole SNP calling stuff (we don't want to do it).
Did we miss something ? Is there a standard, well documented method out there ?