Comments (6)
Found this paper quite helpful in understanding pLI (and its many shortcomings as a metric).
Some additional (or alternative) metrics to consider:
- Variant Effect Predictor: now has a plugin for incorporating precomputed AlphaMissense scores!
ensemblVEP
is a bioc package for interfacing with VEP annotations.
from rare_disease_celltyping.
Ok, so while the data in VEP is super useful, the VEP software to access these annotations is a hot garbage fire that is virtually uninstallable. I tried everything under the sun:
https://gist.github.com/bschilder/8a64d266e0e3ab18075274ad539985ac
However, I was able to extract the AlphaMissense predictions directly! Turns out they already computed per gene scores for the entire protein-coding genome here (see their README):
AlphaMissense_gene_hg19.tsv.gz, AlphaMissense_gene_hg38.tsv.gz
Gene-level average predictions, which were computed by taking the mean
alphamissense_pathogenicity over all possible missense variants in a transcript
(canonical transcript).
With a little extra postprocessing, I got the gene symbols:
am <- data.table::fread("https://storage.googleapis.com/dm_alphamissense/AlphaMissense_gene_hg38.tsv.gz")
am$enst_id <- stringr::str_split(am$transcript_id,"\\.", simplify = TRUE)[,1]
map <- orthogene::map_genes(genes = unique(am$enst_id),
target = "ENST",
species="human",
drop_na = FALSE,
mthreshold = Inf)
am_mapped <- unique(map[,c("input","name")]) |>
data.table::data.table(key = "input") |>
data.table::merge.data.table(am, by.x = "input", by.y = "enst_id")
am_mapped
pLI is still problably worth looking at, but I think ML-based AlphaMissense metric circumvents many of the shortcomings of the rule-based pLI metric.
from rare_disease_celltyping.
Found the latest pLI data from gnomad as well:
https://gnomad.broadinstitute.org/downloads/#v4-constraint
Importing that now for comparison with AlphaMissense.
readme <- suppressWarnings(
readLines("https://storage.googleapis.com/gcp-public-data--gnomad/release/v4.0/constraint/README.txt")
)
pli <- data.table::fread("https://storage.googleapis.com/gcp-public-data--gnomad/release/v4.0/constraint/gnomad.v4.0.constraint_metrics.tsv")
data.table::setorderv(pli, "mane_select",order=-1)
mane <- pli[mane_select==TRUE, lapply(.SD, mean, na.rm=TRUE),
.SDcols = is.numeric, by="gene"][, mane_select:=TRUE]
pli_agg <- data.table::rbindlist(
list(
mane,
pli[!gene %in% mane$gene, lapply(.SD, mean, na.rm=TRUE),
.SDcols = is.numeric, by="gene"][, mane_select:=FALSE]
)
)
from rare_disease_celltyping.
from rare_disease_celltyping.
Just having a look into what I did previously when looking at pLI and genes under selective pressure.
I used the pLI for human transcripts from this study: The mutational constraint spectrum quantified from variation in 141,456 humans.
I'm attaching the relevant supplementary table:
supplementary_dataset_11_full_constraint_metrics.tsv.zip.
But as you've shared @bschilder, there is a more up to date version of pLI data.
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How would an AI model give us population frequency? I thought current generation AI models of protein folding are also really bad at predicting variant effects?
@NathanSkene Are you talking about variant population frequency, phenotype frequency, or disease frequency?
In any case, none of these were the intended usage of pLI as outlined here:
#50 (comment)
Also see here for my explanation of why pLI would not be appropriate for estimating population prevalence. Instead, getting epidemiological stats on population prevalence would make much more sense.
from rare_disease_celltyping.
Related Issues (20)
- Identify variant-level mechanisms of each rare disease HOT 3
- Update website with the results from the new scRNA-seq datasets HOT 1
- Assess our results against known phenotype-celltype links HOT 4
- Regenerate manuscript figures with new results HOT 2
- Rewrite manuscript HOT 2
- Remake equations with color coding HOT 1
- Adjust congenital onset figure HOT 1
- Remove diagnosis/prognosis figures
- Redo Monarch recall stats HOT 1
- Create static versions of network plots
- Adjust ontology levels figure HOT 5
- Rework target prioritisation figure HOT 1
- Assess distribution of congenital phenotypes HOT 7
- Target prioritisation pipeline figure HOT 5
- Move AD/PD networks to supplementary materials HOT 1
- Include animal model availability in target prioritisation pipeline HOT 1
- Add section on 'Spinocerebellar atrophy' phenotype HOT 1
- Adjust 'Recurrent Neisserial infections' network plot HOT 3
- Consider adding more severity-related figures
- Consider extending fetal vs. adult cell type analyses HOT 1
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