9bfd58221b1539193cb7f0a317b4e959c1c7e49a
max
Thu May 21 01:00:45 2026 -0700
varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
diff --git src/hg/makeDb/trackDb/human/finngen.html src/hg/makeDb/trackDb/human/finngen.html
index 539efc2f9d1..5250a73ebb5 100644
--- src/hg/makeDb/trackDb/human/finngen.html
+++ src/hg/makeDb/trackDb/human/finngen.html
@@ -1,56 +1,56 @@
<h2>Description</h2>
<p>
<a href="https://www.finngen.fi/en" target="_blank">FinnGen</a> is a public-private partnership
that combines genotype data from Finnish biobanks with digital health record data from Finnish
-health registries. The R12 release contains imputed variants from 500,348 biobank samples obtained
-using genotyping arrays. The imputation used phased variants obtained from 8,554 high-quality
-whole genome sequences, also from Finland. This represents approximately 10% of the Finnish
+health registries. The R12 release contains imputed variants from 500,348 biobank samples typed on
+genotyping arrays. The imputation used phased variants from 8,554 high-quality
+whole genome sequences, also from Finland. That is roughly 10% of the Finnish
population. Phenotype links can be viewed at the
<a href="https://r12.finngen.fi/" target="_blank">FinnGen PheWeb</a>.
</p>
<h2>Data Access</h2>
<p>
Due to license restrictions, the data for this track cannot be downloaded from the UCSC
Genome Browser. The Table Browser, Data Integrator, and download server are not available
for this track.
</p>
<p>
TSV data can be requested via the form at
<a href="https://finngen.gitbook.io/documentation/data-download" target="_blank">FinnGen</a>,
which triggers an automated email containing the download link.
A script in our GitHub repo converts this file to VCF (see Methods below).
</p>
<h2>Methods</h2>
<p>
FinnGen participants were genotyped using a custom Axiom FinnGen1 array, supplemented by legacy
collections genotyped with other arrays. Imputation used a population-specific reference panel of
high-coverage (25–30x) whole-genome sequences from Finnish individuals. Ancestry outliers were
removed via PCA against 1000 Genomes reference samples, and 5,780 duplicates and monozygotic twins
were excluded. Variant quality was assessed using VQSR.
</p>
<p>
R12 annotated variants were downloaded from the Google Cloud bucket link received through an email
and converted to VCF with a
<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/finngen_to_vcf.py"
target="_blank">custom Python script</a>.
-We provide documentation that indicates how all source files of the varFreqs track were converted in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc file</a> of the track.
-For some tracks, python scripts were necessary and are also available from <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target="_blank">GitHub</a>.
+The conversion steps for all source files of the varFreqs track are recorded in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc file</a> of the track.
+Some tracks also need python scripts, which live on <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target="_blank">GitHub</a>.
</p>
<h2>Credits</h2>
<p>
-We want to acknowledge the participants and investigators of the FinnGen study.
+Thanks to the participants and investigators of the FinnGen study.
</p>
<h2>References</h2>
<p>
Kurki MI, Karjalainen J, Palta P, Sipilä TP, Kristiansson K, Donner KM, Reeve MP, Laivuori H,
Aavikko M, Kaunisto MA <em>et al</em>.
<a href="https://doi.org/10.1038/s41586-022-05473-8" target="_blank">
FinnGen provides genetic insights from a well-phenotyped isolated population</a>.
<em>Nature</em>. 2023 Jan;613(7944):508-518.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36653562" target="_blank">36653562</a>; PMC: <a
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9849126/" target="_blank">PMC9849126</a>
</p>