Conversation
✅ Deploy Preview for strchive ready!
To edit notification comments on pull requests, go to your Netlify project configuration. |
data/STRchive-loci.json
Outdated
| "mechanism_detail": "LoF [@pmid:38467784].", | ||
| "source": [], | ||
| "details": null, | ||
| "details": "2-3 motifs are benign, 12-17 have not undergone clinical evaluation and are therefore designated as intermediate, and 30-125 repeats are pathogenic. 4-11 and 18-29 repeats have not been studied or reported. The length of the pathogenic allele affects age of onset and severity, but severity also varies between families [@pmid:18325013; @genereviews:NBK1142].", |
There was a problem hiding this comment.
On web preview the citations are "3,2", should I flip the order or does it not matter
There was a problem hiding this comment.
The citation number is based on the overall order across all the fields. In this case, NBK1142 was cited earlier up in the age_onset field, so that's why it is number 2. You are welcome to flip them for neatness, but it's totally optional.
hdashnow
left a comment
hdashnow
left a comment
There was a problem hiding this comment.
Awesome! A few suggestions in comments.
data/STRchive-loci.json
Outdated
| "mechanism_detail": "LoF [@pmid:38467784].", | ||
| "source": [], | ||
| "details": null, | ||
| "details": "2-3 motifs are benign, 12-17 have not undergone clinical evaluation and are therefore designated as intermediate, and 30-125 repeats are pathogenic. 4-11 and 18-29 repeats have not been studied or reported. The length of the pathogenic allele affects age of onset and severity, but severity also varies between families [@pmid:18325013; @genereviews:NBK1142].", |
There was a problem hiding this comment.
The citation number is based on the overall order across all the fields. In this case, NBK1142 was cited earlier up in the age_onset field, so that's why it is number 2. You are welcome to flip them for neatness, but it's totally optional.
data/STRchive-loci.json
Outdated
| "mechanism_detail": "LoF [@pmid:38467784].", | ||
| "source": [], | ||
| "details": null, | ||
| "details": "2-3 motifs are benign, 12-17 have not undergone clinical evaluation and are therefore designated as intermediate, and 30-125 repeats are pathogenic. 4-11 and 18-29 repeats have not been studied or reported. The length of the pathogenic allele affects age of onset and severity, but severity also varies between families [@pmid:18325013; @genereviews:NBK1142].", |
There was a problem hiding this comment.
Looking at PMID: 18325013, I'm finding the way they describe the different middle ranges a bit confusing.
For this bit "Alleles of 12-17 dodecamer repeats have been observed, but individuals with alleles in this range have not undergone thorough clinical evaluation for signs and symptoms of EPM1"
I think we'd just not count them in any of the ranges because we don't know what they mean. So probably intermediate range should be null/null.
Then in the description here I would rephrase a little to put the key info up front next to the citation and group the unknown ranges. Maybe something like this?
"alleles containing 2-3 motifs are considered benign, while alleles with 30-125 repeats are fully penetrant [@pmid:18325013]. Alleles in the range 12-17 have been observed, however the individuals carrying them have not undergone clinical evaluation. Alleles in the range 4-11 and 18-29 repeats have not been reported to date."
There was a problem hiding this comment.
It would also be nice to start the details section with something like this phrase from the paper so they know what dodecamer means:
Affected individuals "have an unstable expansion of a 12-nucleotide (dodecamer) repeat"
CITATION.cff
Outdated
| title: STRchive | ||
| version: 2.5.1 | ||
| date-released: "2025-07-08" | ||
| version: 2.5.2 |
There was a problem hiding this comment.
Since there's a change to the HTT min pathogenic range, I think this should be a major version change. So 2.6.0.
hdashnow
left a comment
hdashnow
left a comment
There was a problem hiding this comment.
A few more minor edits. I'll try to figure out why it's failing. Odds are it's something I did.
data/STRchive-loci.json
Outdated
| "novel": null, | ||
| "mechanism": "LoF", | ||
| "mechanism_detail": "LoF [@pmid:38467784].", | ||
| "mechanism_detail": "The repeat expanison causes significantly reduced esxpression of cystatin-B protein [@genereviews:NBK1142].", |
There was a problem hiding this comment.
typo:
esxpression -> expression
| "mechanism_detail": "The repeat expanison causes significantly reduced esxpression of cystatin-B protein [@genereviews:NBK1142].", | ||
| "source": [], | ||
| "details": null, | ||
| "details": "Affected individuals have an unstable 12-nucleotide (dodecomer) repeat expansion. Alleles containing 2-3 motifs are considered benign, while alleles with 30-125 repeats are fully penetrant [@pmid:18325013]. Alleles in the range 12-17 repeats have been observed, however the individuals carrying them have not undergone clinical evaluation. Alleles in the range 4-11 and 18-29 repeats have not been reported to date.", |
data/STRchive-loci.json
Outdated
| "mechanism_detail": "While the primary pathogenic mechanism is gain of function of the protein product, pathogenesis is complex and multifactorial [@pmid:27940602].", | ||
| "source": [], | ||
| "details": "27-35 motifs are unstable/premutations, while 36-39 motifs are associated with reduced penetrance and mild phenotypes [@pmid:39572770]. >60 motifs associated with onset age <20 years [@genereviews:NBK1305]. Only CAG expansions are considered pathogenic, but interruptions impact pathogenicity (e.g. CAA) [@pmid:35245110]. Only fathers with premutations are considered at risk of transmitting pathogenic alleles [@pmid:19507258]. CAG repeats in the non-HD range (>= 21 repeats) may modulate psychiatric disease risk in an age-dependent manner [@pmid:39572770]", | ||
| "details": "27-35 motifs are unstable/premutations, while 36-39 motifs are associated with reduced penetrance and mild phenotypes [@pmid:39572770], and alleles over 40 repeats are typically full penetrant [@genereviews:NBK1305]. >60 motifs associated with onset age <20 years [@genereviews:NBK1305]. Only CAG expansions are considered pathogenic, but interruptions impact pathogenicity (e.g. CAA) [@pmid:35245110]. Only fathers with premutations are considered at risk of transmitting pathogenic alleles [@pmid:19507258]. CAG repeats in the non-HD range (>= 21 repeats) may modulate psychiatric disease risk in an age-dependent manner [@pmid:39572770]", |
There was a problem hiding this comment.
full penetrant -> fully penetrant
There was a problem hiding this comment.
geez I can't type today!
Added EPM1 details field, updating Huntington's so motif ranges match, added new GnomAD links (#222).
2 participants
Added EPM1 details field, updating Huntington's so motif ranges match, added new GnomAD links (#222).
Description
Summarize the changes
Fixes: #222
Minor Changes
Checklist
CITATION.cff, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X.