FRA7A and TYMS#370
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I fixed the json format so now the website renders and you can see everything. 
Looks like this locus is listed twice. I assume one is a typo. Sorry if it was my fault!
They are different, so would you like to check which info to keep from each? |
| { | ||
| "Evidence type": "Regulatory impact", | ||
| "Score": 0.5, | ||
| "Citation": "pmid:24763282", |
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This paper is "FRA2A is a CGG repeat expansion associated with silencing of AFF3", see above.
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Just a silly mistake! This was meant to cite pmid:25196122 (see criTRia page)
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| { | ||
| "Evidence type": "Cell culture", | ||
| "Score": 0.5, | ||
| "Citation": "pmid:24763282", |
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This paper is "FRA2A is a CGG repeat expansion associated with silencing of AFF3"
Was this supposed to be a different PMID, or was this chunk supposed to be part of a different locus curation?
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Different locus... although I'm not sure which one
hdashnow
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I think some of the citations numbers were swapped between the two loci. Can you please double-check I've fixed them correctly?
| { | ||
| "Evidence type": "Cell culture", | ||
| "Score": 0.5, | ||
| "Citation": "pmid:24763282", |
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| { | ||
| "Evidence type": "Regulatory impact", | ||
| "Score": 0.5, | ||
| "Citation": "pmid:24763282", |
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| "Citation": "pmid:25196122", | ||
| "Evidence detail": "poorly matched but highly significant", | ||
| "evidence_category": "Statistics", | ||
| "Evidence detail": "Poorly matched controls and small power, but did find statistical significance.", |
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Is this about this part of the paper? I think it should be described as rare in controls instead.
PCR-based amplification of the FRA7A-associated (CGG)12 repeat in 176 individuals revealed 14 different alleles with repeat sizes ranging from five to 22 units (Supp. Materials and Methods). The most common allele contained seven repeat units (Fig. 1E). There were 35 apparent homozygous control individuals. The PCR assay used in this analysis would not detect a full mutation and thus individuals heterozygous for a full expansion of the allele would appear homozygous. However, the number of observed homozygous individuals (35) did not differ significantly from the number predicted (31.2) from the allele frequencies derived from the control group (P = 0.45; Supp. Table S1). It thus seems unlikely that full expansion mutations are present in the control group. This conclusion is supported by the rarity of FRA7A in clinical cytogenetic analysis with no other cases being detected in >9,000 analyses performed using similar culture conditions in children with neurodevelopmental disorders in the laboratory that identified FRA7A in the proband.
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Yes it is, I'm happy with that wording
| "Evidence type": "Regulatory impact", | ||
| "Score": 0.5, | ||
| "Citation": "pmid:25196122", | ||
| "Evidence detail": "Evidence of effect of premutation alleles.", |
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I don't really get what's going on with the premutation in this paper???
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I read it as them saying the premutation allele is super unstable, and they could not confidently claim that it did or didn't cause disease because of that. I was citing the paper for the methylation evidence toward altered expression. Anyways, I have no clue what's happening with the premutation but I think their proband evidence is good enough to score
FRA7A and TYMS loci
Co-authored-by: Harriet Dashnow <h.dashnow@gmail.com>
FRA7A and TYMS loci ## Major Changes - Added FRA7A_ZNF13 - Added CPUM_TYMS # Checklist - [x] All changes are well summarized - [ ] Check all tests pass - [ ] Check that the website preview looks good - [ ] Update the STRchive version in `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. - [ ] Ask someone to review this PR --------- Co-authored-by: Harriet Dashnow <h.dashnow@gmail.com> Co-authored-by: hdashnow <3794821+hdashnow@users.noreply.github.com>
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FRA7A and TYMS loci
Major 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.