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Revised May Lit Check #182

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Merged
hdashnow merged 3 commits into from
May 10, 2025
Merged

Revised May Lit Check #182

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Macayla-May-Lit.json
Macayla-weiner May 9, 2025
6219faf
Macayla Updated STRchive-lit.json
Macayla-weiner May 9, 2025
433b7c1
Update STRchive-loci.json
Macayla-weiner May 9, 2025
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16 changes: 8 additions & 8 deletions data/STRchive-loci.json
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Expand Up @@ -44,7 +44,7 @@
"details": "Characterized in eight unrelated families which were used to establish benign (3-44) and pathogenic (118-694) ranges [@pmid:39068203].",
"omim": [],
"prevalence": null,
"prevalence_details": "Found in individuals of European ancestry [@pmid:38876750].",
"prevalence_details": "Found in individuals of European, Japanese, and Chinese ancestry [@pmid:38876750].",
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@hdashnow hdashnow May 9, 2025

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Which paper is this from?

"stripy": [],
"gnomad": [],
"genereviews": [],
Expand Down Expand Up @@ -1511,7 +1511,7 @@
"typ_age_onset_max": 30.0,
"novel": "ref",
"mechanism": "GoF",
"mechanism_detail": "RNA gain-of-function: RNA gelation leading to misregulation of alternative splicing [@pmid:36169768]. Expanded-repeat RNA sequesters the muscleblind-like (MBNL) family of RNA-binding proteins as part of the disruption of pre-mRNA processing, contributing to cardiac phenotypes [@pmid:39932794].",
"mechanism_detail": "RNA gain-of-function: RNA gelation leading to misregulation of alternative splicing [@pmid:36169768]. Expanded-repeat RNA sequesters the muscleblind-like (MBNL) family of RNA-binding proteins as part of the disruption of pre-mRNA processing, contributing to cardiac phenotypes [@pmid:39932794]. Loss of MBNL proteins has been linked to mis-splicing of Autism spectrum-risk genes such as SCN2A, ANK2, and SHANK2, possibly leading to Autism-related traits [@pmid:40259070]",
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Looks good!

"source": [],
"details": "Overview of disease locus through 2024, including largest pathogenic allele of 4,000, described in Rimoldi et al review [@pmid:39643839]. Intermediate alleles (35-49) associated with premutation [@genereviews:NBK1165]. 3%-8% of DM1 expansions contain interrupting variant repeats such as CCG and CGG, associated with later onset and milder phenotype; the variant repeat GCGGCA has also been reported [@pmid:32851192; @doi:10.1016/j.mcp.2024.102005]. In another study, interruptions of the CTG repeat with CCG, GGC, CTC or CAG motifs are estimated to occur in 3-11% of DM1 patients [@pmid:35741732]. Expansions within gene ZNF850 may function as DM1 modifiers [@doi:10.1093/hmg/ddae186].",
"omim": ["160900"],
Expand All @@ -1529,7 +1529,7 @@
"webstr_hg38": ["5650727"],
"webstr_hg19": ["Expansion_DM1/DMPK"],
"tr_atlas": ["TR156684"],
"disease_description": "Steinert disease, also known as myotonic dystrophy type 1, is a muscle disease characterized by myotonia and by multiorgan damage that combines various degrees of muscle weakness, arrhythmia and/or cardiac conduction disorders, cataract, endocrine damage, sleep disorders and baldness [@mondo:0008056].",
"disease_description": "Steinert disease, also known as myotonic dystrophy type 1, is a muscle disease characterized by myotonia and by multiorgan damage that combines various degrees of muscle weakness, arrhythmia and/or cardiac conduction disorders, cataract, endocrine damage, sleep disorders and baldness [@mondo:0008056]. It has also been linked to Autism Spectrum Disorder and related traits [@pmid:29361396; @pmid:8810716; @pmid:27695335; @pmid:29871899; @pmid:37209486], the presence of which may be associated with age of onset of DM1 [@pmid:40259070].",
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Suggested rewording:
It has also been linked to Autism and related traits, especially in individuals with earlier DM1 onset [@pmid:40259070; @pmid:29361396; @pmid:8810716; @pmid:27695335; @pmid:29871899; @pmid:37209486]."

"locus_tags": ["somatic_instability", "anticipation", "maternal_expansion", "length_affects_onset", "length_affects_phenotype", "length_affects_severity", "motif_affects_instability", "motif_affects_onset", "motif_affects_phenotype", "motif_affects_severity"],
"disease_tags": ["myotonic_dystrophy"],
"references": ["genereviews:NBK1165", "pmid:38454488", "pmid:36169768", "pmid:39932794", "pmid:39643839", "pmid:32851192", "doi:10.1016/j.mcp.2024.102005", "pmid:35741732", "doi:10.1093/hmg/ddae186", "pmid:29100084", "pmid:31159885", "pmid:35483324", "pmid:1310900", "mondo:0008056"],
Expand Down Expand Up @@ -1644,7 +1644,7 @@
"details": "Higher repeat size is associated with earlier age of onset [@pmid:39263992]. The 250-300 repeats range is linked to incomplete penetrance and >300 repeats with complete penetrance in some studies and resources [@genereviews:NBK599589; @pmid:37399286; @pmid:39227614]. However, our thresholds are taken from suggestions made by Mohren et al upon evaluation of 169 cases and 802 controls; the authors propose lower thresholds based on pathogenic cases of shorter pure repeats [@pmid:39227614]. Additionally, this study suggests that benign motifs may disrupt the formation of secondary structures in DNA/RNA, leading to reduced pathogenicity. The affect of interruptions on penetrance and onset has been shown in patients, with uninterrupted expansions apparently necessary for disease [@pmid:40007153]. Variation in flanking regions appear to correlate with repeat size [@pmid:39227614; @pmid:38937606]. Intermediate alleles make pose as susceptibility factors or be associated with a phenotypic spectrum (multiple system atrophy) [@pmid:39227614; @pmid:39604554].",
"omim": ["620174"],
"prevalence": null,
"prevalence_details": "Intermediate expansions 1-2% of population, but non-GAA-pure without relation to ataxia [@genereviews:NBK599589]. Found in multiple ethnicities [@pmid:38876750]; diagnosed patients in America, Brazil, Japan, Germany, Spain, Canada, France, Austria and Australia [@genereviews:NBK599589].",
"prevalence_details": "Intermediate expansions 1-2% of population, but non-GAA-pure without relation to ataxia [@genereviews:NBK599589]. Found in multiple ethnicities [@pmid:38876750]; diagnosed patients in America, Brazil, Japan, Germany, Spain, Canada, France, Austria, Australia, and Italy [@genereviews:NBK599589; @pmid:38886208].",
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I think this citation needs to be added for the Australian cohort:
@pmid:37267898

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@Macayla-weiner Macayla-weiner May 9, 2025

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Australian cohort was already there, the only edit I made there was putting a comma and moving the "and" after. I cannot view that article you've linked but if it details the cohort, I'll add it

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Yes, please!

"stripy": ["FGF14"],
"gnomad": [],
"genereviews": ["NBK599589"],
Expand Down Expand Up @@ -2281,7 +2281,7 @@
"mechanism": "GoF/LoF",
"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 assocated 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]. >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]",
"omim": ["143100"],
"prevalence": "1/10000",
"prevalence_details": "6.5-15/100,000 [@pmid:29100084]. 9.71-17:100,000 (European) vs. 0.1-2/100,000 (African), as many as 1 in 400 have reduced penetrance (0.2-2% for 36-38 CAG) HTT alleles [@genereviews:NBK1305]. Found across ethnicities/ancestries, with population-dependent prevalence [@genereviews:NBK1305].",
Expand Down Expand Up @@ -2348,7 +2348,7 @@
"details": "Intermediate alleles (29-39) may either be premutations or associated with reduced penetrance; the longest pathogenic expansion (40+ motifs) to date is 60 repeats [@genereviews:NBK1529]",
"omim": ["606438"],
"prevalence": null,
"prevalence_details": "<1/1,000,000 [@orphanet:98934]. Largely in individuals of African ancestry [@genereviews:NBK1529].",
"prevalence_details": "<1/1,000,000 [@orphanet:98934]. Largely in individuals of African ancestry [@genereviews:NBK1529]. JPH3 is a possible founder mutation in individuals of African ancestry [@pmid:40187026].",
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Looks good

"stripy": ["JPH3"],
"gnomad": ["JPH3"],
"genereviews": ["NBK1529"],
Expand Down Expand Up @@ -4384,8 +4384,8 @@
"pathogenic_max": 74.0,
"ref_copies": 21.3,
"motif_len": 3,
"age_onset": "Typical: 37- 56; Range: 15 - 60 [@pmid:38035881; @pmid:38973251].",
"age_onset_min": 15,
"age_onset": "Typical: 37- 56; Range: 12 - 60 [@pmid:39666847; @pmid:38973251].",
"age_onset_min": 12,
"age_onset_max": 60,
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Also update max to 65 from @pmid:39666847

"typ_age_onset_min": 37.0,
"typ_age_onset_max": 56.0,
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