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Update Literature (#217)
**Please edit this description as you work on this PR** ## Description July Literature Update ## Minor Changes - Fetch latest literature - Merging locus updates from #220 ## Checklist - [x] Check I've included all literature since the last "Literature Update" PR (may need to diff against an earlier version) - [x] Check for updates to existing loci - [x] Check for potential new loci - [x] Add any changes to `STRchive-loci.json` as commits to this branch/PR - [x] If anything needs to be discussed further before adding to STRchive, add it to [Discussions](https://github.com/dashnowlab/STRchive/discussions) - [x] Check all tests pass e.g. the website built - [x] Check that the website preview looks good - [x] 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. - [x] Ask someone to review this PR --------- Co-authored-by: hdashnow <3794821+hdashnow@users.noreply.github.com> Co-authored-by: Macayla Ann Weiner <macanncash@gmail.com>
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‎CITATION.cff‎

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title: STRchive
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version: 2.5.0
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date-released: "2025-07-01"
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version: 2.5.1
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date-released: "2025-07-08"
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url: https://github.com/dashnowlab/STRchive
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authors:
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- family-names: Dashnow
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title: "STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci"
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issue: 1
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volume: 17
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year: 2025
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year: 2025

‎data/STRchive-citations.json‎

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‎data/STRchive-disease-loci.T2T-chm13.TRGT.bed‎

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@@ -54,7 +54,7 @@ chr17 17754961 17755053 ID=FAME8_RAI1;MOTIFS=ATTTT,TTTCA,TTTTA;STRUC=<TR>
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chr17 81047404 81047534 ID=RCPS_EIF4A3;MOTIFS=CCTCGCTGCGCCGCTGCCGA,CCTCGCTGTGCCGCTGCCGA;STRUC=<TR>
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chr18 821235 821905 ID=CPUM_TYMS;MOTIFS=GATGGT;STRUC=<TR>
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chr18 55789233 55789288 ID=FECD3_TCF4;MOTIFS=CAG;STRUC=<TR>
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chr19 4494212 4497342 ID=PLIN4_MRUPAV;MOTIFS=TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC;STRUC=<TR>
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chr19 4494212 4497342 ID=MRUPAV_PLIN4;MOTIFS=TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC;STRUC=<TR>
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chr19 13333136 13333176 ID=SCA6_CACNA1A;MOTIFS=CTG;STRUC=<TR>
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chr19 14622655 14622692 ID=OPDM2_GIPC1;MOTIFS=CCG;STRUC=<TR>
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chr19 18921630 18921645 ID=EDM1-PSACH_COMP;MOTIFS=GTC;STRUC=<TR>

‎data/STRchive-disease-loci.T2T-chm13.bed‎

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@@ -55,7 +55,7 @@ chr17 17754961 17755053 FAME8_RAI1 RAI1 TTTTA TTTCA 9 AD Familial adult myocloni
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chr17 81047404 81047534 RCPS_EIF4A3 EIF4A3 CCTCGCTGTGCCGCTGCCGA CCTCGCTGTGCCGCTGCCGA 14 AR Richieri-Costa-Pereira syndrome
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chr18 821235 821905 CPUM_TYMS TYMS GATGGT GATGGT 210 AR Congenital Progressive Universal Melanosis
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chr18 55789233 55789288 FECD3_TCF4 TCF4 CAG CAG 51 AD Fuchs endothelial corneal dystrophy 3
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chr19 4494212 4497342 PLIN4_MRUPAV PLIN4 TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC 39 AD Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
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chr19 4494212 4497342 MRUPAV_PLIN4 PLIN4 TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC 39 AD Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
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chr19 13333136 13333176 SCA6_CACNA1A CACNA1A CTG CTG 21 AD Spinocerebellar ataxia type 6
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chr19 14622655 14622692 OPDM2_GIPC1 GIPC1 CCG CCG 73 AD Oculopharyngodistal myopathy type 2
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chr19 18921630 18921645 EDM1-PSACH_COMP COMP GTC GTC 6 AD Multiple epiphyseal dysplasia, Pseudoachondroplasia

‎data/STRchive-disease-loci.hg19.TRGT.bed‎

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chr17 78120808 78120938 ID=RCPS_EIF4A3;MOTIFS=CCTCGCTGCGCCGCTGCCGA,CCTCGCTGTGCCGCTGCCGA;STRUC=<TR>
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chr18 666891 667632 ID=CPUM_TYMS;MOTIFS=GATGGT;STRUC=<TR>
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chr18 53253384 53253460 ID=FECD3_TCF4;MOTIFS=CAG;STRUC=<TR>
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chr19 4510739 4513671 ID=PLIN4_MRUPAV;MOTIFS=TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC;STRUC=<TR>
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chr19 4510739 4513671 ID=MRUPAV_PLIN4;MOTIFS=TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC;STRUC=<TR>
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chr19 13318672 13318712 ID=SCA6_CACNA1A;MOTIFS=CTG;STRUC=<TR>
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chr19 14606853 14606887 ID=OPDM2_GIPC1;MOTIFS=CCG;STRUC=<TR>
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chr19 18896844 18896860 ID=EDM1-PSACH_COMP;MOTIFS=GTC;STRUC=<TR>

‎data/STRchive-disease-loci.hg19.bed‎

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chr17 78120808 78120938 RCPS_EIF4A3 EIF4A3 CCTCGCTGTGCCGCTGCCGA CCTCGCTGTGCCGCTGCCGA 14 AR Richieri-Costa-Pereira syndrome
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chr18 666891 667632 CPUM_TYMS TYMS GATGGT GATGGT 210 AR Congenital Progressive Universal Melanosis
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chr18 53253384 53253460 FECD3_TCF4 TCF4 CAG CAG 51 AD Fuchs endothelial corneal dystrophy 3
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chr19 4510739 4513671 PLIN4_MRUPAV PLIN4 TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC 39 AD Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
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chr19 4510739 4513671 MRUPAV_PLIN4 PLIN4 TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC 39 AD Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
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chr19 13318672 13318712 SCA6_CACNA1A CACNA1A CTG CTG 21 AD Spinocerebellar ataxia type 6
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chr19 14606853 14606887 OPDM2_GIPC1 GIPC1 CCG CCG 73 AD Oculopharyngodistal myopathy type 2
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chr19 18896844 18896860 EDM1-PSACH_COMP COMP GTC GTC 6 AD Multiple epiphyseal dysplasia, Pseudoachondroplasia

‎data/STRchive-disease-loci.hg38.TRGT.bed‎

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@@ -54,7 +54,7 @@ chr17 17808358 17808460 ID=FAME8_RAI1;MOTIFS=ATTTT,TTTCA,TTTTA;STRUC=<TR>
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chr17 80147009 80147139 ID=RCPS_EIF4A3;MOTIFS=CCTCGCTGCGCCGCTGCCGA,CCTCGCTGTGCCGCTGCCGA;STRUC=<TR>
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chr18 666891 667632 ID=CPUM_TYMS;MOTIFS=GATGGT;STRUC=<TR>
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chr18 55586153 55586229 ID=FECD3_TCF4;MOTIFS=CAG;STRUC=<TR>
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chr19 4510727 4513659 ID=PLIN4_MRUPAV;MOTIFS=TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC;STRUC=<TR>
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chr19 4510727 4513659 ID=MRUPAV_PLIN4;MOTIFS=TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC;STRUC=<TR>
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chr19 13207858 13207898 ID=SCA6_CACNA1A;MOTIFS=CTG;STRUC=<TR>
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chr19 14496041 14496075 ID=OPDM2_GIPC1;MOTIFS=CCG;STRUC=<TR>
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chr19 18786034 18786050 ID=EDM1-PSACH_COMP;MOTIFS=GTC;STRUC=<TR>

‎data/STRchive-disease-loci.hg38.bed‎

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@@ -55,7 +55,7 @@ chr17 17808358 17808460 FAME8_RAI1 RAI1 TTTTA TTTCA 9 AD Familial adult myocloni
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chr17 80147009 80147139 RCPS_EIF4A3 EIF4A3 CCTCGCTGTGCCGCTGCCGA CCTCGCTGTGCCGCTGCCGA 14 AR Richieri-Costa-Pereira syndrome
5656
chr18 666891 667632 CPUM_TYMS TYMS GATGGT GATGGT 210 AR Congenital Progressive Universal Melanosis
5757
chr18 55586153 55586229 FECD3_TCF4 TCF4 CAG CAG 51 AD Fuchs endothelial corneal dystrophy 3
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chr19 4510727 4513659 PLIN4_MRUPAV PLIN4 TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC 39 AD Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
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chr19 4510727 4513659 MRUPAV_PLIN4 PLIN4 TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC 39 AD Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
5959
chr19 13207858 13207898 SCA6_CACNA1A CACNA1A CTG CTG 21 AD Spinocerebellar ataxia type 6
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chr19 14496041 14496075 OPDM2_GIPC1 GIPC1 CCG CCG 73 AD Oculopharyngodistal myopathy type 2
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chr19 18786034 18786050 EDM1-PSACH_COMP COMP GTC GTC 6 AD Multiple epiphyseal dysplasia, Pseudoachondroplasia

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