v2.24.0

This release includes a major site refactor, modernizing the frontend codebase, improvements to motif standardization logic, and automation updates to the curation pipeline.

Key Changes:

• Site fully refactored with TypeScript and Tailwind CSS
• Motif frame is now standardized based on gene direction
• criTRia-curations.tsv integrated into Snakefile for automatic updates

Major Changes

• Site Refactor (#493) — The entire /site folder has been overhauled. The frontend has been converted from vanilla CSS to Tailwind and migrated to TypeScript for improved type safety. The locus page layout has been made more static with less conditional rendering, providing a more consistent experience when comparing loci across tabs. Theme colors and styles have also been refreshed. Closes #343.
• Motif Frame Standardization (#486) — ⚠️ Breaking behaviour change: gene direction motifs now overwrite reference direction when the two differ. Motifs are converted to a canonical set based on gene direction, and gene_orientation is now the source of truth that reference_orientation is derived from. The check_loci motif frame determining functions have been updated to align with standard frames documented in the schema file. Form entry and schema instructions have been updated accordingly.

Minor Changes

• criTRia-curations.tsv automation (#496) — The curations file is now included in the Snakefile and will be updated automatically as part of the pipeline.
• Minor formatting fixes in check_loci.

What's Changed

• update criTRia-curations.tsv and include it in the Snakefile by @hdashnow in #496
• Draft code to standardize frame of motifs by @gaberbz in #486
• Refactor site by @vincerubinetti in #493

Full Changelog: v2.23.0...v2.24.0

v2.23.0

This release is a broad content and curation update that expands STRchive’s schema and locus annotations, especially through the addition of a new Detection section and more detection/sizing information across much of the resource. It also adds new loci, including GOLGA8A and CSNK1E, and continues wider criTRia cleanup and literature-driven updates across many entries.

A notable point in this release is the handling of FRA12A_DIP2B: it was first added to criTRia as Limited and then revised to reflect conflicting evidence / disputed status, making that change in interpretation explicit.

Major Changes

• Added a new Detection section to the site and schema
• Added detection/sizing information to most loci
• Added new loci:
  • GOLGA8A associated with atypical FTLD-U risk
  • CSNK1E associated with progressive myoclonic epilepsy
  • FRA12A_DIP2B to criTRia, later updated with conflicting evidence/disputed status
• Expanded June literature curation with diagnostic relevance updates across many loci
• Renamed MIR7-2_CHNG3 to CHNG3_MIR7-2
• Continued broad criTRia expansion/cleanup across many locus-disease entries

Minor Changes

• Updated criTRia evidence details and descriptions across many curated loci, including DM2, ATXN3, FMR1, DMD, POLG, ZIC3, LRP12, NOTCH2NLC, NUTM2B-AS1, PABPN1, JPH3, CBL, TCF4, ZIC2, ATXN1, ATN1, ATXN10, TBX1, HOXD13, TBP, ATXN8OS, HOXA13, FGF14, BEAN1, NOP56, THAP11, CACNA1A, SOX3, and TYMS
• Added/cleaned up CPUM and XLID curations
• Updated the criTRia table script
• Removed unsupported regulatory-impact evidence from CJD_PRNP
• Added missing PMIDs/references and various wording, formatting, and schema-alignment fixes
• June literature updates included:
  • detection info for most loci
  • SCA12_PPP2R2B age of onset max changed to 62
  • MODY8_CEL mechanism changed to GoF
  • expanded diagnostic/mechanistic details for loci including C9orf72, CEL, DM2_CNBP, FGF14, HTT, NOTCH2NLC, and PABPN1

What's Changed

• Rename MIR7-2 ID by @hdashnow in #481
• DM2_CNPB-critria-update by @elbayaliyev in #483
• SCA3_ATXN3-critria-update by @elbayaliyev in #485
• Update Literature by @github-actions[bot] in #487
• Adding conflicting evidence to FRA12A_DIP2B by @gaberbz in #490
• Diagnostic_Relevance_and_June_Lit by @gaberbz in #491

Full Changelog: v2.22.0...v2.23.0

v2.22.0

What's Changed

• Curation details by @hdashnow in #376
• DMD_DMD-critria-update by @elbayaliyev in #464
• FGF14_SCA27B-critria-update by @elbayaliyev in #450
• Adding GOLGA8A by @strchive-bot in #418
• SCA51_THAP11-critria-update by @elbayaliyev in #456
• OPDM1_LRP12-critria-update by @elbayaliyev in #412
• TOF_TBX1-critria-update by @elbayaliyev in #436
• ZFHX3_SCA4-critria-update by @elbayaliyev in #459
• SCA7-ATXN7-critria-update by @elbayaliyev in #443
• TCF4_FECD3-critria-update by @elbayaliyev in #396
• remove regulatory impact from CJD_PRNP by @hdashnow in #470
• HDL2_JPH3-critria-update by @elbayaliyev in #400
• CBL_JBS-critria-evidence-update by @elbayaliyev in #375
• VACTERLX_ZIC3-critria-update by @elbayaliyev in #435
• ARX_EIEE1 curation update by @hdashnow in #471
• XLID_SOX3 and CPUM_TYMS.json by @Macayla-weiner in #467
• EPM_CSNK1E by @strchive-bot in #468
• TYMS_CPUM-critria-update by @elbayaliyev in #475
• XLID_SOX3-critria-update by @elbayaliyev in #474
• NOTCH2NLC_NIID-critria-update by @elbayaliyev in #410
• SCA1_ATXN1-critria-update by @elbayaliyev in #425
• DRPLA_ATN1-critria-update by @elbayaliyev in #430
• SCA8_ATXN8OS-critria-update by @elbayaliyev in #442
• SCA10_ATXN10-critria-update by @elbayaliyev in #434
• SCA17-TBP-critria-update by @elbayaliyev in #440
• SCA31_BEAN1-critria-update by @elbayaliyev in #452
• Update criTRia-curations.json by @elbayaliyev in #461
• SCA6_CACNA1A-critria-update by @elbayaliyev in #458
• SCA36_NOP56-critria-update by @elbayaliyev in #454
• HOXD_SD5-critria-update by @elbayaliyev in #438
• POLG_CPEO-critria-update by @elbayaliyev in #466
• HOXA13 / HFG-I -critria-update by @elbayaliyev in #446
• HOXA13_HFG-III-critria-update by @elbayaliyev in #448
• NUTM2B-AS1_OPML1-critria-update by @elbayaliyev in #421
• FMR1_FXTAS,POF1-critria-update by @elbayaliyev in #432
• PABPN1_OPMD criTRia curation update by @elbayaliyev in #419
• ZIC2-HPE5-critria-update by @elbayaliyev in #406
• FRA12A_DIP2B-criTRia by @gaberbz in #469
• FXS_FM1-critria-update by @elbayaliyev in #463
• CriTRia table script update by @hdashnow in #478

New Contributors

• @gaberbz made their first contribution in #469

Full Changelog: v2.21.0...v2.22.0

v2.21.0

What's Changed

• Add GSS to CJD and note spectrum by @Macayla-weiner in #416
• May Literature Update (#387) by @gaberbz in #391
• Update Literature by @github-actions[bot] in #347

Major Changes

• FMR1 premature ovarian insufficiency risk now noted starting at 36 repeats
• GIPC1 minimum age now 2 years
• RFC1 phenotype expanded to include new neuropathies
• Add GSS to CJD

Minor Changes

• C9orf72 details updated to note rare non HD chorea presentation
• C9orf72, CACNA1A, and HTT details now include presymptomatic cerebellar atrophy
• FGF14 phenotype expanded to include episodic dysarthria and visual disturbances
• C9orf72 details updated to note earlier onset and faster progression than other ALS
• C9orf72 mechanism updated with CNS somatic expansion
• CNBP mechanism now includes nucleolar stress, autophagy dysregulation, and stress granule formation findings
• DMPK mechanism updated with MBNL1/MBNL2 dimerization
• Added supporting citation for ambiguity of C9orf72
• GIPC1 details updated with asymptomatic 650-repeat carrier observation
• GIPC1 phenotype expansion to include ataxia
• NOTCH2NLC mechanism updated with nucleolar stress and altered chromatin structure
• HTT mechanism updated with proposed somatic expansion contribution to age dependent onset
• HTT gramatical edit
• NOTCH2NLC details updated with renal, bladder, and GI involvement potentially preceding neurologic manifestations

Full Changelog: v2.20.0...v2.21.0

v2.20.0

What's Changed

• 3 new provisional TR disease loci were added:
  • FAM193B and TBC1D7 are associated with OPDM
  • CEL is associated with MODY8
• Updates to the criTRia evidence descriptions and in some cases score adjustments for DAB1, NIPA, DMD, POLG, NAXE, and others with minor edits.
• New locus submission form fixed

Major Changes

• Add FAM193B and TBC1D7 by @Macayla-weiner in #352
• Add MODY8 locus again by @strchive-bot in #357

Minor Changes

• Add parse markdown util func by @vincerubinetti in #349
• fix locus form when adding new locus by @vincerubinetti in #354
• Naxe critria update by @hdashnow in #361
• Update Conflicting criTRia-curations.json by @Macayla-weiner in #363
• NIPA_ALS1-critria-update by @elbayaliyev in #366
• Update DAB1/SCA37 criTRia curation by @elbayaliyev in #360

Full Changelog: v2.19.0...v2.20.0

v2.19.0

What's Changed

• Simplify and validate criTRia format by @hdashnow in #345

Major Changes

• Merge Values, Evidence detail, and Notes into a single "Evidence
  details" field
• Create schema
• Validate format against schema
• Update score values as data is updated
• Add validation/update into Snakemake
• Round scores to the closest integer before comparing to classification ranges

Evidence category changes

Locus	Old category	New Category
FRA2A_AFF3	Moderate	Definitive
JBS_CBL	Strong	Definitive
SCA27B_FGF14	Strong	Definitive
HFG_HOXA13-II	Moderate	Limited
HFG_HOXA13-III	Moderate	Limited
NME_NAXE	Moderate	Limited
MRUPAV_PLIN4	Strong	Definitive
FAME2_STARD7	Moderate	Strong
FAME4_YEATS2	Moderate	Limited
HPE5_ZIC2	Moderate	Definitive

Minor Changes

• Fixes to curation data to make it valid with the new schema e.g. date
  formatting, citation formatting, and inheritance abbreviations.

Full Changelog: v2.18.0...v2.19.0

v2.18.0

What's Changed

• add association_type and evidence fields to STRchive-loci by @hdashnow in #332

Major Changes

• Number of criTRia curated loci increased from 55 to 74 (12 from ClinGen, 19 by @laurelhiatt and @Macayla-weiner)
• criTRia curations populated into STRchive locus pages
• Display improvements for curation data by @vincerubinetti
• Add provisional evidence category

Minor Changes

• Data cleanup and cross-links
• Auto-populate curations from criTRia
• Remove previous evidence tags

Full Changelog: v2.17.2...v2.18.0

v2.17.2

What's Changed

• Update Literature by @github-actions[bot] in #336
• April lit review + interruption data by @Macayla-weiner in #337

Minor Changes

• interruptions for NIPA1, NOTCH2NLC, SAMD12, FXN, FMR1, HTT, RILPL1,
  THAP11, ATXN1, ATXN 10, ATXN2, FGF14, ATXN3, NOP56, ATXN8OS, RAI1, and
  TBP
• RAI1 typo fixed

Related issues: #203 #286

Full Changelog: v2.17.1...v2.17.2

v2.17.1

What's Changed

• Update Literature by @github-actions[bot] in #326
• add interruption fields by @hdashnow in #335
• March Lit update by @Macayla-weiner in #334

Minor Changes

• ATXN2 intermediate range now 29-24
• ATXN2 locus details cleaned up to be a touch to be less repetitive
• SCA7 motif updated for clarity from GCA to CAG
• interruption field added to json (backwards compatible, not yet displayed)

Full Changelog: v2.17.0...v2.17.1

v2.17.0

What's Changed

Introducing "criTRia" locus-disease curations by @Macayla-weiner and @laurelhiatt. This version introduces the framework and a first draft of curations for 55 loci. More detail and curations to follow.

Major Changes

• criTRia page by @hdashnow and @vincerubinetti in #328

Full Changelog: v2.16.0...v2.17.0