cccurj
Quantitative Biology > Genomics

[Submitted on 19 Oct 2026]

Republished example · not submitted to CCCURJ. This work, written by or with California Community College students, first appeared in Research Square (preprint) on September 22, 2026 under CC BY 4.0. It is shown here unchanged, with the openly licensed PDF, as an example of the research CCC students do; its authors did not submit it and CCCURJ editors did not review it. Read and cite the original.

Guide reselection expands canonical PAM candidates in an HGD editing resource for alkaptonuria

William Zane Duncan, Annie de Paula Bento, Laura Nadia Cabrera, Quoc Huy Hoang, Maddison Lila Kahn, Zhuolang Li, Raj Mathur, Malaika Theresa Mekkattuparamban, Cristian Emanuel Vasquez, Yuritzia Alexandra Zaragoza, Giorgio Lagna
Rare monogenic diseases offer defined molecular targets, but sequence-level editing options require explicit selection and verification. Using artificial intelligence assisted analysis and public tools within a community-college research cohort, we assembled an editing resource for the homogentisate 1,2-dioxygenase gene (HGD) in alkaptonuria. The inventory contained 278 variants and represented 268 of 271 eligible records in a defined ClinVar census. We compared filtering fixed prime-editing designs with re-selection requiring canonical NGG protospacer-adjacent motifs at both guide targets. Re-selection preserved 93 compatible configurations and added 140, all using a second nick without predicted edited-allele discrimination (PE3), while retaining 92 predicted allele-discriminating configurations (PE3b). Under a shared genomic count screen including NGG, NAG and NGA sites, 70 preserved and 79 added configurations remained. With an unchanged base-editing arm, combined representation increased from 110 to 188 variants, or 106 to 180 of 271 eligible ClinVar records. Preserving fixed configurations makes nonnegative gain structural; a 33-setting threshold grid quantified additional representation, with gains of 2–121. Conservative base-window exclusions and a prime-only control retained the increase. Sequence reconstruction and independent PrimeDesign comparisons checked component conventions. The result identifies nicking-guide selection as a source of additional canonical candidates and motivates planned tests of editing activity, product purity and restoration of HGD function.
Artifact type:Research in progress
Comments:20 pages. Republished from a Research Square preprint (posted September 22, 2026) under CC BY 4.0; not submitted to CCCURJ
Subjects:Genomics (q-bio.GN); Quantitative Methods (q-bio.QM)
Cite as:the original, https://doi.org/10.21203/rs.3.rs-11097253/v1
Related DOI:https://doi.org/10.21203/rs.3.rs-11097253/v1

Submission history

From: CCCURJ editors (republished)
[v1] Mon, 19 Oct 2026 17:00:00 UTC (2,233 KB)

Report a concern about this paper or its authors (plagiarism, fabricated results, misconduct)

Bibliographic and Citation Tools

BibTeX citation

@misc{duncan2026guide,
      title={Guide reselection expands canonical PAM candidates in an HGD editing resource for alkaptonuria},
      author={William Zane Duncan and Annie de Paula Bento and Laura Nadia Cabrera and Quoc Huy Hoang and Maddison Lila Kahn and Zhuolang Li and Raj Mathur and Malaika Theresa Mekkattuparamban and Cristian Emanuel Vasquez and Yuritzia Alexandra Zaragoza and Giorgio Lagna},
      year={2026},
      howpublished={Research Square (preprint)},
      doi={10.21203/rs.3.rs-11097253/v1},
      url={https://doi.org/10.21203/rs.3.rs-11097253/v1},
}