---
title: "Quantitative Methods new submissions"
description: "Today's new preprints in Quantitative Methods (q-bio.QM) on CCCURJ, the open-access archive of research by California Community College students."
url: "https://cccurj.org/list/q-bio.QM/new"
license: "CC BY 4.0"
---

# Quantitative Methods

## New submissions

Showing new listings for Monday, 19 October 2026

Total of 1 entries | [Cross submissions](https://cccurj.org/list/q-bio.QM/new#cross)

### Cross submissions (showing 1 of 1 entries)

**[\[1\]](https://cccurj.org/list/q-bio.QM/new#item1) [CCCURJ:2610.00014](https://cccurj.org/abs/2610.00014) (cross-list from q-bio.GN) [[pdf](https://cccurj.org/pdf/2610.00014)]**

[Research in progress](https://cccurj.org/help/artifacts#research-in-progress) Guide reselection expands canonical PAM candidates in an HGD editing resource for alkaptonuria

[William Zane Duncan](https://cccurj.org/search#William_Zane_Duncan), [Annie de Paula Bento](https://cccurj.org/search#Annie_de_Paula_Bento), [Laura Nadia Cabrera](https://cccurj.org/search#Laura_Nadia_Cabrera), [Quoc Huy Hoang](https://cccurj.org/search#Quoc_Huy_Hoang), [Maddison Lila Kahn](https://cccurj.org/search#Maddison_Lila_Kahn), [Zhuolang Li](https://cccurj.org/search#Zhuolang_Li), [Raj Mathur](https://cccurj.org/search#Raj_Mathur), [Malaika Theresa Mekkattuparamban](https://cccurj.org/search#Malaika_Theresa_Mekkattuparamban), [Cristian Emanuel Vasquez](https://cccurj.org/search#Cristian_Emanuel_Vasquez), [Yuritzia Alexandra Zaragoza](https://cccurj.org/search#Yuritzia_Alexandra_Zaragoza), [Giorgio Lagna](https://cccurj.org/search#Giorgio_Lagna)

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)

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.

Total of 1 entries | [recent](https://cccurj.org/list/q-bio.QM/recent) | [RSS feed](https://cccurj.org/rss/q-bio.QM)