This repository contains the code and analysis pipeline used to evaluate faecal and urinary amino acids as non-invasive biomarkers for detecting colorectal neoplasia in individuals with Lynch syndrome.
The study investigates whether metabolomic alterations, particularly amino acid profiles measured using liquid chromatography-tandem mass spectrometry (LC-MS/MS), can improve colorectal cancer (CRC) surveillance and potentially refine colonoscopy-based screening strategies.
Individuals with Lynch syndrome undergo regular colonoscopy surveillance to reduce colorectal cancer risk. However:
- Colonoscopy surveillance is burdensome.
- Post-colonoscopy colorectal cancers still occur.
- Additional non-invasive biomarkers may improve risk stratification.
Previous studies have demonstrated that gut metabolomic changes, including amino acid alterations, may serve as promising biomarkers for both advanced and non-advanced sporadic colorectal neoplasia.
To evaluate the diagnostic potential of:
- Faecal amino acids
- Urinary amino acids
- Faecal amino acids combined with FIT (Faecal Immunochemical Test)
for detecting relevant colorectal neoplasia in individuals with Lynch syndrome.
Participants with Lynch syndrome provided:
- Faecal samples
- Urine samples
at the following time points:
- 3 months before surveillance colonoscopy
- 3–6 months after surveillance colonoscopy
Cases and controls were matched based on:
- Age
- Sex
- Smoking status
- Dietary characteristics
Relevant neoplasia was defined as:
- Colorectal cancer (CRC)
- Adenomas
- Advanced serrated polyps
Twenty amino acids were quantified in:
- Faecal samples
- Urinary samples
using:
Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)
Diagnostic models were developed using:
- Random Forest classification
- Cross-validation procedures
- Receiver Operating Characteristic (ROC) analysis
Models evaluated:
- Faecal amino acids
- Faecal amino acids + FIT (2.55 μg Hb/g faeces threshold)
- Urinary amino acids
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