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Updated: Mar 9, 2026

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Published on: November 5, 2019

Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data.

Nilgun Donmez^1,2, Salem Malikic^1,2, Alexander W Wyatt^2,3

¹1 School of Computing Science, Simon Fraser University , Burnaby, Canada .

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|January 6, 2017

Summary

This summary is machine-generated.

This study introduces CTPsingle, a new method for analyzing cancer evolution. CTPsingle accurately infers tumor purity and subclonal composition from single, low-coverage sequencing data.

Keywords:

DNA sequencing cancer progression intra-tumor heterogeneity

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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Area of Science:

Oncology
Genomics
Bioinformatics

Background:

Intra-tumor heterogeneity is crucial for understanding cancer evolution.
Somatic mutations aid in estimating tumor purity and subclonal architecture.
Current methods often require ultra-deep sequencing from multiple tumor samples, limiting practical application.

Purpose of the Study:

To develop a method for inferring intra-tumor heterogeneity from single, low-coverage sequencing data.
To enable accurate estimation of tumor purity and subclonal composition using CTPsingle.
To overcome the limitations of multi-sample and ultra-deep sequencing requirements.

Main Methods:

CTPsingle utilizes low-coverage sequencing data from a single tumor sample.
The method focuses on inferring subclonal composition and tumor purity.
Computational analysis of variant allele frequencies is employed.

Main Results:

CTPsingle accurately infers tumor purity and clonality from single samples.
The method demonstrates high accuracy even with low-coverage sequencing (approximately 30×).
Successful reconstruction of subclonal composition is achieved.

Conclusions:

CTPsingle provides a valuable tool for studying intra-tumor heterogeneity.
The method expands the feasibility of subclonal analysis to more cancer types and research settings.
Accurate inference is possible with cost-effective, single-sample, low-coverage sequencing.