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Related Experiment Video

Updated: Apr 19, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

Allele-specific copy number profiling by next-generation DNA sequencing.

Hao Chen¹, John M Bell², Nicolas A Zavala²

¹Department of Statistics, University of California, One Shields Avenue, Davis, CA 95616, USA.

Nucleic Acids Research

|December 6, 2014

Summary

A new method called falcon accurately estimates allele-specific copy number changes in tumors using next-generation sequencing. This technique aids in understanding tumor evolution and clonal history.

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

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Published on: April 11, 2016

Area of Science:

Genomics
Cancer Biology
Bioinformatics

Background:

Tumor progression involves genomic alterations like amplifications and deletions.
Allele-specific copy number estimation is crucial for tumor genome characterization and inferring clonal history.

Purpose of the Study:

To introduce falcon, a novel method for detecting somatic allele-specific copy number changes.
To improve the characterization of tumor genomes and their clonal development.

Main Methods:

Utilizes a change-point model on a bivariate mixed Binomial process.
Explicitly models copy numbers of two chromosome haplotypes and corrects for allele-specific coverage biases.
Employs a modified Bayesian information criterion for model selection.

Main Results:

falcon effectively pools evidence from low-coverage sites using Binomial distribution, outperforming normal approximations.
Demonstrated accuracy on in silico spike-in data.
Applied to analyze copy number changes in pre-malignant and late-stage colorectal adenocarcinoma samples.

Conclusions:

falcon provides detailed insights into the clonal history of colon cancer.
The method enhances the understanding of genomic instability in tumor development.