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Related Experiment Video

Updated: Jun 13, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing.

John C Castle¹, Matthew Biery, Heather Bouzek

¹Rosetta Inpharmatics LLC, Merck & Co., Inc., Seattle, Washington 98109, USA. castle@uni-mainz.de

|April 20, 2010

Summary

This study introduces a new, cost-efficient sequencing assay for profiling DNA copy number variations, including mitochondrial and telomeric DNA. The platform offers improved accuracy and is adaptable for laboratory automation.

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Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA

Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA

Published on: November 14, 2017

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

DNA copy number variations (CNVs) are common in populations and linked to various diseases.
Existing methods for CNV profiling can be costly and lack efficiency.
There is a need for improved, automatable, and accurate platforms for DNA copy number analysis.

Purpose of the Study:

To develop an improved, lab-automatable, cost-efficient, and accurate platform for profiling DNA copy number.
To create a sequencing-based assay capable of analyzing nuclear, mitochondrial, and telomeric DNA copy number.

Main Methods:

Development of a novel sequencing-based assay.
Incorporation of techniques from RNA expression profiling.
Assay of UMC-11 cells using next-generation sequencing (NGS) with 5 million 33 nt reads.

Main Results:

Demonstrated significant copy number variation in UMC-11 cells, including deletions and amplifications up to 29 copies.
Identified a 5-fold increase in mitochondrial DNA and a 4-fold decrease in telomeric DNA compared to control DNA.
Determined that UMC-11 cells originated from a male individual.

Conclusions:

The developed assay provides absolute copy number with error estimates (p-value).
The platform exhibits higher accuracy than array-based methods, especially at high copy numbers.
It enables profiling of mitochondrial levels and telomeric length, with tunable genomic resolution and cost based on sequencing depth.