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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
Real Time RT-PCR02:57

Real Time RT-PCR

Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
The real-time quantification of the number of amplified products is...
Genome Copying Errors02:46

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.

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Related Experiment Video

Updated: Jun 10, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

rSW-seq: algorithm for detection of copy number alterations in deep sequencing data.

Tae-Min Kim1, Lovelace J Luquette, Ruibin Xi

  • 1Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, Massachusetts 02115, USA.

BMC Bioinformatics
|August 20, 2010
PubMed
Summary

We developed rSW-seq, an efficient method for detecting DNA copy number alterations in cancer genomes using sequencing data. This approach offers high sensitivity and precision for characterizing chromosomal changes.

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Last Updated: Jun 10, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
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Detection of Copy Number Alterations Using Single Cell Sequencing

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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Advances in sequencing technologies generate large-scale genome data.
  • DNA copy number profiling is crucial for cancer genome characterization.
  • Robust methods for screening chromosomal alterations are needed for accurate cancer genome analysis.

Purpose of the Study:

  • To develop and validate an efficient method for identifying copy number alterations in tumor genomes.
  • To compare the performance of the developed method against existing algorithms and microarray-based results.

Main Methods:

  • Application of the Smith-Waterman algorithm to single-end sequencing data for copy number alteration identification.
  • Refinement of the algorithm into rSW-seq (recursive Smith-Waterman-seq) to detect complex alterations.
  • Validation using simulated datasets, public datasets, and comparison with microarray data.

Main Results:

  • The algorithm demonstrated >90% sensitivity and >90% precision in detecting copy number changes with approximately 500 reads.
  • rSW-seq effectively identifies complex alterations common in human cancer genomes.
  • Sequencing-based profiles showed comparable results to microarray-based analyses.

Conclusions:

  • rSW-seq is proposed as an efficient and accurate method for detecting copy number changes in tumor genomes.
  • The method provides a robust tool for detailed cancer genome characterization.