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Related Concept Videos

Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
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%...
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.
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...
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...

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Related Experiment Video

Updated: May 19, 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

Reconstructing DNA copy number by joint segmentation of multiple sequences.

Zhongyang Zhang1, Kenneth Lange, Chiara Sabatti

  • 1Department of Statistics, University of California, Los Angeles, CA, USA.

BMC Bioinformatics
|August 18, 2012
PubMed
Summary

We developed generalized fused lasso (GFL), a novel segmentation method to identify copy number variant regions. GFL offers high accuracy and efficiency for analyzing DNA copy number variations in cancer research.

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Published on: October 18, 2013

Area of Science:

  • Genomics
  • Cancer Biology
  • Bioinformatics

Background:

  • DNA copy number variations (CNVs) provide insights into genome evolution and cancer development.
  • CNVs aid in localizing tumor suppressor genes and identifying disease-associated genomic alterations.
  • High-throughput technologies and algorithms are crucial for detecting CNVs.

Purpose of the Study:

  • To develop a method for detecting regions with common copy number variation within a sample.
  • To address the analysis of copy number polymorphisms, related samples, technical replicates, and cancer subpopulations.

Main Methods:

  • Introduced generalized fused lasso (GFL), a segmentation method for reconstructing copy number variant regions.
  • GFL utilizes penalized estimation and processes multiple signals concurrently.
  • The method is computationally efficient and comparable to existing state-of-the-art techniques.

Main Results:

  • GFL demonstrates sensitivity and specificity levels on par with specialized methodologies.
  • The method's effectiveness was validated using both simulated and real-world datasets.
  • Identified copy number variant regions with high accuracy.

Conclusions:

  • The GFL framework is adaptable to various data types from diverse technologies.
  • Its speed and versatility make GFL ideal for initial screening of large genomic datasets.
  • Facilitates efficient analysis of copy number variations in cancer research.