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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%...
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.
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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.
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.
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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Related Experiment Video

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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

A computational framework discovers new copy number variants with functional importance.

Samprit Banerjee1, Derek Oldridge, Maria Poptsova

  • 1Department of Public Health, Weill Cornell Medical College, New York, New York, United States of America.

Plos One
|April 12, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a computational framework, IgC2N, to identify and genotype small germline copy number variants (CNVs). The framework improves characterization of genomic variability and reveals smaller CNVs

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Area of Science:

  • Genomics
  • Bioinformatics
  • Population Genetics

Background:

  • Structural variants, particularly copy number variants (CNVs), are key contributors to genomic variability.
  • Existing methods require better characterization of small CNVs (<500 bp).

Purpose of the Study:

  • To develop and validate a computational framework (IgC2N) for discovering and genotyping germline CNVs, with a focus on small variants.
  • To characterize novel CNVs and assess their functional impact on gene regulation.

Main Methods:

  • A three-step computational framework (IgC2N) was developed for CNV detection and genotyping.
  • Applied to genome-wide data from 1250 HapMap individuals, with validation using high-density marker data and RNA-sequencing.

Main Results:

  • Discovered and characterized novel germline CNVs, including their size, frequency, type, and formation mechanism.
  • Validated a majority of detected variants, with higher validation rates for larger variants (>1 kb).
  • Demonstrated that smaller CNVs (<1 Kb) are significantly more likely to regulate gene transcripts (p=2.04e-08).

Conclusions:

  • The IgC2N framework effectively detects novel germline CNVs relevant to disease susceptibility.
  • Genetic variants, especially smaller CNVs, play a crucial role in gene regulatory networks.