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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%...
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,...
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.
Karyotyping01:17

Karyotyping

Describing the number and physical features of chromosomes can reveal abnormalities that underlie genetic diseases. This description is facilitated by special staining techniques that produce a particular banding pattern on each chromosome. State-of-the-art techniques make this approach even more powerful, enabling the detection of individual genes that cause disease.A Simple Chromosome Staining Technique Provides Valuable Scientific InsightSome genetic diseases can be detected by looking at...
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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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.

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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

Characterization of missing human genome sequences and copy-number polymorphic insertions.

Jeffrey M Kidd1, Nick Sampas, Francesca Antonacci

  • 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, USA.

Nature Methods
|May 5, 2010
PubMed
Summary

Researchers discovered 2,363 new human genomic insertion sequences, revealing significant structural variations. Many insertions were missing or misassigned in the reference genome, impacting copy-number polymorphism analysis.

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Area of Science:

  • Genomics
  • Human Genetics
  • Bioinformatics

Background:

  • Human genomic structural variation is extensive, suggesting undiscovered genomic regions.
  • Current reference genomes may lack complete annotation and characterization of all sequences.

Purpose of the Study:

  • To present a resource and analysis of newly identified insertion sequences.
  • To characterize the accuracy of existing genome assemblies and identify novel genomic elements.

Main Methods:

  • Analysis of 2,363 new insertion sequences across 720 genomic loci.
  • Comparison with de novo sequence assemblies from next-generation sequencing (NGS) data.
  • Complete sequencing of 156 insertions and genotyping using breakpoint mapping of NGS datasets.

Main Results:

  • A substantial fraction of new insertions were missing, fragmented, or misassigned in the reference genome.
  • 18-37% of new insertions were copy-number polymorphic, with population stratification observed.
  • Novel exons and conserved noncoding sequences were identified in previously unrepresented regions.

Conclusions:

  • The human genome contains significant uncharacterized structural variation.
  • New insertion sequences offer insights into novel exons and noncoding elements.
  • Developed methods enable accurate genotyping of previously inaccessible genomic regions.