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

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Published on: February 17, 2017

Algorithm implementation for CNV discovery using Affymetrix and Illumina SNP array data.

Laura Winchester1, Jiannis Ragoussis

  • 1Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK.

Methods in Molecular Biology (Clifton, N.J.)
|January 10, 2012
PubMed
Summary
This summary is machine-generated.

This study details methods for detecting copy number (CN) changes using SNP array data from Affymetrix and Illumina platforms. It emphasizes quality control and discusses algorithms for accurate genomic segment CN analysis.

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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • SNP arrays are used for genotyping and determining genomic copy number.
  • Accurate copy number (CN) detection is crucial for understanding genomic alterations.

Purpose of the Study:

  • To describe methods for detecting copy number (CN) changes using SNP array intensity data.
  • To examine options and challenges for Affymetrix and Illumina genotyping platforms.
  • To provide guidelines for quality control and algorithm selection in CN analysis.

Main Methods:

  • Analysis of intensity data from SNP arrays.
  • Incorporation of data from Affymetrix and Illumina genotyping platforms.
  • Evaluation of various algorithms for CN detection.

Main Results:

  • Established methods for copy number (CN) change detection using SNP array data.
  • Identified critical quality control steps for reliable CN analysis.
  • Reviewed available algorithms and suggested further analysis protocols.

Conclusions:

  • SNP array intensity data provides a robust method for copy number (CN) variation analysis.
  • Rigorous quality control and appropriate algorithm selection are essential for accurate results.
  • The discussed methods and guidelines support reliable genomic segment CN determination.