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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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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%...
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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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,...
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Genome Copying Errors02:46

Genome Copying Errors

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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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Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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RNA-seq03:21

RNA-seq

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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...
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Next-generation Sequencing03:00

Next-generation Sequencing

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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....
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Related Experiment Video

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Detection of Copy Number Alterations Using Single Cell Sequencing
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Determining multiallelic complex copy number and sequence variation from high coverage exome sequencing data.

Diego Forni1,2, Diana Martin1, Razan Abujaber1

  • 1Department of Genetics, University of Leicester, Leicester, UK.

BMC Genomics
|November 4, 2015
PubMed
Summary
This summary is machine-generated.

Copy number variation (CNV) typing methods are improving with high-throughput sequencing. This study reveals novel sequence variants in the beta-defensin region, highlighting CNVs as a significant source of genomic diversity.

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Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma
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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Area of Science:

  • Genomics
  • Human Genetics

Background:

  • Copy number variation (CNV) is a key genomic variation type, but accurate typing methods are still developing.
  • High-throughput sequencing offers new approaches for CNV analysis using read depth and sequence data.

Purpose of the Study:

  • To infer diploid copy number and call sequence variants in the beta-defensin genomic region using exome sequencing data.
  • To investigate the genomic diversity within this complex, multicopy region.

Main Methods:

  • Utilized high-coverage exome sequences from the 1000 Genomes project (Phase 3).
  • Inferred diploid copy number and identified sequence variants in the beta-defensin region across 1285 samples.
  • Validated copy number and sequence calls using Nanostring nCounter, paralogue ratio tests, and cloned PCR products.

Main Results:

  • Successfully called copy number and sequence variation for beta-defensin genes in 1285 individuals from 26 populations.
  • Identified novel sequence variants, many rare, predicted to alter beta-defensin protein sequences and function.
  • These variants may influence antimicrobial properties, immune response, and fertility.

Conclusions:

  • Sequence variation within multiallelic copy number variations (CNVs) is an underappreciated source of genomic diversity.
  • 81% of identified sequence variants in this region were novel and not previously cataloged in dbSNP.