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Comparing Copy Number Variations and SNPs

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-SNPs

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-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

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...

RNA-seq

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...

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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
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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...

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Updated: Apr 26, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Forensic application of SNP-based resequencing array for individual identification.

Sohee Cho¹, Hyung Jin Yu², Jisung Han²

¹Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, Republic of Korea.

Forensic Science International. Genetics

|August 2, 2014

Summary

This summary is machine-generated.

Forensic investigations can now utilize a new platform for analyzing single nucleotide polymorphisms (SNPs). This method accurately types degraded DNA samples, complementing existing short tandem repeat (STR) analysis.

Keywords:

DNA chip Human identification Resequencing array Single nucleotide polymorphism

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Last Updated: Apr 26, 2026

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Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Area of Science:

Forensic Science
Genetics
Molecular Biology

Background:

Single nucleotide polymorphisms (SNPs) are crucial genetic markers in forensic investigations.
Accurate analysis of SNPs requires efficient multi-amplification technology and reliable platforms.
Existing methods may face challenges with degraded or limited DNA samples.

Purpose of the Study:

To develop and validate a novel platform for forensic SNP analysis.
To assess the platform's performance with challenging DNA samples, including degraded and bone-extracted DNA.
To evaluate the potential of this platform to augment current forensic techniques.

Main Methods:

Development of a platform utilizing Affymetrix resequencing arrays.
Multiplex PCR amplification of 169 selected SNP markers.
SNP marker selection based on population genetics parameters (Fst, LD R², MAF) from the 1000 Genomes database.
Testing with low DNA quantities (approx. 10pg) and artificially degraded samples.

Main Results:

The platform successfully typed over 120 out of 169 SNPs with approximately 10pg of DNA.
High typing success rates were observed even with artificially degraded DNA samples.
Comparable success rates were achieved with DNA extracted from bone samples.

Conclusions:

The developed platform demonstrates significant potential for forensic applications, particularly with challenging samples like degraded DNA and bone.
This SNP analysis platform can serve as a valuable adjunct to established short tandem repeat (STR) profiling methods.
The platform's adaptability suggests future applications in diverse forensic and genetic analysis areas.