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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,...

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Updated: May 20, 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

Efficiency and power as a function of sequence coverage, SNP array density, and imputation.

Jason Flannick¹, Joshua M Korn, Pierre Fontanillas

¹Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.

Plos Computational Biology

|July 19, 2012

Summary

This summary is machine-generated.

Combining low-coverage sequencing and SNP arrays improves genotype accuracy, especially for rare genetic variations. This integrated approach enhances genetic studies and genotype calling methods.

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Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

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Last Updated: May 20, 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

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Area of Science:

Genomics
Statistical Genetics
Bioinformatics

Background:

High-coverage whole genome sequencing offers comprehensive genetic variation data but can be inefficient.
Lower-coverage sequencing and SNP arrays, coupled with imputation, are cost-effective alternatives for large-scale genetic studies.
Existing methods may not fully leverage the complementary strengths of different genotyping technologies.

Purpose of the Study:

To develop and evaluate a statistical framework for joint genotype estimation from diverse data sources.
To compare the performance of low-coverage sequencing, SNP arrays, and their combination for genotype calling.
To assess the impact of combining data on sensitivity, specificity, and error detection.

Main Methods:

Developed a statistical framework for joint genotype calling from sequence reads, array intensities, and imputation data.
Evaluated the framework using European samples.
Compared imputation accuracy using 1x sequencing, 1M SNP arrays, and combined approaches.

Main Results:

Imputation with 1x sequencing or 1M SNP arrays showed comparable sensitivity (89%) and specificity (99.6%).
Adding low-coverage sequence reads to dense SNP arrays significantly increased sensitivity for low-frequency polymorphisms (MAF < 5%).
Joint analysis reduced genotype errors and identified novel error modes at discordant sites.

Conclusions:

Combining low-coverage sequencing with SNP arrays offers a powerful strategy for accurate genotype calling, particularly for rare variants.
The developed joint framework improves genotype accuracy and aids in understanding error patterns.
This approach has implications for optimizing next-generation sequencing in genome-wide association studies and advancing genotype calling methodologies.