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Updated: May 15, 2026
09:45
Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
ParseCNV integrative copy number variation association software with quality tracking.
Joseph T Glessner1, Jin Li, Hakon Hakonarson
1Department of Pediatrics, Division of Human Genetics, The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. glessner@chop.edu
Nucleic Acids Research
|January 8, 2013
Summary
ParseCNV software enhances copy number variation (CNV) association studies by providing probe-based statistics for CNV occurrence and regions (CNVRs). It improves upon existing tools by offering quality tracking and uncertainty evaluation for reliable results.
Area of Science:
- Genetics
- Bioinformatics
- Computational Biology
Background:
- Copy number variations (CNVs) are significant in genetic studies, but tools for CNV association analysis are limited.
- Existing software often lacks comprehensive statistics, quality control, and robust handling of complex CNV overlaps.
Purpose of the Study:
- To introduce ParseCNV, a novel software tool designed for robust CNV association studies.
- To address the limitations of current software in analyzing CNV occurrence and regions (CNVRs).
Main Methods:
- ParseCNV processes CNV calls to generate probe-based statistics for case-control and family-based studies.
- It dynamically defines CNV regions (CNVRs) to manage complex overlaps and association precision.
- The software incorporates quality tracking and uncertainty evaluation for CNV associations.
Main Results:
- ParseCNV avoids convergence failures and fitting weaknesses seen in other tools like CNVtools and CNVassoc.
- It provides state-specific CNVR statistics, unlike Plink's combined approach.
- Utilizing ParseCNV with optimal quality control leads to 90% validation of CNVs by polymerase chain reaction.
Conclusions:
- ParseCNV offers a unique and comprehensive solution for CNV association studies.
- The software enhances the reliability of CNV association findings through integrated quality assessment.
- ParseCNV is freely available, facilitating its adoption in genetic research.
Related Concept Videos
02:26Comparing 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%...
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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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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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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Although all next-generation methods use different technologies, they all share a set of standard features.
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