Comparing Software for Analyzing Genomic Copy Number Variation
Author Information
Author(s): Eckel-Passow Jeanette E, Atkinson Elizabeth J, Maharjan Sooraj, Kardia Sharon LR, de Andrade Mariza
Primary Institution: Mayo Clinic
Hypothesis
Which software packages are optimal for estimating copy number variation from Affymetrix SNP arrays?
Conclusion
PennCNV and Aroma.Affymetrix are the best software options for analyzing locus-level copy number data.
Supporting Evidence
- PennCNV detected more CNVs than CRLMM/VanillaIce.
- APT had median locus-level copy numbers closest to a value of two.
- Only PennCNV provides copy number specific quality-control metrics.
Takeaway
This study looked at different computer programs to see which ones are best at figuring out how many copies of genes people have. It found that some programs do a better job than others.
Methodology
The study compared four software packages using a dataset of 1,418 samples to evaluate bias, variance, and concordance in copy number data.
Potential Biases
The software packages may have different biases affecting the results.
Limitations
The study did not validate the detected CNVs with an independent technology.
Participant Demographics
1,418 non-Hispanic white adults from the GENOA study.
Digital Object Identifier (DOI)
Want to read the original?
Access the complete publication on the publisher's website