Comparing Copy Number Calling Algorithms with Quantitative PCR
Author Information
Author(s): Britney L Grayson, Thomas M Aune
Primary Institution: Vanderbilt University School of Medicine
Hypothesis
We hypothesized that quantitative PCR could finitely determine copy number and assess the validity of calling algorithms.
Conclusion
Birdsuite showed the greatest agreement with quantitative PCR in determining copy numbers.
Supporting Evidence
- Birdsuite had a 91% agreement with quantitative PCR for copy number calls.
- Partek Genomics Suite and GTC showed lower agreement rates of 76% and 79% respectively with quantitative PCR.
- The study analyzed 77 genomic DNA samples from patients.
Takeaway
This study looked at how well different computer programs can find changes in DNA compared to a lab test, and found one program was the best at matching the lab results.
Methodology
Data from 29 Affymetrix SNP 6.0 arrays were analyzed using three programs and compared to quantitative PCR results.
Potential Biases
Potential bias due to reliance on pooled reference files for some algorithms.
Limitations
The study's findings may not be generalizable beyond the specific algorithms and methods used.
Participant Demographics
Participants were recruited from the Clinical Research Center at Vanderbilt University.
Digital Object Identifier (DOI)
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