The impact of errors in copy number variation detection algorithms on association results.
The inaccuracy of copy number variation (CNV) detection on single nucleotide polymorphism (SNP) arrays has recently been brought to attention. Such high error rates will undoubtedly have ramifications on downstream association testing. We examined this effect for a wide range of scenarios and found...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3327691?pdf=render |
| _version_ | 1828452377158483968 |
|---|---|
| author | Nathan E Wineinger Hemant K Tiwari |
| author_facet | Nathan E Wineinger Hemant K Tiwari |
| author_sort | Nathan E Wineinger |
| collection | DOAJ |
| description | The inaccuracy of copy number variation (CNV) detection on single nucleotide polymorphism (SNP) arrays has recently been brought to attention. Such high error rates will undoubtedly have ramifications on downstream association testing. We examined this effect for a wide range of scenarios and found a noticeable decrease in power for error rates typical of CNV calling algorithms. We compared power using CNV calls to the log relative ratio and found the latter to be superior when error rates are moderate to large or when the CNV size is small. It is our recommendation that CNV researchers use intensity measurements as an alternative to CNV calls in these scenarios. |
| first_indexed | 2024-12-10T23:52:32Z |
| format | Article |
| id | doaj.art-c78d7659b9234d9fbb8b0dece5a4dbf0 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T23:52:32Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-c78d7659b9234d9fbb8b0dece5a4dbf02022-12-22T01:28:42ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0174e3239610.1371/journal.pone.0032396The impact of errors in copy number variation detection algorithms on association results.Nathan E WineingerHemant K TiwariThe inaccuracy of copy number variation (CNV) detection on single nucleotide polymorphism (SNP) arrays has recently been brought to attention. Such high error rates will undoubtedly have ramifications on downstream association testing. We examined this effect for a wide range of scenarios and found a noticeable decrease in power for error rates typical of CNV calling algorithms. We compared power using CNV calls to the log relative ratio and found the latter to be superior when error rates are moderate to large or when the CNV size is small. It is our recommendation that CNV researchers use intensity measurements as an alternative to CNV calls in these scenarios.http://europepmc.org/articles/PMC3327691?pdf=render |
| spellingShingle | Nathan E Wineinger Hemant K Tiwari The impact of errors in copy number variation detection algorithms on association results. PLoS ONE |
| title | The impact of errors in copy number variation detection algorithms on association results. |
| title_full | The impact of errors in copy number variation detection algorithms on association results. |
| title_fullStr | The impact of errors in copy number variation detection algorithms on association results. |
| title_full_unstemmed | The impact of errors in copy number variation detection algorithms on association results. |
| title_short | The impact of errors in copy number variation detection algorithms on association results. |
| title_sort | impact of errors in copy number variation detection algorithms on association results |
| url | http://europepmc.org/articles/PMC3327691?pdf=render |
| work_keys_str_mv | AT nathanewineinger theimpactoferrorsincopynumbervariationdetectionalgorithmsonassociationresults AT hemantktiwari theimpactoferrorsincopynumbervariationdetectionalgorithmsonassociationresults AT nathanewineinger impactoferrorsincopynumbervariationdetectionalgorithmsonassociationresults AT hemantktiwari impactoferrorsincopynumbervariationdetectionalgorithmsonassociationresults |