Attack of the clones: the influence of PCR clones on RAD-seq genotype calls

Session: Application of Genomic Tools to Inform Management of the Great Lakes (2)

Peter Euclide, University of Wisconsin Steven's Point, [email protected]
Wesley Larson, U.S. Geological Survey, [email protected]
Matthew Bootsma, Wisconsin Cooperative Fisheries Research Unit, [email protected]
Mariah Meek, Michigan State University, [email protected]
Garrett Mckinney, NOAA, [email protected]

Abstract

Interpretation of genomic data requires an understanding of the sources of bias that can influence results. One source of bias often cited are PCR clones or duplicates. PCR clones are common in restriction site associated sequencing (RAD-seq) which is increasingly used in fisheries science. We evaluate the influence PCR clones have on four RAD-seq datasets. Datasets were compared before and after clones were removed to estimate an expected number of clones present in RAD-seq datasets, quantify how often clones cause genotype calls to change, explore why some genotypes are more vulnerable to clones than others, and test if clones bias genetic diversity estimates. We discovered that RAD-seq datasets contain 30 – 60% PCR clones, but very few genotypes actually change once clones are removed (5-10%), and less than 0.2% change between a heterozygote and a homozygote. Removing PCR clones has little influence on estimates of diversity. As such, while steps should be taken to limit PCR clones during library preparation, PCR clones are likely not a substantial source of bias for most RAD-seq studies.

Twitter handle of presenter
@peuclide