AUTHOR=Fountain Emily D. , Zhou Li-Chen , Karklus Alyssa , Liu Qun-Xiu , Meyers James , Fontanilla Ian K. C. , Rafael Emmanuel Francisco , Yu Jian-Yi , Zhang Qiong , Zhu Xiang-Lei , Pei En-Le , Yuan Yao-Hua , Banes Graham L. TITLE=Cross-Species Application of Illumina iScan Microarrays for Cost-Effective, High-Throughput SNP Discovery JOURNAL=Frontiers in Ecology and Evolution VOLUME=9 YEAR=2021 URL=https://www.frontiersin.org/journals/ecology-and-evolution/articles/10.3389/fevo.2021.629252 DOI=10.3389/fevo.2021.629252 ISSN=2296-701X ABSTRACT=

Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single-nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily converted to human-readable genotypes or be merged with pre-existing data. To address this, we present and validate a novel pipeline to facilitate data analysis from cross-species application of Illumina microarrays. This facilitates the generation of a compatible VCF from iScan data and the merging of this with a second VCF comprising genotypes derived from other samples and sources. Our pipeline includes a custom script, iScanVCFMerge (presented as a Python package), which we validate using iScan data from three great ape genera. We conclude that cross-species application of microarrays can be a rapid, cost-effective approach for SNP discovery in non-model organisms. Our pipeline surmounts the common challenges of integrating iScan genotypes with pre-existing data.