TY - JOUR AU - Walter, Nicole AR AU - Bottomly, Daniel AU - Laderas, Ted AU - Mooney, Michael A. AU - Darakjian, Priscila AU - Searles, Robert P. AU - Harrington, Christina A. AU - McWeeney, Shannon K. AU - Hitzemann, Robert AU - Buck, Kari J. PY - 2009 DA - 2009/08/17 TI - High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs JO - BMC Genomics SP - 379 VL - 10 IS - 1 AB - Allelic variation is the cornerstone of genetically determined differences in gene expression, gene product structure, physiology, and behavior. However, allelic variation, particularly cryptic (unknown or not annotated) variation, is problematic for follow up analyses. Polymorphisms result in a high incidence of false positive and false negative results in hybridization based analyses and hinder the identification of the true variation underlying genetically determined differences in physiology and behavior. Given the proliferation of mouse genetic models (e.g., knockout models, selectively bred lines, heterogeneous stocks derived from standard inbred strains and wild mice) and the wealth of gene expression microarray and phenotypic studies using genetic models, the impact of naturally-occurring polymorphisms on these data is critical. With the advent of next-generation, high-throughput sequencing, we are now in a position to determine to what extent polymorphisms are currently cryptic in such models and their impact on downstream analyses. SN - 1471-2164 UR - https://doi.org/10.1186/1471-2164-10-379 DO - 10.1186/1471-2164-10-379 ID - Walter2009 ER -