@article{bischoff_tsai_hardison_york_freking_nonneman_rohrer_piedrahita_2008, title={Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays}, volume={9}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/1471-2164-9-252}, DOI={10.1186/1471-2164-9-252}, abstractNote={Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed with Affymetrix porcine microarrays is presented. A linear mixed model analysis was used to identify significant breed-by-probe interactions.Gene specific linear mixed models were fit to each of the log2 transformed probe intensities on these arrays, using fixed effects for breed, probe, breed-by-probe interaction, and a random effect for array. After surveying the day 25 placental transcriptome, 857 probes with a q-value < or = 0.05 and |fold change| > or = 2 for the breed-by-probe interaction were identified as candidates containing SFP. To address the quality of the bioinformatics approach, universal pyrosequencing assays were designed from Affymetrix exemplar sequences to independently assess polymorphisms within a subset of probes for validation. Additionally probes were randomly selected for sequencing to determine an unbiased confirmation rate. In most cases, the 25-mer probe sequence printed on the microarray diverged from Meishan, not occidental crosses. This analysis was used to define a set of highly reliable predicted SFPs according to their probability scores.By applying a SFP detection method to two mammalian breeds for the first time, we detected transition and transversion single nucleotide polymorphisms, as well as insertions/deletions which can be used to rapidly develop markers for genetic mapping and association analysis in species where high density genotyping platforms are otherwise unavailable.SNPs and INDELS discovered by this approach have been publicly deposited in NCBI's SNP repository dbSNP. This method is an attractive bioinformatics tool for uncovering breed-by-probe interactions, for rapidly identifying expressed SNPs, for investigating potential functional correlations between gene expression and breed polymorphisms, and is robust enough to be used on any Affymetrix gene expression platform.}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Bischoff, Steve R and Tsai, Shengdar and Hardison, Nicholas E and York, Abby M and Freking, Brad A and Nonneman, Dan and Rohrer, Gary and Piedrahita, Jorge A}, year={2008}, pages={252} }
 @article{estrada_collins_york_bischoff_sommer_tsai_petters_piedrahita_2008, title={Successful cloning of the Yucatan minipig using commercial/occidental breeds as oocyte donors and embryo recipients}, volume={10}, ISSN={["1536-2302"]}, DOI={10.1089/clo.2008.0005}, abstractNote={The widespread application of porcine SCNT to biomedical research is being hampered by the large adult size (300-600 lbs) of the commercial breeds commonly used for SCNT. The Yucatan minipig, in contrast, has an adult weight of 140-150 lbs and a long history of utility in biomedical research. In order to combine the wide availability of commercial swine with the biomedical value of the Yucatan minipig, we utilized SCNT using the Yucatan as nuclear donors and commercial swine as both oocyte donors and recipients. Of six recipient gilts receiving 631 SCNT embryos, three went to term and delivered seven piglets, four of which survived to adulthood. Additionally, we obtained fetal fibroblasts from a cloned Yucatan and used them for a second round of SCNT. Of three recipients receiving 315 reconstructed embryos, one went to term and delivered three piglets, one of which survived to adulthood. Both microsatellite and D-loop sequence analysis confirmed that all of the piglets generated were nuclear-mitochondrial hybrids carrying Yucatan nuclear DNA and commercial breed mitochondrial DNA. This report shows that it is possible to produce viable Yucatan SCNT clones and opens up the possibility of developing valuable biomedical models in this porcine breed.}, number={2}, journal={CLONING AND STEM CELLS}, author={Estrada, Jose L. and Collins, Bruce and York, Abby and Bischoff, Steve and Sommer, Jeff and Tsai, Shengdar and Petters, Robert M. and Piedrahita, Jorge A.}, year={2008}, month={Jun}, pages={287–296} }