Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency

The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values (FIS) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE) or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, FST and allelic number of close lineage populations.

P3-14-21: Neoadjuvant Therapy Response, Subtype and BRCA Status in an Underserved Population

Background

Preoperative (neoadjuvant) chemotherapy is typically used for larger operable breast cancer cases, and the degree of pathological response correlates with long term outcome. Therapeutic response also depends on biological and molecular subtype and is increasingly studied in the research setting to identify prognostic biomarkers and potential therapeutic targets. Little is known about the interactions of neoadjuvant response with biomarker subtypes and genetic predisposition in underserved and minority populations.

Methods: IRB approval was obtained to capture demographic, clinicopathological and genetic testing data on patients diagnosed with invasive breast cancer and treated with preoperative chemotherapy and definitive surgery between 2005 and 2010 at Los Angeles County Medical Center, which serves a primarily Hispanic and indigent population. Treatment followed NCCN guidelines with the exception that not all patients with HER2+ disease received trastuzumab. Genetic counseling and testing has been available at this center since 2007. Pathological complete response (pCR) was defined as no residual invasive disease in breast or nodes. Chi-square or Fisher's Exact test was used to examine associations between pCR and clinical factors, and logistic regression analyses were applied to assess each variable's contribution to pCR.

Results: Among 104 patients, of whom 79% were Hispanic, the overall pCR rate was 27%. Significantly higher pCR rates were seen in age ≥50, clinical N0, HER2+, triple negative, and lumpectomy cases. No differences in pCR rate was seen in Hispanics vs. others, Grade III vs. I and II or in the 9 BRCA mutations carriers among 45 tested compared to no mutation or those not tested. Of the 43 patients with HER2+ disease, the pCR rate was higher in the 32 patients who received trastuzumab (pCR 50.0 vs. 27.3%). Subset pCR rates and odds ratios (OR) of achieving pCR are shown below: