Allele quantification using molecular inversion probes (MIP)

Detection of genomic copy number changes has been an important research area, especially in cancer. Several high-throughput technologies have been developed to detect these changes. Features that are important for the utility of technologies assessing copy number changes include the ability to interrogate regions of interest at the desired density as well as the ability to differentiate the two homologs. In addition, assessing formaldehyde fixed and paraffin embedded (FFPE) samples allows the utilization of the vast majority of cancer samples. To address these points we demonstrate the use of molecular inversion probe (MIP) technology to the study of copy number. MIP is a high-throughput genotyping technology capable of interrogating >20 000 single nucleotide polymorphisms in the same tube. We have shown the ability of MIP at this multiplex level to provide copy number measurements while obtaining the allele information. In addition we have demonstrated a proof of principle for copy number analysis in FFPE samples

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

BACKGROUND:A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue.RESULTS:Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE.CONCLUSION:MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]

Faculty roles and role preferences in ten fields of professional study

Teaching faculty in ten entry-level professional fields reported varying amounts of time devoted to teaching, research, consulting, and professional practice but did not differ in time devoted to administration. The faculty member's own role view was most closely related to time use, but for time spent in teaching and research, faculty age and institutional type (but not gender) were also significant predictors. Even after several general demographic characteristics and environmental variables that potentially differentiate professional from discipline-based faculty are taken into account, different professional fields may be characterized by group climates which influence or reinforce certain faculty roles.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43598/1/11162_2004_Article_BF00991875.pd

Administration Guide for the Opinions about Deaf People Scale: A Scale To Measure Hearing Adults' Beliefs about the Capabilities of Deaf Adults

Guides - Non-Classroom; Reports - Evaluative; Tests/QuestionnairesInstructions for the administration of the Opinions about Deaf People Scale are given. This scale measures the beliefs of hearing adults about the capabilities of deaf adults. The somewhat ambiguous title of the instrument is designed to avoid leading respondents to respond in socially desirable ways. The instrument is based on misconceptions hearing adults might hold about the capabilities of deaf adults. The scale can be administered individually or to a group. It is a summative scale, and each subject's score can be calculated by adding the points for all 20 items. A low score reflects a positive attitude about the capabilities of the deaf, while a high score reflects a negative attitude. A scoring key is included. A pilot test with 290 college students supported construct validity and suggested one general deaf capabilities factor, with a few items that correlate moderately to strongly with an intelligence factor. The scale is in Appendix A. (SLD)N