Intercenter Reliability and Validity of the Rhesus Macaque GeneChip

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2007 Mar 3

PMID 17328815

Citations 12

Authors

Fenghai Duan

Eliot R Spindel

Yu-Hua Li

Robert B Norgren Jr

Affiliations

Soon will be listed here.

Abstract

Background: The non-human primate (NHP) research community has been intensely interested in obtaining whole-genome expression arrays for their work. Recently, novel approaches were used to generate the DNA sequence information for a rhesus GeneChip. To test the reliability of the rhesus GeneChip across different centers, RNA was isolated from five sources: cerebral cortex, pancreas, thymus, testis, and an immortalized fibroblast cell line. Aliquots of this RNA were sent to each of three centers: Yerkes National Primate Research Center, Oregon National Primate Research Center and the University of Nebraska Medical Center. Each center labeled the samples and hybridized them with two rhesus macaque GeneChips. In addition, rhesus samples were hybridzed with human GeneChips to compare with samples hybridized with the rhesus GeneChip.

Results: The results indicate that center effects were minimal and the rhesus GeneChip appears highly reliable. To test the validity of the rhesus GeneChip, five of the most differentially expressed genes among tissues identified in the reliability experiments were chosen for analysis with Quantitative PCR. For all 5 genes, the qPCR and GeneChip results were in agreement with regard to differential expression between tissues. Significantly more probesets were called present when rhesus samples were hybridized with the rhesus GeneChip than when these same samples were hybridized with a human GeneChip.

Conclusion: The rhesus GeneChip is both a reliable and a valid tool for examining gene expression and represents a significant improvement over the use of the human GeneChip for rhesus macaque gene expression studies.

Citing Articles

Gene expression dataset for whole cochlea of Macaca fascicularis.

Mutai H, Miya F, Shibata H, Yasutomi Y, Tsunoda T, Matsunaga T Sci Rep. 2018; 8(1):15554.

PMID: 30349143 PMC: 6197234. DOI: 10.1038/s41598-018-33985-9.

Genomic Tools for the Use of Nonhuman Primates in Translational Research.

Harding J ILAR J. 2017; 58(1):59-68.

PMID: 28838069 PMC: 6279127. DOI: 10.1093/ilar/ilw042.

Improving genome assemblies and annotations for nonhuman primates.

Norgren Jr R ILAR J. 2013; 54(2):144-53.

PMID: 24174438 PMC: 3814395. DOI: 10.1093/ilar/ilt037.

The Rhesus macaque (Macaca mulatta) sperm proteome.

Skerget S, Rosenow M, Polpitiya A, Petritis K, Dorus S, Karr T Mol Cell Proteomics. 2013; 12(11):3052-67.

PMID: 23816990 PMC: 3820923. DOI: 10.1074/mcp.M112.026476.

Limitations of the rhesus macaque draft genome assembly and annotation.

Zhang X, Goodsell J, Norgren Jr R BMC Genomics. 2012; 13:206.

PMID: 22646658 PMC: 3426473. DOI: 10.1186/1471-2164-13-206.

References

Wang Z, Lewis M, Nau M, Arnold A, Vahey M . Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip platforms for the optimization of the assessment of expression patterns in non human primate (NHP) samples. BMC Bioinformatics. 2004; 5:165. PMC: 526766. DOI: 10.1186/1471-2105-5-165. View

Shi L, Reid L, Jones W, Shippy R, Warrington J, Baker S . The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006; 24(9):1151-61. PMC: 3272078. DOI: 10.1038/nbt1239. View

Wang Y, Barbacioru C, Hyland F, Xiao W, Hunkapiller K, Blake J . Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays. BMC Genomics. 2006; 7:59. PMC: 1435885. DOI: 10.1186/1471-2164-7-59. View

Spindel E, Pauley M, Jia Y, Gravett C, Thompson S, Boyle N . Leveraging human genomic information to identify nonhuman primate sequences for expression array development. BMC Genomics. 2005; 6:160. PMC: 1314899. DOI: 10.1186/1471-2164-6-160. View

Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S . Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. PMC: 545600. DOI: 10.1186/gb-2004-5-10-r80. View

Qin L, Beyer R, Hudson F, Linford N, Morris D, Kerr K . Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. BMC Bioinformatics. 2006; 7:23. PMC: 1360686. DOI: 10.1186/1471-2105-7-23. View

Smyth G . Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2006; 3:Article3. DOI: 10.2202/1544-6115.1027. View

Draghici S, Khatri P, Eklund A, Szallasi Z . Reliability and reproducibility issues in DNA microarray measurements. Trends Genet. 2005; 22(2):101-9. PMC: 2386979. DOI: 10.1016/j.tig.2005.12.005. View

Jeong J, Lee K, Kwak I, White L, Hilsenbeck S, Lydon J . Identification of murine uterine genes regulated in a ligand-dependent manner by the progesterone receptor. Endocrinology. 2005; 146(8):3490-505. DOI: 10.1210/en.2005-0016. View

10.

Yoshida S, Mears A, Friedman J, Carter T, He S, Oh E . Expression profiling of the developing and mature Nrl-/- mouse retina: identification of retinal disease candidates and transcriptional regulatory targets of Nrl. Hum Mol Genet. 2004; 13(14):1487-503. DOI: 10.1093/hmg/ddh160. View

11.

Chismar J, Mondala T, Fox H, Roberts E, Langford D, Masliah E . Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations. Biotechniques. 2002; 33(3):516-8, 520, 522 passim. DOI: 10.2144/02333st01. View

12.

Bammler T, Beyer R, Bhattacharya S, Boorman G, Boyles A, Bradford B . Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods. 2005; 2(5):351-6. DOI: 10.1038/nmeth754. View

13.

Tusher V, Tibshirani R, Chu G . Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A. 2001; 98(9):5116-21. PMC: 33173. DOI: 10.1073/pnas.091062498. View

14.

Larkin J, Frank B, Gavras H, Sultana R, Quackenbush J . Independence and reproducibility across microarray platforms. Nat Methods. 2005; 2(5):337-44. DOI: 10.1038/nmeth757. View

15.

Barrett T, Suzek T, Troup D, Wilhite S, Ngau W, Ledoux P . NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res. 2004; 33(Database issue):D562-6. PMC: 539976. DOI: 10.1093/nar/gki022. View

16.

Irizarry R, Bolstad B, Collin F, Cope L, Hobbs B, Speed T . Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003; 31(4):e15. PMC: 150247. DOI: 10.1093/nar/gng015. View

17.

Irizarry R, Warren D, Spencer F, Kim I, Biswal S, Frank B . Multiple-laboratory comparison of microarray platforms. Nat Methods. 2005; 2(5):345-50. DOI: 10.1038/nmeth756. View