Banking placental tissue: An optimized collection procedure for genome-wide analysis of nucleic acids

Placenta

Volumn 35, Issue 8, 2014, Pages 645-654

  Wolfe, L M ^a   Thiagarajan, R D ^a   Boscolo, F ^a,b   Tache V ^a,c   Coleman, R L ^b   Kim, J ^d   Kwan, W K ^a   Loring, J F ^b   Parast, M ^d   Laurent, L C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DNA methylation; DNAgard; Gene expression; Microarray; Placenta; RNA integrity; RNAlater; Snap freezing

Indexed keywords

DNA; NUCLEIC ACID; RNA; MESSENGER RNA;

ARTICLE; COMPARATIVE STUDY; DNA METHYLATION; FEMALE; FIRST TRIMESTER PREGNANCY; GENE EXPRESSION; GENETIC ASSOCIATION; HUMAN; HUMAN TISSUE; LIMIT OF QUANTITATION; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PLACENTA; PLACENTA DISORDER; PLACENTAL DELIVERY; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; QUALITY CONTROL; RNA EXTRACTION; THIRD TRIMESTER PREGNANCY; EVALUATION STUDY; GENE EXPRESSION PROFILING; GENOMICS; HEALTH CARE FACILITY; LABORATORY DIAGNOSIS; PREGNANCY;

DNA METHYLATION; FEMALE; GENE EXPRESSION PROFILING; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMANS; PLACENTA; PREGNANCY; PREGNANCY TRIMESTER, FIRST; PREGNANCY TRIMESTER, THIRD; RNA, MESSENGER; SPECIMEN HANDLING; TISSUE BANKS;

EID: 84905400543     PISSN: 01434004     EISSN: 15323102     Source Type: Journal    
DOI: 10.1016/j.placenta.2014.05.005     Document Type: Article

References (27)

1. Y. Zhou, M. McMaster, K. Woo, M. Janatpour, J. Perry, and T. Karpanen et al. Vascular endothelial growth factor ligands and receptors that regulate human cytotrophoblast survival are dysregulated in severe preeclampsia and hemolysis, elevated liver enzymes, and low platelets syndrome Am J Pathol 160 4 2002 Apr 1405 1423 [PubMed PMID: 11943725. Pubmed Central PMCID: 3277330]
2. O. Basso, S. Rasmussen, C.R. Weinberg, A.J. Wilcox, L.M. Irgens, and R. Skjaerven Trends in fetal and infant survival following preeclampsia JAMA 296 11 2006 Sep 20 1357 1362 PubMed PMID: 16985227
3. M. Habli, R.J. Levine, C. Qian, and B. Sibai Neonatal outcomes in pregnancies with preeclampsia or gestational hypertension and in normotensive pregnancies that delivered at 35, 36, or 37 weeks of gestation Am J Obstet Gynecol 197 4 2007 Oct 406e1 406e7 [PubMed PMID: 17904980]
4. A.A. Baschat, U. Gembruch, I. Reiss, L. Gortner, C.P. Weiner, and C.R. Harman Relationship between arterial and venous Doppler and perinatal outcome in fetal growth restriction Ultrasound Obstet Gynecol 16 5 2000 Oct 407 413 [PubMed PMID: 11169323]
5. I.M. Bernstein, J.D. Horbar, G.J. Badger, A. Ohlsson, and A. Golan Morbidity and mortality among very-low-birth-weight neonates with intrauterine growth restriction. The Vermont Oxford Network Am J Obstet Gynecol 182 1 Pt 1 2000 Jan 198 206 [PubMed PMID: 10649179]
6. T.J. Garite, R. Clark, and J.A. Thorp Intrauterine growth restriction increases morbidity and mortality among premature neonates Am J Obstet Gynecol 191 2 2004 Aug 481 487 [PubMed PMID: 15343225]
7. F. Lackman, V. Capewell, B. Richardson, O. daSilva, and R. Gagnon The risks of spontaneous preterm delivery and perinatal mortality in relation to size at birth according to fetal versus neonatal growth standards Am J Obstet Gynecol 184 5 2001 Apr 946 953 [PubMed PMID: 11303203]
8. D.D. McIntire, S.L. Bloom, B.M. Casey, and K.J. Leveno Birth weight in relation to morbidity and mortality among newborn infants N Engl J Med 340 16 1999 Apr 22 1234 1238 [PubMed PMID: 10210706]
9. O. Lapaire, S. Grill, S. Lalevee, V. Kolla, I. Hosli, and S. Hahn Microarray screening for novel preeclampsia biomarker candidates Fetal Diagn Ther 31 3 2012 147 153 [PubMed PMID: 22472943]
10. C.L. Howerton, C.P. Morgan, D.B. Fischer, and T.L. Bale O-GlcNAc transferase (OGT) as a placental biomarker of maternal stress and reprogramming of CNS gene transcription in development Proc Natl Acad Sci U S A 110 13 2013 Mar 26 5169 5174 [PubMed PMID: 23487789. Pubmed Central PMCID: 3612602]
11. S.E. Maynard, J.Y. Min, J. Merchan, K.H. Lim, J. Li, and S. Mondal et al. Excess placental soluble fms-like tyrosine kinase 1 (sFlt1) may contribute to endothelial dysfunction, hypertension, and proteinuria in preeclampsia J Clin Invest 111 5 2003 Mar 649 658 [PubMed PMID: 12618519. Pubmed Central PMCID: 151901]
12. D.K. Bourque, L. Avila, M. Penaherrera, P. von Dadelszen, and W.P. Robinson Decreased placental methylation at the H19/IGF2 imprinting control region is associated with normotensive intrauterine growth restriction but not preeclampsia Placenta 31 3 2010 Mar 197 202 [PubMed PMID: 20060582]
13. R.K. Yuen, M.S. Penaherrera, P. von Dadelszen, D.E. McFadden, and W.P. Robinson DNA methylation profiling of human placentas reveals promoter hypomethylation of multiple genes in early-onset preeclampsia Eur J Hum Genet 18 9 2010 Sep 1006 1012 [PubMed PMID: 20442742. Pubmed Central PMCID: 2987406]
14. X. Huang, M. Baumann, L. Nikitina, F. Wenger, D. Surbek, and M. Korner et al. RNA degradation differentially affects quantitative mRNA measurements of endogenous reference genes in human placenta Placenta 34 7 2013 Jul 544 547 [PubMed PMID: 23623484]
15. R Development Core Team R: a language and environment for statistical computing 3.0.1 ed. 2013 R Foundation for Statistical Computing Vienna, Austria
16. W.E. Johnson, C. Li, and A. Rabinovic Adjusting batch effects in microarray expression data using empirical Bayes methods Biostatistics 8 1 2007 Jan 118 127 [PubMed PMID: 16632515]
17. T. Hulsen, J. de Vlieg, and W. Alkema BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams BMC Genomics 9 2008 488 [PubMed PMID: 18925949. Pubmed Central PMCID: 2584113]
18. J. Maksimovic, L. Gordon, and A. Oshlack SWAN: subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips Genome Biol 13 6 2012 R44 [PubMed PMID: 22703947. Pubmed Central PMCID: 3446316]
19. M.A. Perlmutter, C.J. Best, J.W. Gillespie, Y. Gathright, S. Gonzalez, and A. Velasco et al. Comparison of snap freezing versus ethanol fixation for gene expression profiling of tissue specimens J Mol Diagn 6 4 2004 Nov 371 377 [PubMed PMID: 15507677. Pubmed Central PMCID: 1867483]
20. A. Schroeder, O. Mueller, S. Stocker, R. Salowsky, M. Leiber, and M. Gassmann et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements BMC Mol Biol 7 2006 3 [PubMed PMID: 16448564. Pubmed Central PMCID: 1413964]
21. I. Fajardy, E. Moitrot, A. Vambergue, M. Vandersippe-Millot, P. Deruelle, and J. Rousseaux Time course analysis of RNA stability in human placenta BMC Mol Biol 10 2009 21 [PubMed PMID: 19284566. Pubmed Central PMCID: 2664811]
22. L. Avila, R.K. Yuen, D. Diego-Alvarez, M.S. Penaherrera, R. Jiang, and W.P. Robinson Evaluating DNA methylation and gene expression variability in the human term placenta Placenta 31 12 2010 Dec 1070 1077 [PubMed PMID: 20947161]
23. G.J. Burton, N.J. Sebire, L. Myatt, D. Tannetta, Y.L. Wang, and Y. Sadovsky et al. Optimising sample collection for placental research Placenta 35 1 2014 Jan 9 22 [PubMed PMID: 24290528]
24. C. Hatzis, H. Sun, H. Yao, R.E. Hubbard, F. Meric-Bernstam, and G.V. Babiera et al. Effects of tissue handling on RNA integrity and microarray measurements from resected breast cancers J Natl Cancer Inst 103 24 2011 Dec 21 1871 1883 [PubMed PMID: 22034635. Pubmed Central PMCID: 3243675]
25. D. Chowdary, J. Lathrop, J. Skelton, K. Curtin, T. Briggs, and Y. Zhang et al. Prognostic gene expression signatures can be measured in tissues collected in RNAlater preservative J Mol Diagn 8 1 2006 Feb 31 39 [PubMed PMID: 16436632. Pubmed Central PMCID: 1867564]
26. K.L. Thompson, P.S. Pine, B.A. Rosenzweig, Y. Turpaz, and J. Retief Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA BMC Biotechnol 7 2007 57 [PubMed PMID: 17854504. Pubmed Central PMCID: 2082023]
27. M.L. Jobarteh, S.E. Moore, C. Kennedy, L. Gambling, and H.J. McArdle The effect of delay in collection and processing on RNA integrity in human placenta: experiences from rural Africa Placenta 35 1 2014 Jan 72 74 [PubMed PMID: 24125806. Pubmed Central PMCID: 3928992]