Reduction of systematic bias in transcriptome data from human peripheral blood mononuclear cells for transportation and biobanking

PLoS ONE

Volumn 9, Issue 8, 2014, Pages

  Ohmomo, Hideki ^a   Hachiya, Tsuyoshi ^a   Shiwa, Yu ^a   Furukawa, Ryohei ^a   Ono, Kanako ^a   Ito, Shigeki ^a   Ishida, Yoji ^a   Satoh, Mamoru ^a   Hitomi, Jiro ^a   Sobue, Kenji ^a   Shimizu, Atsushi ^a  

^a IWATE MEDICAL UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; BLOOD SAMPLING; BLOOD STORAGE; CONTROLLED STUDY; DATA ANALYSIS; FREEZING; GENE EXPRESSION; HUMAN; HUMAN CELL; PERIPHERAL BLOOD MONONUCLEAR CELL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA DEGRADATION; RNA EXTRACTION; RNA SEQUENCE; STATISTICAL BIAS; TRANSCRIPTOMICS; ADULT; BLOOD BANK; CYTOLOGY; FEMALE; MALE; METABOLISM; MIDDLE AGED; MONONUCLEAR CELL; RNA STABILITY; SEQUENCE ANALYSIS;

ADULT; BLOOD BANKS; BLOOD PRESERVATION; FEMALE; HUMANS; LEUKOCYTES, MONONUCLEAR; MALE; MIDDLE AGED; RNA STABILITY; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84905484324     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0104283     Document Type: Article

References (25)

1. Nakamura M, Tanaka F, Nakajima S, Honma M, Sakai T, et al. (2012) Comparison of the incidence of acute decompensated heart failure before and after the major tsunami in Northeast Japan. Am J Cardiol 110: 1856-1860.
2. Omama S, Yoshida Y, Ogasawara K, Ogawa A, Ishibashi Y, et al. (2013) Influence of the great East Japan earthquake and tsunami 2011 on occurrence of cerebrovascular diseases in Iwate, Japan. Stroke 44: 1518-1524.
3. Aoki T, Fukumoto Y, Yasuda S, Sakata Y, Ito K, et al. (2012) The Great East Japan Earthquake Disaster and cardiovascular diseases. Eur Heart J 33: 2796-2803.
4. Usami M, Iwadare Y, Kodaira M, Watanabe K, Aoki M, et al. (2012) Relationships between traumatic symptoms and environmental damage conditions among children 8 months after the 2011 Japan earthquake and tsunami. PLoS One 7: e50721.
5. Steinberg K, Beck J, Nickerson D, Garcia-Closas M, Gallagher M, et al. (2002) DNA banking for epidemiologic studies: a review of current practices. Epidemiology 13: 246-254. (Pubitemid 34415843)
6. Nederhand RJ, Droog S, Kluft C, Simoons ML, de Maat MP, et al. (2003) Logistics and quality control for DNA sampling in large multicenter studies. J Thromb Haemost 1: 987-991.
7. Elliott P, Peakman TC; UK BioBank. (2008) The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine. Int J Epidemiol 37: 234-244. (Pubitemid 351494195)
8. Wihlberg K, Hugget J, Sanders R, Whale AS, Bushell C, et al. (2012) Quality assessment of biobanked nucleic acid extracts for downstream molecular analysis. Biopreserv Biobank 10: 266-275.
9. Abe Al-Soud W, Rådström P. (2000) Effects of amplificators on diagnostic PCR in the presence of blood, feces and meat. J Clin Microbiol 38: 4463-4470.
10. Wright C, Bergstrom D, Dai H, Marton M, Morris M, et al. (2008) Characterization of globin RNA interference in gene expression profiling of whole-blood samples. Clin Chem 54: 396-405. (Pubitemid 351302623)
11. Debey S, Schoenbeck U, Hellmich M, Gathof BS, Pillai R, et al. (2004) Comparison of different isolation techniques prior gene expression profileing of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types. Parmacogenomics 4: 193-207. (Pubitemid 38786558)
12. Debey S, Zander T, Brors B, Popov A, Eils R, et al. (2006) A highly standardized, robust, and cost-effective method for genome-wide transcriptome analysis of peripheral blood applicable to large-scale clinical trials. Genomics 87: 653-664.
13. Bayatti, Cooper-Knock J, Bury JJ, Wyles M, Heath PR, et al. (2014) Comparison of blood RNA extraction methods used for gene expression profiling in amytrophic lateral sclerosis. PLoS One 27: e87508.
14. Asare AL, Kolchinsky SA, Gao Z, Wang R, Raddassi K, et al. (2008) Differential gene expression profiles are dependent upon method of peripheral blood collection and RNA isolation. BMC Genomics 9: 474.
15. Vartanian K, Slottke R, Johnstone T, Casale A, Planck SR, et al. (2009) Gene expression profileing of whole blood: comparison of target preparation methods for accurate and reproducible microarray analysis. BMC Genomics 10: 2.
16. Burczynski ME, Twine NC, Dukart G, Marshall B, Hidalgo M, et al. (2005) Transcriptional profiles in peripheral blood mononuclear cells prognostic of clinical outcomes in patients with advanced renal cell carcinoma. Clin Cancer Res 11: 1181-1189. (Pubitemid 40175769)
17. Baine MJ, Chakraborty S, Smith LM, Mallya K, Sasson AR, et al. (2011) Transcriptional profiling or peripheral blood mononuclear cells in pancreatic cancer patients identifies novel genes with potential diagnostic utility. PLoS One 6: e17014.
18. Pawlowski NA, Kaplan G, Hamill AL, Cohn ZA, Scott WA. (1983) Arachidonic acid metabolism by human monocytes. Studies with platelet-depleted cultures. J Exp Med 158: 393-412. (Pubitemid 13049396)
19. Rainen L, Oelmueller U, Jurgensen S, Wyrich R, Ballas C, et al. (2002) Stabilization of mRNA expression in whole blood samples. Clin Chem 48: 1883-1890. (Pubitemid 35222745)
20. Schmittgen TS, Livak KJ. (2008) Analysing real-time PCR data by the comparative C(T) method. Nat Protoc 3: 1101-1108.
21. Langmead B, Trapnell C, Pop M, Salzberg SL. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
22. Trapnell C, Pachter L, Salzberg SL. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
23. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079.
24. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
25. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, et al. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31: 46-53.