Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: Preliminary assessment of cross-platform concordance

Genomics

Volumn 102, Issue 1, 2013, Pages 8-14

  Kelly, Andrew D ^a   Hill, Katherine E ^a   Correll, Mick ^b   Hu, Lan ^b   Wang, Yaoyu E ^b   Rubio, Renee ^b   Duan, Shenghua ^b   Quackenbush, John ^b   Spentzos, Dimitrios ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

Microarrays; Paraffin tissue; RNA sequencing

Indexed keywords

MICRORNA;

ADOLESCENT; ARTICLE; CHILD; CONTROLLED STUDY; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENETIC PROCEDURES; HUMAN; HUMAN TISSUE; LEIOMYOSARCOMA; LIPOSARCOMA; MICROARRAY ANALYSIS; NEXT GENERATION SEQUENCING; NUCLEOTIDE SEQUENCE; OSTEOSARCOMA; PRESCHOOL CHILD; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; QUANTITATIVE ASSAY; REAL TIME POLYMERASE CHAIN REACTION; RELIABILITY; SCHOOL CHILD; SIGNAL TRANSDUCTION; TRANSCRIPTOMICS; TRANSLATIONAL RESEARCH;

BREAST NEOPLASMS; CRYOPRESERVATION; DNA, COMPLEMENTARY; FEMALE; FORMALDEHYDE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICROARRAY ANALYSIS; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PARAFFIN EMBEDDING; RNA, MESSENGER; TISSUE FIXATION;

EID: 84878507923     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2013.03.008     Document Type: Article

References (19)

1. Meyerson M., Gabriel S., Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet. 2010, 11:685-696.
2. Hawkins R.D., Hon G.C., Ren B. Next-generation genomics: an integrative approach. Nat. Rev. Genet. 2010, 11:476-486.
3. Chon H.S., Lancaster J.M. Microarray-based gene expression studies in ovarian cancer. Cancer Control 2011, 18:8-15.
4. Lallemant B., Evrard A., Chambon G., Sabra O., Kacha S., Lallemant J.G., Lumbroso S., Brouillet J.P. Gene expression profiling in head and neck squamous cell carcinoma: clinical perspectives. Head Neck 2010, 32:1712-1719.
5. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
6. Hurd P.J., Nelson C.J. Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct. Genomic Proteomic 2009, 8:174-183.
7. Xu W., Seok J., Mindrinos M.N., Schweitzer A.C., Jiang H., Wilhelmy J., Clark T.A., Kapur K., Xing Y., Faham M., Storey J.D., Moldawer L.L., Maier R.V., Tompkins R.G., Wong W.H., Davis R.W., Xiao W. Human transcriptome array for high-throughput clinical studies. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:3707-3712.
8. Fan J.B., Yeakley J.M., Bibikova M., Chudin E., Wickham E., Chen J., Doucet D., Rigault P., Zhang B., Shen R., McBride C., Li H.R., Fu X.D., Oliphant A., Barker D.L., Chee M.S. A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res. 2004, 14:878-885.
9. Chen J., Lozach J., Garcia E.W., Barnes B., Luo S., Mikoulitch I., Zhou L., Schroth G., Fan J.B. Highly sensitive and specific microRNA expression profiling using BeadArray technology. Nucleic Acids Res. 2008, 36:e87.
10. Marioni J.C., Mason C.E., Mane S.M., Stephens M., Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008, 18:1509-1517.
11. Du P., Kibbe W.A., Lin S.M. lumi: a pipeline for processing Illumina microarray. Bioinformatics 2008, 24:1547-1548.
12. Lin S.M., Du P., Huber W., Kibbe W.A. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res. 2008, 36:e11.
13. Edgar R., Domrachev M., Lash A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30:207-210.
14. Kozomara A., Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2010, 39:D152-D157.
15. Wang W.C., Lin F.M., Chang W.C., Lin K.Y., Huang H.D., Lin N.S. miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinforma. 2009, 10:328.
16. Roberts A., Pachter L. RNA-Seq and find: entering the RNA deep field. Genome Med. 2011, 3:74.
17. Labaj P.P., Leparc G.G., Linggi B.E., Markillie L.M., Wiley H.S., Kreil D.P. Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. Bioinformatics 2011, 27:i383-i391.
18. McIntyre L.M., Lopiano K.K., Morse A.M., Amin V., Oberg A.L., Young L.J., Nuzhdin S.V. RNA-seq: technical variability and sampling. BMC Genomics 2011, 12:293.
19. Beck A.H., Weng Z., Witten D.M., Zhu S., Foley J.W., Lacroute P., Smith C.L., Tibshirani R., van de Rijn M., Sidow A., West R.B. 3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One 2010, 5:e8768.