Isolating Viral and Host RNA Sequences from Archival Material and Production of CDNA Libraries for High-Throughput DNA Sequencing

Overview

Journal Curr Protoc Microbiol

Specialty Microbiology

Date 2015 Sep 8

PMID 26344216

Citations 3

Authors

Yongli Xiao

Zong-Mei Sheng

Jeffery K Taubenberger

Affiliations

Soon will be listed here.

Abstract

The vast majority of surgical biopsy and post-mortem tissue samples are formalin-fixed and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. As an example, the viral RNA genome of the 1918 pandemic influenza A virus was previously determined in a 9-year effort by overlapping RT-PCR from post-mortem samples. Using the protocols described here, the full genome of the 1918 virus was determined at high coverage in one high-throughput sequencing run of a cDNA library derived from total RNA of a 1918 FFPE sample after duplex-specific nuclease treatments. This basic methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of infectious diseases.

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References

Zhulidov P, Bogdanova E, Shcheglov A, Vagner L, Khaspekov G, Kozhemyako V . Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res. 2004; 32(3):e37. PMC: 373426. DOI: 10.1093/nar/gnh031. View

Wood H, Belvedere O, Conway C, Daly C, Chalkley R, Bickerdike M . Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Res. 2010; 38(14):e151. PMC: 2919738. DOI: 10.1093/nar/gkq510. View

Yi H, Cho Y, Won S, Lee J, Yu H, Kim S . Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq. Nucleic Acids Res. 2011; 39(20):e140. PMC: 3203590. DOI: 10.1093/nar/gkr617. View

Foss R, Guha-Thakurta N, Conran R, Gutman P . Effects of fixative and fixation time on the extraction and polymerase chain reaction amplification of RNA from paraffin-embedded tissue. Comparison of two housekeeping gene mRNA controls. Diagn Mol Pathol. 1994; 3(3):148-55. DOI: 10.1097/00019606-199409000-00003. View

Weng L, Wu X, Gao H, Mu B, Li X, Wang J . MicroRNA profiling of clear cell renal cell carcinoma by whole-genome small RNA deep sequencing of paired frozen and formalin-fixed, paraffin-embedded tissue specimens. J Pathol. 2010; 222(1):41-51. DOI: 10.1002/path.2736. View

Tang W, David F, Wilson M, Barwick B, Leyland-Jones B, Bouzyk M . DNA extraction from formalin-fixed, paraffin-embedded tissue. Cold Spring Harb Protoc. 2010; 2009(2):pdb.prot5138. DOI: 10.1101/pdb.prot5138. View

Masuda N, Ohnishi T, Kawamoto S, Monden M, Okubo K . Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res. 1999; 27(22):4436-43. PMC: 148727. DOI: 10.1093/nar/27.22.4436. View

Fox C, Johnson F, Whiting J, Roller P . Formaldehyde fixation. J Histochem Cytochem. 1985; 33(8):845-53. DOI: 10.1177/33.8.3894502. View

KRAFFT , Duncan , Bijwaard , Taubenberger , Lichy . Optimization of the Isolation and Amplification of RNA From Formalin-fixed, Paraffin-embedded Tissue: The Armed Forces Institute of Pathology Experience and Literature Review. Mol Diagn. 1999; 2(3):217-230. DOI: 10.1054/MODI00200217. View

10.

Baldwin D, Feldman M, Alwine J, Robertson E . Metagenomic assay for identification of microbial pathogens in tumor tissues. mBio. 2014; 5(5):e01714-14. PMC: 4172075. DOI: 10.1128/mBio.01714-14. View

11.

Taubenberger J, Reid A, Krafft A, Bijwaard K, Fanning T . Initial genetic characterization of the 1918 "Spanish" influenza virus. Science. 1997; 275(5307):1793-6. DOI: 10.1126/science.275.5307.1793. View

12.

Zhao W, He X, Hoadley K, Parker J, Hayes D, Perou C . Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling. BMC Genomics. 2014; 15:419. PMC: 4070569. DOI: 10.1186/1471-2164-15-419. View

13.

Schweiger M, Kerick M, Timmermann B, Albrecht M, Borodina T, Parkhomchuk D . Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. PLoS One. 2009; 4(5):e5548. PMC: 2678265. DOI: 10.1371/journal.pone.0005548. View

14.

Firth C, Lipkin W . The genomics of emerging pathogens. Annu Rev Genomics Hum Genet. 2013; 14:281-300. DOI: 10.1146/annurev-genom-091212-153446. View

15.

Service R . Gene sequencing. The race for the $1000 genome. Science. 2006; 311(5767):1544-6. DOI: 10.1126/science.311.5767.1544. View

16.

Evers D, Fowler C, Cunningham B, Mason J, OLeary T . The effect of formaldehyde fixation on RNA: optimization of formaldehyde adduct removal. J Mol Diagn. 2011; 13(3):282-8. PMC: 3077733. DOI: 10.1016/j.jmoldx.2011.01.010. View

17.

Singh R, Patel K, Routbort M, Reddy N, Barkoh B, Handal B . Clinical validation of a next-generation sequencing screen for mutational hotspots in 46 cancer-related genes. J Mol Diagn. 2013; 15(5):607-22. DOI: 10.1016/j.jmoldx.2013.05.003. View

18.

Xiao Y, Kash J, Beres S, Sheng Z, Musser J, Taubenberger J . High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic. J Pathol. 2012; 229(4):535-45. PMC: 3731037. DOI: 10.1002/path.4145. View

19.

McKinney M, Moon S, Kulesh D, Larsen T, Schoepp R . Detection of viral RNA from paraffin-embedded tissues after prolonged formalin fixation. J Clin Virol. 2008; 44(1):39-42. DOI: 10.1016/j.jcv.2008.09.003. View

20.

Bibby K . Metagenomic identification of viral pathogens. Trends Biotechnol. 2013; 31(5):275-9. DOI: 10.1016/j.tibtech.2013.01.016. View