A method for metagenomics of helicobacter pylori from archived formalin-fixed gastric biopsies permitting longitudinal studies of carcinogenic risk

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Zheng, Zongli ^a   Andersson, Anders F ^b   Ye, Weimin ^a   Nyrén, Olof ^a   Normark, Staffan ^a,c   Engstrand, Lars ^a,c  

^a KAROLINSKA INSTITUTE   (Sweden)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^c SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FORMALDEHYDE; PARAFFIN;

ARTICLE; CARCINOGENICITY; CONTROLLED STUDY; DNA EXTRACTION; GASTROSCOPY; GENE AMPLIFICATION; GENE MAPPING; GENE SEQUENCE; HELICOBACTER INFECTION; HELICOBACTER PYLORI; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN TISSUE; LASER CAPTURE MICRODISSECTION; LONGITUDINAL STUDY; METAGENOMICS; NONHUMAN; SEQUENCE ALIGNMENT; STOMACH BIOPSY; BIOPSY; CHEMISTRY; GENETICS; IMMUNOHISTOCHEMISTRY; IN VITRO STUDY; METABOLISM; METHODOLOGY; MICROBIOLOGY; STOMACH TUMOR; TISSUE FIXATION;

HELICOBACTER PYLORI;

BIOPSY; FORMALDEHYDE; HELICOBACTER PYLORI; HUMANS; IMMUNOHISTOCHEMISTRY; LASER CAPTURE MICRODISSECTION; METAGENOMICS; PARAFFIN EMBEDDING; STOMACH NEOPLASMS; TISSUE FIXATION;

EID: 80054843451     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026442     Document Type: Article

References (12)

1. Falush D, Kraft C, Taylor NS, Correa P, Fox JG, et al. (2001) Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc Natl Acad Sci U S A 98: 15056-15061.
2. Israel DA, Salama N, Krishna U, Rieger UM, Atherton JC, et al. (2001) Helicobacter pylori genetic diversity within the gastric niche of a single human host. Proc Natl Acad Sci U S A 98: 14625-14630.
3. Pinard R, de Winter A, Sarkis GJ, Gerstein MB, Tartaro KR, et al. (2006) Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. B M C Genomics 7: 216.
4. Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, et al. (2010) Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res 20: 1420-1431.
5. Zheng Z, Advani A, Melefors O, Glavas S, Nordstrom H, et al. (2010) Titration-free massively parallel pyrosequencing using trace amounts of starting material. Nucleic Acids Res 38: e137.
6. Zheng Z, Advani A, Melefors O, Glavas S, Nordstrom H, et al. (2011) Titration-free 454 sequencing using Y adapters. Nat Protoc: 6: 1367- 1376.
7. Enroth H, Kraaz W, Engstrand L, Nyren O, Rohan T, (2000) Helicobacter pylori strain types and risk of gastric cancer: a case-control study. Cancer Epidemiol Biomarkers Prev 9: 981-985.
8. Quach N, Goodman MF, Shibata D, (2004) In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR. B M C Clin Pathol 4: 1.
9. Andersen LP, Rasmussen L, (2009) Helicobacter pylori-coccoid forms and biofilm formation. F E M S Immunol Med Microbiol 56: 112-115.
10. Enroth H, Wreiber K, Rigo R, Risberg D, Uribe A, et al. (1999) In vitro aging of Helicobacter pylori: Changes in morphology, intracellular composition and surface properties. Helicobacter 4: 7-16.
11. Wang Y, Antonopoulos DA, Zhu X, Harrell L, Hanan I, et al. (2010) Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Appl Microbiol Biotechnol.
12. Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, et al. (2000) A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci U S A 97: 14668-14673.