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Cancerbiome: Characterization of the cancer-associated microbiome

Cancerbiome: Characterization of the cancer-associated microbiome

Objective

Deep environmental sequencing (metagenomics) will be used to characterize microbial communities associated with 3 different cancer types: cervical cancer, oral squamous cell carcinoma and colorectal cancer. For all 3 types, non-invasive molecular diagnostics and prognostics are feasible via utilization of vaginal, oral and faecal samples, respectively. The project consequently aims to identify microbial markers in these ¿readouts¿ that correlate with cancer presence or progression. Microbial markers can be individual species or specific community compositions, but also particular genes or pathways. The microbial communities will be sampled locally at tumor surfaces and in healthy control tissues. After DNA extraction and sequencing, a complex bioinformatics pipeline will be developed to characterise the microbiomes and to identify the cancer-specific functional and phylogenetic markers therein. For colorectal cancer, the project intends to go into more details in that it tries i) to establish a correlation of microbiota with cancer progression and it ii) explores differences between distinct cancer subtypes. For each of the 3 cancer types, at least two samples from 40 individuals will be sequenced (as well as controls) at a depth of at least 5Gb each using Illumina technology. This is expected to be sufficient for the identification of microbial markers and also allows superficial genotyping of the individuals at ca 2-3x coverage as a by-product (the samples will contain considerable amounts of human DNA). Further analyses will be designed to study the potential of certain microbial species or community compositions to enhance or even cause one or more of the 3 cancers. The discovery of such causations will open up research towards directed antimicrobial treatment.
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Principal Investigator

Peer Bork (Dr.)

Host institution

EUROPEAN MOLECULAR BIOLOGY LABORATORY

Address

Meyerhofstrasse 1
69117 Heidelberg

Germany

Activity type

Higher or Secondary Education Establishments

EU Contribution

€ 2 233 740

Principal Investigator

Peer Bork (Dr.)

Administrative Contact

Jillian Rowe (Ms.)

Beneficiaries (1)

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EUROPEAN MOLECULAR BIOLOGY LABORATORY

Germany

EU Contribution

€ 2 233 740

Project information

Grant agreement ID: 268985

Status

Closed project

  • Start date

    1 July 2011

  • End date

    30 June 2016

Funded under:

FP7-IDEAS-ERC

  • Overall budget:

    € 2 233 740

  • EU contribution

    € 2 233 740

Hosted by:

EUROPEAN MOLECULAR BIOLOGY LABORATORY

Germany