Formalin-fixed paraffin embedded colorectal cancer and healthy colonic tissue sample collection 1
Formalin-fixed paraffin embedded (FFPE) tissues from colorectal cancer patients (n=14) and healthy controls (n=13) were obtained from pathology archives for 16S rRNA amplicon sequencing. The FFPE tissue collection includes n=14 colorectal cancer (CRC), n=14 normal adjacent (ADJ) and n=13 healthy control tissues. DNA extraction negatives consisted of blank (n=3) and water (n=3) controls that were concurrently processed with the tissues. Additional controls consisted of empty paraffin samples (n=6).
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Erasmus University Medical Center
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dig-wur-nl-wurpubs-5977722024-10-10 Lam, Suk Yee Ioannou, Athanasia Konstanti, Prokopis Visseren, Thijmen Doukas, Michail Peppelenbosch, Maikel Petrus Belzer, Clara Fuhler, Gwenny Manel Dataset Formalin-fixed paraffin embedded colorectal cancer and healthy colonic tissue sample collection 1 2021 Formalin-fixed paraffin embedded (FFPE) tissues from colorectal cancer patients (n=14) and healthy controls (n=13) were obtained from pathology archives for 16S rRNA amplicon sequencing. The FFPE tissue collection includes n=14 colorectal cancer (CRC), n=14 normal adjacent (ADJ) and n=13 healthy control tissues. DNA extraction negatives consisted of blank (n=3) and water (n=3) controls that were concurrently processed with the tissues. Additional controls consisted of empty paraffin samples (n=6). Abstract Background Formalin-fixed paraffin embedded (FFPE) tissues may provide an exciting resource to study microbial associations in human disease, but the use of these low biomass specimens remains challenging. We aimed to reduce unintentional bacterial interference in molecular analysis of FFPE tissues and investigated the feasibility of conducting quantitative polymerase chain reaction (qPCR) and 16S rRNA amplicon sequencing using 14 colorectal cancer, 14 normal adjacent and 13 healthy control tissues. Results Bacterial contaminants from the laboratory environment and the co-extraction of human DNA can affect bacterial analysis. The application of undiluted template improves bacterial DNA amplification, allowing the detection of specific bacterial markers (Escherichia coli and Faecalibacterium prausnitzii) by qPCR. Nested and non-nested PCR-based 16S rRNA amplicon sequencing approaches were employed, showing that bacterial communities of tissues and paired paraffin controls cluster separately at genus level on weighted Unifrac in both non-nested (R2 = 0.045; Pr(> F) = 0.053) and nested (R2 = 0.299; Pr(> F) = 0.001) PCR datasets. Nevertheless, considerable overlap of bacterial genera within tissues was seen with paraffin, DNA extraction negatives (non-nested PCR) or PCR negatives (nested PCR). Following mathematical decontamination, no differences in α- and β diversity were found between tumor, normal adjacent and control tissues. Conclusions Bacterial marker analysis by qPCR seems feasible using non-normalized template, but 16S rRNA amplicon sequencing remains challenging. Critical evaluation of laboratory procedures and incorporation of positive and negative controls for bacterial analysis of FFPE tissues are essential for quality control and to account for bacterial contaminants. Erasmus University Medical Center text/html https://research.wur.nl/en/datasets/formalin-fixed-paraffin-embedded-colorectal-cancer-and-healthy-co https://edepot.wur.nl/570517 Medical Multispecies Raw sequence reads Wageningen University & Research |
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Medical Multispecies Raw sequence reads Medical Multispecies Raw sequence reads Lam, Suk Yee Ioannou, Athanasia Konstanti, Prokopis Visseren, Thijmen Doukas, Michail Peppelenbosch, Maikel Petrus Belzer, Clara Fuhler, Gwenny Manel Formalin-fixed paraffin embedded colorectal cancer and healthy colonic tissue sample collection 1 |
| description |
Formalin-fixed paraffin embedded (FFPE) tissues from colorectal cancer patients (n=14) and healthy controls (n=13) were obtained from pathology archives for 16S rRNA amplicon sequencing. The FFPE tissue collection includes n=14 colorectal cancer (CRC), n=14 normal adjacent (ADJ) and n=13 healthy control tissues. DNA extraction negatives consisted of blank (n=3) and water (n=3) controls that were concurrently processed with the tissues. Additional controls consisted of empty paraffin samples (n=6). |
| format |
Dataset |
| topic_facet |
Medical Multispecies Raw sequence reads |
| author |
Lam, Suk Yee Ioannou, Athanasia Konstanti, Prokopis Visseren, Thijmen Doukas, Michail Peppelenbosch, Maikel Petrus Belzer, Clara Fuhler, Gwenny Manel |
| author_facet |
Lam, Suk Yee Ioannou, Athanasia Konstanti, Prokopis Visseren, Thijmen Doukas, Michail Peppelenbosch, Maikel Petrus Belzer, Clara Fuhler, Gwenny Manel |
| author_sort |
Lam, Suk Yee |
| title |
Formalin-fixed paraffin embedded colorectal cancer and healthy colonic tissue sample collection 1 |
| title_short |
Formalin-fixed paraffin embedded colorectal cancer and healthy colonic tissue sample collection 1 |
| title_full |
Formalin-fixed paraffin embedded colorectal cancer and healthy colonic tissue sample collection 1 |
| title_fullStr |
Formalin-fixed paraffin embedded colorectal cancer and healthy colonic tissue sample collection 1 |
| title_full_unstemmed |
Formalin-fixed paraffin embedded colorectal cancer and healthy colonic tissue sample collection 1 |
| title_sort |
formalin-fixed paraffin embedded colorectal cancer and healthy colonic tissue sample collection 1 |
| publisher |
Erasmus University Medical Center |
| url |
https://research.wur.nl/en/datasets/formalin-fixed-paraffin-embedded-colorectal-cancer-and-healthy-co |
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1816153644048842752 |