Lynch syndrome CRC tumour vs distal tissue microbiome, Spain
97 FFPE samples from Lynch syndrome colorectal cancer patients in Spain, comparing tumour and distal non-tumour tissue microbiota using shotgun metagenomics in a case-control design. machine-written summary
97 samples · 97 runs · ES · Age unknown · 2021 · 0.84 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 485 sample values (collection date, country, latitude, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 389 sample values (age, health condition, health condition detail, location region, sex) · PMC7801721 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population colorectal_cancer · Tumour vs distal tissue sampled from surgical resection
“had developed CRC and had undergone surgical resection” — abstract:33432015 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
48 of 49 people sampled more than once (96 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 1 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 1 | 1% | ||||
| country | 97 | 100% | 97 | |||
| health_condition | 97 | 100% | 97 | |||
| subject_id | 97 | 100% | 97 | |||
| collection_date | 97 | 100% | 97 | |||
| detailed_location | 97 | 100% | ||||
| health_condition_detail | 97 | 100% | 97 | |||
| latitude | 97 | 100% | 97 | |||
| location_region | 97 | 100% | 97 | |||
| longitude | 97 | 100% | 97 | |||
| sex | 97 | 100% | 97 | |||
| age_at_collection_days | 1 | 1% | 1 |
- Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients. 2021 PMID 33432015 PMC7801721 own_data
Archive description
A total of 98 samples from 49 patients diagnosed with Lynch syndrome and having developed colorectal cancer were collected for this study.From each patient, two formalin-fixed and paraffin embedded (FFPE) samples, collected from the surgically removed piece of the gut were obtained, one from the tumour itself and one from a distal section of non-affected tissue. For all samples, the metagenomic taxonomic and gene shot-gun analysis of the microbiota was carried out by a metagenomic approach, using a shotgun sequencing with the Illumina NextSeq with 150 bp x2 chemistry.After sequencing 94 samples were paired (tumour and distal tissue from the same subject) and two contained only the tumour sample, since the distal pieced failed in the sequencing, totalizing the 96 deposited samples.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “collected from the surgically removed piece of the gut”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5951992 | age_at_collection_days | 25202.2 | R3 | 0.75 | paper.body.body.Table 1[Age] | 69 |
| SAMEA5951920 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMEA5951920 | country | ES | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Spain |
| SAMEA5951920 | health_condition | colorectal_cancer | R3 | 0.60 | paper.fulltext.results | 49 LS patients surgically treated between 1996 and 2017 |
| SAMEA5951920 | health_condition_detail | Lynch syndrome patients who had developed colorectal cancer (CRC) | R3 | 0.60 | paper.fulltext.results | 49 LS patients surgically treated between 1996 and 2017 |
| SAMEA5951920 | latitude | 39.4767 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.476667 0.374444 |
| SAMEA5951920 | location_region | Valencian Community | R3 | 0.70 | paper.fulltext.methods | Program of Genetic Counseling in Cancer of the Valencian Community |
| SAMEA5951920 | longitude | 0.3744 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.476667 0.374444 |
| SAMEA5951920 | sex | female | R3 | 0.75 | paper.body.body.Table 1[Gender] | F |
| SAMEA5951920 | subject_id | 930900 | R1 | 0.70 | sample.name_rule:sample_alias | 930900TS_R |
Sequencing
97 runs over 97 samples · mean 1.12 Gbp per run (median 0.84 Gbp, total 108.68 Gbp; 97 runs with a base count) · layout PAIRED 97 · platform ILLUMINA 97 · models NextSeq 500 (97) · 9% of runs with a Sandpiper profile · first public 2021-02-15
Authors (7)
Debesa-Tur G first · Pérez-Brocal V · Ruiz-Ruiz S · Castillejo A · Latorre A · Soto JL · Moya A last
Downloads
PRJEB34333.csv.gz (3.3 KB) · parquet (74.6 KB) — all 97 samples, every field with route and confidence · PRJEB34333_determinations.csv.gz (6.2 KB) — 874 evidence rows