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PRJNA996050 SRP450099

Vermiform appendix microbiome in pancreatic vs colon cancer

Fecal metagenomic profiling of vermiform appendix from adult patients with pancreatic or colon cancer

27 fecal samples from the vermiform appendix of adult pancreatic and colon adenocarcinoma patients in Rotterdam, Netherlands, analyzed to compare microbiome profiles between the two groups in a case-control design. machine-written summary

27 samples · 27 runs · NL · Adult · 2023 · 3.69 Gbp / sample

ENA BioProject Sample sheet Registry Download Flag an issue

Sources

✓Sequence archive 162○Abstract / description○Full text✓Supplementary tables 135–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	162 sample values (collection date, country, latitude, location locality, location region, longitude)
○ Abstract / description	read; no usable statement
○ Full text	read; no usable statement or table · PMC10667699
✓ Supplementary tables	135 sample values (age, health condition, health condition detail, sex, subject id)
– 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

Samples at a glance

1 sampling locations · 1 country

Age

elderly16

adult11

Condition

other_cancer14

colorectal_cancer13

Sex

female14

male13

Country

NL27

Body site

primary27

Collected 2019–2022

Sequencing depth per sample · this project all projects

Community composition

Escherichia 6.9%Blautia_A 5.2%Bacteroides 5.0%Faecalibacterium 4.5%Alistipes 3.5%Bifidobacterium 3.4%Phocaeicola 3.4%Mediterraneibacter 2.6%Pseudomonas 2.2%Streptococcus 2.1%Collinsella 1.8%Vescimonas 1.6%not assigned to a genus 10.4%other genera 47.4%

Genera, mean relative abundance over 21 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1	R2
age_category	27	100%
country	27	100%	27
health_condition	27	100%		27
subject_id	27	100%		27
age_at_collection_days	27	100%		27
collection_date	27	100%	27
detailed_location	27	100%
health_condition_detail	27	100%		27
latitude	27	100%	27
location_locality	27	100%	27
location_region	27	100%	27
longitude	27	100%	27
sex	27	100%		27

Papers (1)

B cell immune profiles in dysbiotic vermiform appendixes of pancreatic cancer patients. 2023 PMID 38022530 PMC10667699 own_data

Details

Archive description

In this study the fecal content of normal vermiform appendix was collected from n=14 adult pancreatic adenocarcinoma patients and age matched n=13 colon adenocarcinoma patients for metagenomic analysis, to compare microbiome profiles between the two patient groups.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

host external_curation.infant_catalog · “infant triage reason_code age_unknown_no_evidence”
body site study.title · “Fecal metagenomic profiling of”
body site study.description · “this study the fecal content of normal”
life stage study.title · “vermiform appendix from adult patients with pancreatic”
life stage study.description · “collected from n=14 adult pancreatic adenocarcinoma patients”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN36511239	age_at_collection_days	30316	R2	0.85	paper.supp.DataSheet_1.docx[table4!Age [years]]	83
SAMN36511239	collection_date	2019-02-18	R1	0.90	biosample.attribute:collection_date	2019-02-18
SAMN36511239	country	NL	R1	0.90	sample.attr.geo_loc_name	Netherlands: Rotterdam
SAMN36511239	health_condition	other_cancer	R2	0.85	paper.supp.DataSheet_1.docx[table4!Disease]	Local PDAC
SAMN36511239	health_condition_detail	Local PDAC	R2	0.85	paper.supp.DataSheet_1.docx[table4!Disease]	Local PDAC
SAMN36511239	latitude	51.9100	R1	0.90	biosample.attribute:lat_lon	51.91 N 4.47 E
SAMN36511239	location_locality	Rotterdam	R1	0.85	biosample.attribute:geo_loc_name	Netherlands: Rotterdam
SAMN36511239	location_region	South Holland	R1	0.60	biosample.attribute:lat_lon	51.91 N 4.47 E
SAMN36511239	longitude	4.4700	R1	0.90	biosample.attribute:lat_lon	51.91 N 4.47 E
SAMN36511239	sex	male	R2	0.85	paper.supp.DataSheet_1.docx[table4!Sex]	M
SAMN36511239	subject_id	APP-001	R2	0.85	paper.supp.DataSheet_1.docx[table4!Study ID]	APP-001

Sequencing

27 runs over 27 samples · mean 3.89 Gbp per run (median 3.69 Gbp, total 105.04 Gbp; 27 runs with a base count) · layout PAIRED 27 · platform ILLUMINA 27 · models Illumina HiSeq X (25), NextSeq 2000 (2) · 89% of runs with a Sandpiper profile · first public 2023-11-15

Authors (20)

Vietsch EE first · Latifi D · Verheij M · van der Oost EWA · de Wilde RF · Haen R · van den Boom AL · Koerkamp BG · Doornebosch PG · van Verschuer VMT · Ooms AHAG · Mohammad F · Willemsen M · Aerts JGJV · Krog RT · de Miranda NFCC · van den Bosch TPP · Mueller YM · Katsikis PD · van Eijck CHJ last

Downloads

PRJNA996050.csv.gz (2.0 KB) · parquet (72.0 KB) — all 27 samples, every field with route and confidence · PRJNA996050_determinations.csv.gz (3.3 KB) — 297 evidence rows

Samples (27 · every field this project has values for · hover a cell for its source)

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