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PRJNA1222800 SRP563407

Fecal metagenomes, HER2-negative metastatic breast cancer, USA

Fecal metagenomes from patients with HER2-negative metastatic breast cancer

23 baseline fecal metagenome samples from adult and elderly patients in the USA with HER2-negative metastatic breast cancer and high tumor mutational burden, enrolled in an interventional trial of nivolumab plus low-dose ipilimumab. machine-written summary

23 samples · 23 runs · US · Age unknown · 2025 · 14.36 Gbp / sample

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Sources

✓Sequence archive 230○Abstract / description✓Full text 46○Supplementary tables–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	230 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location region)
○ Abstract / description	read; no usable statement
✓ Full text	46 sample values (sex, subject id) · PMC12075640
○ 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

Interventions

intervention — arms not resolved

Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population other_cancer · Nivolumab plus low-dose ipilimumab, phase II trial, 2 years

“received nivolumab (3 mg/kg biweekly) and low-dose ipilimumab” — bioproject.description (study level; per-sample arms are in the intervention column below)

Samples at a glance

1 sampling locations · 1 country

Age

adult13

elderly10

Condition

other_cancer23

Sex

female23

Country

US23

Body site

primary23

Sequencing depth per sample · this project all projects

Community composition

Bacteroides 12.0%Blautia_A 7.1%Faecalibacterium 6.6%Phocaeicola 6.6%Alistipes 5.1%Akkermansia 4.0%Roseburia 3.3%Ruminococcoides 2.6%Bifidobacterium 2.3%Parabacteroides 1.7%Gemmiger 1.6%Mediterraneibacter 1.6%not assigned to a genus 2.9%other genera 42.6%

Genera, mean relative abundance over 17 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	R3
age_category	23	100%
country	23	100%	23
health_condition	23	100%	23
subject_id	23	100%		23
age_at_collection_days	23	100%	23
bmi	23	100%	23
collection_date	23	100%	23
detailed_location	23	100%
health_condition_detail	23	100%	23
latitude	23	100%	23
location_region	23	100%	23
longitude	23	100%	23
sex	23	100%		23
timepoint_label	23	100%	23

Papers (1)

Nivolumab plus low-dose ipilimumab in hypermutated HER2-negative metastatic breast cancer: a phase II trial (NIMBUS). 2025 PMID 40360544 PMC12075640 own_data

Details

Archive description

This dataset comprises fecal metagenomes collected from patients at baseline in the phase II NIMBUS trial. Patients with HER2-negative metastatic breast cancer and high tumor mutational burden (TMB >9mut/Mb) received nivolumab (3 mg/kg biweekly) and low-dose ipilimumab (1 mg/kg every 6 weeks) for 2 years or until progression.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of elderly and adult by opus_adjudicated with confidence 0.85. Assay shotgun_dna.

host run.host_tax_id · “9606”
host study.title · “Fecal metagenomes from patients”
body site study.title · “Fecal metagenomes”
life stage sample.attr.host_age · “64 (n=12/23)”
life stage sample.attr.host_age · “36 (n=10/23)”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN46790270	age_at_collection_days	25550.0	R1	0.85	sample.attr.host_age	70
SAMN46790270	bmi	30.12	R1	0.90	sample.attr.host_body_mass_index	30.1213
SAMN46790270	collection_date	2022	R1	0.90	biosample.attribute:collection_date	2022
SAMN46790270	country	US	R1	0.90	sample.attr.geo_loc_name	USA
SAMN46790270	health_condition	other_cancer	R1	0.85	biosample_attr	breast cancer
SAMN46790270	health_condition_detail	breast cancer	R1	0.90	sample.attr.host_disease	breast cancer
SAMN46790270	latitude	42.3550	R1	0.90	biosample.attribute:lat_lon	42.355 N 71.05 W
SAMN46790270	location_region	Massachusetts	R1	0.60	biosample.attribute:lat_lon	42.355 N 71.05 W
SAMN46790270	longitude	-71.0500	R1	0.90	biosample.attribute:lat_lon	42.355 N 71.05 W
SAMN46790270	sex	female	R3	0.60	paper.fulltext.results	The sex of all patients was female
SAMN46790270	subject_id	SAMN46790270	R3	0.75	design.one_sample_per_subject:fulltext	23 baseline samples for 23 patients. In this study, we analyzed only the baseline samples.
SAMN46790270	timepoint_label	Baseline	R1	0.70	sample.name_rule:title	18-561_1_DF-100_Baseline

Sequencing

23 runs over 23 samples · mean 15.04 Gbp per run (median 14.36 Gbp, total 345.89 Gbp; 23 runs with a base count) · layout PAIRED 23 · platform ILLUMINA 23 · models Illumina NovaSeq 6000 (23) · 74% of runs with a Sandpiper profile · first public 2025-02-14 – 2025-02-15

Authors (22)

Barroso-Sousa R first · Zanudo JGT · Li T · Reddy SM · Emens LA · Kuntz TM · Silva CAC · AlDubayan SH · Chu H · Overmoyer B · Lange P · DiLullo MK · Montesion M · Kasparian J · Hughes ME · Attaya V · Basta A · Lin NU · Tayob N · Jeselsohn R · Mittendorf EA · Tolaney SM last

Downloads

PRJNA1222800.csv.gz (1.8 KB) · parquet (72.0 KB) — all 23 samples, every field with route and confidence · PRJNA1222800_determinations.csv.gz (3.2 KB) — 276 evidence rows

Samples (23 · every field this project has values for · hover a cell for its source)

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