Rectal microbiome in cervical cancer patients, Texas, USA
41 rectal swab samples from adult cervical cancer patients at a Texas cancer center, collected pre-treatment; shotgun metagenome sequencing in a case-control study of gut microbiome and chemoradiation response. machine-written summary
41 samples · 41 runs · US · Adult · 2021 · 5.96 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 246 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 41 sample values (location site) |
| ○ Full text | read; no usable statement or table · PMC10841640, PMC9438314 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 82 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 35 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 | 41 | 100% | ||||
| country | 41 | 100% | 41 | |||
| health_condition | 41 | 100% | 41 | |||
| subject_id | 41 | 100% | 41 | |||
| collection_date | 41 | 100% | 41 | |||
| detailed_location | 41 | 100% | ||||
| health_condition_detail | 41 | 100% | 41 | |||
| latitude | 41 | 100% | 41 | |||
| location_region | 41 | 100% | 41 | |||
| location_site | 41 | 100% | 41 | |||
| longitude | 41 | 100% | 41 |
- Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure. 2022 PMID 36050658 PMC9438314 own_data
- Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring. 2023 PMID 37863066 PMC10841640 own_data
Archive description
Forty-one patients admitted to the University of Texas, M.D. Anderson Cancer Center with diagnosis cervical cancer participated in the study. The patients were enrolled on an Institutional Review Board (IRB) approved protocol. Informed consent was obtained to collect rectal swabs. All patient samples were acquired prior to receiving any treatment. Samples were collected from each out of 41 patients by a clinician performing rectal exams using a matrix-designed quick-release Isohelix swab. The swabs were initially stored in proteinase K and lysis buffer (Isohelix) within 1 h of sample collection and then were frozen and kept at -80C. Whole Genome Shotgun sequencing was performed on genomic bacterial DNA (gDNA), which was extracted to maximize bacterial DNA yield from specimens while keeping background amplification to a minimum. Libraries were constructed from each sample using the KAPA Hyper Prep Kit (Kapa Biosystems, Wilmington, MA, USA) and sequenced using the Illumina HiSeqX platform with the 2 x 150 bp paired-end read protocol.
How this project entered the registry
Classified as human gut / stool / vaginal / urogenital 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_adult_only”
- body site study.title · “Metagenome Sequencing of Rectal Swab Samples from”
- body site study.description · “obtained to collect rectal swabs. All patient”
- body site study.title · “Swab Samples from Cervical Cancer Patients”
- body site study.description · “Center with diagnosis cervical cancer participated in”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17976249 | collection_date | 2015-10-27 | R1 | 0.90 | biosample.attribute:collection_date | 2015-10-27 |
| SAMN17976249 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Texas |
| SAMN17976249 | health_condition | other_cancer | R2 | 0.75 | external.gmrepo source | phenotype: Uterine Cervical Neoplasms |
| SAMN17976249 | health_condition_detail | Uterine Cervical Neoplasms | R2 | 0.75 | external.gmrepo source | phenotype: Uterine Cervical Neoplasms |
| SAMN17976249 | latitude | 29.7074 | R1 | 0.90 | biosample.attribute:lat_lon | 29.70742858 N 95.39693898 W |
| SAMN17976249 | location_region | Texas | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Texas |
| SAMN17976249 | location_site | University of Texas, M.D. Anderson Cancer Center | R4 | 0.45 | ena.study_description | University of Texas, M.D. Anderson Cancer Center |
| SAMN17976249 | longitude | -95.3969 | R1 | 0.90 | biosample.attribute:lat_lon | 29.70742858 N 95.39693898 W |
| SAMN17976249 | subject_id | p702-Klopp-03 | R1 | 0.70 | sample.name_rule:alias | p702-Klopp-03-R-T1 |
Sequencing
41 runs over 41 samples · mean 6.67 Gbp per run (median 5.96 Gbp, total 273.45 Gbp; 41 runs with a base count) · layout PAIRED 41 · platform ILLUMINA 41 · models HiSeq X Ten (41) · 85% of runs with a Sandpiper profile · first public 2021-02-19 – 2021-03-01
Authors (61)
Karpinets TV first · Wu X · Solley T · El Alam MB · Sims TT · Yoshida-Court K · Lynn E · Ahmed-Kaddar M · Biegert G · Yue J · Song X · Sun H · Petrosino JF · Mezzari MP · Okhuysen P · Eifel PJ · Jhingran A · Lin LL · Schmeler KM · Ramondetta L · Ajami N · Jenq RR · Futreal A · Zhang J · Klopp AH · Colbert LE last · Wang R · Karpinets T · Lo D · Lynn EJ · Harris TA · Elnaggar JH · Tomasic K · Bronk JK · Sammouri J · Yanamandra AV · Olvera AV · Carlin LG · Sims T · Delgado Medrano AY · Napravnik TC · O'Hara M · Lin D · Abana CO · Li HX · Joyner M · Lin L · Ramondetta LM · Futreal AM · Mathew G · Dorta-Estremera S · Ajami NJ · Wong M · Taniguchi C · Sastry KJ · Okhuysen PC · Martinez SA · Tan L · Mahmud I · Lorenzi PL · Wargo JA
Downloads
PRJNA702617.csv.gz (2.3 KB) · parquet (72.5 KB) — all 41 samples, every field with route and confidence · PRJNA702617_determinations.csv.gz (4.0 KB) — 369 evidence rows