Home › Studies › PRJNA1037036
PRJNA1037036 SRP470716

Gut virome in pediatric ASD vs neurotypical children, Hong Kong

human stool sample

Case-control metagenomic study of 124 stool samples from children in Hong Kong, comparing gut DNA virome composition between those with autism spectrum disorder and age- and gender-matched typically developing controls. machine-written summary

124 samples · 124 runs · Child · 2024 · 6.80 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 496○Abstract / description✓Full text 124○Supplementary tables✓External resources 248–User contribution–Human verified

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

what each source gave
✓ Sequence archive496 sample values (age, collection date, sex, subject id)
○ Abstract / descriptionread; no usable statement
✓ Full text124 sample values (antibiotic exposure) · PMC10897546
○ Supplementary tablesfiles read; no table could be matched to the samples
✓ External resources248 sample values (health condition, health condition detail) · from GMrepo v3
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
Age
child121
infant3
Condition
healthy_control64
neurological_psychiatric60
Sex
male104
female20
Body site
primary124
Collected 2017–2019
2017: 19 samples2018: 79 samples2019: 26 samples20172019
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)all projects, 1–3 Gbp: 124,983 samples (22 %)all projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 124 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 6.80 Gbp per sample0130Gbp
! Self-contradictory metadata

country: sequence archive and GMrepo disagree for 124 samples (e.g. HK vs CN) — withheld.

The sources disagree on 124 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).

Contradicted values (40 of 124)
samplefieldvalueother valuehandling
SAMN38156470countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156471countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156472countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156473countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156474countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156475countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156476countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156477countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156478countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156479countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156480countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156481countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156482countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156483countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156484countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156485countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156486countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156487countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156488countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156489countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156490countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156491countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156492countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156493countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156494countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156495countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156496countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156497countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156498countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156499countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156500countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156501countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156502countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156503countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156504countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156505countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156506countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156507countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156508countryHK (sequence archive)CN (GMrepo)withheld: neither value published
SAMN38156509countryHK (sequence archive)CN (GMrepo)withheld: neither value published
Sampling design and relatedness

longitudinal

34 of 90 people sampled more than once (68 samples; median 2, up to 2 per person) · follow-up median 13 mo (max 3.1 y) · median interval between samples 13 mo (time from age at collection).

009009: day 0009: day 694010010: day 0010: day 1126012012: day 0012: day 153014014: day 0014: day 731017017: day 0017: day 61018018: day 0018: day 576021021: day 0021: day 275025025: day 0025: day 23026026: day 0026: day 943028028: day 0028: day 460029029: day 0029: day 147030030: day 0030: day 366033033: day 0033: day 352036036: day 0036: day 30038038: day 0038: day 93042042: day 0042: day 610044044: day 0044: day 367045045: day 0045: day 156050050: day 0050: day 246052052: day 0052: day 822053053: day 0053: day 427054054: day 0054: day 456059059: day 0059: day 1128060060: day 0060: day 272062062: day 0062: day 735063063: day 0063: day 243064064: day 0064: day 519065065: day 0065: day 425066066: day 0066: day 789070070: day 0070: day 913071071: day 0071: day 167073073: day 0073: day 61074074: day 0074: day 152076076: day 0076: day 10960 d9 mo19 mo2.3 y3.1 y

Each row is one person (34 shown); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition
Bacteroides 33.6%Phocaeicola 25.6%Prevotella 4.9%Parabacteroides 3.5%Fimenecus 2.4%Alistipes 2.3%Faecalibacterium 2.2%Roseburia 1.9%Ruminococcoides 1.2%Parasutterella 1.0%Lachnospira 1.0%Akkermansia 0.9%not assigned to a genus 5.8%other genera 13.7%

Genera, mean relative abundance over 114 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category124 100%
country0 0%
health_condition124 100%124
subject_id124 100%124
age_at_collection_days124 100%124
antibiotic_exposure124 100%124
collection_date124 100%124
health_condition_detail124 100%124
sex124 100%124
Papers (1)
  • Alterations in fecal virome and bacteriome virome interplay in children with autism spectrum disorder. 2024 PMID 38307030 PMC10897546 own_data
Details
Archive description

metagenomics data for pediatric ASD children and neurotypical children

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of child and infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.

  • host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
  • body site study.title · “human stool sample”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
  • life stage study.description · “metagenomics data for pediatric ASD children and”
  • life stage sample.attr.age · “4.916666666666667 (n=18/124)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN38156470age_at_collection_days1856.0R10.85sample.attr.age5.083333333333333
SAMN38156470antibiotic_exposurenoR30.70paper.fulltext.methodsusage of antibiotics and antifungal medications
SAMN38156470collection_date2017-11-03R10.90biosample.attribute:collection_date2017-11-03
SAMN38156470health_conditionneurological_psychiatricR20.75external.gmrepo sourcephenotype: Autism Spectrum Disorder
SAMN38156470health_condition_detailAutism Spectrum DisorderR20.75external.gmrepo sourcephenotype: Autism Spectrum Disorder
SAMN38156470sexmaleR10.90sample.attr.sexmale
SAMN38156470subject_idPWHRCA001R10.70sample.name_rule:library_namePWHRCA001
SAMN38156473subject_id006R10.70sample.name_rule:aliasPWHRCA006
Sequencing

124 runs over 124 samples · mean 6.77 Gbp per run (median 6.80 Gbp, total 839.65 Gbp; 124 runs with a base count) · layout PAIRED 124 · platform ILLUMINA 124 · models Illumina NovaSeq 6000 (124) · 93% of runs with a Sandpiper profile · first public 2024-07-01

Authors (11)

Wan Y first · Zhang L · Xu Z · Su Q · Leung TF · Chan D · Wong OWH · Chan S · Chan FKL · Tun HM · Ng SC last

Downloads

PRJNA1037036.csv.gz (5.0 KB) · parquet (76.3 KB) — all 124 samples, every field with route and confidence · PRJNA1037036_determinations.csv.gz (9.1 KB) — 868 evidence rows

Samples (124 · every field this project has values for · hover a cell for its source)
Loading the sample table…