Datasets/HTA12

Washington University Human Tumor Atlas Research Center

MixedMachine-extracted

Human Tumor Atlas NetworkAvailable from HTANWashington University

Can it answer my research question?Who has used it Get the data

Can it answer your research question?

0 of 6 supported

Overall survival
Limited
A follow-up table exists for 50% of cases; its individual fields were not measured.API
Progression or recurrence
Limited
A follow-up table exists for 50% of cases; its individual fields were not measured.API
Treatment response
Limited
A therapy table exists for 68% of cases; its individual fields were not measured.API
Which drug was given
Limited
A therapy table exists for 68% of cases; its individual fields were not measured.API
Stage-adjusted modelling
Limited
A diagnosis table exists for 100% of cases; its individual fields were not measured.API
Analysis by race or ethnicity
Limited
A demographics table exists for 100% of cases; its individual fields were not measured.API

Judged from the repository’s own field completeness (thresholds). “Not measured” means we have not probed that field for this record, not that the data lack it.

At a glance

Every percentage is the repository’s own record of what is filled in

CasesAPI

295

Measurement types

9,484 files

Follow-upAPI

Present

no survival endpoint

Treatment responseAPI

Unknown

SubjectCALC

Subject derived from title

Derived from the title, not stated by the repository, and never used to place this dataset in an answer shortlist.

As filed by the repository

The repository publishes no disease classification.

Who is in the cohort

The repository’s harmonized records carry no demographics for this dataset.

What was measured, and on how many

6 measurement types, none covering the whole cohort.

Single-cell / single-nucleus RNA sequencingcount not published
Single-cell ATAC sequencingscarcecount not published
10x Visium spatial transcriptomicsscarcecount not published
Bulk DNA sequencingcount not published
Bulk RNA sequencingcount not published
Multiplexed tissue imagingscarcecount not published

Platform, files and data levels

Assay	Platform	Files	Levels
Single-cell / single-nucleus RNA sequencingAPI	-	2,099	level 1, level 2, level 3, level 4
Single-cell ATAC sequencingAPI	-	1,811	level 1, level 2, level 3, level 4
10x Visium spatial transcriptomicsAPI	-	1,492	level 1, level 2, level 3, level 4
Bulk DNA sequencingAPI	-	1,037	level 1
Bulk RNA sequencingAPI	-	488	level 1
Multiplexed tissue imagingAPI	-	220	level 2, level 3, level 4

How complete all 6 clinical fields are - 2 informative for at least 80% of cases

A field counts as informative only when it holds a real value. “Not reported” blocks an analysis just as a missing field does. Fields marked 1:n can hold several records per case, so they show the share of cases with any record.

Informative - a usable valuePresent but uninformative - “not reported” or “unknown”Absent - no value recorded

Follow-up

Follow-upAPI50%

Treatment

TherapyAPI68%

Diagnosis

Diagnosis1:nAPI100%

Demographics

DemographicsAPI100%

Exposure

Exposure historyAPI36%

Other

Family historyAPI53%

Access

MixedSome components are open; others need approval.API

Level 1-2 sequencing data are controlled through dbGaP; level 3-4 derived data and most imaging are downloadable from Synapse after registering and accepting the HTAN data use terms.

Open components: level 3-4 derived data; most imaging
Controlled components: level 1-2 sequencing (dbGaP)
License: HTAN data use terms; CC BY 4.0 for many level 3-4 products
Citation requirement: Cite the atlas publication and acknowledge HTAN per the network's publication policy.

What it is good for

Written and checked by a reviewer, not generated from metadata.

No reviewed research questions yet. The measurements and field completeness above are machine-extracted and still useful for judging fit.

What it cannot tell you

Written by a reviewer against the source, not inferred from what is missing.

No reviewed limitations yet. Check the field completeness chart above before committing to an analysis. Low coverage on an endpoint you need is the most common blocker.

Who has used it

Articles that analyzed these data, counted separately from articles that only cited the paper. Only the first counts as reuse.

Analyzed the dataCALC

could not be measured for this dataset

Declared using it

named in a data availability statement

Cited the paper

676

attention to the publication, not reuse of the data

Against expectation

Not assessed

Reuse cannot be traced for this dataset

No accession is specific enough to search the literature for, so we cannot tell how often these data have been reused. That is a limit of the measurement, not a finding about the dataset. It is also a barrier in itself: a researcher cannot find prior work to build on.

Reuse assessment

Not assessed: this dataset has no accession specific enough for citation-based reuse tracing, so a shortfall cannot be measured.

Compared against rgi-huber-v2. See Methods for the model.

Original publications

Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages
Michael D. Iglesia et al.Nature cancer202413 citationsPMID 39478117FILE
Tumour evolution and microenvironment interactions in 2D and 3D space
Chia-Kuei Mo et al.Nature202494 citationsPMID 39478210FILE
Epigenetic regulation during cancer transitions across 11 tumour types
Nadezhda V Terekhanova et al.Nature2023124 citationsPMID 37914932FILE
Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma
Yige Wu et al.Nature communications202335 citationsPMID 36973268FILE
Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer
Daniel Cui Zhou et al.Nature genetics2022150 citationsPMID 35995947FILE

Articles that analyzed the data

Not searchable. See the note above.

Community examples

Share your example

Analyses someone ran on these data end to end, each with a receipt recording when it ran, against which packages and for how long.

Nobody has shared an analysis of this dataset yet. The examples on other datasets cover the common patterns and can be adapted - and if you adapt one, it belongs here.

Start here

Starter code generated from this record’s own identifiers, then the access steps.

Get the data in code

HTAN: fetch files from Synapsepython

pip install synapseclient. Register at synapse.org and accept the HTAN terms first. Level 1 and 2 sequencing is controlled through dbGaP.

import synapseclient

syn = synapseclient.login()          # uses ~/.synapseConfig or SYNAPSE_AUTH_TOKEN
for sid in ["syn39159015","syn39159784","syn39159835","syn39159871"]:
    entity = syn.get(sid, downloadLocation="./htan")
    print(sid, entity.name)
# Browse the atlas at https://humantumoratlas.org/explore

This page as data: limitations firstbash

curl -s https://cd2s.vercel.app/data/datasets/htan-washington-university-human-tumor-atlas-research-center.json | python3 -c '
import json, sys
r = json.load(sys.stdin)
for l in r["limitations"]:
    print(l["severity"].upper(), "-", l["statement"][:120])
print("survival endpoint:", r["longitudinal"]["has_survival_endpoint"], "| treatment response:", r["longitudinal"]["has_treatment_response"])'

Access steps

1
Register at Synapse and accept the HTAN termsFor people15 minutes
One free account covers the atlas; the terms are click-through, not a data access request.
Requires: Synapse account
https://humantumoratlas.org/data-access
Generated from repository policy. Check the linked policy before downloading.
2
Download the available files from SynapseFor peopleminutes to hours
Derived data and other released files become available after the terms are accepted.
```
synapse get syn39159015
```
https://help.synapse.org/docs/Getting-Started.2055471150.html
Generated from repository policy. Check the linked policy before downloading.
3
Request controlled sequencing through dbGaP when neededFor peopledays to a few weeks
Raw and aligned sequencing may require an approved request; derived analyses often do not.
Requires: eRA Commons account, approved dbGaP request
https://humantumoratlas.org/data-access
Generated from repository policy. Check the linked policy before downloading.
4
Give an agent a Synapse token, not a passwordFor agents
Unauthenticated calls return metadata and no files, so an agent should report the credential requirement explicitly.
Requires: SYNAPSE_AUTH_TOKEN
```
export SYNAPSE_AUTH_TOKEN=...
synapse get syn39159015
```
https://help.synapse.org/docs/Getting-Started.2055471150.html
Generated from repository policy. Check the linked policy before downloading.

Provenance

All of it, and more, is in this record’s JSON.

Identifiers

IdentifierHTA12 API
Synapsesyn39159015 API
Synapsesyn39159784 API
Synapsesyn39159835 API
Synapsesyn39159871 API
Synapsesyn39159904 API
Synapsesyn39168749 API
Synapsesyn39168806 API
Synapsesyn39168815 API
Synapsesyn39168925 API
Synapsesyn39169269 API
Synapsesyn39169760 API
Synapsesyn39169783 API

Versions and verification

Metadata retrieved: 18 Sept 2026
Review status: Machine-extracted
Data generation funding: Funded data generation

Funding

Awards resolved through NIH RePORTER. Awards that paid to generate these data are listed apart from awards that paid to reuse them. Both are returns on NCI investment, but different ones.

Funded data generation

U2CCA233303Biospecimen Acquisition, Processing, and Classification UnitRyan C Fields, Li DingFY2018-2023FILE
U24CA211006Deep Discovery and Clinical Interpretation of Germline and Somatic Cancer DriversLi Ding, Ramaswamy GovindanFY2016-2020API
U24CA209837Washington University Co-Clinical Imaging Research ResourceLi Ding, Shunqiang LiFY2017-2026API
R01CA273194FFNP-PET as a predictive biomarker of response to endocrine therapy approaches in advanced breast cancerFARROKH DEHDASHTI, Cynthia X MaFY2022-2025API
R01CA260855NANOPHOTOSENSITIZERS FOR REGENERATIVE PHOTOTHERAPYSamuel AchilefuFY2021-2025API
P30CA091842Clinical Protocol and Data ManagementAmanda Fishback Cashen, Adetunji T ToriolaFY2019-2026API
U24CA264027Pathway, Network and Spatiotemporal Integration of Cancer Genomics DataBenjamin Raphael, Jen Jen YehFY2021-2025API
U24CA248453Comprehensive and Robust Tools for Analysis of Tumor Heterogeneity and EvolutionBenjamin RaphaelFY2020-2026API
U24CA210972Proteogenomic Data Analysis for Cancer Systems Biology and Clinical TranslationLi Ding, David FenyoFY2016-2020API
R01CA260112Impact of cancer predisposition on oncogenic process, microenvironment, and treatmentFENG CHEN, Li DingFY2022-2026API

and 5 more

For software record JSON