Datasets/HTA13

TNP SARDANA

MixedMachine-extracted

Human Tumor Atlas NetworkAvailable from HTANTrans-Network Project

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 100% of cases; its individual fields were not measured.API
Progression or recurrence
Limited
A follow-up table exists for 100% of cases; its individual fields were not measured.API
Treatment response
Limited
A therapy table exists for 100% of cases; its individual fields were not measured.API
Which drug was given
Limited
A therapy table exists for 100% 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

Measurement types

718 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

1 measurement type, none covering the whole cohort.

Multiplexed tissue imagingscarcecount not published

Platform, files and data levels

Assay	Platform	Files	Levels
Multiplexed tissue imagingAPI	-	301	level 2, level 3, level 4

How complete all 7 clinical fields are - 7 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-upAPI100%

Treatment

TherapyAPI100%

Diagnosis

DiagnosisAPI100%

Demographics

DemographicsAPI100%

Exposure

Exposure historyAPI100%

Molecular markers

Clinical molecular test1:nAPI100%

Other

Family historyAPI100%

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

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.

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 ["syn41745520","syn41745688","syn41745802","syn41745888"]:
    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-tnp-sardana.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 syn41745520
```
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 syn41745520
```
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

IdentifierHTA13 API
Synapsesyn41745520 API
Synapsesyn41745688 API
Synapsesyn41745802 API
Synapsesyn41745888 API
Synapsesyn41745941 API
Synapsesyn41745973 API
Synapsesyn41745996 API
Synapsesyn41746009 API
Synapsesyn41746037 API
Synapsesyn41746051 API
Synapsesyn41746067 API
Synapsesyn47878101 API

Versions and verification

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

For software record JSON