Neuroblastoma mutation landscape report
Executive summary
This report documents the first local Neuroblastoma mutation-landscape release in BioTransfer. Five public cBioPortal cohorts are connected with source IDs, retrieval dates and patient/sample denominators. Headline gene frequencies use the MSK 2023 reference cohort (176 unique patients); cohort-specific values remain separate.
The page covers ALK, MYCN, ATRX, TERT, TP53, PHOX2B and BARD1. A zero means no call in the selected mutation profile, while a null means that the source did not support the requested metric.
Scope and current data status
The intended scope includes SNVs, small indels, amplification, copy-number gain, deletion, structural variants, rearrangements and fusions. Mutational signatures are reserved for a later release.
The local snapshot contains five cBioPortal cohorts on hg19. TARGET and MSK include repeat samples, so patient and sample counts are shown separately. Unknown is represented as null, with a status such as unknown, not_assayed or unavailable; it is never converted into zero. The chromosome-wise rollup covers the seven selected genes and loaded representative events, not a genome-wide call set.
Observed data versus interpretation
Observed data
- Five dated cBioPortal study snapshots are loaded.
- ALK is observed in 29/176 MSK patients (16.48%); ATRX in 15/176 (8.52%).
- Representative ALK, MYCN, ATRX, TERT, TP53 and PHOX2B variant rows are retained with hg19 coordinates.
- GISTIC copy-number calls are loaded for TARGET/MSK, and structural-variant/fusion annotations for Broad/MSK, with event-specific denominators.
- No trial, approval or treatment conclusion is made from mutation calls alone.
BioTransfer-derived interpretation
A clinically useful comparison of recurrent events, drivers and therapeutic actionability must wait for normalized cohort records, event-specific tested denominators and linked evidence. Somatic observations must remain separate from germline susceptibility evidence, especially for PHOX2B and BARD1.
Cohort and provenance requirements
Each imported cohort must retain its source name, source URL, accession/study ID, source version, retrieval date, licence, assay type, sequencing method, genome build, disease subtype, age group and primary/metastatic status. Each observation must preserve raw, normalized and derived representations.
Frequencies are only valid when numerator and denominator use the same counting unit. Multiple samples from one patient must not inflate a patient-level numerator. Cohorts cannot be pooled until sample overlap, disease definitions and assay coverage are reconciled.
Normalization rules
The importer must retain the source genome build and record any GRCh37/GRCh38 conversion, left normalization, transcript mapping and HGVS representation. SNV/indel, CNV, structural-variant and fusion records must keep event-appropriate representations rather than being forced into one SNV shape.
Limitations in this release
- This is a cBioPortal public API snapshot retrieved 2026-09-08; the local page does not refresh source data at request time.
- Headline gene metrics use the MSK 2023 mutation profile as a reference cohort (176 unique patients); historical cohorts remain separate.
- Cohort patient counts are deduplicated within each study's sequenced sample list. Cross-study overlap has not been checked, so no pooled patient total is reported.
- Copy-number calls are available for TARGET and MSK; structural-variant/fusion profiles are available for Broad 2013 and MSK 2023. Other cohorts do not have these profiles connected.
- GISTIC values are discrete copy-number calls and SV fusion annotations do not establish a functional driver fusion.
- Chromosome rollups cover the seven selected genes and events anchored to those genes; they are not a genome-wide mutation burden or Manhattan plot.
- A zero is a no-call in the selected cBioPortal profile, not proof that the alteration is absent from Neuroblastoma or from unassayed samples.
- TARGET data carry OCG use and publication terms; original study and data-use conditions apply.
- Coordinates are retained on the source hg19 build; no liftover or transcript remapping was performed in this snapshot.
- Drug approval in another disease, a Neuroblastoma trial and established Neuroblastoma actionability are separate evidence categories.
Next data-import step
The next local release should add broader gene coverage, richer copy-number and structural-variant records, clinical-evidence adapters, and a cross-study patient-overlap check before enabling any pooled estimate. The same contract can subsequently support other cancers without changing the page model.