open-neo/open-neo-public-test-data

Open-Neo HCC1395/HCC1395BL Public WGS Test Data

This dataset provides a public paired whole-genome test case for validating the Open-Neo installation, input-QC, DNA evidence, purity/CNV, HLA, candidate generation, presentation, ranking, and reporting paths.

Samples

Role	Sample	BioSample	Source material
Tumor	HCC1395 (WGS_EA_T_1)	SAMN10102573	Breast carcinoma cell line, ATCC CRL-2324
Matched normal	HCC1395BL (WGS_EA_N_1)	SAMN10102574	B-lymphoblast cell line, ATCC CRL-2325, same donor

These are established public cell-line samples. This repository does not contain patient names, contact information, clinical records, or the source spreadsheet used to locate the files.

Files

The files are stored under data/hcc1395_hcc1395bl/:

• WGS_EA_T_1.bwa.dedup.bam and .bai: coordinate-sorted tumor WGS alignment.
• WGS_EA_N_1.bwa.dedup.bam and .bai: coordinate-sorted matched-normal WGS alignment.
• WGS_EA_T_1-somatic.somatic.pass.vcf.gz and .tbi: paired somatic PASS calls.
• data_manifest.tsv: public identifiers, roles, paths, sizes, and validation states.
• open_neo_sample.example.yaml: an editable Skill 2 input template.

The BAMs and VCF use GRCh38 with chr-prefixed contigs. Before upload, both BAM/BAI pairs passed samtools quickcheck and samtools idxstats; the VCF passed gzip validation and contained 108,080 records with sample columns WGS_EA_N_1 and WGS_EA_T_1.

Somatic Calling Summary

The supplied somatic VCF was generated from the paired BAMs using a chromosome-scattered GATK Mutect2 workflow on GRCh38, with a panel of normals and the gnomAD germline resource. Scattered calls and statistics were merged, processed by FilterMutectCalls, and restricted to PASS records. Environment- specific licensed wrappers and internal server paths are intentionally not distributed.

Download

Install the Hugging Face CLI and download only this test case:

hf download open-neo/open-neo-public-test-data \
  --repo-type dataset \
  --include "data/hcc1395_hcc1395bl/*" \
  --local-dir open-neo-public-test-data

The two BAMs total more than 200 GB. Confirm available disk space before downloading. For Open-Neo, keep the BAMs, BAI files, VCF, and TBI together.

Open-Neo Use

Edit open_neo_sample.example.yaml so each path points to the downloaded local file, then run Skill 2 (open-neo-run) using that sample manifest. This is a DNA-only public test case; RNA-dependent fusion, splice, expression, RNA VAF, and RNA-junction evidence should be reported as unavailable rather than as negative biological findings.

Scope And Limitations

• This dataset is for software validation and research benchmarking, not clinical diagnosis or treatment selection.
• Cell-line behavior and variant profiles do not represent a primary tumor.
• The repository republishes derived files from publicly registered biological materials. No new rights are claimed over the underlying sequence data.
• Users are responsible for reviewing and complying with the terms of the original NCBI/SRA records, ATCC materials, and their institution.

References

• NCBI BioSample: SAMN10102573
• NCBI BioSample: SAMN10102574
• NCBI BioProject: PRJNA489865