NBDC Research ID: hum0455.v3
SUMMARY
Aims: Small cell carcinoma and large cell neuroendocrine carcinoma (LCNEC) fall under high-grade neuroendocrine carcinomas (HGNEC). HGNEC, characterized by poor prognosis and high treatment resistance, presents subtypes withinSCLC based on ASCL1, NEUROD1, POU2F3, and YAP1 expression levels, each influencing prognosis differently. LCNEC exhibits heterogeneous distribution of these factors, hypothesized to contribute to treatment resistance. Incorporating whole-genome sequencing and spatial transcriptomics, we'll investigate this variability. Leveraging tumor tissue morphology, we'll analyze single-cell factor expression correlations and gene expressions in the microenvironment, aiming to identify new HGNEC therapeutic targets and understand treatment resistance.
Methods: Whole-genome sequencing, High-performance in situ gene expression mapping Xenium (10x Genomics), Visium Spatial Gene Expression data (10X Genomics), Single-cell RNA sequencing data derived from nuclei (10X Genomics), STOMICS spatial transcritome data (BGI)
Participants/Materials: Samples from 10 + 10 + 13 patients with pulmonary neuroendocrine carcinoma operated on at the University of Tsukuba and Jichi Medical University Hospital
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000732 | NGS (WGS) | Controlled-access (Type I) | 2025/08/04 |
| JGAS000733 | Xenium In Situ Gene Expression | Controlled-access (Type I) | 2025/08/04 |
| JGAS000784 | NGS (WGS) | Controlled-access (Type I) | 2026/02/20 |
| JGAS000832 |
Xenium In Situ Gene Expression |
Controlled-access (Type I) | 2026/04/09 |
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MOLECULAR DATA
| Participants/Materials |
pulmonary neuroendocrine carcinoma (ICD10: C34): 10 + 10 cases frozen specimens - tumor tissues: 10 + 10 samples - non-tumor tissues: 10 + 10 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | DNAs extracted from frozen specimen |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Nano DNA Library Prep kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000865: 3.9 TB (fastq) JGAD000926: 3.9 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
pulmonary neuroendocrine carcinoma (ICD10: C34): 21 cases frozen specimens - tumor tissues: 21 samples - non-tumor tissues: 21 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Nanopore [PromethION] |
| Library Source | DNAs extracted from frozen specimen |
| Cell Lines | - |
| Library Construction (kit name) | Ligation Sequencing Kit V14 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Mapping Methods | Guppy (version 6.4.6 and 6.5.7), Minimap2 (version 2.24) |
| Mapping Quality | - |
| Reference Genome Sequence | hg38 |
| Coverage (Depth) | - |
| Algorithms for Calculating Methylation-rate (software) | Modkit (version 0.3.1) |
| Reference Genome Sequence | hg38.p12 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000974 |
| Total Data Volume | 7.7 TB (fastq, bed) |
| Comments (Policies) | NBDC policy |
WGS (JGAS000832: Novaseq 6000)
| Participants/Materials |
pulmonary neuroendocrine carcinoma (ICD10: C34): 1 case frozen specimens - tumor tissues: 1 sample - non-tumor tissues: 1 sample |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | DNAs extracted from frozen specimen |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Nano DNA Library Prep kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000974 |
| Total Data Volume | 7.7 TB (fastq) |
| Comments (Policies) | NBDC policy |
Xenium In Situ Gene Expression (JGAS000733)
| Participants/Materials |
pulmonary neuroendocrine carcinoma (ICD10: C34): 1 case FFPE specimen - tumor tissue: 1 sample |
| Targets | Xenium In Situ Gene Expression |
| Target Loci for Capture Methods | 302 genes (Human Lung panel: 202 genes, custom: 100 genes） |
| Platform | 10x Genomics [Xenium] |
| Source | FFPE specimen |
| Cell Lines | - |
| Reagents (Panel, Kit, Version) | Xenium Slides & Sample Prep Reagents Xenium Decoding Reagents Xenium Decoding Consumables |
| Software | xenium-1.3.0.6 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000866 |
| Total Data Volume | 11.8 GB (csv, h5, html, json, mtx, tiff, parquet, tsv, xenium, zarr） |
| Comments (Policies) | NBDC policy |
Xenium In Situ Gene Expression (JGAS000832)
| Participants/Materials |
pulmonary neuroendocrine carcinoma (ICD10: C34): 33 cases FFPE specimen - tumor tissue: 36 samples |
| Targets | Xenium In Situ Gene Expression |
| Target Loci for Capture Methods | 302 genes (Human Lung panel: 202 genes, custom: 100 genes） |
| Platform | 10x Genomics [Xenium] |
| Source | FFPE specimen |
| Cell Lines | - |
| Reagents (Panel, Kit, Version) | Xenium Slides & Sample Prep Reagents Xenium Decoding Reagents Xenium Decoding Consumables |
| Software | xenium-1.3.0.6, xenium-1.4.0.7, xenium-1.7.1.0, xenium-2.0.0.10 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000974 |
| Total Data Volume | 7.7 TB (csv, h5, html, json, mtx, tiff, parquet, tsv, xenium, zarr） |
| Comments (Policies) | NBDC policy |
Visium Spatial Gene Expression, Histological image (JGAS000832)
| Participants/Materials |
pulmonary neuroendocrine carcinoma (ICD10: C34): 19 cases - tumor tissues: 19 samples |
| Targets | Visium Spatial Gene Expression, Histological image |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Visium Spatial Gene Expression Reagent Kits |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 118 bp |
| Software | spaceranger-1.3.1 |
| Reference | GRCh38-2020-A |
| Tissue Image | hematoxylin-eosin staining |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000974 |
| Total Data Volume | 7.7 TB (fastq, tsv, mtx, json, png, csv) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
pulmonary neuroendocrine carcinoma (ICD10: C34): 6 cases - tumor tissues: 6 samples |
| Targets | snRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Nuclei Isolation Kit, Chromium GEM-X Single Cell 3' Reagent Kits v4 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 118 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000974 |
| Total Data Volume | 7.7 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
pulmonary neuroendocrine carcinoma (ICD10: C34): 2 cases - tumor tissues: 2 samples |
| Targets | STOmics |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-T7] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Stereo-Seq Transcriptomics Set |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 135 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000974 |
| Total Data Volume | 7.7 TB (fastq, h5, ipr, tiff, csv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Daisuke Matsubara
Affiliation: Department of diagnostic pathology, The university of Tsukuba
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Promotion of Cancer Research and Therapeutic Evolution, Japan Agency for Medical Research and Development (AMED) | Study of heterogeneity of genomic and epigenomic aberrations and association with microenvironment in lung cancer tissues | JP24ama221522 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Clinicopathologic, Cellular, and Molecular Analyses of Pulmonary Neuroendocrine Carcinoma With High Expression of Hepatocyte Nuclear Factor 4 Alpha | doi:10.1016/j.labinv.2025.104210 | JGAD000865 JGAD000866 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
