NBDC Research ID: hum0068.v8
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SUMMARY
Aims: Establishing a method for detecting variations of lung adenocarcinoma
Methods: [PCR amplicon Seq] Amplicon sequencing by using of MinION (Nanopore)
[WGS] Whole-genome sequencing for identification and characterization of a novel class of structual aberrations in cancers by using of NovaSeq and PromethION.
[RNA-seq] RNA sequencing by using of NovaSeq, HiSeq and PromethION.
[scDNA-seq] Single cell DNA sequencing by using of NovaSeq.
[Target Capture] Target capture sequencing by using of NovaSeq.
[Visium Spatial Gene Expression] Spatial transcriptome sequencing Visium (10x Genomics)
[Multiplex Fluorescence Immunostaining] Multiplex fluorescence immunostaining by PhenoCycler (Akoya Biosciences)
[Xenium In Situ Gene Expression] High-performance in situ gene expression mapping Xenium (10x Genomics)
Participants/Materials: Lung adenocarcinoma
URL: http://kero.hgc.jp/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000065 | NGS (PCR amplicon Seq) | Controlled-access (Type I) | 2017/07/10 |
| JGAS000065 | Controlled-access (Type I) | 2020/10/19 | |
| JGAS000349 | Controlled-access (Type I) | 2021/12/14 | |
| JGAS000349 (Data addition) | Controlled-access (Type I) | 2022/03/23 | |
| JGAD000670 | Processed data of JGAD000252 by JGA | Controlled-access (Type I) | 2022/12/27 |
| JGAS000570 |
NGS (RNA-seq : NovaSeq 6000, HiSeq 2000) |
Controlled-access (Type I) | 2023/02/10 |
| JGAS000570 (Data addition) | Xenium In Situ Gene Expression | Controlled-access (Type I) | 2023/06/19 |
| JGAS000570 (Data addition) | Xenium In Situ Gene Expression | Controlled-access (Type I) | 2023/09/22 |
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MOLECULAR DATA
| Participants/Materials | lung adenocarcinoma (ICD10: C349): 8 cases (7 samples) |
| Targets | PCR amplicon Seq |
| Target Loci for Capture Methods |
sample 1: Amplicons from EML4-ALK positive case (EML4-ALK region) and KIF5B-RET positive case (KIF5B-RET region) were mixed (1 sample) sample 2 - 7: Amplicons from 6 cases (EGFR and KRAS regions) |
| Platform | Nanopore [MinION] |
| Library Source | cDNA were synthesized from mRNA extracted from lung adenocarcinomas |
| Cell Lines | - |
| Library Construction (kit name) | Nanopore Sequencing Kit (Oxford Nanopore Technologies) |
| Fragmentation Methods | PCR |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 367 Mb |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000065 |
| Total Data Volume | 889 MB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 21 + 56 cases (42 + 112 samples) tumor tissues: 21 + 56 samples normal tissues: 21 + 56 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor and normal tissues of lung adenocarcinomas |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Nano DNA Library Prep kit, TruSeq DNA PCR-Free Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 2.8 Tb |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Dataset ID of the Processed data by JGA | |
| Total Data Volume |
2 + 23.9 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 21 + 42 cases (41 + 8 + 81 samples) tumor tissues: 21 + 4 + 42 samples normal tissues: 20 + 4 + 39 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Nanopore [PromethION] |
| Library Source | DNAs extracted from tumor and normal tissues of lung adenocarcinomas |
| Cell Lines | - |
| Library Construction (kit name) | SQK-LSK109 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 2.7 Tb |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume | 2.4 + 1.4 + 23.9 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 6 cases (12 samples) tumor tissues: 6 samples normal tissues: 6 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Nanopore [PromethION] |
| Library Source | RNAs extracted from tumor and normal tissues of lung adenocarcinomas |
| Cell Lines | - |
| Library Construction (kit name) | SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, SQK-LSK109 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 850 bp on average |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000463 |
| Total Data Volume | 1.4 TB (fastq) |
| Comments (Policies) | NBDC policy |
RNA-seq: NovaSeq 6000, HiSeq 2000
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 6 + 5 + 26 cases (12 + 5 + 26 samples) tumor tissues: 6 + 5 + 26 samples normal tissues: 6 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000, HiSeq 2000] |
| Library Source | RNAs extracted from tumor and normal tissues of lung adenocarcinomas |
| Cell Lines | - |
| Library Construction (kit name) | SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, Nextera XT DNA Library Preparation Kit, TruSeq Stranded mRNA Library Prep, TruSeq Stranded Total RNA Library Prep Gold, SMART-Seq Stranded Kit |
| Fragmentation Methods | Tagmentation (Nextera XT DNA Library Preparation Kit) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume | 1.4 TB + 941.7 GB + 23.9 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 2 cases tumor tissues: 2 samples |
| Targets | scDNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from single cells in tumor tissues of lung adenocarcinomas |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Single Cell DNA Reagent Kits (10x Genomics) |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000463 |
| Total Data Volume | 941.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 36 cases tumor tissues: 36 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods |
NCC Oncopanel v2 https://www.ncc.go.jp/en/information/press_release/20190717/20190717152024.html |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor tissues of lung adenocarcinomas |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect NCC oncopanel |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000696 |
| Total Data Volume | 23.9 TB (fastq) |
| Comments (Policies) | NBDC policy |
Visium Spatial Gene Expression, Histological image
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 3 cases tumor tissues: 3 samples |
| Targets | Visium Spatial Gene Expression, Histological image |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from tumor tissues of lung adenocarcinomas |
| 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 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000696 |
| Total Data Volume | 102.1 GB (fastq, png, json, csv) |
| Comments (Policies) | NBDC policy |
Multiplex Fluorescence Immunostaining
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 3 cases tumor tissues: 3 samples |
| Targets | Multiplex Fluorescence Immunostaining |
| Target Loci for Capture Methods | cycle/probe information |
| Platform | Akoya Biosciences [PhenoCycler] |
| Library Source | tumor tissues of lung adenocarcinomas |
| Cell Lines | - |
| Cell Treatment Method (kit name) | Staining Kit for PhenoCycler |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000696 |
| Total Data Volume | 102.1 GB (qptiff) |
| Comments (Policies) | NBDC policy |
Xenium In Situ Gene Expression
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 1 + 1 cases tumor tissues: 1 + 1 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 Analyzer] |
| Source | tumor tissues of lung adenocarcinomas |
| Cell Lines | - |
| Reagents (Panel, Kit, Version) |
Xenium Slides & Sample Prep Reagents Xenium Decoding Reagents Xenium Decoding Consumables |
| Software |
xenium-1.1.0.2 xenium-1.5.1.2 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000696 |
| Total Data Volume | lung adenocarcinoma: 16.1 + 2.1 GB (csv, h5, html, json, mtx, tiff, parquet, tsv, xenium, zarr) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takashi Kono
Affiliation: Division of Genome Biology, National Cancer Center Research Institute
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Platform for Advanced Genome Science | 16H06279 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Conquering cancer through neo-dimensional systems understanding; Sequencing and phasing cancer mutations using a nanopore sequencer MinION | 16H01582 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Stratification of cancer patients by novel genomic aberrations using long-read sequencing technologies | JP19cm0106539 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Study of genomic evolution of non-small cell lung cancers using long read sequencing technologies | JP21cm0106582 |
| Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED) | Study of heterogeneity of genomic and epigenomic aberrations and association with microenvironment in lung cancer tissues | JP23ama221522 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer. | doi: 10.1093/dnares/dsx027 | JGAD000065 |
| 2 | Long-read sequencing for non-small-cell lung cancer genomes | doi: 10.1101/gr.261941.120 | JGAD000252 JGAD000253 |
| 3 | Phasing analysis of lung cancer genomes using a long read sequencer | doi: 10.1038/s41467-022-31133-6 | JGAD000252 JGAD000253 JGAD000463 |
| 4 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Hirofumi Nakaoka | Department of Cancer Genome Research, Sasaki Institute | Japan | Genetic analysis of lung cancer | JGAD000252 | 2022/08/06-2023/03/31 |
