NBDC Research ID: hum0068.v9

 

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 IDType of DataCriteriaRelease Date
JGAS000065 NGS (PCR amplicon Seq) Controlled-access (Type I) 2017/07/10
JGAS000065

NGS (WGS: NovaSeq 6000)

NGS (WGS: PromethION)

Controlled-access (Type I) 2020/10/19
JGAS000349

NGS (RNA-seq: PromethION)

NGS (RNA-seq: NovaSeq 6000)

NGS (WGS: PromethION)

Controlled-access (Type I) 2021/12/14
JGAS000349 (Data addition)

NGS (scDNA-seq : NovaSeq 6000)

NGS (RNA-seq : NovaSeq 6000)

Controlled-access (Type I) 2022/03/23
JGAD000670 Processed data of JGAD000252 by JGA Controlled-access (Type I) 2022/12/27
JGAS000570

NGS (WGS: NovaSeq 6000)

NGS (WGS: PromethION)

NGS (RNA-seq : NovaSeq 6000, HiSeq 2000)

NGS (Target Capture)

NGS (Visium Spatial Gene Expression), Histological image

Multiplex Fluorescence Immunostaining

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
JGAS000677

NGS (Visium Spatial Gene Expression), Histological image

Multiplex Fluorescence Immunostaining

Xenium In Situ Gene Expression

Controlled-access (Type I) 2024/04/10

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

PCR amplicon Seq

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) -
Japanese Genotype-phenotype Archive Dataset ID JGAD000065
Total Data Volume 889 MB (fastq)
Comments (Policies) NBDC policy

 

WGS: NovaSeq 6000

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) -
Japanese Genotype-phenotype Archive Dataset ID

JGAD000252

JGAD000696

Dataset ID of the Processed data by JGA

JGAD000670

The way to Process

Total Data Volume

2 + 23.9 TB (fastq)

Comments (Policies) NBDC policy

 

WGS: PromethION

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) -
Japanese Genotype-phenotype Archive Dataset ID

JGAD000253

JGAD000463

JGAD000696

Total Data Volume 2.4 + 1.4 + 23.9 TB (fastq)
Comments (Policies) NBDC policy

 

RNA-seq: PromethION

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

JGAD000463

JGAD000696

Total Data Volume 1.4 TB + 941.7 GB + 23.9 TB (fastq)
Comments (Policies) NBDC policy

 

scDNA-seq

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

 

Target Capture

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 + 19 cases

          tumor tissues: 3 + 25 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

JGAD000807

Total Data Volume

JGAD000696:102.1 GB (fastq, png, json, csv)

JGAD000807:1.1 TB (fastq, png, json, csv)

Comments (Policies) NBDC policy

 

Multiplex Fluorescence Immunostaining

Participants/Materials

lung adenocarcinoma (ICD10: C349): 3 + 6 cases

          tumor tissues: 3 + 6 samples

Targets Multiplex Fluorescence Immunostaining
Target Loci for Capture Methods

cycle/probe information for JGAD000696

cycle/probe information for JGAD000807

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

JGAD000807

Total Data Volume

JGAD000696: 102.1 GB (qptiff)

JGAD000807: 10.4 GB (qptiff, xlsx)

Comments (Policies) NBDC policy

 

Xenium In Situ Gene Expression

Participants/Materials

lung adenocarcinoma (ICD10: C349): 1 + 1 + 10 cases

          tumor tissues: 1 + 1 + 10 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

JGAD000807

Total Data Volume

JGAD000696: 16.1 + 2.1 GB (csv, h5, html, json, mtx, tiff, parquet, tsv, xenium, zarr)

JGAD000807: 55.8 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):

NameTitleProject 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

TitleDOIDataset 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 Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma doi: 10.1038/s41467-023-43732-y JGAD000252
JGAD000253
JGAD000463
JGAD000696

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData 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
Kenichi Yoshida Division of Cancer Evolution, National Cancer Center Research Institute Japan A multicenter study on genomic analysis of solid tumors JGAD000065,
JGAD000252,
JGAD000253,
JGAD000463,
JGAD000696,
JGAD000807
2024/08/01-2028/03/31