NBDC Research ID: hum0068.v4

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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 and PromethION.

                 [scDNA-seq] Single cell DNA sequencing by using of NovaSeq.

Participants/Materials: Lung adenocarcinoma

URL: http://kero.hgc.jp/

 

Data Set 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

*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: 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 Data set ID JGAD000065
Total Data Volume 889 MB (fastq)
Comments (Policies) NBDC policy

 

WGS: NovaSeq 6000

Participants/Materials

lung adenocarcinoma (ICD10: C349): 21 cases (42 samples)

          tumor tissues: 21 samples

          normal tissues: 21 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
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 2.8 Tb
Japanese Genotype-phenotype Archive Data set ID

JGAD000252

Total Data Volume

2 TB (fastq)

Comments (Policies) NBDC policy

 

WGS: PromethION

Participants/Materials

lung adenocarcinoma (ICD10: C349): 21 cases (41 + 8 samples)

          tumor tissues: 21 + 4 samples

          normal tissues: 20 + 4 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 Data set ID

JGAD000253

JGAD000463

Total Data Volume 2.4 + 1.4 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 Data set ID JGAD000463
Total Data Volume 1.4 TB (fastq)
Comments (Policies) NBDC policy

 

RNA-seq: NovaSeq 6000

Participants/Materials

lung adenocarcinoma (ICD10: C349): 6 + 5 cases (12 + 5 samples)

          tumor tissues: 6 + 5 samples

          normal tissues: 6 samples

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
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
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 Data set ID JGAD000463
Total Data Volume 1.4 TB + 941.7 GB (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 Data set ID JGAD000463
Total Data Volume 941.7 GB (fastq)
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 19cm0106539h0002
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

 

PUBLICATIONS

TitleDOIData Set 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

 

USRES (Controlled-Access Data)

Principal InvestigatorAffiliationResearch TitleData in Use (Data Set ID)Period of Data Use