NBDC Research ID: hum0094.v10
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SUMMARY
Aims: Identification of oncogenic alteration in breast cancer, lung adenocarcinoma, colorectal cancer (CRC) and pulmonary pleomorphic carcinoma through genomic analysis. To identify new biomarkers of desmoid tumor by investigating the molecular profiles in combination with the clinicopathological characteristics.
Methods: Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), RNA-seq and Target Capture sequencing were performed with HiSeq 2000/2500. Methylation analysis was performed with Infinium MethylationEPIC Kit. SNP array was performed with HumanOmni2.5-8. Genomic DNA was purified from each sample; We sequenced those genomic DNAs using 10X Genomics sequencing technologies, and analyzed genomic structural variations. Long-read sequencing was performed with the Pacific Biosciences Single-Molecule Real-Time (SMRT) sequencing technology.
Participants/Materials: Surgically resected breast cancer, lung adenocarcinoma, CRC and desmoid tumor tissues and paired non-tumor tissues or peripheral blood cells (as normal tissues)
WGS: Triple negative breast cancer: 16 cases (JGAS000095)
Lung adenocarcinoma: 7 cases (JGAS000360)
MSI-H CRC: 12 cases (JGAS000360)
Triple negative breast cancer: 11 cases (JGAS000360)
Colorectal cancer: 21 cases (JGAS000335)
WES: Triple negative breast cancer: 36 cases (including 16 cases used for WGS, 23 cases used for RNA-seq) (JGAS000095)
Lung adenocarcinoma: 43 cases (JGAS000105) + 126 cases (JGAS000215)
MSI-H CRC: 149 cases (JGAS000113)
CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 casess (JGAS000128)
Desmoid tumor: 64 cases (JGAS000270)
Pulmonary pleomorphic carcinoma: 19 cases (JGAS000297)
Colorectal cancer: 128 cases (JGAS000335)
RNA-seq: Triple negative breast cancer: 23 cases (JGAS000095)
Estrogen receptor-positive breast cancer: 17 cases (JGAS000095)
Human epidermal growth factor receptor 2 (HER2)-positive breast cancer: 15 cases (JGAS000095)
Lung adenocarcinoma: 43 cases (JGAS000105) + 126 cases (JGAS000215)
MSI-H CRC: 94 cases (JGAS000113)
CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 cases (JGAS000128)
Desmoid tumor: 55 cases (JGAS000270)
Pulmonary pleomorphic carcinoma: 33 cases (JGAS000297)
Colorectal cancer: 141 cases (JGAS000335)
RNA access: MSI-H CRC: 18 cases (JGAS000113)
Methylation array: MSI-H CRC: 93 cases (JGAS000113)
SNP array: MSI-H CRC: 25 cases (JGAS000113)
Target Capture: Pulmonary pleomorphic carcinoma: 20 cases (JGAS000297)
Colorectal cancer: 31 cases (JGAS000335)
Iso-seq: Triple negative breast cancer: 14 cases (JGAS000095)
Estrogen receptor-positive breast cancer: 8 cases (JGAS000095)
URL： https://www.ncc.go.jp/en/ri/division/genetics/index.html
| Data Set ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000095 | NGS (WGS, Exome, RNA-seq) | Controlled Access (Type I) | 2017/09/04 |
| JGAS000105 | NGS (Exome, RNA-seq) | Controlled Access (Type I) | 2018/01/22 |
| JGAS000113 |
NGS (Exome, RNA-seq, RNA access), |
Controlled Access (Type I) | 2019/02/12 |
| JGAS000128 | NGS (Exome, RNA-seq) | Controlled Access (Type I) | 2020/08/14 |
| JGAS000215 | NGS (Exome, RNA-seq) | Controlled Access (Type I) | 2020/10/26 |
| JGAS000270 | NGS (Exome, RNA-seq) | Controlled Access (Type I) | 2021/01/29 |
| JGAS000297 | NGS (Exome, RNA-seq, Target Capture) | Controlled Access (Type I) | 2021/07/02 |
| JGAS000360 | NGS (WGS) | Controlled Access (Type I) | 2021/10/22 |
| JGAS000095 (Data addition) | NGS (Iso-seq, RNA-seq) | Controlled Access (Type I) | 2021/10/26 |
| JGAS000335 | NGS (WGS, Exome, RNA-seq, Target Capture) | Controlled Access (Type I) | 2022/05/23 |
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MOLECULAR DATA
| Participants/Materials | Triple negative breast cancer (ICD10: C50): 16 cases |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | DNAs extracted from tumor tissues and paired non-tumor tissues or peripheral blood cells as non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext® Ultra™ DNA Library Prep Kit for Illumina® |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 103 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000095 |
| Total Data Volume | 8.94 TB (bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Triple negative breast cancer (ICD10: C50): 36 cases Lung adenocarcinoma (ICD10: C349): 43 cases MSI-H CRC (ICD10: C18, 19, 20): 149 cases CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 cases (ICD10: C18, 19, 20) Lung adenocarcinoma (ICD10: C34): 126 cases Desmoid tumor (ICD10: D48.1): 64 cases Pulmonary pleomorphic carcinoma (NCBI MedGen UID: 87198): 19 cases [30 samples] (tumor tissue: 12 cases [12 samples], non-tumor tissue: 18 cases [18 samples], paired samples from 11 cases) Colorectal cancer (ICD10: C189): 128 cases [141 samples] |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | DNAs extracted from tumor tissues and paired non-tumor tissues or peripheral blood cells as non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext® Ultra™ DNA Library Prep Kit for Illumina®, SureSelect Human All Exon V5, SureSelect Human All Exon V6 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
breast cancer and lung adenocarcinoma: 103 bp MSI-H CRC: 104 bp or 135 bp CRC: 100 bp or 103 bp lung adenocarcinoma (JGAD000301): 134 bp or 137 bp desmoid tumor: 134 bp or 137 bp pulmonary pleomorphic carcinoma: 133 bp colorectal cancer: 125 bp, 150 bp or 151 bp |
| Japanese Genotype-phenotype Archive Data set ID |
Triple negative breast cancer: JGAD000095 Lung adenocarcinoma: JGAD000110 MSI-H CRC: JGAD000122 CRC: JGAD000139 Lung adenocarcinoma: JGAD000301 Desmoid tumor: JGAD000376 Pulmonary pleomorphic carcinoma: JGAD000407 Colorectal cancer: JGAD000446 |
| Total Data Volume |
JGAD000095: 8.94 TB (bam [ref: hg19]) JGAD000110: 955.16 GB (bam [ref: hg19/hg38]) JGAD000122: 5.99 TB (bam [ref: hg38]) JGAD000139: 1.36 TB (bam [ref: hg38]) JGAD000301: 5 TB (bam [ref: hg38]) JGAD000376: 2.8 TB (bam [ref: hg38]) JGAD000407: 786.9 GB (bam [ref: hg19/hg38]) JGAD000446: 7.5 TB (bam [ref: hg38]) |
| Comments (Policies) |
NBDC policy (JGAD000095, JGAD000122, JGAD000139, JGAD000301, JGAD000376, JGAD000407, JGAD000446) NBDC policy & Company User Limit (JGAD000110) |
| Participants/Materials |
Triple negative breast cancer (ICD10: C50): 23 cases (including 2 cases for JGAD000457) Estrogen receptor-positive breast cancer (ICD10: C50): 17 cases HER2-positive breast cance (ICD10: C50)r: 15 cases Lung adenocarcinoma (ICD10: C349): 43 cases MSI-H CRC (ICD10: C18, 19, 20): 94 cases CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 cases (ICD10: C18, 19, 20) Lung adenocarcinoma (ICD10: C34): 126 cases Desmoid tumor (ICD10: D48.1): 55 cases Pulmonary pleomorphic carcinoma (NCBI MedGen UID: 87198): 33 cases [48 samples] (fresh frozen samples: 12 cases [12 samples], FFPE samples: 21 cases [36 samples]) Colorectal cancer (ICD10: C189): 141 cases [170 samples] (including 14 cases used for RNA-seq only) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) |
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® FFPE samples of pulmonary pleomorphic carcinoma: TruSeq RNA Access Library Prep kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
Breast cancer and lung adenocarcinoma: 103 bp MSI-H CRC: 104 bp or 135 bp CRC (JGAD000139): 133 bp Lung adenocarcinoma (JGAD000301): 134 bp or 137 bp Desmoid tumor: 134 bp or 137 bp Pulmonary pleomorphic carcinoma: 132 bp or 133 bp Breast cancer (JGAD000457): 100 bp Colorectal cancer: 125 bp or 127 bp |
| Japanese Genotype-phenotype Archive Data set ID |
Breast cancers: JGAD000095, JGAD000457 Lung adenocarcinoma: JGAD000111 MSI-H CRC: JGAD000122 CRC: JGAD000139 Lung adenocarcinoma: JGAD000301 Desmoid tumor: JGAD000376 Pulmonary pleomorphic carcinoma: JGAD000407 Colorectal cancer: JGAD000446 |
| Total Data Volume |
JGAD000095: 8.94 TB (fastq) JGAD000111: 1.31 TB (fastq) JGAD000122: 5.99 TB (fastq) JGAD000139: 1.91 TB (fastq) JGAD000301: 5 TB (fastq) JGAD000376: 2.8 TB (fastq) JGAD000407: 786.9 GB (fastq) JGAD000446: 7.5 TB (fastq) JGAD000457: 41.2 GB (fastq) |
| Comments (Policies) |
NBDC policy (JGAD000095, JGAD000122, JGAD000139, JGAD000301, JGAD000376, JGAD000407, JGAD000446, JGAD000457) NBDC policy & Company User Limit (JGAD000111) |
| Participants/Materials | MSI-H CRC (ICD10: C18, 19, 20): 18 cases |
| Targets | RNA access |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq® RNA Access Library Prep Kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 104 bp or 135 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000122 (fastq) |
| Total Data Volume | 5.99 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
MSI-H CRC (ICD10: C18, 19, 20): 93 cases normal tissues: 20 samples |
| Targets | Methylation array |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium Human MethylationEPIC BeadChip] |
| Source | DNAs extracted from tumor tissues and paired non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Infinium Human MethylationEPIC BeadChip Kit |
| Algorithms for Calculating Methylation-rate (software) | GenomeStudio (Illumina) |
| Filtering Methods | Detection P-value >= 0.05 |
| Normalization of microarray | - |
| Probe Number | 867,926 Probe Numbers |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000122 |
| Total Data Volume | 5.99 TB (tsv) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | MSI-H CRC (ICD10: C18, 19, 20): 25 cases |
| Targets | genome wide CNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanOmni2.5-8 BeadChip] |
| Source | DNAs extracted from tumor tissues and paired non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Infinium HumanOmni2.5-8 kit |
| Algorithm for detecting CNVs (software) | GenomeStudio (Illumina) |
| Filtering Methods | As described in 'Illumina Infinium Assay Ver.2.1.' |
| CNV number | - |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000122 |
| Total Data Volume | 5.99 TB (tsv) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pulmonary pleomorphic carcinoma (NCBI MedGen UID: 87198): 20 cases [50 samples] (tumor tissue: 20 cases [37 samples], non-tumor tissue: 13 cases [13 samples], paired samples from 13 cases) Colorectal cancer (ICD10: C189): 31 cases [49 samples] |
| Targets | Target Capture |
| Target Loci for Capture Methods |
Todai OncoPanel |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor tissues and paired non-tumor tissues (FFPE) |
| Cell Lines | - |
| Library Construction (kit name) | SureSelectXT Custom kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
Pulmonary pleomorphic carcinoma: 132 bp or 133 bp Colorectal cancer: 125 bp |
| Japanese Genotype-phenotype Archive Data set ID |
Pulmonary pleomorphic carcinoma: JGAD000407 Colorectal cancer: JGAD000446 |
| Total Data Volume |
JGAD000407: 786.9 GB (bam [ref: hg19/hg38]) JGAD000446: 7.5 TB (bam [ref: hg38) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Lung adenocarcinoma (ICD10: C34): 7 cases (tumor tissues and paired non-tumor tissues for 3 cases; tumor tissues only for 4 cases) MSI-H CRC (ICD10: C18, C19, C20): 12 cases (tumor tissues and paired non-tumor tissues) Triple negative breast cancer (ICD10: C50): 11 cases (tumor tissues only) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | 10x Genomics [Chromium Controller] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | 10x Genomics Chromium Genome Sequencing Solution |
| Fragmentation Methods | 10x Genomics Chromium Genome Sequencing Solution |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 125 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000474 |
| Total Data Volume | 3.3 TB (fastq, bed, vcf [ref：hg38]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Triple negative breast cancer (ICD10: C50): 14 cases Estrogen receptor-positive breast cancer (ICD10: C50): 8 cases |
| Targets | Iso-seq |
| Target Loci for Capture Methods | - |
| Platform | PacBio [Sequel] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SMRTbell Template Prep Kit 1.0 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000457 |
| Total Data Volume | 41.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Colorectal cancer (ICD10: C189): 21 cases (including 3 cases used for WES, 18 cases used for TGS) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq6000] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA PCR-free Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000446 |
| Total Data Volume | 7.5 TB (bam [ref：hg38]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hiroyuki Mano
Affiliation: Division of Cellular Signaling, National Cancer Center Research Institute
Project / Group Name: -
URL： https://www.ncc.go.jp/en/ri/division/genetics/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Leading Advanced Projects for medical innovation, The Japan Agency for Medical Research and Development (AMED) | Project for novel therapeutic targets in cancer | - |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Oncogenic mutations of RAC small GTPases in Human cancers | 26430106 |
| Grant from The Princess Takamatsu Cancer Research Fund | Analysis of molecular mechanisms of oncogenic activity of RAC small GTPase | - |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Elucidation of initiation and progression mechanism of human epithelial tumors towards identification of novel therapeutic targets | JP17cm0106502 |
| Program for an Integrated Database of Clinical and Genomic Information, Japan Agency for Medical Research and Development (AMED) | Establishment of infrastructure for genomic medicine and construction of knowledge database | JP18kk0205003 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Implementation of precision medicine by the application of an innovative method for functional evaluation of oncogenes. | JP18ck0106252 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Comprehensive exploration of biomarkers by high-throughput functional analysis for the strategic drug development | JP20ck0106536 |
| Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED) | Informatics for analyzing de novo human genome assemblies | JP19km0405204 |
PUBLICATIONS
| Title | DOI | Data Set ID | |
|---|---|---|---|
| 1 | Integrative analysis of genomic alterations in triple-negative breast cancer in association with homologous recombination deficiency | doi: 10.1371/journal.pgen.1006853 | JGAD000095 |
| 2 | Inactivating mutations and hypermethylation of the NKX2-1/TTF-1 gene in non-terminal respiratory unit-type lung adenocarcinomas. | doi: 10.1111/cas.13313 | JGAD000110, JGAD000111 |
| 3 | Fusion Kinases Identified by Genomic Analyses of Sporadic Microsatellite Instability-High Colorectal Cancers | doi: 10.1158/1078-0432.CCR-18-1574 | JGAD000122 |
| 4 | Genomic profiles of colorectal carcinoma with liver metastases and newly identified fusion genes | doi: 10.1111/cas.14127 | JGAD000139 |
| 5 | Identification of Novel CD74-NRG2α Fusion From Comprehensive Profiling of Lung Adenocarcinoma in Japanese Never or Light Smokers | doi: 10.1016/j.jtho.2020.01.021 | JGAD000301 |
| 6 | Comprehensive molecular and clinicopathological profiling of desmoid tumors | doi: 10.1016/j.ejca.2020.12.001 | JGAD000376 |
| 7 | Comprehensive molecular profiling of pulmonary pleomorphic carcinoma. | doi: 10.1038/s41698-021-00201-3 | JGAD000407 |
| 8 | Multi-sample Full-length Transcriptome Analysis of 22 Breast Cancer Clinical Specimens with Long-Read Sequencing | doi: 10.1101/2020.07.15.199851 | JGAD000457 |
| 9 | Exploration of predictive biomarkers for postoperative recurrence of stage II/III colorectal cancer using genomic sequencing | doi: 10.1002/cam4.4710 | JGAD000446 |
USERS (Controlled-Access Data)
| Principal Investigator | Affiliation | Research Title | Data in Use (Data Set ID) | Period of Data Use |
|---|---|---|---|---|
| Subhajyoti De | Rutgers Cancer Institute, Rutgers the State University of New Jersey | JGAD000095 | 2018/08/06-2021/05/31 | |
| Youping Deng | Department of Complementary and Integrative Medicine, University of Hawai Manoa | JGAD000110, JGAD000111 | 2018/10/04-2025/07/10 | |
| Tetsuya Sato | Research Department, Miraca Research Institute G.K. | Search for Lynch syndrome colorectal cancer-related genes using contolled-access clinical sequence data | JGAD000095, JGAD000122 | 2019/08/05-2020/03/31 |
| Kouya Shiraishi | Division of Genome Biology, National Cancer Research Institute | Elucidation of immune-system networks between host and tumor based on genomic analysis | JGAD000095, JGAD000110, JGAD000111, JGAD000122 | 2019/08/05-2023/03/31 |
| Ruping Sun | Department of laboratory medicine and pathology, University of Minnesota | Accounting for Copy Number States in Quantifying Tumor Heterogeneity | JGAD000095 | 2020/03/19-2022/08/01 |
| Masaki Mandai | Kyoto University Faculty of Medicene, department of Gynecology and Obstetrics | Integrated analyses of omics (genomics, transcriptomics, proteomics and metabolomics) associated with clinical variables for developing indivisualizedtreatment in gynecological malignancy | JGAD000095, JGAD000110, JGAD000111, JGAD000122 | 2020/03/13-2025/03/31 |
