NBDC Research ID: hum0516.v1
SUMMARY
Aims: Breast cancer is one of the most common cancers occurring worldwide in women. Even after curative treatment based on clinical subtypes according to molecular features, the risk of relapse still remains. Cell-free DNA (cfDNA) is an emerging tool for clinical cancer detection to monitor the risk of recurrence, therapeutic efficacy and tumor progression. In occurrence of relapse, genomic, transcriptomic and epigenetic profiles are altered, and reflected in cfDNA fragmentation patterns. In this study, we focus on the transcriptionally dynamic loci associated with therapy resistance in breast cancer, and develop the target sequencing approach using cfDNAs to detect individuals with recurrent/metastatic breast cancer.
Methods: cfDNA target sequencing
Participants/Materials: 150 blood samples obtained from 99 patients with primary breast cancer (pBC) and 34 patients with recurrent/metastatic breast cancer (mBC)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000812 | NGS (Target Capture) | Controlled-access (Type I) | 2026/05/20 |
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MOLECULAR DATA
| Participants/Materials |
breast cancer (ICD10: C50.9): 127 cases pBC 99 cases: 105 samples mBC 34 cases: 45 samples Details: 99 pBC patients, 99: before initial treatment, 6: plus after the neoadjuvant therapy. 34 mBC patients, at time point observed recurrence/distant metastasis (one; 25 samples, two; 7 samples and three; 2 samples). Of these samples, 6 patients had samples with both pBC and mBC. |
| Targets | Target Capture |
| Target Loci for Capture Methods | 26 genes (RERE, APH1A, AHNAK, SYTL2, CYP1A1, CLN3, ESRP2, DBNDD1, USP34, MFSD10, LRBA, BRD8, VPS28, KDM2A, SIDT2, ERBB2, TUBG2, CASP14, KYNU, ATIC, SLC12A5, CCDC50, SYNPO2, ESR1, SDK1, and AVL9) |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | cfDNA in blood |
| Cell Lines | - |
| Library Construction (kit name) | KAPA Hyper Prep Kit, xGen Duplex Seq Adapter-Tech Access |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100bp x 2 |
| Mapping Methods | Burrows–Wheeler aligner (BWA; version 0.5.9-r16) |
| Mapping Quality | MAPQ filtering was not applied. |
| Reference Genome Sequence | GRCh37 |
| Coverage (Depth) | 200x |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000954 |
| Total Data Volume | 68.8 GB (bam) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Sugiko Watanabe
Affiliation: Institute of Molecular Embryology and Genetics, Kumamoto university
Project / Group Name: Department of medical cell biology
URL： https://www.imeg.kumamoto-u.ac.jp/en/bunya_top/medical_cell_biology/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Analysis of cell-free DNA targeted sequence to develop of novel strategies for endocrine therapy-resistant breast cancer | 23K06699 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Platform for Advanced Genome Science | 16H06279 (PAGS) |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Molecular mechanism of accumulation of cytoplasmic chromatin in senescent cells, related to carcinogenesis | 20K07589 |
| Princess Takamatsu Cancer Research Fund | Next-Generation Extranuclear Genome Sequencing for Detecting Genome Instability in Cellular Senescence and Molecular Mechanisms of Cancer Genomic Structural Variations | 20-25240 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Molecular basis of senescence-associated secretory phenotype and its medical application | 24K02240 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Transcriptionally informed nucleosome profiling of circulating cell-free DNA predicts breast cancer recurrence. | JGAD000954 | |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
