Omics · study · 2026
Native American ancestry-enriched eQTLs regulate HER2 amplicon genes and are associated with breast cancer outcomes in Colombian women
Listed in NCBI GEO
Women with higher Native American (NA) ancestry are more likely to develop HER2-positive breast tumors and exhibit increased ERBB2 expression.
Description
We performed RNA sequencing of tumor and adjacent non-tumoral breast tissue from Colombian women with invasive breast cancer. Germline genotypes were obtained from RNA-seq data using the GATK4 pipeline.
Local ancestry was inferred with RFMix. eQTL analyses identified trans-eQTLs rs77910576 (7p21.1) and rs12144827 (1p13.3) associated with increased expression of HER2 amplicon genes, supporting a role for ancestry-specific regulatory variation in shaping breast cancer biology.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE343nnn/GSE343732 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE343732 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1512471 ncbi.nlm.nih.gov/bioproject/PRJNA1512471 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Homo sapiens
- From keywords
- Life Sciences
- Inferred from text
- Cancer 75% · RNA sequencing 75% · Sequencing 75%
Provenance · 1 source records, 10 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE343732 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[disease].local:disease:cancer | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[organism].NCBITaxon:9606 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |