Data · dataset · 2024
GWAS summary statistics of PhD Thesis "Identifying Genetic Factors Associated with Breast or Ovarian Cancer Risk in BRCA1 Pathogenic Variant Carriers"
Listed in Riga Stradins University dataverse
In this study, we conducted a genome-wide association study (GWAS) involving 406 female carriers of BRCA1 pathogenic variants (PV) (c.4035del or c.5266dup) in Latvian population.
Description
The cohort included individuals affected by breast cancer (BC) or ovarian cancer (OC) and unaffected individuals. We compared three groups: (1) carriers affected with cancer (BC or OC) vs. unaffected individuals, (2) carriers affected with BC vs. unaffected individuals, and (3) carriers affected with OC vs. unaffected individuals.
Genotyping of all study samples was performed using the Infinium OncoArray-500K BeadChip (Illumina, San Diego, CA, USA) at the Institute of Oncology and Molecular Genetics, Rīga Stradiņš University. The dataset underwent standard genotype quality control (QC), followed by imputation of missing genotypes using the Estonian population-based high-coverage whole-genome sequencing (WGS) dataset (n = 2244) as a reference panel.
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Association analysis was performed using the R v4.0.2 package SAIGE v0.38 to implement a mixed logistic regression model, adjusted for relatedness, the first four principal components (PCs), age at recruitment/disease onset, and BRCA1 PV type.
Links
Where it is published
- Dataverse dataset page dataverse.rsu.lv/dataset.xhtml?persistentId=doi%3A10.48510%2FFK2%2FTEJ5PK ↗
landing page · from dataverse rsu lv
- DOI doi.org/10.48510/fk2/tej5pk ↗
DOI / persistent id · from dataverse rsu lv
Catalogue records · 1
- Dataverse API dataverse.rsu.lv/api/datasets/:persistentId/?persistentId=doi%3A10.48510%2FFK2%… ↗
metadata API · from dataverse rsu lv
Topics
- Stated by source
- Medicine, Health and Life Sciences
- From keywords
- Life Sciences · Medicine & Health
- Inferred from text
- Cancer 75% · Disease 75% · Genome sequencing 65% · Oncology and carcinogenesis 75% · Sequencing 75%
Provenance · 1 source records, 14 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Riga Stradins University dataverse | doi:10.48510/FK2/TEJ5PK | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[disease].local:disease:cancer | enrichment · dataverse rsu lv | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[disease].local:disease:disease | enrichment · dataverse rsu lv | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].anzsrc:group:3211 | enrichment · dataverse rsu lv | taxonomy-embedding@1.1.0 | title+keywords+description (75%) |
| concepts[field].dataverse_subject:medicine-health-and-life-sciences | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | /subjects |
| concepts[modality].local:modality:genome-sequencing | enrichment · dataverse rsu lv | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:sequencing | enrichment · dataverse rsu lv | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | |
| description | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | /description |
| publication_date | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | |
| title | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | /name |
| updated_date | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | |
| version_label | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 |