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E50a5f0d-c339-4494-9d1d-f2b7961701dd - samples

ABSTRACT: Paired end shallow whole genome sequencing (sWGS) data (FASTQ) for the identification of genomewide somatic copy number alterations (SCNA) and the estimation of tumor fractions.

PROVIDER: EGAD00001010293 | EGA |

REPOSITORIES: EGA

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ena-DATASET-MUG-02-12-2021-20:16:00:427-345 - samples

Project description:Paired end shallow whole genome sequencing (sWGS) data for the identification of genomewide somatic copy number alterations (SCNA) and the estimation of tumor fractions.

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Association of self-identified race and genetic ancestry with the immunogenomic landscape of primary prostate cancer

Project description:The genomic and immune landscapes of prostate cancer differ by self-identified race. However, few studies have examined the genome-wide copy number landscape and immune content of matched cohorts with genetic ancestry data and clinical outcomes. Here, we assessed prostate cancer somatic copy number alterations (sCNA) and tumor immune content of a grade-matched, surgically-treated cohort of 145 self-identified Black (BL) and 145 self-identified white (WH) patients with genetic ancestry estimation. A generalized linear model adjusted with age, pre-operative PSA, and Grade Group and filtered for germline copy number variations (gCNV) identified 143 loci where copy number varied significantly by percent African ancestry, clustering on chromosomes 6p, 10q, 11p, 12p, and 17p. Multivariable Cox regression models adjusted for age, pre-operative PSA levels, and Grade Group revealed that chromosome 8q gains (including MYC) were significantly associated with biochemical recurrence and metastasis, independent of genetic ancestry. Finally, regulatory T-cell density in BL and WH patients was significantly correlated with percent genome altered, and these findings were validated in the TCGA cohort. Taken together, our findings identify specific sCNA linked to genetic ancestry and outcome in primary prostate cancer and demonstrate that regulatory T-cell infiltrate varies by global sCNA burden in primary disease.

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