Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes

• Published in: Nature communications Vol. 12; no. 1; pp. 6946 - 15
• Main Authors: Ansari-Pour, Naser, Zheng, Yonglan, Yoshimatsu, Toshio F., Sanni, Ayodele, Ajani, Mustapha, Reynier, Jean-Baptiste, Tapinos, Avraam, Pitt, Jason J., Dentro, Stefan, Woodard, Anna, Rajagopal, Padma Sheila, Fitzgerald, Dominic, Gruber, Andreas J., Odetunde, Abayomi, Popoola, Abiodun, Falusi, Adeyinka G., Babalola, Chinedum Peace, Ogundiran, Temidayo, Ibrahim, Nasiru, Barretina, Jordi, Van Loo, Peter, Chen, Mengjie, White, Kevin P., Ojengbede, Oladosu, Obafunwa, John, Huo, Dezheng, Wedge, David C., Olopade, Olufunmilayo I.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 26.11.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 45; 45/23; 45/91; 631/114/2785; 631/67/69; 692/4028/67/1347; Adult; Aged; Biomarkers, Tumor - genetics; Biopsy; Black People - ethnology; Black People - genetics; Breast - pathology; Breast cancer; Breast Neoplasms - ethnology; Breast Neoplasms - genetics; Breast Neoplasms - mortality; Breast Neoplasms - pathology; Clonal Evolution; DNA Mutational Analysis; Ethnic factors; Evolution; Female; GATA-3 protein; GATA3 Transcription Factor - genetics; Gene sequencing; Genetic Heterogeneity; Genomes; Genomic Instability; Genomics; Germ-Line Mutation; Health Status Disparities; Heterogeneity; Homologous recombination; Homology; Humanities and Social Sciences; Humans; Medical research; Middle Aged; multidisciplinary; Mutation; Nigeria - epidemiology; Nigeria - ethnology; Patients; Risk Assessment; RNA-Seq; Science; Science (multidisciplinary); Synaptophysin - genetics; Trans-Activators - genetics; Transcriptomes; Tumor Microenvironment - genetics; Tumors; White People - ethnology; White People - genetics; Whole Genome Sequencing; Nigeria
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-27079-w

Black women across the African diaspora experience more aggressive breast cancer with higher mortality rates than white women of European ancestry. Although inter-ethnic germline variation is known, differential somatic evolution has not been investigated in detail. Analysis of deep whole genomes of 97 breast cancers, with RNA-seq in a subset, from women in Nigeria in comparison with The Cancer Genome Atlas (n = 76) reveal a higher rate of genomic instability and increased intra-tumoral heterogeneity as well as a unique genomic subtype defined by early clonal GATA3 mutations with a 10.5-year younger age at diagnosis. We also find non-coding mutations in bona fide drivers ( ZNF217 and SYPL1 ) and a previously unreported INDEL signature strongly associated with African ancestry proportion, underscoring the need to expand inclusion of diverse populations in biomedical research. Finally, we demonstrate that characterizing tumors for homologous recombination deficiency has significant clinical relevance in stratifying patients for potentially life-saving therapies. Breast cancer heterogeneity and tumour evolutionary trajectories remain largely unknown among women of African ancestry. Here, the authors perform whole genome and transcriptome sequencing of Nigerian breast cancer patients and identify unique evolutionary phenomena.