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Muquith M, Hsiehchen D. Landscape and Saturation Analysis of Mutations Associated With Race in Cancer Genomes by Clinical Sequencing. Oncologist 2024; 29:219-226. [PMID: 38297963 PMCID: PMC10911917 DOI: 10.1093/oncolo/oyad341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 12/11/2023] [Indexed: 02/02/2024] Open
Abstract
Differences in cancer genomes between racial groups may impact tumor biology and health disparities. However, the discovery of race-associated mutations is constrained by the limited representation and sample size of different racial groups in prior genomic studies. We evaluated the influence of race on the frequency of gene mutations using the Genomics, Evidence, Neoplasia, Information, Exchange database, a large genomic dataset aggregated from clinical sequencing. Matched cohort analyses were used to identify histology-specific race-associated mutations including increased TERT promoter mutations in Black and Asian patients with gliomas and bladder cancers, and a decreased frequency of mutations in DNA repair pathway genes and subunits of the SWI/SNF chromatin complex in Asian and Black patients across multiple cancer types. The distribution of actionable mutations in oncogenes was also race-specific, demonstrating how targeted therapies may have a disparate impact on racial groups. Down-sampling analyses indicate that larger sample sizes are likely to discover more race-associated mutations. These results provide a resource to understand differences in cancer genomes between racial groups which may inform the design of clinical studies and patient recruitment strategies in biomarker trials.
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Affiliation(s)
- Maishara Muquith
- University of Texas Southwestern Medical School, Dallas, TX, USA
| | - David Hsiehchen
- Division of Hematology and Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Garcia-Souto D, Bruzos AL, Diaz S, Rocha S, Pequeño-Valtierra A, Roman-Lewis CF, Alonso J, Rodriguez R, Costas D, Rodriguez-Castro J, Villanueva A, Silva L, Valencia JM, Annona G, Tarallo A, Ricardo F, Bratoš Cetinić A, Posada D, Pasantes JJ, Tubio JMC. Mitochondrial genome sequencing of marine leukaemias reveals cancer contagion between clam species in the Seas of Southern Europe. eLife 2022; 11:e66946. [PMID: 35040778 PMCID: PMC8765752 DOI: 10.7554/elife.66946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 12/04/2021] [Indexed: 12/30/2022] Open
Abstract
Clonally transmissible cancers are tumour lineages that are transmitted between individuals via the transfer of living cancer cells. In marine bivalves, leukaemia-like transmissible cancers, called hemic neoplasia (HN), have demonstrated the ability to infect individuals from different species. We performed whole-genome sequencing in eight warty venus clams that were diagnosed with HN, from two sampling points located more than 1000 nautical miles away in the Atlantic Ocean and the Mediterranean Sea Coasts of Spain. Mitochondrial genome sequencing analysis from neoplastic animals revealed the coexistence of haplotypes from two different clam species. Phylogenies estimated from mitochondrial and nuclear markers confirmed this leukaemia originated in striped venus clams and later transmitted to clams of the species warty venus, in which it survives as a contagious cancer. The analysis of mitochondrial and nuclear gene sequences supports all studied tumours belong to a single neoplastic lineage that spreads in the Seas of Southern Europe.
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Affiliation(s)
- Daniel Garcia-Souto
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de CompostelaSantiago de CompostelaSpain
- Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger InstituteCambridgeUnited Kingdom
| | - Alicia L Bruzos
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Seila Diaz
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Sara Rocha
- Phylogenomics Lab, Universidade de VigoVigoSpain
| | - Ana Pequeño-Valtierra
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
| | | | - Juana Alonso
- CINBIO, Universidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGOVigoSpain
| | - Rosana Rodriguez
- Centro de Investigación Mariña, Universidade de Vigo, ECIMATVigoSpain
| | - Damian Costas
- Centro de Investigación Mariña, Universidade de Vigo, ECIMATVigoSpain
| | - Jorge Rodriguez-Castro
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
| | | | - Luis Silva
- Instituto Español de Oceanografía (IEO), Centro Oceanográfico de CádizCádizSpain
| | - Jose Maria Valencia
- Laboratori d’Investigacions Marines i Aqüicultura, (LIMIA) - Govern de les Illes BalearsPort d'Andratx, Balearic IslandsSpain
- Instituto de Investigaciones Agroambientales y de Economía del Agua (INAGEA) (INIA-CAIB-UIB)Palma de Mallorca, Balearic IslandsSpain
| | | | | | - Fernando Ricardo
- ECOMARE, Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Santiago University CampusAveiroPortugal
| | | | - David Posada
- CINBIO, Universidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGOVigoSpain
- Department of Biochemistry, Genetics and Immunology, Universidade de VigoVigoSpain
| | - Juan Jose Pasantes
- Department of Biochemistry, Genetics and Immunology, Universidade de VigoVigoSpain
- Centro de Investigación Mariña, Universidade de VigoVigoSpain
| | - Jose MC Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de CompostelaSantiago de CompostelaSpain
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Robine N, Varmus H. New York's Polyethnic-1000: a regional initiative to understand how diverse ancestries influence the risk, progression, and treatment of cancers. Trends Cancer 2021; 8:269-272. [PMID: 34895873 DOI: 10.1016/j.trecan.2021.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/09/2021] [Indexed: 12/22/2022]
Abstract
Research consortia can help to repair deficiencies in knowledge about the influence of inherited genetic diversity on disease. The New York Genome Center (NYGC) recently established Polyethnic-1000 (P-1000), a multi-institutional collaboration to study hereditary factors affecting several types of cancer. Here, we describe its rationale, organization, development, current activities, and prospects.
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Affiliation(s)
| | - Harold Varmus
- New York Genome Center, New York, NY, USA; Weill-Cornell Medicine, New York, NY, USA.
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Abstract
A central goal in cancer genomics is to identify the somatic alterations that underpin tumor initiation and progression. While commonly mutated cancer genes are readily identifiable, those that are rarely mutated across samples are difficult to distinguish from the large numbers of other infrequently mutated genes. We introduce a method, nCOP, that considers per-individual mutational profiles within the context of protein-protein interaction networks in order to identify small connected subnetworks of genes that, while not individually frequently mutated, comprise pathways that are altered across (i.e., "cover") a large fraction of individuals. By analyzing 6,038 samples across 24 different cancer types, we demonstrate that nCOP is highly effective in identifying cancer genes, including those with low mutation frequencies. Overall, our work demonstrates that combining per-individual mutational information with interaction networks is a powerful approach for tackling the mutational heterogeneity observed across cancers.
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Affiliation(s)
- Borislav H Hristov
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Mona Singh
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
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Affiliation(s)
- Ge Gao
- a Department of Laboratory Medicine and Pathology , Mayo Clinic , Rochester , MN , USA
| | - David I Smith
- a Department of Laboratory Medicine and Pathology , Mayo Clinic , Rochester , MN , USA
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