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Kamaraju S, Conroy M, Harris A, Georgen M, Min H, Powell M, Kurzrock R. Challenges to genetic testing for germline mutations associated with breast cancer among African Americans. Cancer Treat Rev 2024; 124:102695. [PMID: 38325071 DOI: 10.1016/j.ctrv.2024.102695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Inequities in preventive cancer screening, diagnosis, treatment, and inferior cancer outcomes continue to pose challenges across the cancer continuum. While the exact reasons for these inferior outcomes are unknown, multiple barriers to various domains of social determinants of health (SDOH) play a vital role, leading to inequities in cancer care. These include barriers to transportation, housing, and food insecurities, contributing to delays in preventive screening and treatment. Furthermore, aggressive biologies also exist across various racial profiles with accompanying germline mutations. For example, African Americans (AAs) have a higher incidence of triple-negative breast cancer subtype and a high prevalence of BRCA1/2 gene mutations, increasing the risk of multiple cancers, warranting high-risk screening for these populations. Unfortunately, other barriers, such as financial insecurities, low health literacy rates, and lack of awareness, lead to delays in cancer screening and genetic testing, even with available high-risk screening and risk reduction procedures. In addition, physicians receive minimal interdisciplinary training to address genetic assessment, interpretation of the results, and almost no additional training in addressing the unique needs of racial minorities, leading to suboptimal delivery of genetic assessment provision resources among AAs. In this review, we discuss the confluence of factors and barriers limiting genetic testing among AAs and highlight the prevalence of germline mutations associated with increased risk of breast cancer among AAs, reflecting the need for multi-panel germline testing as well as education regarding hereditary cancer risks in underserved minorities.
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Affiliation(s)
- S Kamaraju
- Medical College of Wisconsin, Milwaukee, WI, USA; Department of Medicine, Division of Hematology-Oncology, Medical College of Wisconsin, Milwaukee, WI, USA; Froedtert Hospital, Milwaukee, WI, USA.
| | - M Conroy
- Medical College of Wisconsin, Milwaukee, WI, USA; Froedtert Hospital, Milwaukee, WI, USA
| | - A Harris
- Medical College of Wisconsin, Milwaukee, WI, USA; Froedtert Hospital, Milwaukee, WI, USA
| | - M Georgen
- Medical College of Wisconsin, Milwaukee, WI, USA; Department of Medicine, Division of Hematology-Oncology, Medical College of Wisconsin, Milwaukee, WI, USA; Froedtert Hospital, Milwaukee, WI, USA
| | - H Min
- Medical College of Wisconsin, Milwaukee, WI, USA; Froedtert Hospital, Milwaukee, WI, USA
| | - M Powell
- Medical College of Wisconsin, Milwaukee, WI, USA; Froedtert Hospital, Milwaukee, WI, USA
| | - R Kurzrock
- Medical College of Wisconsin, Milwaukee, WI, USA; Department of Medicine, Division of Hematology-Oncology, Medical College of Wisconsin, Milwaukee, WI, USA; Froedtert Hospital, Milwaukee, WI, USA
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2
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Nagy G, Diabate M, Banerjee T, Adamovich AI, Smith N, Jeon H, Dhar S, Liu W, Burgess K, Chung D, Starita LM, Parvin JD. Multiplexed assay of variant effect reveals residues of functional importance in the BRCA1 coiled-coil and serine cluster domains. PLoS One 2023; 18:e0293422. [PMID: 37917606 PMCID: PMC10621863 DOI: 10.1371/journal.pone.0293422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Delineating functionally normal variants from functionally abnormal variants in tumor suppressor proteins is critical for cancer surveillance, prognosis, and treatment options. BRCA1 is a protein that has many variants of uncertain significance which are not yet classified as functionally normal or abnormal. In vitro functional assays can be used to identify the functional impact of a variant when the variant has not yet been categorized through clinical observation. Here we employ a homology-directed repair (HDR) reporter assay to evaluate over 300 missense and nonsense BRCA1 variants between amino acid residues 1280 and 1576, which encompasses the coiled-coil and serine cluster domains. Functionally abnormal variants tended to cluster in residues known to interact with PALB2, which is critical for homology-directed repair. Multiplexed results were confirmed by singleton assay and by ClinVar database variant interpretations. Comparison of multiplexed results to designated benign or likely benign or pathogenic or likely pathogenic variants in the ClinVar database yielded 100% specificity and 100% sensitivity of the multiplexed assay. Clinicians can reference the results of this functional assay for help in guiding cancer treatment and surveillance options. These results are the first to evaluate this domain of BRCA1 using a multiplexed approach and indicate the importance of this domain in the DNA repair process.
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Affiliation(s)
- Gregory Nagy
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Mariame Diabate
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Tapahsama Banerjee
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Aleksandra I. Adamovich
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Nahum Smith
- Department of Genome Sciences, University of Washington and Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Hyeongseon Jeon
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Shruti Dhar
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Wenfang Liu
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Katherine Burgess
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington and Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Jeffrey D. Parvin
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
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Iwai Y, Toumbou K, Zuze T, Morgan JS, Simwinga L, Wright ST, Fedoriw Y, Oladeru OT, Balogun OD, Roberson ML, Olopade OI, Tomoka T, Elmore SN. Breast Cancer Germline Genetic Counseling and Testing for Populations of African Heritage Globally: A Scoping Review on Research, Practice, and Bioethical Considerations. JCO Glob Oncol 2023; 9:e2300154. [PMID: 37944088 PMCID: PMC10645409 DOI: 10.1200/go.23.00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/05/2023] [Accepted: 09/05/2023] [Indexed: 11/12/2023] Open
Abstract
PURPOSE Despite the disproportionately high risk of breast cancer among women of African heritage, little is known about the facilitators and barriers to implementing germline genetic testing and counseling (GT/C). METHODS This scoping review followed guidelines recommended by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews. Published manuscripts from database inception through 2021 were sourced from PubMed, Cumulative Index to Nursing and Allied Health Literature via EBSCO, Embase, Cochrane Library, and Scopus. Search terms were used to retrieve articles addressing (1) African heritage, (2) breast cancer, and (3) GT or GC. The screening involved abstract and title review and full-text review. Data were extracted for all articles meeting the inclusion criteria. RESULTS A total of 154 studies were included. Most studies that took place were conducted in the United States (71.4%), and most first authors (76.9%) were from the United States. GT was conducted in 73 (49.7%) studies. BRCA1/BRCA2 were the most commonly studied genes for germline mutations. GC was conducted in 49 studies (33.3%), and perspectives on GC were evaluated in 43 (29.3%). The use of racial/ethnic categories varied broadly, although African American was most common (40.1%). Racism was mentioned in three studies (2.0%). CONCLUSION There is a growing body of literature on GT/C for breast cancer in women of African heritage. Future studies on GT/C of African populations should consider increased clarity around racial/ethnic categorizations, continued community engagement, and intentional processes for informed consent.
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Affiliation(s)
- Yoshiko Iwai
- University of North Carolina School of Medicine, Chapel Hill, NC
| | | | | | - Jenny S. Morgan
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC
- Department of Clinical Medicine, Indiana University School of Medicine, Indianapolis, IN
- Department of Global Health, Indiana University School of Medicine, Indianapolis, IN
| | | | - Sarah T. Wright
- UNC Health Sciences Library, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Yuri Fedoriw
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Oluwadamilola T. Oladeru
- Department of Radiation Oncology, University of Florida, Gainesville, FL
- Department of Radiation Oncology, Mayo Clinic in Florida, Jacksonville, FL
| | | | - Mya L. Roberson
- Department of Health Policy, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC
| | | | | | - Shekinah N.C. Elmore
- Department of Radiation Oncology, University of North Carolina School of Medicine, Chapel Hill, NC
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White JA, Kaninjing ET, Adeniji KA, Jibrin P, Obafunwa JO, Ogo CN, Mohammed F, Popoola A, Fatiregun OA, Oluwole OP, Karanam B, Elhussin I, Ambs S, Tang W, Davis M, Polak P, Campbell MJ, Brignole KR, Rotimi SO, Dean-Colomb W, Odedina FT, Martin DN, Yates C. Whole-exome Sequencing of Nigerian Prostate Tumors from the Prostate Cancer Transatlantic Consortium (CaPTC) Reveals DNA Repair Genes Associated with African Ancestry. CANCER RESEARCH COMMUNICATIONS 2022; 2:1005-1016. [PMID: 36922933 PMCID: PMC10010347 DOI: 10.1158/2767-9764.crc-22-0136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 12/30/2022]
Abstract
In this study, we used whole-exome sequencing of a cohort of 45 advanced-stage, treatment-naïve Nigerian (NG) primary prostate cancer tumors and 11 unmatched nontumor tissues to compare genomic mutations with African American (AA) and European American (EA) The Cancer Genome Atlas (TCGA) prostate cancer. NG samples were collected from six sites in central and southwest Nigeria. After whole-exome sequencing, samples were processed using GATK best practices. BRCA1 (100%), BARD1 (45%), BRCA2 (27%), and PMS2(18%) had germline alterations in at least two NG nontumor samples. Across 111 germline variants, the AA cohort reflected a pattern [BRCA1 (68%), BARD1 (34%), BRCA2 (28%), and PMS2 (16%)] similar to NG samples. Of the most frequently mutated genes, BRCA1 showed a statistically (P ≤ 0.05) higher germline mutation frequency in men of African ancestry (MAA) and increasing variant frequency with increased African ancestry. Disaggregating gene-level mutation frequencies by variants revealed both ancestry-linked and NG-specific germline variant patterns. Driven by rs799917 (T>C), BRCA1 showed an increasing mutation frequency as African ancestry increased. BRCA2_rs11571831 was present only in MAA, and BRCA2_rs766173 was elevated in NG men. A total of 133 somatic variants were present in 26 prostate cancer-associated genes within the NG tumor cohort. BRCA2 (27%), APC (20%), ATM (20%), BRCA1 (13%), DNAJC6 (13%), EGFR (13%), MAD1L1 (13%), MLH1 (11%), and PMS2 (11%) showed mutation frequencies >10%. Compared with TCGA cohorts, NG tumors showed statistically significant elevated frequencies of BRCA2, APC, and BRCA1. The NG cohort variant pattern shared similarities (cosign similarities ≥0.734) with Catalogue of Somatic Mutations in Cancer signatures 5 and 6, and mutated genes showed significant (q < 0.001) gene ontology (GO) and functional enrichment in mismatch repair and non-homologous repair deficiency pathways. Here, we showed that mutations in DNA damage response genes were higher in NG prostate cancer samples and that a portion of those mutations correlate with African ancestry. Moreover, we identified variants of unknown significance that may contribute to population-specific routes of tumorigenesis and treatment. These results present the most comprehensive characterization of the NG prostate cancer exome to date and highlight the need to increase diversity of study populations. Significance MAA have higher rates of prostate cancer incidence and mortality, however, are severely underrepresented in genomic studies. This is the first study utilizing whole-exome sequencing in NG men to identify West African ancestry-linked variant patterns that impact DNA damage repair pathways.
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Affiliation(s)
- Jason A White
- Tuskegee University, Center for Cancer Research, Tuskegee, Alabama
| | | | | | | | - John O Obafunwa
- Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | | | | | | | | | | | - Isra Elhussin
- Tuskegee University, Center for Cancer Research, Tuskegee, Alabama
| | - Stefan Ambs
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Wei Tang
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Melissa Davis
- Department of Surgery, New York Presbyterian - Weill Cornell Medicine, New York, New York
| | | | - Moray J Campbell
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | | | | | - Windy Dean-Colomb
- Tuskegee University, Center for Cancer Research, Tuskegee, Alabama.,Piedmont Medical Oncology - Newnan, Newnan, Georgia
| | - Folake T Odedina
- Center for Health Equity and Community Engagement Research, Mayo Clinic, Jacksonville, Florida
| | - Damali N Martin
- Division of Cancer Control and Population Sciences, NCI, Rockville, Maryland
| | - Clayton Yates
- Tuskegee University, Center for Cancer Research, Tuskegee, Alabama
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5
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Akesson LS, Rius R, Brown NJ, Rosenbaum J, Donoghue S, Stormon M, Chai C, Bordador E, Guo Y, Hakonarson H, Compton AG, Thorburn DR, Amarasekera S, Marum J, Monaco A, Lee C, Chong B, Lunke S, Stark Z, Christodoulou J. Distinct diagnostic trajectories in NBAS-associated acute liver failure highlights the need for timely functional studies. JIMD Rep 2022; 63:240-249. [PMID: 35433172 PMCID: PMC8995841 DOI: 10.1002/jmd2.12280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 11/22/2022] Open
Abstract
Variants of uncertain significance (VUS) are commonly found following genomic sequencing, particularly in ethnically diverse populations that are underrepresented in large population databases. Functional characterization of VUS may assist in variant reclassification, however these studies are not readily available and often rely on research funding and good will. We present four individuals from three families at different stages of their diagnostic trajectory with recurrent acute liver failure (RALF) and biallelic NBAS variants, confirmed by either trio analysis or cDNA studies. Functional characterization was undertaken, measuring NBAS and p31 levels by Western blotting, demonstrating reduced NBAS levels in two of three families, and reduced p31 levels in all three families. These results provided functional characterization of the molecular impact of a missense VUS, allowing reclassification of the variant and molecular confirmation of NBAS-associated RALF. Importantly, p31 was decreased in all individuals, including an individual with two missense variants where NBAS protein levels were preserved. These results highlight the importance of access to timely functional studies after identification of putative variants, and the importance of considering a range of assays to validate variants whose pathogenicity is uncertain. We suggest that funding models for genomic sequencing should consider incorporating capabilities for adjunct RNA, protein, biochemical, and other specialized tests to increase the diagnostic yield which will lead to improved medical care, increased equity, and access to molecular diagnoses for all patients.
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Affiliation(s)
- Lauren S. Akesson
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- SA PathologySA HealthAdelaideSAAustralia
- School of Biomedicine, Faculty of Medicine, Dentistry and Health SciencesUniversity of AdelaideAdelaideAustraliaAustralia
| | - Rocio Rius
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Brain and Mitochondrial Research GroupMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
| | - Natasha J. Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - Jeremy Rosenbaum
- Department of GastroenterologyRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Sarah Donoghue
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of Metabolic MedicineRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Michael Stormon
- Department of GastroenterologyChildren's Hospital WestmeadSydneyNew South WalesAustralia
- Discipline of Child & Adolescent Health, Sydney Medical SchoolUniversity of SydneySydneyNew South WalesAustralia
| | - Charmaine Chai
- Department of GastroenterologyChildren's Hospital WestmeadSydneyNew South WalesAustralia
| | - Esmeralda Bordador
- Department of Metabolic MedicineRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Yiran Guo
- Center for Applied GenomicsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
- Center for Data‐Driven Discovery in BiomedicineChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Hakon Hakonarson
- Center for Applied GenomicsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
- Department of Pediatrics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Alison G. Compton
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Brain and Mitochondrial Research GroupMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
| | - David R. Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Brain and Mitochondrial Research GroupMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
| | - Sumudu Amarasekera
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Brain and Mitochondrial Research GroupMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
| | - Justine Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Alisha Monaco
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Crystle Lee
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PathologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Brain and Mitochondrial Research GroupMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
- Discipline of Child & Adolescent Health, Sydney Medical SchoolUniversity of SydneySydneyNew South WalesAustralia
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6
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Myer PA, Lee JK, Madison RW, Pradhan K, Newberg JY, Isasi CR, Klempner SJ, Frampton GM, Ross JS, Venstrom JM, Schrock AB, Das S, Augenlicht L, Verma A, Greally JM, Raj SM, Goel S, Ali SM. The Genomics of Colorectal Cancer in Populations with African and European Ancestry. Cancer Discov 2022; 12:1282-1293. [PMID: 35176763 DOI: 10.1158/2159-8290.cd-21-0813] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/28/2021] [Accepted: 02/11/2022] [Indexed: 11/16/2022]
Abstract
Blacks have a higher incidence of colorectal cancer (CRC) and worse survival rates when compared to Whites. Comprehensive genomic profiling was performed in 46,140 colorectal adenocarcinoma cases. Ancestry-informative markers identified 5,301 patients of African descent (AFR) and 33,770 patients of European descent (EUR). AFR were younger, had fewer MSI-H tumors, and had significantly more frequent alterations in KRAS, APC, and PIK3CA. AFR had increased frequency of KRAS mutations specifically KRAS G12D and KRAS G13. There were no differences in rates of actionable kinase driver alterations (HER2, MET, NTRK, ALK, ROS1, RET). In patients with young onset CRC (<50 years), AFR and EUR had similar frequency of MSI-H and TMB-H tumors, and strikingly different trends in APC mutations by age, as well as differences in MAPK pathway alterations. These findings inform treatment decisions, impact prognosis, and underscore the need for model systems representative of our diverse US population.
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Affiliation(s)
| | | | | | - Kith Pradhan
- Albert Einstein College of Medicine, bronx, United States
| | | | | | | | | | | | - Jeffrey M Venstrom
- University of California, San Francisco, San Francisco, CA, United States
| | | | - Sudipto Das
- Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Amit Verma
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York, United States
| | - John M Greally
- Albert Einstein College of Medicine, Bronx, United States
| | | | - Sanjay Goel
- Montefiore Medical Center, and Albert Einstein College of Medicine, Bronx, NY, United States
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7
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Galisa SLG, Jacob PL, de Farias AA, Lemes RB, Alves LU, Nóbrega JCL, Zatz M, Santos S, Weller M. Haplotypes of single cancer driver genes and their local ancestry in a highly admixed long-lived population of Northeast Brazil. Genet Mol Biol 2022; 45:e20210172. [PMID: 35112701 PMCID: PMC8811751 DOI: 10.1590/1678-4685-gmb-2021-0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/17/2021] [Indexed: 12/02/2022] Open
Abstract
Admixed populations have not been examined in detail in cancer genetic studies. Here, we inferred the local ancestry of cancer-associated single nucleotide polymorphisms (SNPs) and haplotypes of a highly admixed Brazilian population. SNP array was used to genotype 73 unrelated individuals aged 80-102 years. Local ancestry inference was performed by merging genotyped regions with phase three data from the 1000 Genomes Project Consortium using RFmix. The average ancestry tract length was 9.12-81.71 megabases. Strong linkage disequilibrium was detected in 48 haplotypes containing 35 SNPs in 10 cancer driver genes. All together, 19 risk and eight protective alleles were identified in 23 out of 48 haplotypes. Homozygous individuals were mainly of European ancestry, whereas heterozygotes had at least one Native American and one African ancestry tract. Native-American ancestry for homozygous individuals with risk alleles for HNF1B, CDH1, and BRCA1 was inferred for the first time. Results indicated that analysis of SNP polymorphism in the present admixed population has a high potential to identify new ancestry-associated alleles and haplotypes that modify cancer susceptibility differentially in distinct human populations. Future case-control studies with populations with a complex history of admixture could help elucidate ancestry-associated biological differences in cancer incidence and therapeutic outcomes.
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Affiliation(s)
- Steffany Larissa Galdino Galisa
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
| | - Priscila Lima Jacob
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
| | - Allysson Allan de Farias
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
- Universidade de São Paulo (USP), Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Renan Barbosa Lemes
- Universidade de São Paulo (USP), Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Leandro Ucela Alves
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
- Universidade de São Paulo (USP), Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Júlia Cristina Leite Nóbrega
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
| | - Mayana Zatz
- Universidade de São Paulo (USP), Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Silvana Santos
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
- Universidade Estadual da Paraíba (UEPB), Departamento de Biologia,
Campina Grande, PB, Brazil
| | - Mathias Weller
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em
Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB,
Brazil
- Universidade Estadual da Paraíba (UEPB), Departamento de Biologia,
Campina Grande, PB, Brazil
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8
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Herzog JS, Chavarri-Guerra Y, Castillo D, Abugattas J, Villarreal-Garza C, Sand S, Clague-Dehart J, Alvarez-Gómez RM, Wegman-Ostrosky T, Mohar A, Mora P, Del Toro-Valero A, Daneri-Navarro A, Rodriguez Y, Cruz-Correa M, Ashton-Prolla P, Alemar B, Mejia R, Gallardo L, Shaw R, Yang K, Cervantes A, Tsang K, Nehoray B, Barrera Saldana H, Neuhausen S, Weitzel JN. Genetic epidemiology of BRCA1- and BRCA2-associated cancer across Latin America. NPJ Breast Cancer 2021; 7:107. [PMID: 34413315 PMCID: PMC8377150 DOI: 10.1038/s41523-021-00317-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 07/26/2021] [Indexed: 12/11/2022] Open
Abstract
The prevalence and contribution of BRCA1/2 (BRCA) pathogenic variants (PVs) to the cancer burden in Latin America are not well understood. This study aims to address this disparity. BRCA analyses were performed on prospectively enrolled Latin American Clinical Cancer Genomics Community Research Network participants via a combination of methods: a Hispanic Mutation Panel (HISPANEL) on MassARRAY; semiconductor sequencing; and copy number variant (CNV) detection. BRCA PV probability was calculated using BRCAPRO. Among 1,627 participants (95.2% with cancer), we detected 236 (14.5%) BRCA PVs; 160 BRCA1 (31% CNVs); 76 BRCA2 PV frequency varied by country: 26% Brazil, 9% Colombia, 13% Peru, and 17% Mexico. Recurrent PVs (seen ≥3 times), some region-specific, represented 42.8% (101/236) of PVs. There was no ClinVar entry for 14% (17/125) of unique PVs, and 57% (111/196) of unique VUS. The area under the ROC curve for BRCAPRO was 0.76. In summary, we implemented a low-cost BRCA testing strategy and documented a significant burden of non-ClinVar reported BRCA PVs among Latin Americans. There are recurrent, population-specific PVs and CNVs, and we note that the BRCAPRO mutation probability model performs adequately. This study helps address the gap in our understanding of BRCA-associated cancer in Latin America.
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Affiliation(s)
| | - Yanin Chavarri-Guerra
- Instituto Nacional de Ciencias Medicas y Nutrición, Salvador Zubiran, Mexico City, Mexico
| | | | | | - Cynthia Villarreal-Garza
- Hospital Zambrano Hellion TecSalud, Tecnologico de Monterrey, Monterrey, Mexico
- Instituto Nacional de Cancerología, México City, México
| | | | - Jessica Clague-Dehart
- City of Hope, Duarte, CA, USA
- School of Community & Global Health, Claremont Graduate University, Claremont, CA, USA
| | | | | | - Alejandro Mohar
- Instituto Nacional de Cancerología, México City, México
- Instituto de Investigaciones Biomédicas, Mexico City, Mexico
| | - Pamela Mora
- Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Azucena Del Toro-Valero
- Instituto Jalisciense de Cancerología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, México City, México
| | - Adrian Daneri-Navarro
- Instituto Jalisciense de Cancerología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, México City, México
| | | | - Marcia Cruz-Correa
- University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico
| | - Patricia Ashton-Prolla
- Hospital de Clínicas de Porto Alegre and Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Bárbara Alemar
- Hospital de Clínicas de Porto Alegre and Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Roche Pharmaceutical, Basel, Switzerland
| | | | | | - Robin Shaw
- Instituto Nacional de Cancerología, México City, México
| | | | | | | | | | | | | | - Jeffrey N Weitzel
- Latin American School of Oncology (Escuela Latinoamericana de Oncología), Tuxla Gutiérrez, Chiapas, Mexico.
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9
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Zhu H, Welinsky S, Soper ER, Brown KL, Abul-Husn NS, Lucas AL. Genetic Variants in Patients With a Family History of Pancreatic Cancer: Impact of Multigene Panel Testing. Pancreas 2021; 50:602-606. [PMID: 33939675 DOI: 10.1097/mpa.0000000000001804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVES Up to 15% of pancreatic cancer is hereditary. We aim to study the prevalence of pathogenic germline variants (PGVs) in patients referred for genetic counseling with a family history (FH) of pancreatic cancer. METHODS We performed a retrospective single institution cohort study of individuals who underwent cancer genetic counseling with a FH of pancreatic cancer. RESULTS We identified 314 patients. Genetic testing was performed in 291 (92.7%) and 187 (59.6%) underwent expanded multigene panel testing. Fifty-four PGVs were found in 53 (16.9%) individuals; PGVs in BRCA1/2 (37%) were most common. Seventy-two variants of uncertain significance (VUS) were found in 58 (18.5%) individuals; VUS in ATM (16.7%) were the most common. Of the 112 (35.4%) with a first-degree family member with pancreatic cancer, 14 PGVs were identified in 14 (12.5%) individuals and 28 VUS were identified in 21 (18.8%) individuals. After genetic testing, 47 (15.0%) individuals met International Cancer of the Pancreas Screening criteria and 67 (21.3%) met American College of Gastroenterology criteria for pancreatic surveillance. CONCLUSIONS Genetic testing of individuals with a FH of pancreatic cancer represents an opportunity to identify individuals who may be candidates for pancreatic surveillance.
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Affiliation(s)
- Huili Zhu
- From the Department of Medicine, Icahn School of Medicine at Mount Sinai
| | - Sara Welinsky
- Division of Gastroenterology, Columbia University Medical Center
| | | | - Karen L Brown
- Division of Medical Genetics and Genomics, Department of Genetics and Genomic Sciences
| | | | - Aimee L Lucas
- Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY
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10
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Identification of Variants (rs11571707, rs144848, and rs11571769) in the BRCA2 Gene Associated with Hereditary Breast Cancer in Indigenous Populations of the Brazilian Amazon. Genes (Basel) 2021; 12:genes12020142. [PMID: 33499154 PMCID: PMC7911168 DOI: 10.3390/genes12020142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/09/2022] Open
Abstract
Estimates show that 5–10% of breast cancer cases are hereditary, caused by genetic variants in autosomal dominant genes; of these, 16% are due to germline mutations in the BRCA1 and BRCA2 genes. The comprehension of the mutation profile of these genes in the Brazilian population, particularly in Amazonian Amerindian groups, is scarce. We investigated fifteen polymorphisms in the BRCA1 and BRCA2 genes in Amazonian Amerindians and compared the results with the findings of global populations publicly available in the 1000 Genomes Project database. Our study shows that three variants (rs11571769, rs144848, and rs11571707) of the BRCA2 gene, commonly associated with hereditary breast cancer, had a significantly higher allele frequency in the Amazonian Amerindian individuals in comparison with the African, American, European, and Asian groups analyzed. These data outline the singular genetic profiles of the indigenous population from the Brazilian Amazon region. The knowledge about BRCA1 and BRCA2 variants is critical to establish public policies for hereditary breast cancer screening in Amerindian groups and populations admixed with them, such as the Brazilian population.
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11
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Lovejoy LA, Rummel SK, Turner CE, Shriver CD, Ellsworth RE. Frequency and spectrum of mutations across 94 cancer predisposition genes in African American women with invasive breast cancer. Fam Cancer 2020; 20:181-187. [PMID: 33083949 DOI: 10.1007/s10689-020-00213-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/14/2020] [Indexed: 11/28/2022]
Abstract
African American women are at increased risk of being diagnosed at a young age and/or with triple negative breast cancer, both factors which are included in current guidelines for identifying women who may benefit from genetic testing. Commercial breast cancer predisposition genetic panels, based largely on data derived from women of European ancestry, may not capture the full spectrum of cancer predisposition genes associated with breast cancer in African American women. Between 2001 and 2018, 488 unselected African American women with invasive breast cancer enrolled in the Clinical Breast Care Project. National Comprehensive Cancer Network (NCCN) Hereditary Cancer testing criteria version 1.2020 were applied to determine genetic risk. Targeted sequencing was performed using the TruSight Cancer panel and variants classified using the ClinVar database. Using NCCN criteria, 64.1% of African American women would be eligible for genetic testing. Fifty pathogenic or likely pathogenic mutations were detected in 19 genes with the highest frequencies in BRCA2 (29.4%) and BRCA1 (15.7%). Mutation frequencies in test-eligible and test-ineligible women were 13.1% and 3.5%, respectively. One-third of women harbored variants that could not be classified. While these data do not suggest a need to expand current commercial gene panels, NCCN criteria would fail to identify 12.5% of African American women with mutations in hereditary cancer predisposing genes.
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Affiliation(s)
- Leann A Lovejoy
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, 620 Seventh Street, Windber, PA, 15963, USA
| | - Seth K Rummel
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, 620 Seventh Street, Windber, PA, 15963, USA
| | - Clesson E Turner
- Murtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Department of Pediatrics, Uniformed Services University, Bethesda, MD, USA
| | - Craig D Shriver
- Murtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Department of Surgery, Uniformed Services Univesity, Bethesda, MD, USA
| | - Rachel E Ellsworth
- Murtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA. .,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
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12
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Gene panel screening for insight towards breast cancer susceptibility in different ethnicities. PLoS One 2020; 15:e0238295. [PMID: 32866190 PMCID: PMC7458311 DOI: 10.1371/journal.pone.0238295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 08/13/2020] [Indexed: 11/19/2022] Open
Abstract
African American breast cancer genetics is less understood compared to European American breast cancer susceptibility. Despite the many advantages of gene panel screening, studies investigating African American inherited breast cancer risk and comparing variant contributions between ethnicities are infrequent. Thus, 97 breast cancer-affected individuals of African and European descent from the Alabama Hereditary Cancer Cohort were screened using the research-based gene-panel, B.O.P. (Breast, Ovarian, and Prostate cancer). Upon sequencing and bioinformatic processing, rare coding variants in 14 cancer susceptibility genes were categorized according to the American College of Medical Genetics guidelines and compared between ethnicities. Overall, 107 different variants were identified, the majority of which were benign/likely benign. A pathogenic/likely pathogenic variant was detected in 8.6% and 6.5% of African American and European American cases, respectively, which was not statistically significant. However, African Americans were more likely to have at least one variant of uncertain significance (VUS; p-value 0.006); they also had significantly more VUSs in BRCA1/2 compared to European Americans (p-value 0.015). Additionally, 51.4% of African Americans and 32.3% of European Americans harbored multiple rare variants, and African Americans were more likely to have at least one VUS and one benign/likely benign variant (p-value 0.032), as well as multiple benign/likely benign variants (p-value 0.089). Moreover, of the 15 variants detected in multiple breast cancer cases, ATM c.2289T>C (p.F763L), a VUS, along with two likely benign variants, BRCA2 c.2926_2927delinsAT (p.S976I) and RAD51D c.251T>A (p.L84H), were determined to be associated with African American breast cancer risk when compared to ethnic-specific controls. Ultimately, B.O.P. screening provides essential insight towards the variant contributions in clinically relevant cancer susceptibility genes and differences between ethnicities, stressing the need for future research to elucidate inherited breast cancer risk.
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13
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Abul-Husn NS, Soper ER, Odgis JA, Cullina S, Bobo D, Moscati A, Rodriguez JE, Loos RJF, Cho JH, Belbin GM, Suckiel SA, Kenny EE. Exome sequencing reveals a high prevalence of BRCA1 and BRCA2 founder variants in a diverse population-based biobank. Genome Med 2019; 12:2. [PMID: 31892343 PMCID: PMC6938627 DOI: 10.1186/s13073-019-0691-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/13/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Pathogenic variants in BRCA1 and BRCA2 (BRCA1/2) lead to increased risk of breast, ovarian, and other cancers, but most variant-positive individuals in the general population are unaware of their risk, and little is known about prevalence in non-European populations. We investigated BRCA1/2 prevalence and impact in the electronic health record (EHR)-linked BioMe Biobank in New York City. METHODS Exome sequence data from 30,223 adult BioMe participants were evaluated for pathogenic variants in BRCA1/2. Prevalence estimates were made in population groups defined by genetic ancestry and self-report. EHR data were used to evaluate clinical characteristics of variant-positive individuals. RESULTS There were 218 (0.7%) individuals harboring expected pathogenic variants, resulting in an overall prevalence of 1 in 139. The highest prevalence was in individuals with Ashkenazi Jewish (AJ; 1 in 49), Filipino and other Southeast Asian (1 in 81), and non-AJ European (1 in 103) ancestry. Among 218 variant-positive individuals, 112 (51.4%) harbored known founder variants: 80 had AJ founder variants (BRCA1 c.5266dupC and c.68_69delAG, and BRCA2 c.5946delT), 8 had a Puerto Rican founder variant (BRCA2 c.3922G>T), and 24 had one of 19 other founder variants. Non-European populations were more likely to harbor BRCA1/2 variants that were not classified in ClinVar or that had uncertain or conflicting evidence for pathogenicity (uncertain/conflicting). Within mixed ancestry populations, such as Hispanic/Latinos with genetic ancestry from Africa, Europe, and the Americas, there was a strong correlation between the proportion of African genetic ancestry and the likelihood of harboring an uncertain/conflicting variant. Approximately 28% of variant-positive individuals had a personal history, and 45% had a personal or family history of BRCA1/2-associated cancers. Approximately 27% of variant-positive individuals had prior clinical genetic testing for BRCA1/2. However, individuals with AJ founder variants were twice as likely to have had a clinical test (39%) than those with other pathogenic variants (20%). CONCLUSIONS These findings deepen our knowledge about BRCA1/2 variants and associated cancer risk in diverse populations, indicate a gap in knowledge about potential cancer-related variants in non-European populations, and suggest that genomic screening in diverse patient populations may be an effective tool to identify at-risk individuals.
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Affiliation(s)
- Noura S Abul-Husn
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Emily R Soper
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jacqueline A Odgis
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sinead Cullina
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dean Bobo
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arden Moscati
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica E Rodriguez
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gillian M Belbin
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sabrina A Suckiel
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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14
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Adedokun B, Zheng Y, Ndom P, Gakwaya A, Makumbi T, Zhou AY, Yoshimatsu TF, Rodriguez A, Madduri RK, Foster IT, Sallam A, Olopade OI, Huo D. Prevalence of Inherited Mutations in Breast Cancer Predisposition Genes among Women in Uganda and Cameroon. Cancer Epidemiol Biomarkers Prev 2019; 29:359-367. [PMID: 31871109 DOI: 10.1158/1055-9965.epi-19-0506] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/23/2019] [Accepted: 12/09/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Sub-Saharan Africa (SSA) has a high proportion of premenopausal hormone receptor negative breast cancer. Previous studies reported a strikingly high prevalence of germline mutations in BRCA1 and BRCA2 among Nigerian patients with breast cancer. It is unknown if this exists in other SSA countries. METHODS Breast cancer cases, unselected for age at diagnosis and family history, were recruited from tertiary hospitals in Kampala, Uganda and Yaoundé, Cameroon. Controls were women without breast cancer recruited from the same hospitals and age-matched to cases. A multigene sequencing panel was used to test for germline mutations. RESULTS There were 196 cases and 185 controls with a mean age of 46.2 and 46.6 years for cases and controls, respectively. Among cases, 15.8% carried a pathogenic or likely pathogenic mutation in a breast cancer susceptibility gene: 5.6% in BRCA1, 5.6% in BRCA2, 1.5% in ATM, 1% in PALB2, 0.5% in BARD1, 0.5% in CDH1, and 0.5% in TP53. Among controls, 1.6% carried a mutation in one of these genes. Cases were 11-fold more likely to carry a mutation compared with controls (OR = 11.34; 95% confidence interval, 3.44-59.06; P < 0.001). The mean age of cases with BRCA1 mutations was 38.3 years compared with 46.7 years among other cases without such mutations (P = 0.03). CONCLUSIONS Our findings replicate the earlier report of a high proportion of mutations in BRCA1/2 among patients with symptomatic breast cancer in SSA. IMPACT Given the high burden of inherited breast cancer in SSA countries, genetic risk assessment could be integrated into national cancer control plans.
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Affiliation(s)
- Babatunde Adedokun
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Paul Ndom
- Hôpital Général Yaoundé, Yaoundé, Cameroon
| | | | | | | | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
| | | | - Ravi K Madduri
- Globus, The University of Chicago, Chicago, Illinois.,Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois
| | - Ian T Foster
- Globus, The University of Chicago, Chicago, Illinois.,Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois
| | - Aminah Sallam
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois.,Yale School of Medicine, New Haven, Connecticut
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois. .,Department of Public Health Sciences, The University of Chicago, Chicago, Illinois
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15
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Ross LF, Clayton EW. Ethical Issues in Newborn Sequencing Research: The Case Study of BabySeq. Pediatrics 2019; 144:peds.2019-1031. [PMID: 31719124 PMCID: PMC6889970 DOI: 10.1542/peds.2019-1031] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/05/2019] [Indexed: 12/12/2022] Open
Abstract
The BabySeq Project is a study funded by the National Institutes of Health and aimed at exploring the medical, behavioral, and economic impacts of integrating genomic sequencing into the care of both healthy newborns and newborns who are sick. Infants were randomly assigned to receive standard of care or standard of care plus sequencing. The protocol and consent specified that only childhood-onset conditions would be returned. When 1 child was found to carry a BRCA2 mutation despite a negative family history, the research team experienced moral distress about nondisclosure and sought institutional review board permission to disclose. The protocol was then modified to require participants to agree to receive results for adult-onset-only conditions as a precondition to study enrollment. The BabySeq team asserted that their new protocol was in the child's best interest because having one's parents alive and well provides both an individual child benefit and a "family benefit." We begin with a short description of BabySeq and the controversy regarding predictive genetic testing of children for adult-onset conditions. We then examine the ethical problems with (1) the revised BabySeq protocol and (2) the concept of family benefit as a justification for the return of adult-onset-only conditions. We reject family benefit as a moral reason to expand genomic sequencing of children beyond conditions that present in childhood. We also argue that researchers should design their pediatric studies to avoid, when possible, identifying adult-onset-only genetic variants and that parents should not be offered the return of this information if discovered unless relevant for the child's current or imminent health.
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Affiliation(s)
- Lainie Friedman Ross
- MacLean Center for Clinical Medical Ethics and Departments of Pediatrics, Medicine, and Surgery, The University of Chicago, Chicago, Illinois; and
| | - Ellen Wright Clayton
- Department of Pediatrics, Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, Tennessee
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16
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Meisel JL, O'Regan RM. Race, breast cancer, and prognosis: Where biology is queen? Cancer 2019; 125:3104-3106. [DOI: 10.1002/cncr.32294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/10/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Jane L. Meisel
- Department of Hematology and Medical Oncology Winship Cancer Institute, Emory University Atlanta Georgia
| | - Ruth M. O'Regan
- Department of Medicine and Carbone Cancer Center University of Wisconsin Madison Wisconsin
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17
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Samtani R, Saksena D. BRCA gene mutations: A population based review. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Kaufman M, Cruz A, Thompson J, Reddy S, Bansal N, Cohen JG, Wu Y, Vadgama J, Farias-Eisner R. A review of the effects of healthcare disparities on the experience and survival of ovarian cancer patients of different racial and ethnic backgrounds. ACTA ACUST UNITED AC 2019; 5. [PMID: 31236478 PMCID: PMC6590085 DOI: 10.20517/2394-4722.2018.25] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ovarian cancer (OC) is a serious condition that often presents at advanced stages and has high mortality rates, with the current mode of early-stage screening lacking sensitivity and specificity. OC often presents asymptomatically, which renders early diagnosis difficult. Furthermore, many patients lack significant risk factors or family history of the disease. Five-year survival rates differ between patients with OC among racial, ethnic, and social groups as a result of different social barriers. This review article aims to present the currently existing data regarding health care disparities among OC patients of different ethnic, demographic, and socioeconomic backgrounds, and what next steps should be taken to better understand and eventually eliminate these potentially devastating health care disparities. Increasing data support the notion that a combination of genomic, socioeconomic status, social factors, and cultural differences lead to differential treatments and therefore health care disparities. While genomic and biological factors are important, language barriers, geographic and travel barriers, differences in comorbidity likelihood between populations, and different treatment plans seem to have a greater impact on 5-year survival rates of patients from diverse backgrounds. Language barriers limit a shared-decision model of care. Transportation limitations and geographic differences can lead to limited follow-up and insufficient care in resource and equipment restrictive settings. Patients with these barriers also tend to have a higher incidence of comorbidities that raise the mortality rate of OC. Further research needs to explore effective solutions to bridge health care disparities and understand why they occur.
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Affiliation(s)
- Matthew Kaufman
- Obstetrics and Gynecology, University of California, Los Angeles, CA 90024, USA
| | - Ana Cruz
- Obstetrics and Gynecology, University of California, Los Angeles, CA 90024, USA
| | - Janese Thompson
- School of Medicine, Meharry Medical College, Nashville, TN 37208, USA
| | - Srinivasa Reddy
- Obstetrics and Gynecology, University of California, Los Angeles, CA 90024, USA
| | - Nisha Bansal
- Obstetrics and Gynecology, University of California, Los Angeles, CA 90024, USA
| | - Joshua G Cohen
- Obstetrics and Gynecology, University of California, Los Angeles, CA 90024, USA
| | - Yanyuan Wu
- Internal Medicine, Charles Drew University, Los Angeles, CA 90059, USA
| | - Jay Vadgama
- Internal Medicine, Charles Drew University, Los Angeles, CA 90059, USA
| | - Robin Farias-Eisner
- Obstetrics and Gynecology, University of California, Los Angeles, CA 90024, USA
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19
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Non-Platinum Metal Complexes as Potential Anti-Triple Negative Breast Cancer Agents. CRYSTALS 2018. [DOI: 10.3390/cryst8100369] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Breast cancer (BC) is the most common cancer in women worldwide, with a mortality rate that has been forecasted to rise in the next decade. This is especially worrying for people with triple-negative BC (TNBC), because of its unresponsiveness to current therapies. Different drugs to treat TNBC have been assessed, and, although platinum chemotherapy drugs seem to offer some hope, their drawbacks have motivated extensive investigations into alternative metal-based BC therapies. This paper aims to: (i) describe the preliminary in vitro and in vivo anticancer properties of non-platinum metal-based complexes (NPMBC) against TNBC; and (ii) analyze the likely molecular targets involved in their anticancer activity.
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20
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McDonald JT, Kritharis A, Beheshti A, Pilichowska M, Burgess K, Ricks-Santi L, McNiel E, London CA, Ravi D, Evens AM. Comparative oncology DNA sequencing of canine T cell lymphoma via human hotspot panel. Oncotarget 2018; 9:22693-22702. [PMID: 29854308 PMCID: PMC5978258 DOI: 10.18632/oncotarget.25209] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/08/2018] [Indexed: 12/31/2022] Open
Abstract
T-cell lymphoma (TCL) is an uncommon and aggressive form of human cancer. Lymphoma is the most common hematopoietic tumor in canines (companion animals), with TCL representing approximately 30% of diagnoses. Collectively, the canine is an appealing model for cancer research given the spontaneous occurrence of cancer, intact immune system, and phytogenetic proximity to humans. We sought to establish mutational congruence of the canine with known human TCL mutations in order to identify potential actionable oncogenic pathways. Following pathologic confirmation, DNA was sequenced in 16 canine TCL (cTCL) cases using a custom Human Cancer Hotspot Panel of 68 genes commonly mutated in human TCL. Sequencing identified 4,527,638 total reads with average length of 229 bases containing 346 unique variants and 1,474 total variants; each sample had an average of 92 variants. Among these, there were 258 germline and 32 somatic variants. Among the 32 somatic variants there were 8 missense variants, 1 splice junction variant and the remaining were intron or synonymous variants. A frequency of 4 somatic mutations per sample were noted with >7 mutations detected in MET, KDR, STK11 and BRAF. Expression of these associated proteins were also detected via Western blot analyses. In addition, Sanger sequencing confirmed three variants of high quality (MYC, MET, and TP53 missense mutation). Taken together, the mutational spectrum and protein analyses showed mutations in signaling pathways similar to human TCL and also identified novel mutations that may serve as drug targets as well as potential biomarkers.
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Affiliation(s)
| | - Athena Kritharis
- Division of Blood Disorders, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | | | | | - Kristine Burgess
- Cummings School of Veterinary Medicine, Tufts University, Boston, MA, USA
| | | | - Elizabeth McNiel
- Cummings School of Veterinary Medicine, Tufts University, Boston, MA, USA
| | - Cheryl A London
- Cummings School of Veterinary Medicine, Tufts University, Boston, MA, USA
| | - Dashnamoorthy Ravi
- Division of Blood Disorders, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Andrew M Evens
- Division of Blood Disorders, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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Jones T, McCarthy AM, Kim Y, Armstrong K. Predictors of BRCA1/2 genetic testing among Black women with breast cancer: a population-based study. Cancer Med 2017. [PMID: 28627138 PMCID: PMC5504315 DOI: 10.1002/cam4.1120] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Evidence shows that Black women diagnosed with breast cancer are substantially less likely to undergo BRCA testing and other multipanel genetic testing compared to White women, despite having a higher incidence of early-age onset breast cancer and triple-negative breast cancer (TNBC). Our study identifies predictors of BRCA testing among Black women treated for breast cancer and examines differences between BRCA testers and nontesters. We conducted an analysis of 945 Black women ages 18-64 diagnosed with localized or regional-stage invasive breast cancer in Pennsylvania and Florida between 2007 and 2009. Logistic regression was used to identify predictors of BRCA 1/2 testing. Few (27%) (n = 252) of the participants reported having BRCA testing. In the multivariate analysis, we found that perceived benefits of BRCA testing (predisposing factor) ([OR], 1.16; 95% CI: 1.11-1.21; P < 0.001), income (enabling factor) ([OR], 2.10; 95% CI: 1.16-3.80; p = 0.014), and BRCA mutation risk category (need factor) ([OR], 3.78; 95% CI: 2.31-6.19; P < 0.001) predicted BRCA testing. These results suggest that interventions to reduce disparities in BRCA testing should focus on identifying patients with high risk of mutation, increasing patient understanding of the benefits of BRCA testing, and removing financial and other administrative barriers to genetic testing.
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Affiliation(s)
- Tarsha Jones
- Florida Atlantic University, Boca Raton, Florida.,Dana Farber Cancer Institute, Phyllis F. Cantor Center for Research in Nursing and Patient Care Services, Boston, Massachusetts
| | - Anne Marie McCarthy
- Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Younji Kim
- Massachusetts General Hospital, Boston, Massachusetts
| | - Katrina Armstrong
- Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
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