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Liebenberg L, L'Abbé EN, Stull KE. Exploring cranial macromorphoscopic variation and classification accuracy in a South African sample. Int J Legal Med 2024:10.1007/s00414-024-03230-2. [PMID: 38622313 DOI: 10.1007/s00414-024-03230-2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
To date South African forensic anthropologists are only able to successfully apply a metric approach to estimate population affinity when constructing a biological profile from skeletal remains. While a non-metric, or macromorphoscopic approach exists, limited research has been conducted to explore its use in a South African population. This study aimed to explore 17 cranial macromorphoscopic traits to develop improved methodology for the estimation of population affinity among black, white and coloured South Africans and for the method to be compliant with standards of best practice. The trait frequency distributions revealed substantial group variation and overlap, and not a single trait can be considered characteristic of any one population group. Kruskal-Wallis and Dunn's tests demonstrated significant population differences for 13 of the 17 traits. Random forest modelling was used to develop classification models to assess the reliability and accuracy of the traits in identifying population affinity. Overall, the model including all traits obtained a classification accuracy of 79% when assessing population affinity, which is comparable to current craniometric methods. The variable importance indicates that all the traits contributed some information to the model, with the inferior nasal margin, nasal bone contour, and nasal aperture shape ranked the most useful for classification. Thus, this study validates the use of macromorphoscopic traits in a South African sample, and the population-specific data from this study can potentially be incorporated into forensic casework and skeletal analyses in South Africa to improve population affinity estimates.
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Affiliation(s)
- Leandi Liebenberg
- Department of Anatomy, University of Pretoria, Private Bag x323, Arcadia, 0007, South Africa.
- Forensic Anthropology Research Centre, University of Pretoria, Arcadia, South Africa.
| | - Ericka N L'Abbé
- Department of Anatomy, University of Pretoria, Private Bag x323, Arcadia, 0007, South Africa
| | - Kyra E Stull
- Department of Anatomy, University of Pretoria, Private Bag x323, Arcadia, 0007, South Africa
- Department of Anthropology, University of Nevada, Reno, USA
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2
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Bourassa KJ, Halverson TF, Garrett ME, Hair L, Dennis M, Ashley-Koch AE, Beckham JC, Kimbrel NA. Demographic characteristics and epigenetic biological aging among post-9/11 veterans: Associations of DunedinPACE with sex, race, and age. Psychiatry Res 2024; 336:115908. [PMID: 38626626 DOI: 10.1016/j.psychres.2024.115908] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/01/2024] [Accepted: 04/06/2024] [Indexed: 04/18/2024]
Abstract
Measures of epigenetic aging derived from DNA methylation (DNAm) have enabled the assessment of biological aging in new populations and cohorts. In the present study, we used an epigenetic measure of aging, DunedinPACE, to examine rates of aging across demographic groups in a sample of 2,309 United States military veterans from the VISN 6 MIRECC's Post-Deployment Mental Health Study. As assessed by DunedinPACE, female veterans were aging faster than male veterans (β = 0.39, 95 % CI [0.29, 0.48], p < .001), non-Hispanic Black veterans were aging faster than non-Hispanic White veterans (β = 0.58, 95 % CI [0.50, 0.66], p < .001), and older veterans were biologically aging faster than younger veterans (β = 0.21, 95 % CI [0.18, 0.25], p < .001). In secondary analyses, these differences in rates of aging were not explained by a variety of biopsychosocial covariates. In addition, the percentage of European genetic admixture in non-Hispanic Black veterans was not associated with DunedinPACE. Our findings suggest that female and non-Hispanic Black veterans are at greater risk of accelerated aging among post-9/11 veterans. Interventions that slow aging might provide relatively greater benefit among veterans comprising these at-risk groups.
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Affiliation(s)
- Kyle J Bourassa
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System; Geriatric Research, Education, and Clinical Center, Durham VA Health Care System; Center for the Study of Aging and Human Development, Duke University Medical Center.
| | - Tate F Halverson
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System
| | | | - Lauren Hair
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine
| | - Michelle Dennis
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine
| | | | - Jean C Beckham
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine
| | - Nathan A Kimbrel
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine; VA Health Services Research and Development Center of Innovation to Accelerate Discovery and Practice Transformation, Durham VA Health Care System
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3
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Saenz Hinojosa S, Adrian Jinam T, Hosomichi K, Romero VI. HLA allelic diversity in the Waorani population of Ecuador: Its significance to their ancestry and migration. Hum Immunol 2024:110771. [PMID: 38443236 DOI: 10.1016/j.humimm.2024.110771] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/09/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
The Waorani, an isolated indigenous tribe in Ecuador, have long been characterized by limited genetic diversity, with few studies delving into their genetic background. Human Leukocyte Antigen (HLA) genes which are located in the human major histocompatibility complex (MHC) provides valuable insights into population evolution due to its highly polymorphic nature. However, little is known about the HLA diversity and ancestry of the Waorani population. In this study, we sequenced eight HLA genes using Next Generation Sequencing (NGS) from 134 Waorani individuals and obtained up to four-field HLA allele resolution. Cluster and phylogenetic analysis show that the Waorani are genetically distant from other Ecuador populations, but instead show genetic affinities with the Puyanawa and Terena tribes from Brazil, as well as the Mixe tribe from Mexico. The identification of alleles common within the Waorani population, previously linked to specific health conditions, notably paves the way for future association analyses. This extensive study, employing Next-Generation Sequencing (NGS) technology, significantly enriches the sparse and segmented understanding of HLA diversity in the South American region. Our findings enhance the global comprehension of human genetic diversity and underscore the value of studying indigenous populations. Such research is vital for deepening our insights into human migration patterns and evolutionary processes.
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Affiliation(s)
| | - Timothy Adrian Jinam
- Department of Para-Clinical Sciences, Faculty of Medicine & Health Sciences, University Malaysia Sarawak, Malaysia
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Vanessa I Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador.
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Rollin FG, Mayne G, Cerdena J. Concerns about an ancestry-focused explanation for racialized health disparities. J Reprod Immunol 2024; 162:104194. [PMID: 38241849 DOI: 10.1016/j.jri.2024.104194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Affiliation(s)
- Francois G Rollin
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
| | - Gabriella Mayne
- Department of Health & Behavioral Sciences, University of Colorado, Denver, CO, USA
| | - Jessica Cerdena
- Department of Family Medicine, Middlesex Health, Middletown, CT, USA
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Abualhija D, Gómez García-Donas J, Shepherd S, McGregor S, Franco A, Manica S. Biological profiling using the human mandible. J Oral Biosci 2024; 66:5-12. [PMID: 38036053 DOI: 10.1016/j.job.2023.11.006] [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: 09/20/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND In the absence of soft tissue, skeletal remains are analyzed to identify the deceased. This assessment involves establishing the biological profile that aids medicolegal investigations and fulfils the right of the dead to be identified. Since the mandible is the strongest bone in the skull and easily identifiable, even when fragmented, this study aimed to systematically review its value in constructing the biological profile in the published literature. We searched PubMed, ScienceDirect, Scopus, and Latin American and Caribbean Health Sciences Literature and collected cross-sectional studies published in English before 2021. A risk of bias assessment was completed based on Joanna Briggs Institute's critical appraisal tools. The data are presented descriptively and were analyzed using Microsoft Office Excel 365. HIGHLIGHT Of the 104 eligible articles, 94 examined the sexual dimorphism of the mandible, while 25 attempted to estimate age. Ancestry and stature were the least explored biological characteristics (five and one articles, respectively). A metric analysis was the most common approach (n = 80), followed by morphological analysis and combined morphologic and metric techniques (n = 18 and n = 6, respectively). The results showed no statistically significant correlation between an individual's mandible and stature. Orthopantomogram radiography continues to be the most common radiographic technique for assessing the mandible. CONCLUSION The mandible is reliable when used for sex estimation; however, caution should be exercised in relying solely on it for morphological assessments. This review provides guidance on estimating age, sex, and ancestry directly from mandibular specimens or radiographs.
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Affiliation(s)
- Doha Abualhija
- Centre for Forensic and Legal Medicine and Dentistry, DD1 4HN, University of Dundee, UK.
| | | | - Simon Shepherd
- Department of Oral Surgery and Medicine, DD1 4HN, University of Dundee, UK
| | | | - Ademir Franco
- Centre for Forensic and Legal Medicine and Dentistry, DD1 4HN, University of Dundee, UK
| | - Scheila Manica
- Centre for Forensic and Legal Medicine and Dentistry, DD1 4HN, University of Dundee, UK
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Salinas-Pineda L, Berumen J, Lopez Armenta M, Leon Campos C, Rangel-Villalobos H, Juarez-Torres E, Huerta-Pacheco NS, Aguilar-Velazquez JA, Villavicencio-Queijeiro A, Guardado-Estrada M. Forensic parameters and population structure based on 21 autosomal STRs with the investigator 24plex QS in mestizos from the Mexico City population. Leg Med (Tokyo) 2024; 66:102344. [PMID: 37977100 DOI: 10.1016/j.legalmed.2023.102344] [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: 07/31/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
Allele frequencies and forensic parameters for 21 STR autosomal markers (CSF1PO, D10S1248, D12S391, D13S317,D16S539, D18S51, D19S433, D1S1656,D21S11, D22S1045, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, FGA, SE33, TH01, TPOX and vWA) were reported in 289 unrelated individuals from Mexico City, Mexico. In addition, an interpopulation analysis was performed including other world populations. In brief, the established population database of 21 autosomal STR markers in the present work is adequate for human identification purposes.
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Affiliation(s)
- Lizette Salinas-Pineda
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Jaime Berumen
- Departamento de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Mauro Lopez Armenta
- Laboratorio de Genética, Instituto de Servicios Periciales y Ciencias Forenses del Poder Judicial de la CDMX, Ciudad de México, Mexico
| | - Carolina Leon Campos
- Laboratorio de Genética, Instituto de Servicios Periciales y Ciencias Forenses del Poder Judicial de la CDMX, Ciudad de México, Mexico
| | - Hector Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Mexico
| | | | - N Sofia Huerta-Pacheco
- CONACHYT-Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Jose Alonso Aguilar-Velazquez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Mexico; Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Mexico
| | - Alexa Villavicencio-Queijeiro
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Mariano Guardado-Estrada
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
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Bataba E, Babcock K, Isensee KA, Eldhose B, Kohaar I, Chesnut GT, Dobi A. Germline Mutations and Ancestry in Prostate Cancer. Curr Oncol Rep 2024; 26:175-180. [PMID: 38265515 PMCID: PMC10891190 DOI: 10.1007/s11912-024-01493-x] [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] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
PURPOSE OF REVIEW Prostate cancer is the most frequently diagnosed non-cutaneous malignancy of men in the USA; notably, the incidence is higher among men of African, followed by European and Asian ancestry. Germline mutations and, in particular, mutations in DNA damage repair genes (DDRGs) have been implicated in the pathogenesis of prostate cancer. This review intends to discuss the implication of ancestry on prostate cancer, specifically in regard to lack of diversity in genomic and genetic databases and the ability of providers to properly counsel patients on the significance of cancer genetic results. RECENT FINDINGS Ancestral differences in prostate cancer-associated DDRG germline mutations are increasingly recognized. Guidelines for treatment by the National Comprehensive Cancer Network® (NCCN®) support germline testing in certain patients, and a myriad of genetic testing panels for DDRG mutations are now available in clinical practice. However, the consensus among providers on what genes and mutations to include in the genetic tests has evolved from experience from men of European ancestry (EA). Gaps in ancestry-informed clinical practice exist in genetic risk assessment, implementation of screening, counseling, guiding recommendations, treatment, and clinical trial enrollment. The lack of diversity in tumor genomic and genetic databases may hinder ancestry-specific disease-predisposing alterations from being discovered and targeted in prostate cancer and, therefore, impede the ability of providers to accurately counsel patients on the significance of cancer genetic test results.
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Affiliation(s)
- Eudoxie Bataba
- Walter Reed National Military Medical Center, Bethesda, MD, 20889, USA
| | - Kevin Babcock
- Walter Reed National Military Medical Center, Bethesda, MD, 20889, USA
| | - Kathryn A Isensee
- School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Binil Eldhose
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery at the Uniformed Services University of the Health Sciences, 6720A Rockledge Drive Suite 300, Bethesda, MD, 20817, USA
- Henry Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, 20817, USA
| | - Indu Kohaar
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery at the Uniformed Services University of the Health Sciences, 6720A Rockledge Drive Suite 300, Bethesda, MD, 20817, USA
- Henry Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, 20817, USA
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA
| | - Gregory T Chesnut
- Walter Reed National Military Medical Center, Bethesda, MD, 20889, USA
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery at the Uniformed Services University of the Health Sciences, 6720A Rockledge Drive Suite 300, Bethesda, MD, 20817, USA
| | - Albert Dobi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery at the Uniformed Services University of the Health Sciences, 6720A Rockledge Drive Suite 300, Bethesda, MD, 20817, USA.
- Henry Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, 20817, USA.
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Silva S, Fatumo S, Nitsch D. Mendelian randomization studies on coronary artery disease: a systematic review and meta-analysis. Syst Rev 2024; 13:29. [PMID: 38225600 PMCID: PMC10790478 DOI: 10.1186/s13643-023-02442-8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/20/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Coronary artery disease (CAD) remains one of the leading causes of mortality worldwide. We aimed to summarize what is currently known with regard to causal modifiable risk factors associated with CAD in populations of diverse ancestries through conducting a systematic review and meta-analysis of Mendelian randomization (MR) studies on CAD. METHODS The databases Embase, Medline, Cochrane Library and Web of Science were searched on the 19th and 20th of December 2022 for MR studies with CAD as a primary outcome; keywords of the search strategy included "coronary artery disease" and "mendelian randomization". Studies were included if they were published in the English language, included only human participants, employed Mendelian randomization as the primary methodology and studied CAD as the outcome of interest. The exclusion criteria resulted in the removal of studies that did not align with the predefined inclusion criteria, as well as studies which were systematic reviews themselves, and used the same exposure and outcome source as another study. An ancestry-specific meta-analysis was subsequently conducted on studies which investigated either body mass index, lipid traits, blood pressure or type 2 diabetes as an exposure variable. Assessment of publication bias and sensitivity analyses was conducted for risk of bias assessment in the included studies. RESULTS A total of 1781 studies were identified through the database searches after de-duplication was performed, with 47 studies included in the quantitative synthesis after eligibility screening. Approximately 80% of all included study participants for MR studies on CAD were of European descent irrespective of the exposure of interest, while no study included individuals of African ancestry. We found no evidence of differences in terms of direction of causation between ancestry groups; however, the strength of the respective relationships between each exposure and CAD were different, with this finding most evident when blood pressure was the exposure of interest. CONCLUSIONS Findings from this review suggest that patterns regarding the causational relationship between modifiable risk factors and CAD do not differ in terms of direction when compared across diverse ancestry populations. Differences in the observed strengths of the respective relationships however are indicative of the value of increasing representation in non-European populations, as novel genetic pathways or functional SNPs relating to CAD may be uncovered through a more global analysis. SYSTEMATIC REVIEW REGISTRATION The protocol for this systematic review was registered to the International Prospective Register of Systematic Reviews (PROSPERO) and is publicly available online (CRD42021272726).
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Affiliation(s)
- Sarah Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda.
| | - Segun Fatumo
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda.
| | - Dorothea Nitsch
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
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Kondo J, Tempaku PF, D'Almeida V, Kakazu VA, Andersen ML, Tufik S, Poyares D. Sleep patterns according to genetically determined ethnicity in the population of São Paulo, Brazil. Sleep Med 2024; 113:242-248. [PMID: 38064796 DOI: 10.1016/j.sleep.2023.11.036] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 01/07/2024]
Abstract
Sleep is a behavior expressed differently for each individual. However, studies have shown that some ethnic groups express common sleep patterns, which can be observed in different ethnic groups. Previous studies have shown the existence of sleep disparities in populations of different ethnicities. Most of these studies have considered self-reported ethnicity and assessed sleep subjectively. Therefore, the aim of this study was to evaluate sleep disparities in different ethnic groups based on an analysis of genetic ancestry and the use of objective sleep evaluation. To do this, we used data from the São Paulo Epidemiologic Sleep Study (EPISONO), which was undertaken in Brazil, a country that is known for its ethnic/racial diversity. All individuals completed a series of questionnaires, underwent full polysomnography and had their blood collected for DNA extraction. After genotyping and identifying samples with high-quality DNA suitable for genetic analysis, 31 ancestry-informative markers (AIMs) were selected. These markers exhibited substantial allelic frequency differences, enabling the characterization of the three primary founding populations of modern Brazil - Europeans, West-Africans, and Native Americans. Through this analysis, the genetic contribution of each of these ancestral groups was identified in respect of each participant. Based on this, a latent class cluster analysis (LCCA) was performed to define the three clusters that best classified the sample according to ethnic group: African (n = 255), Caucasian (n = 668) and Native American (n = 83). Applying the adjusted model for the confounding variables (age, socio-economic class and sex), statistically significant differences in sleep variables between ethnicities were found. Africans had higher sleep latency compared to the other groups (β = 4.46, CI = 1.18 to 7.74 and β = 7.83, CI = 3.50 to 12.15), while Caucasians had longer total sleep time (β = -16.47, CI = -29.94 to -2.99) and better sleep efficiency (β = -2.19, CI = -4.35 to -0.02) compared to Africans. Regarding the respiratory arousals index (β = -1.11, IC = -2.07 to -0.16) and periodic leg movements index (β = -7.48, CI = -12.08 to -2.88), both were higher among Caucasians compared to Africans. We were able to conclude that genetic ancestry might modulate sleep structure and the occurrence of sleep disorders.
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Affiliation(s)
- Julia Kondo
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Priscila F Tempaku
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Vânia D'Almeida
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Viviane A Kakazu
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Monica L Andersen
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Sergio Tufik
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Dalva Poyares
- Departamento de Psicobiologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil.
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Parodis I, Lanata C, Nikolopoulos D, Blazer A, Yazdany J. Reframing health disparities in SLE: A critical reassessment of racial and ethnic differences in lupus disease outcomes. Best Pract Res Clin Rheumatol 2023:101894. [PMID: 38057256 DOI: 10.1016/j.berh.2023.101894] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Health disparities in the prevalence and outcomes of systemic lupus erythematosus (SLE) are well documented across racial and ethnic groups. Similar to other chronic diseases, differences in disease severity among individuals with SLE are likely influenced by both genetic predisposition and multiple social determinants of health. However, research in SLE that jointly examines the genetic and environmental contributions to the disease course is limited, resulting in an incomplete understanding of the biologic and social mechanisms that underly health disparities. While research on health disparities can reveal inequalities and inform resource allocation to improve outcomes, research that relies on racial and ethnic categories to describe diverse groups of people can pose challenges. Additionally, results from research comparing outcomes across socially constructed groups without considering other contributing factors can be misleading. We herein comprehensively examine existing literature on health disparities in SLE, including both clinical studies that examine the relationship between self-reported race and ethnicity and disease outcomes and studies that explore the relationships between genomics and lupus outcomes. Having surveyed this body of research, we propose a framework for research examining health disparities in SLE, including ways to mitigate bias in future studies.
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Affiliation(s)
- Ioannis Parodis
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Department of Gastroenterology, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden; Department of Rheumatology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| | - Cristina Lanata
- Genomics of Autoimmune Rheumatic Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dionysis Nikolopoulos
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Department of Gastroenterology, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Ashira Blazer
- Division of Rheumatology, Department of Medicine, Hospital for Special, Surgery, New York, NY, USA
| | - Jinoos Yazdany
- Division of Rheumatology, University of California, San Francisco, USA
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11
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Gislason H. SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands. BMC Genomics 2023; 24:707. [PMID: 37996805 PMCID: PMC10666429 DOI: 10.1186/s12864-023-09763-x] [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: 03/06/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The population of the Faroe Islands is an isolated population but very little is known about it from whole genome sequencing. The population of about 50000 people has a high incidence of rare diseases e.g., 1:300 for Primary Carnitine Deficiency. A screening programme was implemented, and eleven persons were also whole genome sequenced at x37 coverage for diagnostic purposes of those cases that were not affected by the known mutations. The purpose of our study is to utilize the high coverage data to explore the genomic variation and the ancestral history of the population. We study the SNP heterozygosity, the pairwise relatedness from kinship, the inbreeding from runs of homozygosity ROH, and we find the minor allele frequency distribution. We estimate the population ancestry and the timing of the founding event by using the whole genomes from eight consenting individuals. RESULTS We find the number of SNPs and the heterozygosity for the eight individual samples, and for merged samples, for which we also study the relatedness. We find close relatedness between the supposedly unrelated individuals. From ROH, we interpret the high relatedness as an ancient property of the isolated population. A bottleneck event is estimated starting between years [Formula: see text] with a maximum consanguineous population in year [Formula: see text] and similarly consanguineous between years [Formula: see text]. The ancestry analysis shows the population descends from founders of [Formula: see text] European and [Formula: see text] Admixed American ancestry. A distinct clustering near the central European and British populations of the 1000 Genome Project is likely the result of the population isolation and genetic drift. The minor allele frequency distribution suggests many rare variants. CONCLUSIONS The ancestry is mainly European while the inbreeding is higher compared to European populations and population isolates. The Faroese population has inbreeding more like ancient Europeans. We discovered a bottlenecked and consanguineous population event and estimated it starting in the 1st-4th century as compared to the oldest archaeological findings from the 4th-6th century.
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Affiliation(s)
- Hannes Gislason
- Faculty of Science and Technology, University of the Faroe Islands, Tórshavn, Faroe Islands.
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12
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Jain PR, Burch M, Martinez M, Mir P, Fichna JP, Zekanowski C, Rizzo R, Tümer Z, Barta C, Yannaki E, Stamatoyannopoulos J, Drineas P, Paschou P. Can polygenic risk scores help explain disease prevalence differences around the world? A worldwide investigation. BMC Genom Data 2023; 24:70. [PMID: 37986041 PMCID: PMC10662565 DOI: 10.1186/s12863-023-01168-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/20/2023] [Indexed: 11/22/2023] Open
Abstract
Complex disorders are caused by a combination of genetic, environmental and lifestyle factors, and their prevalence can vary greatly across different populations. The extent to which genetic risk, as identified by Genome Wide Association Study (GWAS), correlates to disease prevalence in different populations has not been investigated systematically. Here, we studied 14 different complex disorders and explored whether polygenic risk scores (PRS) based on current GWAS correlate to disease prevalence within Europe and around the world. A clear variation in GWAS-based genetic risk was observed based on ancestry and we identified populations that have a higher genetic liability for developing certain disorders. We found that for four out of the 14 studied disorders, PRS significantly correlates to disease prevalence within Europe. We also found significant correlations between worldwide disease prevalence and PRS for eight of the studied disorders with Multiple Sclerosis genetic risk having the highest correlation to disease prevalence. Based on current GWAS results, the across population differences in genetic risk for certain disorders can potentially be used to understand differences in disease prevalence and identify populations with the highest genetic liability. The study highlights both the limitations of PRS based on current GWAS but also the fact that in some cases, PRS may already have high predictive power. This could be due to the genetic architecture of specific disorders or increased GWAS power in some cases.
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Affiliation(s)
- Pritesh R Jain
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Myson Burch
- Department of Computer Sciences, Purdue University, West Lafayette, IN, USA
| | - Melanie Martinez
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Pablo Mir
- Unidad de Trastornos del Movimiento, Instituto de Biomedicina de Sevilla (IBiS). Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Jakub P Fichna
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Neurogenetics and Functional Genomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Cezary Zekanowski
- Department of Neurogenetics and Functional Genomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Renata Rizzo
- Child and Adolescent Neurology and Psychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Zeynep Tümer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Csaba Barta
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Evangelia Yannaki
- Hematology Department- Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, Thessaloniki, Greece
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Medicine, Division of Oncology, University of Washington, Seattle, WA, USA
| | - Petros Drineas
- Department of Computer Sciences, Purdue University, West Lafayette, IN, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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13
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Peng XP, Al-Ddafari MS, Caballero-Oteyza A, El Mezouar C, Mrovecova P, Dib SE, Massen Z, Smahi MCE, Faiza A, Hassaïne RT, Lefranc G, Aribi M, Grimbacher B. Next generation sequencing (NGS)-based approach to diagnosing Algerian patients with suspected inborn errors of immunity (IEIs). Clin Immunol 2023; 256:109758. [PMID: 37678716 DOI: 10.1016/j.clim.2023.109758] [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: 05/04/2023] [Revised: 07/23/2023] [Accepted: 09/02/2023] [Indexed: 09/09/2023]
Abstract
The advent of next-generation sequencing (NGS) technologies has greatly expanded our understanding of both the clinical spectra and genetic landscape of inborn errors of immunity (IEIs). Endogamous populations may be enriched for unique, ancestry-specific disease-causing variants, a consideration that significantly impacts molecular testing and analysis strategies. Herein, we report on the application of a 2-step NGS-based testing approach beginning with targeted gene panels (TGPs) tailored to specific IEI subtypes and reflexing to whole exome sequencing (WES) if negative for Northwest Algerian patients with suspected IEIs. Our overall diagnostic yield of 57% is comparable to others broadly applying short-read NGS to IEI detection, but data from our localized cohort show some similarities and differences from NGS studies performed on larger regional IEI cohorts. This suggests the importance of tailoring diagnostic strategies to local demographics and needs, but also highlights ongoing concerns inherent to the application of genomics for clinical IEI diagnostics.
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Affiliation(s)
- Xiao P Peng
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
| | - Moudjahed Saleh Al-Ddafari
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Andres Caballero-Oteyza
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany
| | - Chahrazed El Mezouar
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Pavla Mrovecova
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Saad Eddin Dib
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Zoheir Massen
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Mohammed Chems-Eddine Smahi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Specialized Mother-Child Hospital of Tlemcen, Department of Neonatology, Faculty of Medicine, University of Tlemcen, Algeria
| | - Alddafari Faiza
- Department of Internal Medicine, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Tlemcen, Algeria
| | | | - Gérard Lefranc
- Institute of Human Genetics, UMR 9002 CNRS-University of Montpellier, France
| | - Mourad Aribi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria.
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany.
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14
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Khan A, Inkster AM, Peñaherrera MS, King S, Kildea S, Oberlander TF, Olson DM, Vaillancourt C, Brain U, Beraldo EO, Beristain AG, Clifton VL, Del Gobbo GF, Lam WL, Metz GAS, Ng JWY, Price EM, Schuetz JM, Yuan V, Portales-Casamar É, Robinson WP. The application of epiphenotyping approaches to DNA methylation array studies of the human placenta. Epigenetics Chromatin 2023; 16:37. [PMID: 37794499 PMCID: PMC10548571 DOI: 10.1186/s13072-023-00507-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Genome-wide DNA methylation (DNAme) profiling of the placenta with Illumina Infinium Methylation bead arrays is often used to explore the connections between in utero exposures, placental pathology, and fetal development. However, many technical and biological factors can lead to signals of DNAme variation between samples and between cohorts, and understanding and accounting for these factors is essential to ensure meaningful and replicable data analysis. Recently, "epiphenotyping" approaches have been developed whereby DNAme data can be used to impute information about phenotypic variables such as gestational age, sex, cell composition, and ancestry. These epiphenotypes offer avenues to compare phenotypic data across cohorts, and to understand how phenotypic variables relate to DNAme variability. However, the relationships between placental epiphenotyping variables and other technical and biological variables, and their application to downstream epigenome analyses, have not been well studied. RESULTS Using DNAme data from 204 placentas across three cohorts, we applied the PlaNET R package to estimate epiphenotypes gestational age, ancestry, and cell composition in these samples. PlaNET ancestry estimates were highly correlated with independent polymorphic ancestry-informative markers, and epigenetic gestational age, on average, was estimated within 4 days of reported gestational age, underscoring the accuracy of these tools. Cell composition estimates varied both within and between cohorts, as well as over very long placental processing times. Interestingly, the ratio of cytotrophoblast to syncytiotrophoblast proportion decreased with increasing gestational age, and differed slightly by both maternal ethnicity (lower in white vs. non-white) and genetic ancestry (lower in higher probability European ancestry). The cohort of origin and cytotrophoblast proportion were the largest drivers of DNAme variation in this dataset, based on their associations with the first principal component. CONCLUSIONS This work confirms that cohort, array (technical) batch, cell type proportion, self-reported ethnicity, genetic ancestry, and biological sex are important variables to consider in any analyses of Illumina DNAme data. We further demonstrate the specific utility of epiphenotyping tools developed for use with placental DNAme data, and show that these variables (i) provide an independent check of clinically obtained data and (ii) provide a robust approach to compare variables across different datasets. Finally, we present a general framework for the processing and analysis of placental DNAme data, integrating the epiphenotype variables discussed here.
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Affiliation(s)
- A Khan
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Princess Margaret Cancer Center, Toronto, ON, M5G 2C4, Canada
| | - A M Inkster
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - M S Peñaherrera
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - S King
- Department of Psychiatry, McGill University, Montreal, QC, H3A 1A1, Canada
- Psychosocial Research Division, Douglas Hospital Research Centre, Montreal, QC, H4H 1R3, Canada
| | - S Kildea
- Mater Research Institute, University of Queensland, Brisbane, QLD, 4101, Australia
- Molly Wardaguga Research Centre, Charles Darwin University, Brisbane, QLD, 4000, Australia
| | - T F Oberlander
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, BC, V6H 3V4, Canada
| | - D M Olson
- Department of Obstetrics and Gynecology, University of Alberta, 220 HMRC, Edmonton, AB, T6G 2S2, Canada
| | - C Vaillancourt
- Centre Armand Frappier Santé Biotechnologie - INRS and University of Quebec Intersectorial Health Research Network, Laval, QC, H7V 1B7, Canada
| | - U Brain
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, BC, V6H 3V4, Canada
| | - E O Beraldo
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - A G Beristain
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Obstetrics & Gynecology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - V L Clifton
- Mater Research Institute, University of Queensland, Brisbane, QLD, 4101, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD, 4006, Australia
| | - G F Del Gobbo
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, K1H 5B2, Canada
| | - W L Lam
- British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - G A S Metz
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - J W Y Ng
- Faculty of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - E M Price
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, K1H 5B2, Canada
| | - J M Schuetz
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - V Yuan
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - É Portales-Casamar
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada.
- Centre de Recherche du CHU Sainte-Justine, 3175 Côte-Sainte-Catherine Road, Montréal, QC, H3T 1C5, Canada.
| | - W P Robinson
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.
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15
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Allen PC, Roberts K, Rubio JE, Tiwari HK, Absher DM, Cooper SJ, Myers RM, Brown EE. Genome-wide DNA methylation analysis implicates enrichment of interferon pathway in African American patients with Systemic Lupus Erythematosus and European Americans with lupus nephritis. J Autoimmun 2023; 139:103089. [PMID: 37506491 PMCID: PMC10529132 DOI: 10.1016/j.jaut.2023.103089] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
Systemic Lupus Erythematosus (SLE) is a chronic, multisystem, inflammatory autoimmune disease that disproportionately affects women. Trends in SLE prevalence and clinical course differ by ancestry, with those of African American ancestry presenting with more active, severe and rapidly progressive disease than European Americans. Previous research established altered epigenetic signatures in SLE patients compared to controls. However, the contribution of aberrant DNA methylation (DNAm) to the risk of SLE by ancestry and differences among patients with SLE-associated Lupus Nephritis (LN) has not been well described. We evaluated the DNA methylomes of 87 individuals including 41 SLE patients, with and without LN, and 46 controls enrolled in an ancestry diverse, well-characterized cohort study of established SLE (41 SLE patients [20 SLE-LN+, 21 SLE-LN-] and 46 sex-, race- and age-matched controls; 55% African American, 45% European American). Participants were genotyped using the Infinium Global Diversity Array (GDA), and genetic ancestry was estimated using principal components. Genome-wide DNA methylation was initially measured using the Illumina MethylationEPIC 850K Beadchip array followed by methylation-specific qPCR to validate the methylation status at putative loci. Differentially Methylated Positions (DMP) were identified using a case-control approach adjusted for ancestry. We identified a total of 51 DMPs in CpGs among SLE patients compared to controls. Genes proximal to these CpGs were highly enriched for involvement in type I interferon signaling. DMPs among European American SLE patients with LN were similar to African American SLE patients with and without LN. Our findings were validated using an orthogonal, methyl-specific PCR for three SLE-associated DMPs near or proximal to MX1, USP18, and IFITM1. Our study confirms previous reports that DMPs in CpGs associated with SLE are enriched in type I interferon genes. However, we show that European American SLE patients with LN have similar DNAm patterns to African American SLE patients irrespective of LN, suggesting that aberrant DNAm alters activity of type I interferon pathway leading to more severe disease independent of ancestry.
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Affiliation(s)
- Peter C Allen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kevin Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jose E Rubio
- Department of Rheumatology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - Elizabeth E Brown
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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16
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Mercadel AJ, Sanchez-Covarrubias AP, Medina HN, Pinheiro PS, Pinto A, George SHL, Schlumbrecht MP. Intra-racial disaggregation reveals associations between nativity and overall survival in women with endometrial cancer. Gynecol Oncol 2023; 176:98-105. [PMID: 37480810 DOI: 10.1016/j.ygyno.2023.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/16/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/24/2023]
Abstract
OBJECTIVE Prior studies have demonstrated survival differences between Black women with endometrial cancer (EC) born in the US and Caribbean. Our objective was to determine if country of birth influences EC overall survival (OS) in disaggregated subpopulations of Black women. METHODS Using the Florida Cancer Data System, women with EC diagnosed from 1981 to 2017 were identified. Demographic and clinical information were abstracted. Women who self-identified as Black and born in the US (USB), Jamaica (JBB), or Haiti (HBB) were included. Statistical analyses were performed using chi-square, Cox proportional hazards models, and Kaplan-Meier methods with significance set at p < 0.05. RESULTS 3817 women met the inclusion criteria. Compared to USB, JBB and HBB had more high-grade histologies, more advanced stage disease, had a greater proportion of uninsured or Medicaid insured, and had a higher proportion of women who received chemotherapy (all p < 0.05). In multivariate analyses, age (HR 1.03 [1.02-1.05]), regional stage (HR 1.52 [1.22-1.89]), distant stage (HR 3.73 [2.84-4.89]), lymphovascular space invasion (HR 1.96 [1.61-2.39]), receipt of surgery (HR 0.47 [0.29-0.75]), and receipt of chemotherapy (HR 0.77 [0.62-0.95]) were independently associated with OS. Compared to USB, Haitian nativity was an independent negative predictor of OS when evaluating all histologies together (HR 1.54 [1.18-2.00]) and for endometrioid EC specifically (HR 1.77 [1.10-2.83]). Among women with serous EC, HBB had markedly worse median OS (18.5 months [13.4-46.5]) relative to USB (29.9 months [26.3-35.9]) and JBB (41.0 months, [34.1-82.6], p = 0.013). CONCLUSION Country of birth is associated with endometrial cancer survival in Black women, with HBB demonstrating worse outcomes.
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Affiliation(s)
- Alyssa J Mercadel
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, Leonard M. Miller School of Medicine, University of Miami, 1121 NW 14(th) Street, Suite 345C, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, 1475 NW 12(th) Avenue, Miami, FL 33136, USA
| | - Alex P Sanchez-Covarrubias
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, Leonard M. Miller School of Medicine, University of Miami, 1121 NW 14(th) Street, Suite 345C, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, 1475 NW 12(th) Avenue, Miami, FL 33136, USA
| | - Heidy N Medina
- Department of Public Health Sciences, University of Miami School of Medicine, 1120 NW 14(th) Street, CRB 919, Miami, FL 33136, USA
| | - Paulo S Pinheiro
- Sylvester Comprehensive Cancer Center, 1475 NW 12(th) Avenue, Miami, FL 33136, USA; Department of Public Health Sciences, University of Miami School of Medicine, 1120 NW 14(th) Street, CRB 919, Miami, FL 33136, USA
| | - Andre Pinto
- Department of Pathology, University of Miami Miller School of Medicine, 1611 NW 12(th) Avenue, Holtz 2145, Miami, FL 33136, USA
| | - Sophia H L George
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, Leonard M. Miller School of Medicine, University of Miami, 1121 NW 14(th) Street, Suite 345C, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, 1475 NW 12(th) Avenue, Miami, FL 33136, USA
| | - Matthew P Schlumbrecht
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, Leonard M. Miller School of Medicine, University of Miami, 1121 NW 14(th) Street, Suite 345C, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, 1475 NW 12(th) Avenue, Miami, FL 33136, USA.
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17
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Pereson MJ, Sanabria DJ, Torres C, Liotta DJ, Campos RH, Schurr TG, Di Lello FA, Badano I. Evolutionary analysis of JC polyomavirus in Misiones' population yields insight into the population dynamics of the early human dispersal in the Americas. Virology 2023; 585:100-108. [PMID: 37327595 DOI: 10.1016/j.virol.2023.05.009] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND JC polyomavirus (JCV) has an ethno-geographical distribution across human populations. OBJECTIVE Study the origins of the population of Misiones (Argentina) by using JCV as genetic marker. METHODS Viral detection and characterization was conducted by PCR amplification and evolutionary analysis of the intergenic region sequences. RESULTS 22 out of 121 samples were positive for JCV, including 5 viral lineages: MY (n = 8), Eu-a (n = 7), B1-c (n = 4), B1-b (n = 2) and Af2 (n = 1). MY sequences clustered within a branch of Native American origin that diverged from its Asian counterpart about 21,914 years ago (HPD 95% interval 15,383-30,177), followed by a sustained demographic expansion around 5000 years ago. CONCLUSIONS JCV in Misiones reflects the multiethnic origin of the current population, with an important Amerindian contribution. Analysis of the MY viral lineage shows a pattern consistent with the arrival of early human migrations to the Americas and a population expansion by the pre-Columbian native societies.
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Affiliation(s)
- Matias J Pereson
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Daiana J Sanabria
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina
| | - Carolina Torres
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Instituto Nacional de Medicina Tropical-ANLIS ''Dr. Malbrán'', Neuquén y Jujuy S/n, N3370, Puerto Iguazú, Misiones, Argentina
| | - Rodolfo H Campos
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania. Philadelphia, PA 19104-6398, USA
| | - Federico A Di Lello
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Inés Badano
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina; Universidad Nacional de Misiones. Red de Laboratorios. Laboratorio de Antropología Biológica y Bioinformática Aplicada (LABBA). Misiones, Argentina.
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Wendt FR, Pathak GA, Vahey J, Qin X, Koller D, Cabrera-Mendoza B, Haeny A, Harrington KM, Rajeevan N, Duong LM, Levey DF, De Angelis F, De Lillo A, Bigdeli TB, Pyarajan S, Gaziano JM, Gelernter J, Aslan M, Provenzale D, Helmer DA, Hauser ER, Polimanti R. Modeling the longitudinal changes of ancestry diversity in the Million Veteran Program. Hum Genomics 2023; 17:46. [PMID: 37268996 PMCID: PMC10239111 DOI: 10.1186/s40246-023-00487-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 05/05/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND The Million Veteran Program (MVP) participants represent 100 years of US history, including significant social and demographic changes over time. Our study assessed two aspects of the MVP: (i) longitudinal changes in population diversity and (ii) how these changes can be accounted for in genome-wide association studies (GWAS). To investigate these aspects, we divided MVP participants into five birth cohorts (N-range = 123,888 [born from 1943 to 1947] to 136,699 [born from 1948 to 1953]). RESULTS Ancestry groups were defined by (i) HARE (harmonized ancestry and race/ethnicity) and (ii) a random-forest clustering approach using the 1000 Genomes Project and the Human Genome Diversity Project (1kGP + HGDP) reference panels (77 world populations representing six continental groups). In these groups, we performed GWASs of height, a trait potentially affected by population stratification. Birth cohorts demonstrate important trends in ancestry diversity over time. More recent HARE-assigned Europeans, Africans, and Hispanics had lower European ancestry proportions than older birth cohorts (0.010 < Cohen's d < 0.259, p < 7.80 × 10-4). Conversely, HARE-assigned East Asians showed an increase in European ancestry proportion over time. In GWAS of height using HARE assignments, genomic inflation due to population stratification was prevalent across all birth cohorts (linkage disequilibrium score regression intercept = 1.08 ± 0.042). The 1kGP + HGDP-based ancestry assignment significantly reduced the population stratification (mean intercept reduction = 0.045 ± 0.007, p < 0.05) confounding in the GWAS statistics. CONCLUSIONS This study provides a characterization of ancestry diversity of the MVP cohort over time and compares two strategies to infer genetically defined ancestry groups by assessing differences in controlling population stratification in genome-wide association studies.
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Affiliation(s)
- Frank R Wendt
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Gita A Pathak
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Jacqueline Vahey
- Durham VA Medical Center, Durham, NC, USA
- Duke University, Carmichael Building, 300 N Duke St, Durham, NC, 27701, USA
| | - Xuejun Qin
- Durham VA Medical Center, Durham, NC, USA
- Duke University, Carmichael Building, 300 N Duke St, Durham, NC, 27701, USA
| | - Dora Koller
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Brenda Cabrera-Mendoza
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Angela Haeny
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Kelly M Harrington
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Nallakkandi Rajeevan
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
- Yale Center for Medical Informatics, Yale School of Medicine, New Haven, CT, USA
| | - Linh M Duong
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Daniel F Levey
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Flavio De Angelis
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | | | - Tim B Bigdeli
- SUNY Downstate Health Sciences University, Brooklyn, NY, USA
- VA New York Harbor Healthcare System, Brooklyn, NY, USA
| | - Saiju Pyarajan
- Massachusetts Area Veterans Epidemiology, Research, and Information Center (MAVERIC), Jamaica Plain, MA, USA
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard School of Medicine, Boston, MA, USA
| | - John Michael Gaziano
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard School of Medicine, Boston, MA, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, VA CT Healthcare System, West Haven, CT, USA
| | - Mihaela Aslan
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Dawn Provenzale
- Durham VA Medical Center, Durham, NC, USA
- Duke University, Carmichael Building, 300 N Duke St, Durham, NC, 27701, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Drew A Helmer
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth R Hauser
- Durham VA Medical Center, Durham, NC, USA.
- Duke University, Carmichael Building, 300 N Duke St, Durham, NC, 27701, USA.
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.
- VA Cooperative Studies Program Clinical Epidemiology Research Center (CSP-CERC), VA CT Healthcare System, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA.
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Miyashita M, Bell JSK, Wenric S, Karaesmen E, Rhead B, Kase M, Kaneva K, De La Vega FM, Zheng Y, Yoshimatsu TF, Khramtsova G, Liu F, Zhao F, Howard FM, Nanda R, Beaubier N, White KP, Huo D, Olopade OI. Molecular profiling of a real-world breast cancer cohort with genetically inferred ancestries reveals actionable tumor biology differences between European ancestry and African ancestry patient populations. Breast Cancer Res 2023; 25:58. [PMID: 37231433 DOI: 10.1186/s13058-023-01627-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/27/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Endocrine-resistant HR+/HER2- breast cancer (BC) and triple-negative BC (TNBC) are of interest for molecularly informed treatment due to their aggressive natures and limited treatment profiles. Patients of African Ancestry (AA) experience higher rates of TNBC and mortality than European Ancestry (EA) patients, despite lower overall BC incidence. Here, we compare the molecular landscapes of AA and EA patients with HR+/HER2- BC and TNBC in a real-world cohort to promote equity in precision oncology by illuminating the heterogeneity of potentially druggable genomic and transcriptomic pathways. METHODS De-identified records from patients with TNBC or HR+/HER2- BC in the Tempus Database were randomly selected (N = 5000), with most having stage IV disease. Mutations, gene expression, and transcriptional signatures were evaluated from next-generation sequencing data. Genetic ancestry was estimated from DNA-seq. Differences in mutational prevalence, gene expression, and transcriptional signatures between AA and EA were compared. EA patients were used as the reference population for log fold-changes (logFC) in expression. RESULTS After applying inclusion criteria, 3433 samples were evaluated (n = 623 AA and n = 2810 EA). Observed patterns of dysregulated pathways demonstrated significant heterogeneity among the two groups. Notably, PIK3CA mutations were significantly lower in AA HR+/HER2- tumors (AA = 34% vs. EA = 42%, P < 0.05) and the overall cohort (AA = 28% vs. EA = 37%, P = 2.08e-05). Conversely, KMT2C mutation was significantly more frequent in AA than EA TNBC (23% vs. 12%, P < 0.05) and HR+/HER2- (24% vs. 15%, P = 3e-03) tumors. Across all subtypes and stages, over 8000 genes were differentially expressed between the two ancestral groups including RPL10 (logFC = 2.26, P = 1.70e-162), HSPA1A (logFC = - 2.73, P = 2.43e-49), ATRX (logFC = - 1.93, P = 5.89e-83), and NUTM2F (logFC = 2.28, P = 3.22e-196). Ten differentially expressed gene sets were identified among stage IV HR+/HER2- tumors, of which four were considered relevant to BC treatment and were significantly enriched in EA: ERBB2_UP.V1_UP (P = 3.95e-06), LTE2_UP.V1_UP (P = 2.90e-05), HALLMARK_FATTY_ACID_METABOLISM (P = 0.0073), and HALLMARK_ANDROGEN_RESPONSE (P = 0.0074). CONCLUSIONS We observed significant differences in mutational spectra, gene expression, and relevant transcriptional signatures between patients with genetically determined African and European ancestries, particularly within the HR+/HER2- BC and TNBC subtypes. These findings could guide future development of treatment strategies by providing opportunities for biomarker-informed research and, ultimately, clinical decisions for precision oncology care in diverse populations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Fang Liu
- The University of Chicago, Chicago, IL, USA
| | | | | | - Rita Nanda
- The University of Chicago, Chicago, IL, USA
| | | | - Kevin P White
- Tempus Inc, Chicago, IL, USA
- National University Singapore, Queenstown, Singapore
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Díaz-Zuluaga AM, Vélez JI, Cuartas M, Valencia J, Castaño M, Palacio JD, Arcos-Burgos M, López-Jaramillo C. Ancestry component as a major predictor of lithium response in the treatment of bipolar disorder. J Affect Disord 2023; 332:203-209. [PMID: 36997125 DOI: 10.1016/j.jad.2023.03.058] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/10/2023] [Accepted: 03/18/2023] [Indexed: 04/01/2023]
Abstract
BACKGROUND Bipolar Disorder (BD) represents the seventh major cause of disability life-years-adjusted. Lithium remains as a first-line treatment, but clinical improvement occurs only in 30 % of treated patients. Studies suggest that genetics plays a major role in shaping the individual response of BD patients to lithium. METHODS We used machine-learning techniques (Advance Recursive Partitioned Analysis, ARPA) to build a personalized prediction framework of BD lithium response using biological, clinical, and demographical data. Using the Alda scale, we classified 172 BD I-II patients as responders or non-responders to lithium treatment. ARPA methods were used to build individual prediction frameworks and to define variable importance. Two predictive models were evaluated: 1) demographic and clinical data, and 2) demographic, clinical and ancestry data. Model performance was assessed using Receiver Operating Characteristic (ROC) curves. RESULTS The predictive model including ancestry yield the best performance (sensibility = 84.6 %, specificity = 93.8 % and AUC = 89.2 %) compared to the model without ancestry (sensibility = 50 %, Specificity = 94.5 %, and AUC = 72.2 %). This ancestry component best predicted lithium individual response. Clinical variables such as disease duration, the number of depressive episodes, the total number of affective episodes, and the number of manic episodes were also important predictors. CONCLUSION Ancestry component is a major predictor and significantly improves the definition of individual Lithium response in BD patients. We provide classification trees with potential bench application in the clinical setting. While this prediction framework might be applied in specific populations, the used methodology might be of general use in precision and translational medicine.
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Affiliation(s)
- Ana M Díaz-Zuluaga
- Research Group in Psychiatry (GIPSI), Institute of Medical Research, Department of Psychiatry, Faculty of Medicine, University of Antioquia, Medellín, Antioquia, Colombia
| | - Jorge I Vélez
- Department of Industrial Engineering, Universidad del Norte, Km 5 vía Puerto Colombia, 081007 Barranquilla, Colombia
| | - Mauricio Cuartas
- Research Group Studies in Psychology, School of Humanities, Department of Psychology, EAFIT University, Medellín, Antioquia, Colombia
| | - Johanna Valencia
- Research Group in Psychiatry (GIPSI), Institute of Medical Research, Department of Psychiatry, Faculty of Medicine, University of Antioquia, Medellín, Antioquia, Colombia
| | - Mauricio Castaño
- Department of Mental Health and Human Behavior, Universidad de Caldas, Manizales, Caldas, Colombia
| | - Juan David Palacio
- Research Group in Psychiatry (GIPSI), Institute of Medical Research, Department of Psychiatry, Faculty of Medicine, University of Antioquia, Medellín, Antioquia, Colombia
| | - Mauricio Arcos-Burgos
- Research Group in Psychiatry (GIPSI), Institute of Medical Research, Department of Psychiatry, Faculty of Medicine, University of Antioquia, Medellín, Antioquia, Colombia
| | - Carlos López-Jaramillo
- Research Group in Psychiatry (GIPSI), Institute of Medical Research, Department of Psychiatry, Faculty of Medicine, University of Antioquia, Medellín, Antioquia, Colombia.
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Seibert TM, Garraway IP, Plym A, Mahal BA, Giri V, Jacobs MF, Cheng HH, Loeb S, Helfand BT, Eeles RA, Morgan TM. Genetic Risk Prediction for Prostate Cancer: Implications for Early Detection and Prevention. Eur Urol 2023; 83:241-8. [PMID: 36609003 DOI: 10.1016/j.eururo.2022.12.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/15/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023]
Abstract
CONTEXT Prostate cancer (PCa) is a leading cause of death and partially heritable. Genetic risk prediction might be useful for strategies to reduce PCa mortality through early detection and prevention. OBJECTIVE To review evidence for genetic risk prediction for PCa. EVIDENCE ACQUISITION A collaborative literature review was conducted using PubMed and Google Scholar. Search terms included genetic, risk, prediction, and "prostate cancer". Articles addressing screening, early detection, or prevention were prioritized, as were studies involving diverse populations. EVIDENCE SYNTHESIS Rare pathogenic mutations (RPMs), especially in DNA damage repair genes, increase PCa risk. RPMs in BRCA2 are most clearly deleterious, conferring 2-8.6 times higher risk of PCa and a higher risk of aggressive disease. Common genetic variants can be combined into genetic risk scores (GRSs). A high GRS (top 20-25% of the population) confers two to three times higher risk of PCa than average; a very high GRS (top 1-5%) confers six to eight times higher risk. GRSs are not specific for aggressive PCa, possibly due to methodological limitations and/or a field effect of an elevated risk for both low- and high-grade PCa. It is challenging to disentangle genetics from structural racism and social determinants of health to understand PCa racial disparities. GRSs are independently associated with a lethal PCa risk after accounting for family history and race/ancestry. Healthy lifestyle might partially mitigate the risk of lethal PCa. CONCLUSIONS Genetic risk assessment is becoming more common; implementation studies are needed to understand the implications and to avoid exacerbating healthcare disparities. Men with a high genetic risk of PCa can reasonably be encouraged to adhere to a healthy lifestyle. PATIENT SUMMARY Prostate cancer risk is inherited through rare mutations and through the combination of hundreds of common genetic markers. Some men with a high genetic risk (especially BRCA2 mutations) likely benefit from early screening for prostate cancer. The risk of lethal prostate cancer can be reduced through a healthy lifestyle.
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22
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Asghar A, Naaz S, Ansari S, Kumar A, Singh V. The cross-sectional morphology of median nerve in carpal tunnel of healthy, adult population: A systematic review and meta-analysis. Morphologie 2023; 107:99-115. [PMID: 35697557 DOI: 10.1016/j.morpho.2022.05.005] [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: 04/27/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022]
Abstract
The cross-section area is a crucial parameter to assess peripheral neuropathy. The ultrasonographic evaluation of cross-section area of median nerve is a low-cost and readily available tool for diagnosis and assessment. However, the intra-nerve dimensional variability and its normative reference value in a healthy subject are missing. The current meta-analysis aims to capture the median nerve cross-section area for healthy subjects and generate a comprehensive ultrasonographic reference data set for each population. METHODS The full text of manuscripts were collected after short-listing the abstracts collected from search strategy. A quality assurance tool was used to capture the risk of bias of each study after reviewing the included manuscripts. The pooled estimate of cross-section area was stratified according to anatomical landmarks, sex, and ancestry. RESULTS A total of 97 observational studies dealt with 6679 wrists of healthy subjects were included. The pooled estimate of the cross-section area of median nerve at carpal tunnel inlet was 8.54mm2 [95% CI: 8.34-8.74mm2]. The same pooled estimate at carpal tunnel outlet was 8.03mm2 [95% CI: 7.46-8.60mm2]. Both these pooled estimates have significant correlation with mean age of population. Age and sex were two primary predictors of the cross-section of median nerve. The flattening ratio, circularity, and wrist-forearm ratio of median nerve were also computed. CONCLUSION These normative data could serve as a reference for assessing median nerve pathologies, including carpal tunnel syndrome. The ethnic variation of pooled estimate and heterogeneity will guide clinician set up the reference value for diagnostic criteria.
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Affiliation(s)
- A Asghar
- Department of Anatomy, AIIMS Patna, Patna, Bihar 801505, India.
| | - S Naaz
- Department of Anaesthesiology, AIIMS Patna, Patna, Bihar 801505, India
| | - S Ansari
- Consultant Radiologist, Paras HMRI, Hospital Patna, Patna, Bihar, India
| | - A Kumar
- Department of Anatomy, AIIMS Patna, Patna, Bihar 801505, India
| | - V Singh
- Speciality Registrar (Orthopaedics), Homerton University Hospital, London, UK
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Klure DM, Greenhalgh R, Parchman TL, Matocq MD, Galland LM, Shapiro MD, Dearing MD. Hybridization in the absence of an ecotone favors hybrid success in woodrats (Neotoma spp.). Evolution 2023; 77:959-970. [PMID: 36715204 PMCID: PMC10066834 DOI: 10.1093/evolut/qpad012] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/09/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023]
Abstract
Hybridization is a common process that has broadly impacted the evolution of multicellular eukaryotes; however, how ecological factors influence this process remains poorly understood. Here, we report the findings of a 3-year recapture study of the Bryant's woodrat (Neotoma bryanti) and desert woodrat (N. lepida), two species that hybridize within a creosote bush (Larrea tridentata) shrubland in Whitewater, CA, USA. We used a genotype-by-sequencing approach to characterize the ancestry distribution of individuals across this hybrid zone coupled with Cormack-Jolly-Seber modeling to describe demography. We identified a high frequency of hybridization at this site with ~40% of individuals possessing admixed ancestry, which is the result of multigenerational backcrossing and advanced hybrid-hybrid crossing. F1, F2 and advanced generation hybrids had apparent survival rates similar to parental N. bryanti, while parental and backcross N. lepida had lower apparent survival rates and were far less abundant. Compared to bimodal hybrid zones where hybrids are often rare and selected against, we find that hybrids at Whitewater are common and have comparable survival to the dominant parental species, N. bryanti. The frequency of hybridization at Whitewater is therefore likely limited by the abundance of the less common parental species, N. lepida, rather than selection against hybrids.
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Affiliation(s)
- Dylan M Klure
- School of Biological Sciences, University of Utah, 257 S 1400 E rm 201, Salt Lake City, UT
| | - Robert Greenhalgh
- School of Biological Sciences, University of Utah, 257 S 1400 E rm 201, Salt Lake City, UT
| | - Thomas L Parchman
- Department of Biology, University of Nevada Reno, 1664 N. Virginia Street, Reno, NV
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science; Program in Ecology, Evolution and Conservation Biology, University of Nevada Reno, 1664 N. Virginia Street, Reno, NV
| | - Lanie M Galland
- Department of Biology, University of Nevada Reno, 1664 N. Virginia Street, Reno, NV
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, 257 S 1400 E rm 201, Salt Lake City, UT
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, 257 S 1400 E rm 201, Salt Lake City, UT
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Pagadala MS, Linscott JA, Talwar JV, Seibert TM, Rose B, Lynch J, Panizzon M, Hauger R, Hansen MH, Sammon JD, Hayn MH, Kader K, Carter H, Ryan ST. PRState: Incorporating genetic ancestry in prostate cancer risk scores for men of African ancestry. BMC Cancer 2022; 22:1289. [PMID: 36494783 PMCID: PMC9733391 DOI: 10.1186/s12885-022-10258-3] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/30/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Prostate cancer (PrCa) is one of the most genetically driven solid cancers with heritability estimates as high as 57%. Men of African ancestry are at an increased risk of PrCa; however, current polygenic risk score (PRS) models are based on European ancestry groups and may not be broadly applicable. The objective of this study was to construct an African ancestry-specific PrCa PRS (PRState) and evaluate its performance. METHODS African ancestry group of 4,533 individuals in ELLIPSE consortium was used for discovery of African ancestry-specific PrCa SNPs. PRState was constructed as weighted sum of genotypes and effect sizes from genome-wide association study (GWAS) of PrCa in African ancestry group. Performance was evaluated using ROC-AUC analysis. RESULTS We identified African ancestry-specific PrCa risk loci on chromosomes 3, 8, and 11 and constructed a polygenic risk score (PRS) from 10 African ancestry-specific PrCa risk SNPs, achieving an AUC of 0.61 [0.60-0.63] and 0.65 [0.64-0.67], when combined with age and family history. Performance dropped significantly when using ancestry-mismatched PRS models but remained comparable when using trans-ancestry models. Importantly, we validated the PRState score in the Million Veteran Program (MVP), demonstrating improved prediction of PrCa and metastatic PrCa in individuals of African ancestry. CONCLUSIONS African ancestry-specific PRState improves PrCa prediction in African ancestry groups in ELLIPSE consortium and MVP. This study underscores the need for inclusion of individuals of African ancestry in gene variant discovery to optimize PRSs and identifies African ancestry-specific variants for use in future studies.
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Affiliation(s)
- Meghana S Pagadala
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
- Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA.
- Biomedical Science Program, University of California, San Diego, La Jolla, CA, USA.
| | | | - James V Talwar
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Tyler M Seibert
- Department of Radiation Medicine and Applied Sciences, University of California, San Diego, La Jolla, CA, USA
- VA San Diego Healthcare System, La Jolla, CA, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Brent Rose
- Department of Radiation Medicine and Applied Sciences, University of California, San Diego, La Jolla, CA, USA
- VA San Diego Healthcare System, La Jolla, CA, USA
- Department of Urology, University of California San Diego, La Jolla, CA, USA
| | - Julie Lynch
- VA Salt Lake City Healthcare System, Salt Lake City, UT, USA
- School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Matthew Panizzon
- VA San Diego Healthcare System, La Jolla, CA, USA
- Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, CA, USA
| | - Richard Hauger
- VA San Diego Healthcare System, La Jolla, CA, USA
- Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health (CESAMH), San Diego Healthcare System, San Diego, CA, USA
| | - Moritz H Hansen
- Division of Urology, Maine Medical Center, Portland, ME, USA
| | - Jesse D Sammon
- Division of Urology, Maine Medical Center, Portland, ME, USA
| | - Matthew H Hayn
- Division of Urology, Maine Medical Center, Portland, ME, USA
| | - Karim Kader
- Department of Urology, University of California San Diego, La Jolla, CA, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Stephen T Ryan
- Division of Urology, Maine Medical Center, Portland, ME, USA
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Tiner JC, Mechanic LE, Gallicchio L, Gillanders EM, Helzlsouer KJ. Awareness and use of genetic testing: An analysis of the Health Information National Trends Survey 2020. Genet Med 2022; 24:2526-2534. [PMID: 36136089 PMCID: PMC9746668 DOI: 10.1016/j.gim.2022.08.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Genetic testing is a tool used in a variety of settings for medical and nonhealth related purposes. The goal of this analysis was to better understand the awareness and use of genetic testing in the United States. METHODS Data from the 2020 Health Information National Trends Survey 5 cycle 4 were used to assess the awareness and use of genetic testing by demographic characteristics, personal cancer history, and family cancer history. RESULTS Overall, 75% of participants were aware of genetic testing and 19% of participants had genetic testing. Ancestry testing was the most common type of testing that the participants were aware of and had received. Non-Hispanic Asian, Non-Hispanic Black, and Hispanic respondents and participants with incomes less than $20,000 were less likely to be aware of and have received any type of genetic testing than the Non-Hispanic White participants and participants with higher income, respectively. Participants with a family history of cancer were more likely to be aware of cancer genetic testing than those without, and participants with a personal history of cancer were more likely to have had cancer genetic testing. CONCLUSION It appears awareness of genetic testing is increasing in the United States, and differences in awareness persist by race/ethnicity and income.
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Affiliation(s)
- Jessica C Tiner
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Leah E Mechanic
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD.
| | - Lisa Gallicchio
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Elizabeth M Gillanders
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Kathy J Helzlsouer
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
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Cavalcante LN, Porto J, Mazo D, Longatto-Filho A, Stefano JT, Lyra AC, Carrilho FJ, Reis RM, Alves VAF, Sanyal AJ, Oliveira CP. African genetic ancestry is associated with lower frequency of PNPLA3 G allele in non-alcoholic fatty liver in an admixed population. Ann Hepatol 2022; 27:100728. [PMID: 35710086 DOI: 10.1016/j.aohep.2022.100728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/06/2022] [Accepted: 05/19/2022] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND OBJECTIVES PNPLA3 (rs738409) and TM6SF2 (rs58542926) variants, interindividual and ethnic differences may be risk factors for non-alcoholic fatty liver disease (NAFLD). The PNPLA3 G allele is associated with worse NAFLD evolution in Hispanics and Caucasians. TM6SF2 is associated with hypertriglyceridemia, NAFLD, and cardiovascular disease. We aimed to evaluate the association between genetic ancestry by Ancestry Informative Markers (AIM), PNPLA3 and TM6SF2 polymorphisms in patients with biopsy-proven NAFLD in an admixed population. METHODS We included adults with biopsy-proven NAFLD and excluded patients with the presence of other chronic liver disease, alcohol intake >100g/week, HIV, drug-induced fatty liver disease, or liver transplantation. We classified NAFLD using the Non-Alcoholic Steatohepatitis Clinical Research Network (NASH-CRN) histological scoring system. The PNPLA3 (rs738409 c.444C>G) and TM6SF2 (rs58542926 c.449C>T) genotyping were performed by RT-PCR. Genetic ancestry was determined using 46 insertion-deletion AIM; α<0.05 was considered significant. RESULTS A total of 248 patients with NAFLD were enrolled [34 with simple steatosis (NAFL); 214 with NASH]. Overall, we detected a greater European ancestry contribution (0.645), followed by African (0.173), Amerindian (0.095), and East Asian (0.087) ancestry contribution, without differences between NAFL and NASH patients. However, we found a higher African genetic ancestry contribution among patients with NAFL who had the PNPLA3 C/C genotype than those with the G allele (0.216 ± 0.205 versus 0.105 ± 0.101, respectively; p=0.047). Ancestry contributions did not differ among TM6SF2 genotypes. CONCLUSION Among NAFL patients, greater African genetic ancestry was associated to a lower frequency of the PNPLA3 G allele, demonstrating a possible NASH ancestry-related protective factor.
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Affiliation(s)
| | - Jun Porto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos-SP, Brazil
| | - Daniel Mazo
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Laboratory of Clinical and Experimental Gastroenterology (LIM-07), Division of Clinical Gastroenterology and Hepatology, Department of Gastroenterology, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Adhemar Longatto-Filho
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Department of Pathology (LIM-14), Faculty of Medicine, University of São Paulo, Brazil; Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - José Tadeu Stefano
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Laboratory of Clinical and Experimental Gastroenterology (LIM-07), Division of Clinical Gastroenterology and Hepatology, Department of Gastroenterology, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Andre Castro Lyra
- Federal University of Bahia, School of Medicine, Gastroenterology and Hepatology Services & Salvador-BA, Brazil
| | - Flair Jose Carrilho
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Laboratory of Clinical and Experimental Gastroenterology (LIM-07), Division of Clinical Gastroenterology and Hepatology, Department of Gastroenterology, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos-SP, Brazil; Laboratory of Clinical and Experimental Gastroenterology (LIM-07), Division of Clinical Gastroenterology and Hepatology, Department of Gastroenterology, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil; Department of Pathology (LIM-14), Faculty of Medicine, University of São Paulo, Brazil; Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
| | - Venâncio A F Alves
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Department of Pathology (LIM-14), Faculty of Medicine, University of São Paulo, Brazil
| | - Arun J Sanyal
- Institute of Liver Disease and Metabolic Health; Interim Chair, Div. of Gastroenterology; Virginia Commonwealth University, USA
| | - Claudia P Oliveira
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Laboratory of Clinical and Experimental Gastroenterology (LIM-07), Division of Clinical Gastroenterology and Hepatology, Department of Gastroenterology, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
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Kolden MØ, Nymo SH, Øie E. Impact of neighbourhood-level socioeconomic status, traditional coronary risk factors, and ancestry on age at myocardial infarction onset: A population-based register study. BMC Cardiovasc Disord 2022; 22:447. [PMID: 36289452 PMCID: PMC9608887 DOI: 10.1186/s12872-022-02880-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/28/2022] [Indexed: 11/10/2022] Open
Abstract
Background There is consensus that low socioeconomic status (SES) is associated with an increased risk of acute myocardial infarction (AMI), but the extent to which traditional coronary risk factors and other characteristics of low SES mediate this effect remains uncertain. This study examined AMI patients residing in neighbouring city districts with the same local hospital despite having among the most considerable differences in mean SES in Norway. Our purpose was to assess low SES as a coronary risk factor and examine whether traditional coronary risk factors or ancestry mediate this effect. Methods Six hundred six patients (215 and 391 with a low and high neighbourhood-level SES, respectively) admitted to Diakonhjemmet Hospital with non-ST-elevation myocardial infarction (NSTEMI) between 2014 and 2017, entered analysis. Data from the Norwegian Myocardial Infarction Register were used to identify patient characteristics, and the STATA/SE 15.1 software was used to perform the statistical analyses. Results Patients from socioeconomically disadvantaged city-districts had a 4.9 years earlier onset of AMI (68.99 vs. 73.89 years; p < 0.001) and a higher prevalence of previous AMI, known diabetes, and current smokers (36% vs. 27%, 25% vs. 12%, and 33% vs. 17%, respectively; all p ≤ 0.05). When only comparing patients with a first time AMI, an even greater difference in the age at AMI onset was found (6.1 yrs; p < 0.001). The difference in age at AMI onset remained statistically significant when adjusting for traditional coronary risk factors (3.28 yrs; 95% confidence interval (CI) 1.11−5.44; p = 0.003), but not when adjusting for presumed non-Northwest-European ancestry (1.81 yrs; 95% CI −0.55 to 4.17; p = 0.132). Conclusion This study supports earlier research showing an increased risk of AMI in socioeconomically disadvantaged individuals. In our population, presumed non-Northwest-European ancestry could entirely explain the increased risk, whereas traditional coronary risk factors could only partly explain the increased risk.
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Affiliation(s)
- Mathias Øie Kolden
- grid.413684.c0000 0004 0512 8628Department of Internal Medicine, Diakonhjemmet Hospital, Oslo, Norway
| | - Ståle H. Nymo
- grid.413684.c0000 0004 0512 8628Department of Internal Medicine, Diakonhjemmet Hospital, Oslo, Norway
| | - Erik Øie
- grid.413684.c0000 0004 0512 8628Department of Internal Medicine, Diakonhjemmet Hospital, Oslo, Norway
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Elliott HR, Burrows K, Min JL, Tillin T, Mason D, Wright J, Santorelli G, Davey Smith G, Lawlor DA, Hughes AD, Chaturvedi N, Relton CL. Characterisation of ethnic differences in DNA methylation between UK-resident South Asians and Europeans. Clin Epigenetics 2022; 14:130. [PMID: 36243740 PMCID: PMC9571473 DOI: 10.1186/s13148-022-01351-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 06/08/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
Ethnic differences in non-communicable disease risk have been described between individuals of South Asian and European ethnicity that are only partially explained by genetics and other known risk factors. DNA methylation is one underexplored mechanism that may explain differences in disease risk. Currently, there is little knowledge of how DNA methylation varies between South Asian and European ethnicities. This study characterised differences in blood DNA methylation between individuals of self-reported European and South Asian ethnicity from two UK-based cohorts: Southall and Brent Revisited and Born in Bradford. DNA methylation differences between ethnicities were widespread throughout the genome (n = 16,433 CpG sites, 3.4% sites tested). Specifically, 76% of associations were attributable to ethnic differences in cell composition with fewer effects attributable to smoking and genetic variation. Ethnicity-associated CpG sites were enriched for EWAS Catalog phenotypes including metabolites. This work highlights the need to consider ethnic diversity in epigenetic research.
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Affiliation(s)
- Hannah R. Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Josine L. Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Therese Tillin
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Dan Mason
- Bradford Institute for Health Research, Bradford, UK
| | - John Wright
- Bradford Institute for Health Research, Bradford, UK
| | | | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Deborah A. Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Alun D. Hughes
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Nishi Chaturvedi
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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Lopez-Pineda A, Vernekar M, Moreno-Grau S, Rojas-Muñoz A, Moatamed B, Lee MTM, Nava-Aguilar MA, Gonzalez-Arroyo G, Numakura K, Matsuda Y, Ioannidis A, Katsanis N, Takano T, Bustamante CD. Validating and automating learning of cardiometabolic polygenic risk scores from direct-to-consumer genetic and phenotypic data: implications for scaling precision health research. Hum Genomics 2022; 16:37. [PMID: 36076307 PMCID: PMC9452874 DOI: 10.1186/s40246-022-00406-y] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/06/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction A major challenge to enabling precision health at a global scale is the bias between those who enroll in state sponsored genomic research and those suffering from chronic disease. More than 30 million people have been genotyped by direct-to-consumer (DTC) companies such as 23andMe, Ancestry DNA, and MyHeritage, providing a potential mechanism for democratizing access to medical interventions and thus catalyzing improvements in patient outcomes as the cost of data acquisition drops. However, much of these data are sequestered in the initial provider network, without the ability for the scientific community to either access or validate. Here, we present a novel geno-pheno platform that integrates heterogeneous data sources and applies learnings to common chronic disease conditions including Type 2 diabetes (T2D) and hypertension.
Methods We collected genotyped data from a novel DTC platform where participants upload their genotype data files and were invited to answer general health questionnaires regarding cardiometabolic traits over a period of 6 months. Quality control, imputation, and genome-wide association studies were performed on this dataset, and polygenic risk scores were built in a case–control setting using the BASIL algorithm.
Results We collected data on N = 4,550 (389 cases / 4,161 controls) who reported being affected or previously affected for T2D and N = 4,528 (1,027 cases / 3,501 controls) for hypertension. We identified 164 out of 272 variants showing identical effect direction to previously reported genome-significant findings in Europeans. Performance metric of the PRS models was AUC = 0.68, which is comparable to previously published PRS models obtained with larger datasets including clinical biomarkers. Discussion DTC platforms have the potential of inverting research models of genome sequencing and phenotypic data acquisition. Quality control (QC) mechanisms proved to successfully enable traditional GWAS and PRS analyses. The direct participation of individuals has shown the potential to generate rich datasets enabling the creation of PRS cardiometabolic models. More importantly, federated learning of PRS from reuse of DTC data provides a mechanism for scaling precision health care delivery beyond the small number of countries who can afford to finance these efforts directly.
Conclusions The genetics of T2D and hypertension have been studied extensively in controlled datasets, and various polygenic risk scores (PRS) have been developed. We developed predictive tools for both phenotypes trained with heterogeneous genotypic and phenotypic data generated outside of the clinical environment and show that our methods can recapitulate prior findings with fidelity. From these observations, we conclude that it is possible to leverage DTC genetic repositories to identify individuals at risk of debilitating diseases based on their unique genetic landscape so that informed, timely clinical interventions can be incorporated.
Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00406-y.
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Affiliation(s)
- Arturo Lopez-Pineda
- Galatea Bio, Inc., 975 W 22nd Street, Hialeah, Florida, 33010, USA.,Amphora Health, Batallon Independencia 80, Morelia, Michoacan, 58260, Mexico
| | - Manvi Vernekar
- Genomelink, Inc., 2150 Shattuck Avenue, Berkeley, California, 94704, USA.,Awakens Japan K.K., 2-11-3 Meguro, Meguro-ku, Tokyo, 1530063, Japan
| | | | | | - Babak Moatamed
- Galatea Bio, Inc., 975 W 22nd Street, Hialeah, Florida, 33010, USA
| | | | - Marco A Nava-Aguilar
- Galatea Bio, Inc., 975 W 22nd Street, Hialeah, Florida, 33010, USA.,Amphora Health, Batallon Independencia 80, Morelia, Michoacan, 58260, Mexico
| | - Gilberto Gonzalez-Arroyo
- Galatea Bio, Inc., 975 W 22nd Street, Hialeah, Florida, 33010, USA.,Amphora Health, Batallon Independencia 80, Morelia, Michoacan, 58260, Mexico
| | - Kensuke Numakura
- Genomelink, Inc., 2150 Shattuck Avenue, Berkeley, California, 94704, USA.,Awakens Japan K.K., 2-11-3 Meguro, Meguro-ku, Tokyo, 1530063, Japan
| | - Yuta Matsuda
- Genomelink, Inc., 2150 Shattuck Avenue, Berkeley, California, 94704, USA.,Awakens Japan K.K., 2-11-3 Meguro, Meguro-ku, Tokyo, 1530063, Japan
| | - Alexander Ioannidis
- Galatea Bio, Inc., 975 W 22nd Street, Hialeah, Florida, 33010, USA.,Department of Biomedical Data Science, Stanford University School of Medicine, 1265 Welch Road, Stanford, California, 94305, USA
| | | | - Tomohiro Takano
- Genomelink, Inc., 2150 Shattuck Avenue, Berkeley, California, 94704, USA. .,Awakens Japan K.K., 2-11-3 Meguro, Meguro-ku, Tokyo, 1530063, Japan.
| | - Carlos D Bustamante
- Galatea Bio, Inc., 975 W 22nd Street, Hialeah, Florida, 33010, USA. .,Department of Biomedical Data Science, Stanford University School of Medicine, 1265 Welch Road, Stanford, California, 94305, USA. .,Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, California, 94158, USA.
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Kidd KK, Pakstis AJ, Gandotra N, Scharfe C, Podini D. A multipurpose panel of microhaplotypes for use with STR markers in casework. Forensic Sci Int Genet 2022; 60:102729. [PMID: 35696960 DOI: 10.1016/j.fsigen.2022.102729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 03/25/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 11/19/2022]
Abstract
A small panel of highly informative loci that can be genotyped on the same equipment as the standard CODIS short tandem repeat (STR) markers has strong potential for application in forensic casework. Single nucleotide polymorphisms (SNPs) can be typed by a couple of methods on capillary electrophoresis (CE) machines and on sequencers, but the amount of information relative to the laboratory effort has hindered use of SNPs in actual casework. Insertion-deletion markers (InDels) suffer from similar problems. Microhaplotypes (MHs) are much more informative per locus but have similar technical difficulties unless they are typed by massively parallel sequencing (MPS). As forensic labs are acquiring sequencing machines, MHs become more likely to be used in casework, especially if multiplexed with STRs. Here we present the details of a multipurpose panel of 24 MHs with the highest effective number of alleles (Ae) from previous work. An augmented STR panel of 24 loci (20 CODIS markers plus four commonly typed STRs) is also considered. The Ae and ancestry informativeness (In) distributions of these two datasets are compared. The MH panel is shown to have better individualization and population distinction than the augmented CODIS STRs. We note that the 24 MHs should be better for mixture analyses than the STRs. Finally, we suggest that a commercial kit including both the standard CODIS markers and this set of 24 MH would greatly improve the discrimination power over that of current commercial assays.
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Affiliation(s)
- Kenneth K Kidd
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States.
| | - Andrew J Pakstis
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States
| | - Neeru Gandotra
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States
| | - Curt Scharfe
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States
| | - Daniele Podini
- The George Washington University, Department of Forensic Science, 2100 Foxhall Road, NW, Washington, DC 20007, United States
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Raveane A, Molinaro L, Aneli S, Capodiferro MR, de Gennaro L, Ongaro L, Rambaldi Migliore N, Soffiati S, Scarano T, Torroni A, Achilli A, Ventura M, Pagani L, Capelli C, Olivieri A, Bertolini F, Semino O, Montinaro F. Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy. Genomics 2022; 114:110405. [PMID: 35709925 DOI: 10.1016/j.ygeno.2022.110405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022]
Abstract
Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithization and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidences point to a link between Southern Italians and the Balkans still present in modern times. To shed light on these dynamics, we analysed around 700 South Mediterranean genomes combined with informative ancient DNAs. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with a Bronze Age component ultimately originating from the Caucasus with high Iranian and Anatolian Neolithic ancestries. Furthermore, extremely differentiated allele frequencies among Northern and Southern Italy revealed putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits.
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Morishima Y, Morishima S, Stevenson P, Kodera Y, Horowitz M, McKallor C, Malkki M, Spellman SR, Gooley T, Petersdorf EW. Race and Survival in Unrelated Hematopoietic Cell Transplantation. Transplant Cell Ther 2022; 28:357.e1-357.e6. [PMID: 35405366 DOI: 10.1016/j.jtct.2022.03.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/14/2022] [Accepted: 03/30/2022] [Indexed: 11/18/2022]
Abstract
Survival after hematopoietic cell transplantation depends on race/ethnicity and histocompatibility (HLA) between the patient and transplant donor. HLA sequence variation is a genetic construct of continental populations, but its role in accounting for racial disparities of transplant outcome is unknown. To determine disparities in transplant survivorship among patients of diverse race while accounting for patient and donor HLA variation. A total of 26,945 self-described Japanese, U.S. Asian, White, Hispanic, and Black patients received an unrelated donor transplant for the treatment of a life-threatening blood disorder. The risk of mortality with and without adjustment for known HLA risk factors (number and location of donor mismatches; patient HLA-B leader genotype and HLA-DRβ peptide-binding motif) was studied using multivariable models. Survival after HLA-matched transplantation for patients with optimal leader and peptide-binding features was estimated for each race, as was the improvement in survival over calendar-year time by considering year of transplantation as a continuous linear variable. The number, location, and nature of donor HLA mismatches and the frequency of patient HLA-B and HLA-DRB1 sequence motifs differed by race. Japanese patients had superior survival compared to other races without consideration of HLA. After HLA adjustment, three mortality risk strata were identified: Japanese and U.S. Asian (low-risk); White and Hispanic (intermediate-risk), and Black patients (high-risk). Survival for patients with optimal donor and HLA characteristics was superior for Japanese, intermediate for U.S. Asian, White, and Hispanic, and lowest for Black patients. Five-year increments of transplant year were associated with greater decreases in mortality hazards for Black and Hispanic patients than for Japanese, U.S. Asian and White patients. Transplant survivorship disparities are influenced by HLA as a genetic construct of race. A more complete understanding of the factors that influence transplant outcomes provides opportunities to narrow disparities for future patients.
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Affiliation(s)
- Yasuo Morishima
- Department of Promotion for Blood and Marrow Transplantation, Aichi Medical University, Nagakute Japan; Department of Hematology and Oncology, Nakagami Hospital, Okinawa, Japan.
| | - Satoko Morishima
- Division of Endocrinology, Diabetes and Metabolism, Hematology and Rheumatology, Second Department of Internal Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Phil Stevenson
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Yoshihisa Kodera
- Japan Marrow Donor Program, Tokyo, Japan; Center for Hematopoietic Stem Cell Transplantation, Aichi Medical University Hospital, Nagakute, Japan
| | - Mary Horowitz
- Center for International Blood and Marrow Transplant Research, Milwaukee, Wisconsin; Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Caroline McKallor
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mari Malkki
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Ted Gooley
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Effie W Petersdorf
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Medicine, University of Washington, Seattle, Washington.
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Constantinescu AE, Mitchell RE, Zheng J, Bull CJ, Timpson NJ, Amulic B, Vincent EE, Hughes DA. A framework for research into continental ancestry groups of the UK Biobank. Hum Genomics 2022; 16:3. [PMID: 35093177 PMCID: PMC8800339 DOI: 10.1186/s40246-022-00380-5] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/18/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The UK Biobank is a large prospective cohort, based in the UK, that has deep phenotypic and genomic data on roughly a half a million individuals. Included in this resource are data on approximately 78,000 individuals with "non-white British ancestry." While most epidemiology studies have focused predominantly on populations of European ancestry, there is an opportunity to contribute to the study of health and disease for a broader segment of the population by making use of the UK Biobank's "non-white British ancestry" samples. Here, we present an empirical description of the continental ancestry and population structure among the individuals in this UK Biobank subset. RESULTS Reference populations from the 1000 Genomes Project for Africa, Europe, East Asia, and South Asia were used to estimate ancestry for each individual. Those with at least 80% ancestry in one of these four continental ancestry groups were taken forward (N = 62,484). Principal component and K-means clustering analyses were used to identify and characterize population structure within each ancestry group. Of the approximately 78,000 individuals in the UK Biobank that are of "non-white British" ancestry, 50,685, 6653, 2782, and 2364 individuals were associated to the European, African, South Asian, and East Asian continental ancestry groups, respectively. Each continental ancestry group exhibits prominent population structure that is consistent with self-reported country of birth data and geography. CONCLUSIONS Methods outlined here provide an avenue to leverage UK Biobank's deeply phenotyped data allowing researchers to maximize its potential in the study of health and disease in individuals of non-white British ancestry.
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Affiliation(s)
- Andrei-Emil Constantinescu
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
- School of Translational Health Sciences, University of Bristol, Bristol, UK
| | - Ruth E Mitchell
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Jie Zheng
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Caroline J Bull
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
- School of Translational Health Sciences, University of Bristol, Bristol, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Borko Amulic
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Emma E Vincent
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
- School of Translational Health Sciences, University of Bristol, Bristol, UK
| | - David A Hughes
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK.
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK.
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Hatoum AS, Wendt FR, Galimberti M, Polimanti R, Neale B, Kranzler HR, Gelernter J, Edenberg HJ, Agrawal A. Ancestry may confound genetic machine learning: Candidate-gene prediction of opioid use disorder as an example. Drug Alcohol Depend 2021; 229:109115. [PMID: 34710714 PMCID: PMC9358969 DOI: 10.1016/j.drugalcdep.2021.109115] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/29/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Machine learning (ML) models are beginning to proliferate in psychiatry, however machine learning models in psychiatric genetics have not always accounted for ancestry. Using an empirical example of a proposed genetic test for OUD, and exploring a similar test for tobacco dependence and a simulated binary phenotype, we show that genetic prediction using ML is vulnerable to ancestral confounding. METHODS We utilize five ML algorithms trained with 16 brain reward-derived "candidate" SNPs proposed for commercial use and examine their ability to predict OUD vs. ancestry in an out-of-sample test set (N = 1000, stratified into equal groups of n = 250 cases and controls each of European and African ancestry). We rerun analyses with 8 random sets of allele-frequency matched SNPs. We contrast findings with 11 genome-wide significant variants for tobacco smoking. To document generalizability, we generate and test a random phenotype. RESULTS None of the 5 ML algorithms predict OUD better than chance when ancestry was balanced but were confounded with ancestry in an out-of-sample test. In addition, the algorithms preferentially predicted admixed subpopulations. Random sets of variants matched to the candidate SNPs by allele frequency produced similar bias. Genome-wide significant tobacco smoking variants were also confounded by ancestry. Finally, random SNPs predicting a random simulated phenotype show that the bias attributable to ancestral confounding could impact any ML-based genetic prediction. CONCLUSIONS Researchers and clinicians are encouraged to be skeptical of claims of high prediction accuracy from ML-derived genetic algorithms for polygenic traits like addiction, particularly when using candidate variants.
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Affiliation(s)
- Alexander S Hatoum
- Washington University in St. Louis, School of Medicine, Department of Psychiatry, USA.
| | - Frank R Wendt
- Department of Psychiatry, Division of Human Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Marco Galimberti
- Department of Psychiatry, Division of Human Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Renato Polimanti
- Department of Psychiatry, Division of Human Genetics, Yale School of Medicine, New Haven, CT, USA; Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Benjamin Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Henry R Kranzler
- Center for Studies of Addiction, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; VISN 4 MIRECC, Crescenz VAMC, Philadelphia, PA, USA
| | - Joel Gelernter
- Department of Psychiatry, Division of Human Genetics, Yale School of Medicine, New Haven, CT, USA; Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA; Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Howard J Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Arpana Agrawal
- Washington University in St. Louis, School of Medicine, Department of Psychiatry, USA
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Kidd KK, Bulbul O, Gurkan C, Dogan M, Dogan S, Neophytou PI, Cherni L, Gurwitz D, Speed WC, Murtha M, Kidd JR, Pakstis AJ. Genetic relationships of Southwest Asian and Mediterranean populations. Forensic Sci Int Genet 2021; 53:102528. [PMID: 34020230 DOI: 10.1016/j.fsigen.2021.102528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 11/23/2022]
Abstract
The Southwest Asian, circum-Mediterranean, and Southern European populations (collectively, SWAMSE) together with Northern European populations form one of five "continental" groups of global populations in many analyses of population relationships. This region is of great anthropologic and forensic interest but relationships of large numbers of populations within the region have not been able to be cleanly resolved with autosomal genetic markers. To examine the genetic boundaries to the SWAMSE region and whether internal structure can be detected we have assembled data for a total of 151 separate autosomal genetic markers on populations in this region and other parts of the world for a global set of 95 populations. The markers include 83 ancestry informative SNPs as singletons and 68 microhaplotype loci defined by 204 SNPs. The 151 loci are ancestry informative on a global scale, identifying at least five biogeographic clusters. One of those clusters is a clear grouping of 37 populations containing the SWAMSE plus northern European populations to the exclusion of populations in South Central Asia and populations from farther East. A refined analysis of the 37 populations shows the northern European populations clustering separately from the SWAMSE populations. Within Southwest Asia the Samaritans and Shabaks are distinct outliers. The Yemenite Jews, Saudi, Kuwaiti, Palestinian Arabs, and Southern Tunisians cluster together loosely while the remaining populations from Northern Iraq, Mediterranean Europe, the Caucasus region, and Iran cluster in a more complex graded fashion. The majority of the SWAMSE populations from the mainland of Southwest Asia form a cluster with little internal structure reflecting a very complex history of endogamy and migrations. The set of 151 DNA polymorphisms not only distinguishes major geographical regions globally but can distinguish ancestry to a small degree within geographical regions such as SWAMSE. We discuss forensic characteristics of the polymorphisms and also identify those that rank highest by Rosenberg's In measure for the SWAMSE region populations and for the global set of populations analyzed. DATA AVAILABILITY: Genotypes on all 151 markers for all 3790 individuals typed in the Kidd Lab on the 72 Kidd lab populations have been deposited in the Zenodo archive and can be freely accessed at https://doi.org/10.5281/zenodo.4658892. Some of the data has been made public previously as supplemental files appended to publications. Data for the additional individuals included in the analyses was taken from already public datasets as indicated in the text.
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Hardy DS, Racette SB, Garvin JT, Gebrekristos HT, Mersha TB. Ancestry specific associations of a genetic risk score, dietary patterns and metabolic syndrome: a longitudinal ARIC study. BMC Med Genomics 2021; 14:118. [PMID: 33933074 PMCID: PMC8088631 DOI: 10.1186/s12920-021-00961-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/15/2021] [Indexed: 01/08/2023] Open
Abstract
Background Associations have been observed among genetic variants, dietary patterns, and metabolic syndrome (MetS). A gap in knowledge is whether a genetic risk score (GRS) and dietary patterns interact to increase MetS risk among African Americans. We investigated whether MetS risk was influenced by interaction between a GRS and dietary patterns among Whites and African Americans. A secondary aim examined if molecular genetic clusterings differed by racial ancestry. Methods We used longitudinal data over 4-visits (1987–1998) that included 10,681 participants aged 45–64y at baseline from the Atherosclerosis Risk in Communities study (8451 Whites and 2230 African Americans). We constructed a simple-count GRS as the linear weighted sum of high-risk alleles (0, 1, 2) from cardiovascular disease polymorphisms from the genome-wide association studies catalog associated with MetS risk. Three dietary patterns were determined by factor analysis of food frequency questionnaire data: Western, healthy, and high-fat dairy. MetS was defined according to the 2016 National Cholesterol Education Program Adult Treatment Panel III criteria but used 2017 American Heart Association/American College of Cardiology criteria for elevated blood pressure. Analyses included generalized linear model risk ratios (RR), 95% confidence intervals (CI), and Bonferroni correction for multiple testing. Results The Western dietary pattern was associated with higher risk for MetS across increasing GRS tertiles among Whites (p < 0.017). The high-fat dairy pattern was protective against MetS, but its impact was most effective in the lowest GRS tertile in Whites (RR = 0.62; CI: 0.52–0.74) and African Americans (RR = 0.67; CI: 0.49–0.91). Among each racial group within GRS tertiles, the Western dietary pattern was associated with development and cycling of MetS status between visits, and the high-fat dairy pattern with being free from MetS (p < 0.017). The healthy dietary pattern was associated with higher risk of MetS among African Americans which may be explained by higher sucrose intake (p < 0.0001). Fewer genes, but more metabolic pathways for obesity, body fat distribution, and lipid and carbohydrate metabolism were identified in African Americans than Whites. Some polymorphisms were linked to the Western and high-fat dairy patterns. Conclusion The influence of dietary patterns on MetS risk appears to differ by genetic predisposition and racial ancestry. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-00961-8.
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Affiliation(s)
- Dale S Hardy
- Department of Internal Medicine, Morehouse School of Medicine, 720 Westview Drive, Atlanta, GA, 30310, USA.
| | - Susan B Racette
- Program in Physical Therapy and Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Jane T Garvin
- College of Nursing, Augusta University, Augusta, GA, 30912, USA
| | - Hirut T Gebrekristos
- Department of Internal Medicine, Morehouse School of Medicine, 720 Westview Drive, Atlanta, GA, 30310, USA
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, 3333 Burnet Ave, Cincinnati, OH, 45229, USA
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Ukaegbu C, Levi Z, Fehlmann TD, Uno H, Chittenden A, Inra JA, Grover S, Kastrinos F, Syngal S, Yurgelun MB. Characterizing germline APC and MUTYH variants in Ashkenazi Jews compared to other individuals. Fam Cancer 2021; 20:111-116. [PMID: 32743790 PMCID: PMC7854904 DOI: 10.1007/s10689-020-00198-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/25/2020] [Indexed: 12/20/2022]
Abstract
Germline variants in the APC and MUTYH genes contribute to colorectal cancer (CRC) and adenoma risk, though may occur with varying frequencies in individuals of different ancestries. The aim of this study was to evaluate the prevalence of APC, monoallelic MUTYH and biallelic MUTYH germline variants in Ashkenazi Jewish (AJ) and Other Ancestry (OA) individuals with colorectal adenomas. We studied 7225 individuals with colorectal adenomas who had germline APC and MUTYH testing at a commercial laboratory. Cross-sectional medical history data were extracted from provider-completed test requisition forms. We performed bivariate analysis to compare the frequency of APC and MUTYH variants between AJ and OA, and examined APC p.I1307K and monoallelic MUTYH carrier phenotypes using logistic regression. Pathogenic APC variants occurred in 38/285 AJ (13%) and 1342/6940 OA (19%; P = 0.09); biallelic MUTYH variants in 2/285 (1%) AJ and 399/6940 (6%) OA (P < 0.0001); APC p.I1307K in 35/285 (12%) AJ and 29/6940 (1%) OA (P < 0.0001); and monoallelic MUTYH in 2/285 (1%) AJ and 133/6940 (2%) OA (P = 0.06). Monoallelic MUTYH variants were significantly associated with having a personal history of CRC, regardless of ancestry (OR 1.78; 95% CI 1.21-2.49; P < 0.01), but no significant association was found between APC p.I1307K variants and personal history of CRC (OR 1.38; 95% CI 0.79-2.44; P = 0.26). Ashkenazim with colorectal adenomas rarely have monoallelic or biallelic MUTYH variants, suggesting different genetic etiologies for polyposis in AJ compared to OA individuals. AJ ancestry assessment may be important in clinical evaluation for polyposis.
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Affiliation(s)
- Chinedu Ukaegbu
- Division of Population Sciences, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, USA
| | - Zohar Levi
- The Gastroenterology Department, Rabin Medical Center, Petach Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Tara D Fehlmann
- Division of Population Sciences, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Hajime Uno
- Division of Population Sciences, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Anu Chittenden
- Division of Population Sciences, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | | | - Shilpa Grover
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Fay Kastrinos
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, New York, NY, USA
| | - Sapna Syngal
- Division of Population Sciences, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew B Yurgelun
- Division of Population Sciences, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
- Harvard Medical School, Boston, MA, USA.
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Brooks SA. Genomics in the Horse Industry: Discovering New Questions at Every Turn. J Equine Vet Sci 2021; 100:103456. [PMID: 34030792 DOI: 10.1016/j.jevs.2021.103456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 01/25/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 10/21/2022]
Abstract
The sheer diversity of heritable physiological traits, and the ingenuity of genome derived research technologies, extends the study of genetics to impact diverse scientific fields. Equine science is no exception, experiencing a number of genome-enabled discoveries that spur further research in areas like nutrition, reproduction, and exercise physiology. Yet unexpected findings, especially those that over-turn commonly held beliefs in the horse industry, can create challenges in outreach, education and communication with stakeholders. For example, studies of ancient DNA revealed that the oldest domesticated equids in the archeological record were in fact another species, the Przewalski's horse, leaving the origins of our modern horses a mystery yet to be solved. Genomic analysis of ancestry can illuminate relationships older than our prized pedigree records, and in some cases, identify unexpected inconsistencies in those pedigrees. Even our interpretation of what constitutes a genetic disease is changing, as we re-examine common disease alleles; how these alleles impact equine physiology, and how they are perceived by breeders and professionals in the industry. Effectively translating genetic tools for utilization in horse management and preparing our community for the debate surrounding ethical questions that may arise from genomic studies, may be the next great challenges we face as scientists and educators.
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Affiliation(s)
- Samantha A Brooks
- Department of Animal Sciences and the UF Genetics Institute, University of Florida, Gainesville Fl.
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Abou Alaiwi S, Nassar AH, Adib E, Groha SM, Akl EW, McGregor BA, Esplin ED, Yang S, Hatchell K, Fusaro V, Nielsen S, Kwiatkowski DJ, Sonpavde GP, Pomerantz M, Garber JE, Freedman ML, Rana HQ, Gusev A, Choueiri TK. Trans-ethnic variation in germline variants of patients with renal cell carcinoma. Cell Rep 2021; 34:108926. [PMID: 33789101 DOI: 10.1016/j.celrep.2021.108926] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 09/12/2020] [Revised: 10/27/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Prior studies of the renal cell carcinoma (RCC) germline landscape investigated predominantly patients of European ancestry. We examine the frequency of germline pathogenic and likely pathogenic (P/LP) variants in 1,829 patients with RCC from various ancestries. Overall, P/LP variants are found in 17% of patients, among whom 10.3% harbor one or more clinically actionable variants with potential preventive or therapeutic utility. Patients of African ancestry with RCC harbor significantly more P/LP variants in FH compared to patients of non-African ancestry with RCC and African controls from the Genome Aggregation Database (gnomAD). Patients of non-African ancestry have significantly more P/LP variants in CHEK2 compared to patients of African ancestry with RCC and non-Finnish Europeans controls. Non-Africans with RCC have more actionable variants compared to Africans with RCC. This work helps understand the underlying biological differences in RCC between Africans and non-Africans and paves the way to more comprehensive genomic characterization of underrepresented populations.
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Affiliation(s)
- Sarah Abou Alaiwi
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amin H Nassar
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine and Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elio Adib
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine and Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stefan M Groha
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Elie W Akl
- Division of Pulmonary and Critical Care Medicine and Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bradley A McGregor
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Shan Yang
- Invitae Corporation, San Francisco, CA, USA
| | | | | | | | - David J Kwiatkowski
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine and Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Guru P Sonpavde
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark Pomerantz
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Division of Population Sciences, Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Huma Q Rana
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Division of Population Sciences, Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander Gusev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Toni K Choueiri
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine and Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Tamimy Z, Kevenaar ST, Hottenga JJ, Hunter MD, de Zeeuw EL, Neale MC, van Beijsterveldt CEM, Dolan CV, van Bergen E, Boomsma DI. Multilevel Twin Models: Geographical Region as a Third Level Variable. Behav Genet 2021; 51:319-30. [PMID: 33638732 DOI: 10.1007/s10519-021-10047-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/21/2021] [Indexed: 12/24/2022]
Abstract
The classical twin model can be reparametrized as an equivalent multilevel model. The multilevel parameterization has underexplored advantages, such as the possibility to include higher-level clustering variables in which lower levels are nested. When this higher-level clustering is not modeled, its variance is captured by the common environmental variance component. In this paper we illustrate the application of a 3-level multilevel model to twin data by analyzing the regional clustering of 7-year-old children’s height in the Netherlands. Our findings show that 1.8%, of the phenotypic variance in children’s height is attributable to regional clustering, which is 7% of the variance explained by between-family or common environmental components. Since regional clustering may represent ancestry, we also investigate the effect of region after correcting for genetic principal components, in a subsample of participants with genome-wide SNP data. After correction, region no longer explained variation in height. Our results suggest that the phenotypic variance explained by region might represent ancestry effects on height.
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Zhang Y, Wang S, He H, Wang X, Zhu D, Wen X, Zhang S. Evaluation of three microhaplotypes in individual identification and ancestry inference. Forensic Sci Int 2021; 320:110681. [PMID: 33549990 DOI: 10.1016/j.forsciint.2021.110681] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022]
Abstract
Microhaplotype as an emerging genetic marker has attracted more attention in forensic field. The purpose of this study was to evaluate the potential of microhaplotypes in individual identification and ancestry inference in Chinese Hainan Li and 26 1000 G populations. Three microhaplotypes were genotyped from 100 Li individuals using Agena MassARRAY. Moreover, 2504 individuals from 26 populations (1000 Genomes Project database) were enrolled. The genotypes frequencies of microhaplotypes in each population were calculated by the Plink software. We used Structure, Arlequin, and MEGA6 software to analyze the genetic structure, differentiation and genetic background difference, respectively. The forensic parameters of these microhaplotypes were calculated using Modified Powerstats software. The distribution of genotypes frequencies of three microhaplotypes elaborated the high diversities among the Li and 26 1000 G populations. Li population had a close genetic relationship with EAS populations using structure analysis. No differentiation was observed between Li and CHS population by Fst analysis. The NJ tree showed that the genetic background of Li and CHS is most similar. The average heterozygosity (HE), probability of match (PM), power of discrimination (PD), probability of exclusion (PE) and polymorphism information content (PIC) values for the three microhaplotypes in 27 populations were 0.535, 0.497, 0.465, 0.325, and 0.481, respectively. In conclusion, our results revealed three microhaplotypes as individual identification and ancestry inference genetic markers among Li population and 26 1000 G populations. Future studies are needed to confirm our results with larger samples and select much higher forensic efficacy microhaplotypes.
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Affiliation(s)
- Yingai Zhang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China; School of Life and Pharmaceutical Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Shunlan Wang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Haowei He
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Xianwen Wang
- Criminal Technical Detachment, Haikou City Public Security Bureau, Haikou, Hainan, 570208, China
| | - Dan Zhu
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Xiaohong Wen
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Shufang Zhang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China.
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Sendur SN, Yildiz BO. Influence of ethnicity on different aspects of polycystic ovary syndrome: a systematic review. Reprod Biomed Online 2020; 42:799-818. [PMID: 33487557 DOI: 10.1016/j.rbmo.2020.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 08/20/2020] [Revised: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 01/16/2023]
Abstract
This systematic review aimed to assess variations in the clinical presentation and treatment outcomes of patients with polycystic ovary syndrome (PCOS) belonging to different ethnicities. A search was performed for studies comparing various clinical aspects of PCOS in two or more different ethnic groups. After screening 2264 studies, 35 articles were included in the final analysis. In comparison with White women with PCOS (wPCOS), East Asian women with PCOS (eaPCOS) were less hirsute, whereas Hispanic women with PCOS (hPCOS), South Asian women with PCOS (saPCOS) and Middle Eastern women with PCOS (mePCOS) were more hirsute. saPCOS had higher androgen and lower sex hormone-binding globulin (SHBG) concentrations, mePCOS had higher DHEAS concentrations, and hPCOS and Black women with PCOS (bPCOS) had lower SHBG and DHEAS measures than wPCOS. Menstrual disturbances were more frequent in eaPCOS. Both saPCOS and eaPCOS had lower body mass index with increased central adiposity. hPCOS and bPCOS were more obese. saPCOS, mePCOS, hPCOS and bPCOS had a higher prevalence of insulin resistance than wPCOS. bPCOS had a better lipid profile but higher blood pressure and cardiovascular risk. Indigenous Australian women with PCOS were more obese and more insulin resistant with higher androgen concentrations. The clinical phenotype of PCOS therefore shows a wide variation depending on ethnicity.
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Affiliation(s)
- Suleyman N Sendur
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Hacettepe University School of Medicine, Hacettepe Ankara, Turkey
| | - Bulent O Yildiz
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Hacettepe University School of Medicine, Hacettepe Ankara, Turkey.
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Burgueño-Rodríguez G, Méndez Y, Olano N, Dabezies A, Bertoni B, Souto J, Castillo L, da Luz J, Soler AM. Ancestry and TPMT-VNTR Polymorphism: Relationship with Hematological Toxicity in Uruguayan Patients with Acute Lymphoblastic Leukemia. Front Pharmacol 2020; 11:594262. [PMID: 33424606 PMCID: PMC7789872 DOI: 10.3389/fphar.2020.594262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
6-Mercaptopurine (6-MP) is a thiopurine drug widely used in childhood acute lymphoblastic leukemia (ALL) therapy. Genes such as TPMT and NUDT15 have an outstanding role in 6-MP metabolism. Mutations in both genes explain a significant portion of hematological toxicities suffered by ALL Uruguayan pediatric patients. A variable number tandem repeat in the TPMT promoter (TPMT-VNTR) has been associated with TPMT expression. This VNTR has a conservative architecture (AnBmC). To explore new causes of hematological toxicities related to ALL therapy, we genotyped the TPMT-VNTR of 130 Uruguayan pediatric patients. Additionally, individual genetic ancestry was estimated by 45 ancestry-informative markers (AIMs). Hematological toxicity was measured as the number of leukopenia events and 6-MP dose along the maintenance phase. As previously reported, we found TPMT*2 and TPMT*3C alleles were associated to TPMT-VNTR A2BC and AB2C, respectively. However, contrasting with other reports, TPMT*3A allele was found in a heterogeneous genetic background in linkage equilibrium. Patients carrying more than 5 A repeats present a significant higher number of leukopenia events among patients without TPMT and/or NUDT15 variants. Native American ancestry and the number of A repeats were significantly correlated with the number of leukopenia events. However, the correlation between Native American ancestry and the number of leukopenia events was lost when the number of A repeats was considered as covariate. This suggests that TPMT-VNTR alleles are more relevant than Native American ancestry in the hematological toxicity. Our results emphasize that TPMT-VNTR may be used as a pharmacogenetic biomarker to predict 6-MP-related hematological toxicity in ALL childhood therapy.
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Affiliation(s)
- Gabriela Burgueño-Rodríguez
- Laboratorio de Genética Molecular Humana, Centro Universitario Regional (CENUR) Litoral Norte-Sede Salto, Universidad de la República (UdelaR), Salto, Uruguay
| | - Yessika Méndez
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Natalia Olano
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Agustín Dabezies
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Jorge Souto
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Luis Castillo
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Julio da Luz
- Laboratorio de Genética Molecular Humana, Centro Universitario Regional (CENUR) Litoral Norte-Sede Salto, Universidad de la República (UdelaR), Salto, Uruguay
| | - Ana María Soler
- Laboratorio de Genética Molecular Humana, Centro Universitario Regional (CENUR) Litoral Norte-Sede Salto, Universidad de la República (UdelaR), Salto, Uruguay
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Mateen RM, Sabar MF, Hussain S, Parveen R, Hussain M. Familial DNA analysis and criminal investigation: Usage, downsides and privacy concerns. Forensic Sci Int 2020; 318:110576. [PMID: 33234348 DOI: 10.1016/j.forsciint.2020.110576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 09/14/2020] [Revised: 10/07/2020] [Accepted: 11/01/2020] [Indexed: 02/08/2023]
Abstract
Since the discovery of Deoxyribonucleic acid (DNA) capability in forensic investigation, it has been an important part of the criminal justice system. In most criminal cases DNA profile originating from evidence sample collected from the crime scene is compared with the DNA profile from the reference sample. However, when a reference sample is not available for comparison, familial DNA analysis can provide important investigation leads in a criminal investigation process by identifying an individual. Moreover, this analysis is also proving effective in the identification of ethnicity and ancestry of an individual. A number of different methodologies and software are being used for familial DNA analysis. This review describes the importance of familial DNA analysis, methodologies used for familial DNA searching and identification, and its advantages in forensic. Moreover, ethical, legal and social issues associated with familial DNA analysis have also been discussed along with future directions for the proper implementation of this technology.
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Affiliation(s)
- Rana Muhammad Mateen
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | | | - Safdar Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Rukhsana Parveen
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Manzoor Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
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Fortier AL, Kim J, Rosenberg NA. Human-Genetic Ancestry Inference and False Positives in Forensic Familial Searching. G3 (Bethesda) 2020; 10:2893-2902. [PMID: 32586848 PMCID: PMC7407470 DOI: 10.1534/g3.120.401473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/20/2020] [Indexed: 11/18/2022]
Abstract
In forensic familial search methods, a query DNA profile is tested against a database to determine if the query profile represents a close relative of a database entrant. One challenge for familial search is that the calculations may require specification of allele frequencies for the unknown population from which the query profile has originated. The choice of allele frequencies affects the rate at which non-relatives are erroneously classified as relatives, and allele-frequency misspecification can substantially inflate false positive rates compared to use of allele frequencies drawn from the same population as the query profile. Here, we use ancestry inference on the query profile to circumvent the high false positive rates that result from highly misspecified allele frequencies. In particular, we perform ancestry inference on the query profile and make use of allele frequencies based on its inferred genetic ancestry. In a test for sibling matches on profiles that represent unrelated individuals, we demonstrate that false positive rates for familial search with use of ancestry inference to specify the allele frequencies are similar to those seen when allele frequencies align with the population of origin of a profile. Because ancestry inference is possible to perform on query profiles, the extreme allele-frequency misspecifications that produce the highest false positive rates can be avoided. We discuss the implications of the results in the context of concerns about the forensic use of familial searching.
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Affiliation(s)
| | - Jaehee Kim
- Department of Biology, Stanford University, CA 94305
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Marshall C, Taylor R, Sturk-Andreaggi K, Barritt-Ross S, Berg GE, McMahon TP. Mitochondrial DNA haplogrouping to assist with the identification of unknown service members from the World War II Battle of Tarawa. Forensic Sci Int Genet 2020; 47:102291. [PMID: 32315949 DOI: 10.1016/j.fsigen.2020.102291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 01/10/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 11/17/2022]
Abstract
The World War II Battle of Tarawa, 1943, was a devastating conflict that resulted in losses of more than 1100 American and 4690 Japanese troops. The United States government aims to identify and repatriate the remains of all missing American service members through the Defense Prisoner of War/Missing in Action (POW/MIA) Accounting Agency (DPAA) and its partners such as the Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL). Remains associated with the Battle of Tarawa have been recovered from field excavations conducted by History Flight, a DPAA strategic partner, as well as from the National Memorial Cemetery of the Pacific (NMCP) in Hawaii where unknowns have been disinterred for identification. DNA testing at the AFMES-AFDIL has produced mitochondrial DNA (mtDNA) sequences from 1027 case samples to date. Haplogroup assignments indicate that more than one third (36.2 %) of field-collected samples are likely of Asian maternal ancestry. Therefore the field collections from the Tarawa battlefield comprise the remains of American service members but also those of foreign nationals from Asia. The mtDNA of the NMCP unknowns is similar in ancestry proportion to the family reference sample distribution. The DPAA uses the ancestry information gleaned from mtDNA sequence data in conjunction with anthropological evidence to make foreign national determinations. In this way, mtDNA haplogrouping is used to sort the commingled and fragmentary remains recovered from Tarawa between Americans and foreign nationals, which are then repatriated to their country of origin.
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Affiliation(s)
- Charla Marshall
- Armed Forces Medical Examiner System, Dover Air Force Base, DE, USA; SNA International, Alexandria, VA, USA; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
| | - Rebecca Taylor
- Defense POW/MIA Accounting Agency, Joint Base Pearl Harbor-Hickam, HI, USA
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System, Dover Air Force Base, DE, USA; SNA International, Alexandria, VA, USA; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Gregory E Berg
- Defense POW/MIA Accounting Agency, Joint Base Pearl Harbor-Hickam, HI, USA
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de Vries J, Landouré G, Wonkam A. Stigma in African genomics research: Gendered blame, polygamy, ancestry and disease causal beliefs impact on the risk of harm. Soc Sci Med 2020; 258:113091. [PMID: 32521416 PMCID: PMC7396479 DOI: 10.1016/j.socscimed.2020.113091] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022]
Abstract
A recurring concern in genomics research is the possibility that it could lead to stigma for participants, their families and the population groups they belong to. Little evidence exists to explain how and when this ought to be a concern in genomics research in Africa whilst there is growing international evidence drawing into question the direct link between stigma and genetics. In this paper, we interrogate practical instances from African genomics research where stigma was identified as a concern in an attempt to nuance and refine accounts of when stigma should be considered as an ethical issue. The paper describes examples involving gendered blame, polygamy, beliefs in supernatural disease causation and sensitive information about group lineage. We propose that the concern may not be about stigma so much as broader research-related harm, including for instance reputational harm to population groups. Furthermore, we propose to shift the analytical gaze from establishing causal relationships to exploring the intersection of genomics with pre-existing stigma. Finally, we emphasize the importance of ensuring genomics researchers are culturally competent, meaning able to recognise when cultural factors impact on the possibility that genomics research could cause harm.
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Affiliation(s)
- Jantina de Vries
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa.
| | - Guida Landouré
- Faculté de Médecine et d'Odontostomatologie, USTTB, Bamako, Mali; Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Ambroise Wonkam
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa; Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa; Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa
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48
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Abstract
In an examination of three unwrapped mummified children from the Graeco-Roman Period of ancient Egypt there was an unexpected finding of fair hair. In the majority of unwrapped ancient Egyptian mummified bodies the hair was not fair but rather dark brown or black. To determine if exposure to natron during the mummification process was responsible for the fair hair color an experiment was carried out to partially replicate the environment in which bodies were desiccated. Fourteen samples of modern hair from various age groups, sex and ethnicity were subjected to synthetic natron for a period of 40 days to replicate the time taken to mummify a body. Macroscopic and microscopic examinations of samples were employed to ascertain any significant changes in hair color after treatment. Ancient wigs were studied for evidence of post mortem changes to hair color since construction over 2,000 years ago. Results of the study showed no significant lightening of hair color and in several samples the hair significantly darkened as the result of exposure to the natron. There was not any evidence that hair lightened as the result of natural post mortem changes and this was confirmed by the study of the natural hair wigs that had not changed color post mortem. This study concluded that the fair hair observed in the three child mummies was not the result of exposure to natron or post mortem changes but rather it was probably due to ancestry because of the presence of diverse genomes that were introduced into ancient Egypt during the Greco-Roman Period.
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Affiliation(s)
- Janet Davey
- Department of Forensic Medicine, Monash University, Melbourne, Australia. .,Victorian Institute of Forensic Medicine, 65 Kavanagh St., Southbank,, 3006 Victorian, Australia.
| | - Gale Spring
- School of Science, RMIT University, 124 La Trobe St., Melbourne, 3000, Australia
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49
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Andersen JD, Meyer OS, Simão F, Jannuzzi J, Carvalho E, Andersen MM, Pereira V, Børsting C, Morling N, Gusmão L. Skin pigmentation and genetic variants in an admixed Brazilian population of primarily European ancestry. Int J Legal Med 2020; 134:1569-1579. [PMID: 32385594 DOI: 10.1007/s00414-020-02307-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 12/02/2019] [Accepted: 04/22/2020] [Indexed: 01/16/2023]
Abstract
Although many genes have been shown to be associated with human pigmentary traits and forensic prediction assays exist (e.g. HIrisPlex-S), the genetic knowledge about skin colour remains incomplete. The highly admixed Brazilian population is an interesting study population for investigation of the complex genotype-phenotype architecture of human skin colour because of its large variation. Here, we compared variants in 22 pigmentary genes with quantitative skin pigmentation levels on the buttock, arm, and forehead areas of 266 genetically admixed Brazilian individuals. The genetic ancestry of each individual was estimated by typing 46 AIM-InDels. The mean proportion of genetic ancestry was 68.8% European, 20.8% Sub-Saharan African, and 10.4% Native American. A high correlation (adjusted R2 = 0.65, p < 0.05) was observed between nine SNPs and quantitative skin pigmentation using multiple linear regression analysis. The correlations were notably smaller between skin pigmentation and biogeographic ancestry (adjusted R2 = 0.45, p < 0.05), or markers in the leading forensic skin colour prediction system, the HIrisPlex-S (adjusted R2 = 0.54, p < 0.05). Four of the nine SNPs, OCA2 rs1448484 (rank 2), APBA2 rs4424881 (rank 4), MFSD12 rs10424065 (rank 8), and TYRP1 1408799 (rank 9) were not investigated as part of the HIrisPlex-S selection process, and therefore not included in the HIrisPlex-S model. Our results indicate that these SNPs account for a substantial part of the skin colour variation in individuals of admixed ancestry. Hence, we suggest that these SNPs are considered when developing future skin colour prediction models.
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Affiliation(s)
- Jeppe D Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark.
| | - Olivia S Meyer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Filipa Simão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Juliana Jannuzzi
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Elizeu Carvalho
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Mikkel M Andersen
- Department of Mathematical Sciences, Aalborg University, DK-9000, Aalborg, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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50
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Verdugo RA, Di Genova A, Herrera L, Moraga M, Acuña M, Berríos S, Llop E, Valenzuela CY, Bustamante ML, Digman D, Symon A, Asenjo S, López P, Blanco A, Suazo J, Barozet E, Caba F, Villalón M, Alvarado S, Cáceres D, Salgado K, Portales P, Moreno-Estrada A, Gignoux CR, Sandoval K, Bustamante CD, Eng C, Huntsman S, Burchard EG, Loira N, Maass A, Cifuentes L. Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components. Biol Res 2020; 53:15. [PMID: 32299502 PMCID: PMC7161194 DOI: 10.1186/s40659-020-00284-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Background Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south. Results A panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country’s average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors. Conclusions We have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.
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Affiliation(s)
- Ricardo A Verdugo
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Alex Di Genova
- Mathomics, Centro de Modelamiento Matemático y Centro para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Luisa Herrera
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Mauricio Moraga
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Mónica Acuña
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Soledad Berríos
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Elena Llop
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Carlos Y Valenzuela
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - M Leonor Bustamante
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Departamento de Psiquiatría, y Salud Mental Norte, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Dayhana Digman
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Adriana Symon
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Soledad Asenjo
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Pamela López
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Alejandro Blanco
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - José Suazo
- Instituto de Investigación en Ciencias Odontológicas, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - Emmanuelle Barozet
- Departamento de Sociología, Facultad de Ciencias Sociales, Universidad de Chile, Centro de Estudios de Conflicto y Cohesión, Social, Santiago, Chile
| | - Fresia Caba
- Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Marcelo Villalón
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - Sergio Alvarado
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - Dante Cáceres
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - Katherine Salgado
- Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Pilar Portales
- Corporación Municipal de Desarrollo Social, Iquique, Chile
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, 36821, Mexico
| | | | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, 36821, Mexico
| | | | - Celeste Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Nicolás Loira
- Mathomics, Centro de Modelamiento Matemático y Centro para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Alejandro Maass
- Mathomics, Centro de Modelamiento Matemático y Centro para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile.,Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Lucía Cifuentes
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.
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