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de Barros Rodrigues ML, Rodrigues MP, Norton HL, Mendes-Junior CT, Simões AL, Lawson DJ. Large-scale selection of highly informative microhaplotypes for ancestry inference and population specific informativeness. Forensic Sci Int Genet 2024; 74:103153. [PMID: 39378714 DOI: 10.1016/j.fsigen.2024.103153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 09/30/2024] [Accepted: 10/01/2024] [Indexed: 10/10/2024]
Abstract
Microhaplotypes (MHs) describe physically close genetic markers that are inherited together and are gaining prominence due to their efficiency in forensic, clinical, and population studies. They excel in kinship analysis, DNA mixture detection, and ancestry inference, offering advantages in precision over individual SNPs and STRs. In this study, a pipeline was developed to efficiently select highly informative MHs from large-scale genomic datasets. Over 120,000 MHs were identified from almost a million markers, which allow this non-independent information to be efficiently used for inference. The MHs were compared to SNPs in terms of their informativeness and performance of their subsets in ancestry inference and all the results consistently favored MHs. A method for ranking markers by specific population informativeness was also introduced, which showed improvement in the accuracy of Native American ancestry estimation, overcoming the challenges of its underrepresentation in datasets. In conclusion, this study presents a comprehensive way for selecting highly informative MHs for accurate ancestry inference. The proposed approach and the subsets selected by specific population informativeness offer valuable tools for improving ancestry inference accuracy, particularly for admixed populations as demonstrated for a Brazilian dataset.
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Affiliation(s)
- Maria Luisa de Barros Rodrigues
- Programa de Pós-Graduação em Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900, Brazil.
| | | | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, OH 45221, United States
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-901, Brazil
| | - Aguinaldo Luiz Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900, Brazil
| | - Daniel John Lawson
- Institute of Statistical Sciences, School of Mathematics, Woodland Road, University of Bristol, Bristol BS8 1UG, UK; MRC Integrative Epidemiology Unit, School of Medicine, Oakfield Grove, University of Bristol, Bristol BS8 2BN, UK.
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2
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Mucinski JM, Distefano G, Dubé J, Toledo FGS, Coen PM, Goodpaster BH, DeLany JP. Insulin sensitivity and skeletal muscle mitochondrial respiration in Black and White women with obesity. J Clin Endocrinol Metab 2024:dgae600. [PMID: 39207205 DOI: 10.1210/clinem/dgae600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/09/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
OBJECTIVES Non-Hispanic black women (BW) have a greater risk of type 2 diabetes (T2D) and insulin resistance (IR) compared to non-Hispanic white women (WW). The mechanisms leading to these differences are not understood, and it is unclear whether synergistic effects of race and obesity impact disease risk. To understand the interaction of race and weight, hepatic and peripheral IR were compared in WW and BW with and without obesity. METHODS Hepatic and peripheral IR was measured by a labeled, hyperinsulinemic-euglycemic clamp in BW (n=32) and WW (n=32) with and without obesity. Measurements of body composition, cardiorespiratory fitness, and skeletal muscle (SM) respiration were completed. Data were analyzed by mixed model ANOVA. RESULTS Subjects with obesity had greater hepatic and peripheral IR and lower SM respiration (P<0.001). Despite 14% greater insulin (P=0.066), BW tended to have lower peripheral glucose disposal (Rd; P=0.062), which was driven by women without obesity (P=0.002). BW had significantly lower glucose production (P=0.005), hepatic IR (P=0.024), and maximal coupled and uncoupled respiration (P<0.001) than WW. Maximal coupled and uncoupled SM mitochondrial respiration was strongly correlated with peripheral and hepatic IR (P<0.01). CONCLUSION While BW without obesity had lower Rd than WW, race and obesity did not synergistically impact peripheral IR. Paradoxically, WW with obesity had greater hepatic IR compared to BW. Relationships between SM respiration and IR persisted across a range of body weight. These data provide support for therapies in BW, like exercise, that improve SM mitochondrial respiration to reduce IR and T2D risk.
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Affiliation(s)
| | | | - John Dubé
- School of Arts, Science, and Business, Chatham University, Pittsburgh, PA
| | - Frederico G S Toledo
- Division of Endocrinology and Metabolism, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Paul M Coen
- AdventHealth Orlando, Translational Research Institute, Orlando, FL
| | | | - James P DeLany
- AdventHealth Orlando, Translational Research Institute, Orlando, FL
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3
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Shin J, Hammer MJ, Paul SM, Conley YP, Harris C, Oppegaard K, Morse L, Cooper BA, Levine JD, Miaskowski C. Associations Between Preoperative Shortness of Breath and Potassium Channels Gene Variations in Women With Breast Cancer. Biol Res Nurs 2024:10998004241268088. [PMID: 39137431 DOI: 10.1177/10998004241268088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
OBJECTIVES Shortness of breath is a common symptom in patients with cancer. However, the mechanisms that underlie this troublesome symptom are poorly understood. Therefore, this study aimed to determine the prevalence of and associated risk factors for shortness of breath in women prior to breast cancer surgery and identify associations between shortness of breath and polymorphisms for potassium channel genes. METHODS Patients were recruited prior to breast cancer surgery and completed a self-report questionnaire on the occurrence of shortness of breath. Genotyping of single nucleotides polymorphism (SNPs) in potassium channel genes was performed using a custom array. Multiple logistic regression analyses were done to identify associations between the occurrence of shortness of breath and SNPs in ten candidate genes. RESULTS Of the 398 patients, 11.1% reported shortness of breath. These patients had a lower annual household income, a higher comorbidity burden, and a lower functional status. After controlling for functional status, comorbidity burden, genomic estimates of ancestry and self-reported race and ethnicity, the genetic associations that remained significant in the multiple regression analyses were for potassium voltage-gated channel subfamily D (KCND2) rs12673992, potassium voltage-gated channel modifier subfamily S (KCNS1) rs4499491, and potassium two pore channel subfamily K (KCNK2) rs4411107. CONCLUSIONS While these findings warrant replication, they suggest that alterations in potassium channel function may contribute to the occurrence of shortness of breath in women prior to breast cancer surgery.
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Affiliation(s)
- Joosun Shin
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Steven M Paul
- School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Yvette P Conley
- School of Nursing, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carolyn Harris
- School of Nursing, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Lisa Morse
- School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Bruce A Cooper
- School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Jon D Levine
- VA Portland Health Care System, Portland, OR, USA
| | - Christine Miaskowski
- School of Nursing, University of California San Francisco, San Francisco, CA, USA
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
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4
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Miaskowski C, Conley YP, Levine JD, Cooper BA, Paul SM, Hammer MJ, Oppegaard K, Harris C, Shin J, Abrams G, Asakitogum D, Fu MR, Alismal S. Chronic Decrements in Energy in Women with Breast Cancer are Associated with Cytokine Gene Polymorphisms. Semin Oncol Nurs 2024; 40:151652. [PMID: 38834449 DOI: 10.1016/j.soncn.2024.151652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 06/06/2024]
Abstract
OBJECTIVES Decrements in energy were found in 67% of women who underwent breast cancer surgery. However, no information is available on chronic decrements in energy and associations with inflammation. Purposes were to identify latent classes of patients with distinct average energy profiles from prior to through 12 months after breast cancer surgery; evaluate for differences in demographic and clinical characteristics between the two extreme average energy classes; and evaluate for polymorphisms for cytokine genes associated with membership in the Low energy class. METHODS Women (n = 397) completed assessments of energy prior to and for 12 months following breast cancer surgery. Growth mixture modeling was used to identify classes of patients with distinct average energy profiles. Eighty-two single nucleotide polymorphisms (SNPs) among 15 cytokine genes were evaluated. RESULTS Three distinct energy profiles were identified (ie, Low [27.0%], Moderate [54.4%], Changing [18.6%]). Data from patients in the Low and Moderate energy classes were used in the candidate gene analyses. Five SNPs and one haplotype in six different genes remained significant in logistic regression analyses (ie, interleukin [IL]-1β rs1143623, IL1 receptor 1 rs3917332 IL4 rs2243263, IL6 HapA1 [that consisted of rs1800795, rs2069830, rs2069840, rs1554606, rs2069845, rs2069849, and rs2069861], nuclear factor kappa beta subunit 1 rs170731, tumor necrosis factor rs1799964). For several SNPs for IL6, expression quantitative trait locis were identified in subcutaneous and visceral adipose tissue and thyroid tissue. In addition, skeletal muscle was identified as an expression quantitative trait loci for nuclear factor kappa beta subunit 1. CONCLUSIONS Findings suggest that cytokine genes are involved in the mechanisms that underlie chronic decrements in energy in women following breast cancer surgery. Given the roles of subcutaneous and visceral adipose and thyroid tissues in metabolism and energy balance, the findings related to IL6 suggest that these polymorphisms may have a functional role in the development and maintenance of chronic decrements in energy.
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Affiliation(s)
- Christine Miaskowski
- School of Nursing, University of California, San Francisco; School of Medicine, University of California, San Francisco.
| | | | - Jon D Levine
- School of Medicine, University of California, San Francisco
| | - Bruce A Cooper
- School of Nursing, University of California, San Francisco
| | - Steven M Paul
- School of Nursing, University of California, San Francisco
| | | | | | - Carolyn Harris
- School of Nursing, University of Pittsburgh, Pittsburgh, PA
| | | | - Gary Abrams
- School of Medicine, University of California, San Francisco
| | | | - Mei R Fu
- University of Missouri, Kansas City
| | - Sarah Alismal
- Beckman Research Institute, City of Hope, Duarte, CA
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Goli RC, Chishi KG, Ganguly I, Singh S, Dixit S, Rathi P, Diwakar V, Sree C C, Limbalkar OM, Sukhija N, Kanaka K. Global and Local Ancestry and its Importance: A Review. Curr Genomics 2024; 25:237-260. [PMID: 39156729 PMCID: PMC11327809 DOI: 10.2174/0113892029298909240426094055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/02/2024] [Accepted: 03/11/2024] [Indexed: 08/20/2024] Open
Abstract
The fastest way to significantly change the composition of a population is through admixture, an evolutionary mechanism. In animal breeding history, genetic admixture has provided both short-term and long-term advantages by utilizing the phenomenon of complementarity and heterosis in several traits and genetic diversity, respectively. The traditional method of admixture analysis by pedigree records has now been replaced greatly by genome-wide marker data that enables more precise estimations. Among these markers, SNPs have been the popular choice since they are cost-effective, not so laborious, and automation of genotyping is easy. Certain markers can suggest the possibility of a population's origin from a sample of DNA where the source individual is unknown or unwilling to disclose their lineage, which are called Ancestry-Informative Markers (AIMs). Revealing admixture level at the locus-specific level is termed as local ancestry and can be exploited to identify signs of recent selective response and can account for genetic drift. Considering the importance of genetic admixture and local ancestry, in this mini-review, both concepts are illustrated, encompassing basics, their estimation/identification methods, tools/software used and their applications.
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Affiliation(s)
| | - Kiyevi G. Chishi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Indrajit Ganguly
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Sanjeev Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - S.P. Dixit
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Pallavi Rathi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Vikas Diwakar
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Chandana Sree C
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | | | - Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
- Central Tasar Research and Training Institute, Ranchi, 835303, Jharkhand, India
| | - K.K Kanaka
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, 834010, Jharkhand, India
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Miaskowski C, Conley YP, Cooper BA, Paul SM, Smoot BJ, Hammer MJ, Fu M, Levine JD. Identification Of A Higher Risk Lymphedema Phenotype And Associations With Cytokine Gene Polymorphisms. J Pain Symptom Manage 2024; 67:375-383.e3. [PMID: 38307372 DOI: 10.1016/j.jpainsymman.2024.01.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/04/2024]
Abstract
CONTEXT Breast cancer-related lymphedema (BCRL) is chronic condition that occurs in 5% to 75% of women following treatment for breast cancer. However, little is known about the risk factors and mechanisms associated with a worse BCRL profile. OBJECTIVES Identify distinct BCRL profiles in women with the condition (i.e., lower vs. higher risk phenotype) and evaluate for associations with pro- and anti-inflammatory genes. METHODS Latent class profile analysis (LCPA) was used to identify the BCRL profiles using phenotypic characteristics evaluated prior to surgery. Candidate gene analyses were done to identify cytokine genes associated with the two BCRL profiles. RESULTS Of the 155 patients evaluated, 35.5% (n = 55) were in the Lower and 64.5% (n = 100) were in the Higher Risk classes. Risk factors for membership in the Higher class included: lower functional status, having sentinel lymph node biopsy, axillary lymph node dissection, mastectomy, higher number of positive lymph nodes, and receipt of chemotherapy. Polymorphisms for interleukin (IL)1-beta and IL6 were associated with membership in the Higher Risk class. CONCLUSION The readily available and clinically relevant phenotypic characteristics associated with a worse BCRL profile can be used by clinicians to identify higher risk patients. If confirmed, these characteristics can be tested in predictive risk models. In addition, the candidate gene findings may guide the development of mechanistically-based interventions to decrease the risk of BCRL.
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Affiliation(s)
- Christine Miaskowski
- School of Nursing, University of California, San Francisco, CA, USA; School of Medicine, University of California, San Francisco, CA, USA.
| | | | - Bruce A Cooper
- School of Nursing, University of California, San Francisco, CA, USA
| | - Steven M Paul
- School of Nursing, University of California, San Francisco, CA, USA
| | - Betty J Smoot
- School of Medicine, University of California, San Francisco, CA, USA
| | | | - Mei Fu
- School of Nursing and Health Studies, University of Missouri, Kansas City, MO, USA
| | - Jon D Levine
- School of Medicine, University of California, San Francisco, CA, USA
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Murphy K, Shi Q, Hoover DR, Adimora AA, Alcaide ML, Brockmann S, Daubert E, Duggal P, Merenstein D, Dionne JA, Sheth AN, Keller MJ, Herold BC, Anastos K, Aouizerat B. Genetic predictors for bacterial vaginosis in women living with and at risk for HIV infection. Am J Reprod Immunol 2024; 91:e13845. [PMID: 38720636 PMCID: PMC11410097 DOI: 10.1111/aji.13845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 03/24/2024] [Accepted: 04/03/2024] [Indexed: 08/29/2024] Open
Abstract
PROBLEM Bacterial vaginosis (BV) disproportionally impacts Black and Hispanic women, placing them at risk for HIV, sexually transmitted infections and preterm birth. It is unknown whether there are differences by genetic ancestry in BV risk or whether polymorphisms associated with BV risk differ by ancestry. METHODS Women's Interagency HIV Study (WIHS) participants with longitudinal Nugent scores were dichotomized as having (n = 319, Nugent 7-10) or not having BV (n = 367, Nugent 0-3). Genetic ancestry was defined by clustering of principal components from ancestry informative markers and further stratified by BV status. 627 single nucleotide polymorphisms (SNPs) across 41 genes important in mucosal defense were identified in the WIHS GWAS. A logistic regression analysis was adjusted for nongenetic predictors of BV and self-reported race/ethnicity to assess associations between genetic ancestry and genotype. RESULTS Self-reported race and genetic ancestry were associated with BV risk after adjustment for behavioral factors. Polymorphisms in mucosal defense genes including syndecans, cytokines and toll-like receptors (TLRs) were associated with BV in all ancestral groups. CONCLUSIONS The common association of syndecan, cytokine and TLR genes and the importance of immune function and inflammatory pathways in BV, suggests these should be targeted for further research on BV pathogenesis and therapeutics.
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Affiliation(s)
- Kerry Murphy
- Departments of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Quihu Shi
- School of Health Sciences and Practice, New York Medical College, Valhalla, New York, USA
| | - Donald R Hoover
- Department of Statistics and Institute for Health, Health Care Policy and Aging Research Rutgers the State University of New Jersey, Piscataway, New Jersey, USA
| | - Adaora A Adimora
- Department of Medicine, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Maria L Alcaide
- Department of Medicine, Obstetrics & Gynecology and Public Health, University of Miami Miller School of Medicine, Miami, USA
| | - Susan Brockmann
- Health Sciences Center, State University of New York, Brooklyn, New York, USA
| | - Elizabeth Daubert
- Cook County Health/Hektoen Institute of Medicine, Chicago, Illinois, USA
| | - Priya Duggal
- Department of Epidemiology and International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Jodie A Dionne
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Anandi N Sheth
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Marla J Keller
- Departments of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Betsy C Herold
- Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Kathryn Anastos
- Departments of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
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Liao L, Sun Y, Huang L, Ye L, Chen L, Shen M. A novel approach for exploring the regional features of vaginal fluids based on microbial relative abundance and alpha diversity. J Forensic Leg Med 2023; 100:102615. [PMID: 37995431 DOI: 10.1016/j.jflm.2023.102615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/14/2023] [Accepted: 11/05/2023] [Indexed: 11/25/2023]
Abstract
Vaginal fluids are one of the most common biological samples in forensic sexual assault cases, and their characterization is vital to narrow the scope of investigation. Presently, approaches for identifying vaginal fluids in different regions are not only rare but also have certain limitations. However, the microbiome has shown the potential to identify the source of body fluids and reveal the characteristics of individuals. In this study, 16S rRNA gene high-throughput sequencing was used to characterize the vaginal microbial community from three regions, Sichuan, Hainan and Hunan. In addition, data on relative abundance and alpha diversity were used to construct a random forest model. The results revealed that the dominant genera in the three regions were Lactobacillus, followed by Gardnerella. In addition, Ureaplasma, Nitrospira, Nocardiodes, Veillonella and g-norank-f-Vicinamibacteraceae were significantly enriched genera in Sichuan, llumatobacter was enriched in Hainan, and Pseudomonas was enriched in Hunan. The random forest classifier based on combined data on relative abundance and alpha diversity had a good ability to distinguish vaginal fluids with similar dominant microbial compositions in the three regions. The study suggests that combining high-throughput sequencing data with machine learning models has good potential for application in the biogeographic inference of vaginal fluids.
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Affiliation(s)
- Lili Liao
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China; Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yunxia Sun
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Litao Huang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Linying Ye
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Mei Shen
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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Geris JM, Amirian ES, Marquez-Do DA, Guillaud M, Dillon LM, Follen M, Scheurer ME. Polymorphisms in the Nonhomologous End-joining DNA Repair Pathway are Associated with HPV Integration in Cervical Dysplasia. Cancer Prev Res (Phila) 2023; 16:461-469. [PMID: 37217238 PMCID: PMC10524768 DOI: 10.1158/1940-6207.capr-23-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/06/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
Previous evidence indicates that human papillomavirus (HPV) integration status may be associated with cervical cancer development and progression. However, host genetic variation within genes that may play important roles in the viral integration process is understudied. The aim of this study was to examine the association between HPV16 and HPV18 viral integration status and SNPs in nonhomologous-end-joining (NHEJ) DNA repair pathway genes on cervical dysplasia. Women enrolled in two large trials of optical technologies for cervical cancer detection and positive for HPV16 or HPV18 were selected for HPV integration analysis and genotyping. Associations between SNPs and cytology (normal, low-grade, or high-grade lesions) were evaluated. Among women with cervical dysplasia, polytomous logistic regression models were used to evaluate the effect of each SNP on viral integration status. Of the 710 women evaluated [149 high-grade squamous intraepithelial lesion (HSIL), 251; low-grade squamous intraepithelial lesion (LSIL, 310 normal)], 395 (55.6%) were positive for HPV16 and 192 (27%) were positive for HPV18. Tag-SNPs in 13 DNA repair genes, including RAD50, WRN, and XRCC4, were significantly associated with cervical dysplasia. HPV16 integration status was differential across cervical cytology, but overall, most participants had a mix of both episomal and integrated HPV16. Four tag-SNPs in the XRCC4 gene were found to be significantly associated with HPV16 integration status. Our findings indicate that host genetic variation in NHEJ DNA repair pathway genes, specifically XRCC4, are significantly associated with HPV integration, and that these genes may play an important role in determining cervical cancer development and progression. PREVENTION RELEVANCE HPV integration in premalignant lesions and is thought to be an important driver of carcinogenesis. However, it is unclear what factors promote integration. The use of targeted genotyping among women presenting with cervical dysplasia has the potential to be an effective tool in assessing the likelihood of progression to cancer.
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Affiliation(s)
- Jennifer M Geris
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - E Susan Amirian
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | | | - Martial Guillaud
- Department of Cancer Imaging, British Columbia Cancer Research Centre, Vancouver, British Columbia
| | - Laura M Dillon
- Department of Diagnostic and Biomedical Sciences, UTHealth School of Dentistry, Houston, Texas
| | | | - Michael E Scheurer
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
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10
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Harris C, Kober KM, Paul SM, Cooper BA, Shin J, Oppegaard K, Morse L, Calvo-Schimmel A, Conley Y, Levine JD, Miaskowski C. Neurotransmitter Gene Polymorphisms Are Associated with Symptom Clusters in Patients Undergoing Radiation Therapy. Semin Oncol Nurs 2023; 39:151461. [PMID: 37419849 DOI: 10.1016/j.soncn.2023.151461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 07/09/2023]
Abstract
OBJECTIVES Purpose was to evaluate for associations between the severity of three distinct symptom clusters (ie, sickness-behavior, mood-cognitive, treatment-related) and polymorphisms for 16 genes involved in catecholaminergic, GABAergic, and serotonergic neurotransmission. DATA SOURCES Patients with breast and prostate cancer (n = 157) completed study questionnaires at the completion of radiation therapy. Memorial Symptom Assessment Scale was used to assess the severity of 32 common symptoms. Three distinct symptom clusters were identified using exploratory factor analysis. Associations between the symptom cluster severity scores and neurotransmitter gene polymorphisms were evaluated using regression analyses. CONCLUSION Severity scores for the sickness-behavior symptom cluster were associated with polymorphisms for solute carrier family 6 (SLC6A) member 2 (SLC6A2), SLC6A3, SLC6A1, and 5-hydroxytryptamine receptor (HTR) 2A (HTR2A) genes. For the mood-cognitive symptom cluster, severity scores were associated with polymorphisms for adrenoreceptor alpha 1D, SLC6A2, SLC6A3, SLC6A1, HTR2A, and HTR3A. Severity scores for the treatment-related symptom cluster were associated with polymorphisms for SLC6A2, SLC6A3, catechol-o-methyltransferase, SLC6A1, HTR2A, SLC6A4, and tryptophan hydroxylase 2. IMPLICATIONS FOR NURSING PRACTICE Findings suggest that polymorphisms for several neurotransmitter genes are involved in the severity of sickness-behavior, mood-cognitive, and treatment-related symptom clusters in oncology patients at the completion of radiation therapy. Four genes with various associated polymorphisms were common across the three distinct symptom clusters (ie, SLC6A2, SLC6A3, SLC6A1, HTR2A) which suggest that these clusters have common underlying mechanisms.
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Affiliation(s)
- Carolyn Harris
- Department of Health Promotion and Development, School of Nursing, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kord M Kober
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, California
| | - Steven M Paul
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, California
| | - Bruce A Cooper
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, California
| | - Joosun Shin
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, California
| | - Kate Oppegaard
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, California
| | - Lisa Morse
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, California
| | - Alejandra Calvo-Schimmel
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, California
| | - Yvette Conley
- Department of Health Promotion and Development, School of Nursing, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jon D Levine
- Department of Medicine, School of Nursing and School of Medicine, University of California, San Francisco, California
| | - Christine Miaskowski
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, California.
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11
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Sheng Y, Carpenter JS, Smith BJ, Paul SM, Melisko M, Moslehi J, Levine JD, Conley YP, Kober KM, Miaskowski C. A Pilot Study of Associations Between the Occurrence of Palpitations and Cytokine Gene Variations in Women Prior to Breast Cancer Surgery. Biol Res Nurs 2023; 25:289-299. [PMID: 36255356 PMCID: PMC10236444 DOI: 10.1177/10998004221134684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Palpitations are common and have a negative impact on women's quality of life. While evidence suggests that inflammatory mechanisms may play a role in the development of palpitations, no studies have evaluated for this association in patients with breast cancer who report palpitations prior to surgery. The purpose of this pilot study was to evaluate for associations between the occurrence of palpitations and single nucleotide polymorphisms (SNPs) in genes for pro- and anti-inflammatory cytokines, their receptors, and transcriptional regulators. METHODS Patients were recruited prior to surgery and completed a self-report questionnaire on the occurrence of palpitations. Genotyping of SNPs in cytokine genes was performed using a custom array. Multiple logistic regression analyses were done to identify associations between the occurrence of palpitations and SNPs in fifteen candidate genes. RESULTS Of the 82 SNPs evaluated in the bivariate analyses, eleven SNPs in 6 genes were associated with the occurrence of palpitations. After controlling for functional status, the occurrence of back pain, and self-reported and genomic estimates of race/ethnicity, 3 SNPs in 3 different genes (i.e., interleukin (IL) 1-beta (IL1B) rs1143643, IL10 rs3024505, IL13 rs1295686) were associated with the occurrence of palpitations prior to surgery (all p ≤ .038). CONCLUSIONS While these preliminary findings warrant replication, they suggest that inflammatory mechanisms may contribute to the subjective sensation of palpitations in women prior to breast cancer surgery.
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Affiliation(s)
- Ying Sheng
- School of Nursing, Vanderbilt University,
Nashville, TN, USA
| | | | - Brenda J. Smith
- School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Steven M. Paul
- School of Nursing, University of California, San Francisco, CA, USA
| | - Michelle Melisko
- School of Nursing, University of California, San Francisco, CA, USA
| | - Javid Moslehi
- School of Nursing, University of California, San Francisco, CA, USA
| | - Jon D. Levine
- School of Nursing, University of California, San Francisco, CA, USA
| | - Yvette P. Conley
- School of Nursing, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kord M. Kober
- School of Nursing, University of California, San Francisco, CA, USA
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12
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Watherston J, McNevin D. Skull and long bones – Forensic DNA techniques for historic shipwreck human remains. AUST J FORENSIC SCI 2023. [DOI: 10.1080/00450618.2023.2181395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- J. Watherston
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
- Biology Unit, Forensic Science Branch, Nt Police, Fire and Emergency Services, Berrimah, NT, Australia
- College of Health & Human Sciences, Faculty of Science, Charles Darwin University, Casuarina, NT, Australia
| | - D. McNevin
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
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13
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Pilli E, Morelli S, Poggiali B, Alladio E. Biogeographical ancestry, variable selection, and PLS-DA method: a new panel to assess ancestry in forensic samples via MPS technology. Forensic Sci Int Genet 2023; 62:102806. [PMID: 36399972 DOI: 10.1016/j.fsigen.2022.102806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/14/2022]
Abstract
As evidenced by the large number of articles recently published in the literature, forensic scientists are making great efforts to infer externally visible features and biogeographical ancestry (BGA) from DNA analysis. Just as phenotypic, ancestry information obtained from DNA can provide investigative leads to identify the victims (missing/unidentified persons, crime/armed conflict/mass disaster victims) or trace their perpetrators when no matches were found with the reference profile or in the database. Recently, the advent of Massively Parallel Sequencing technologies associated with the possibility of harnessing high-throughput genetic data allowed us to investigate the associations between phenotypic and genomic variations in worldwide human populations and develop new BGA forensic tools capable of simultaneously analyzing up to millions of markers if for example the ancient DNA approach of hybridization capture was adopted to target SNPs of interest. In the present study, a selection of more than 3000 SNPs was performed to create a new BGA panel and the accuracy of the new panel to infer ancestry from unknown samples was evaluated by the PLS-DA method. Subsequently, the panel created was assessed using three variable selection techniques (Backward variable elimination, Genetic Algorithm and Regularized elimination procedure), and the best SNPs in terms of inferring bio-geographical ancestry at inter- and intra-continental level were selected to obtain panels to predict BGA with a reduced number of selected markers to be applied in routine forensic cases where PCR amplification is the best choice to target SNPs.
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Affiliation(s)
- Elena Pilli
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Stefania Morelli
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Brando Poggiali
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
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14
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Haas ND, Viele C, Paul SM, Abrams G, Smoot B, Melisko M, Levine JD, Miaskowski C, Kober KM. Polymorphisms in Cytokine Receptor and Regulator Genes are Associated with Levels of Exercise in Women Prior to Breast Cancer Surgery. Biol Res Nurs 2023; 25:76-87. [PMID: 36036249 DOI: 10.1177/10998004221120091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background: Little is known about the genetic characteristics associated with exercise in women undergoing breast cancer surgery. Purpose: In a sample of women who were evaluated prior to breast cancer surgery (n = 310), we evaluated for differences in demographic and clinical characteristics between patients who did and did not exercise on a regular basis and evaluated for associations between polymorphisms in genes for pro- and anti-inflammatory cytokines, their receptors, and their transcriptional regulators. Methods: Patients completed an investigator-developed exercise questionnaire. Based on the recommended level of exercise (≥150 minutes/week), survivors were classified into no exercise (NoEx), less exercise (LessEx), or recommended exercise (RecEx) groups. Candidate gene analyses were done to identify relationships between polymorphisms and exercise group membership (i.e., NoEx vs. RecEx). Only 23.5% of the total sample met the recommendations for regular exercise. Results: Compared to the RecEx group (n = 78), patients in the NoEx group (n = 120) had less education; were less likely to report being White or Asia/Pacific Islander; more likely to report a lower household income; had a higher body mass index (BMI), had a poorer functional status; had a higher comorbidity burden; were more likely to self-report high blood pressure; and were more likely to have received neoadjuvant chemotherapy. Polymorphisms in IFNGR1 and NFKB1 were associated with membership in the NoEx group. Conclusions: While they warrant replication, our findings suggest that variations in cytokine-related genes may play a role in exercise behavior, and that clinicians need to assess for barriers to regular exercise and educate patients on its benefits.
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Affiliation(s)
- Nadia D Haas
- School of Nursing, 8785University of California, San Francisco, CA, USA
| | - Carol Viele
- School of Nursing, 8785University of California, San Francisco, CA, USA
| | - Steve M Paul
- School of Nursing, 8785University of California, San Francisco, CA, USA
| | - Gary Abrams
- School of Medicine, 8785University of California, San Francisco, CA, USA
| | - Betty Smoot
- School of Medicine, 8785University of California, San Francisco, CA, USA
| | - Michelle Melisko
- School of Medicine, 8785University of California, San Francisco, CA, USA
| | - Jon D Levine
- School of Medicine, 8785University of California, San Francisco, CA, USA
| | - Christine Miaskowski
- School of Nursing, 8785University of California, San Francisco, CA, USA.,School of Medicine, 8785University of California, San Francisco, CA, USA
| | - Kord M Kober
- School of Nursing, 8785University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
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15
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James D, Bonam CM. Biogeographic ancestry information facilitates genetic racial essentialism: Consequences for race‐based judgments. JOURNAL OF APPLIED SOCIAL PSYCHOLOGY 2022. [DOI: 10.1111/jasp.12932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Drexler James
- Department of Psychology University of Minnesota, Twin Cities Minneapolis Minnesota USA
| | - Courtney M. Bonam
- Psychology Department, Critical Race and Ethnic Studies University of California, Santa Cruz Santa Cruz California USA
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16
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Fesenko DO, Ivanovsky ID, Ivanov PL, Zemskova EY, Agapitova AS, Polyakov SA, Fesenko OE, Filippova MA, Zasedatelev AS. A Biochip for Genotyping Polymorphisms Associated with Eye, Hair, Skin Color, AB0 Blood Group, Sex, Y Chromosome Core Haplogroup, and Its Application to Study the Slavic Population. Mol Biol 2022. [DOI: 10.1134/s0026893322050053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Sun K, Yao Y, Yun L, Zhang C, Xie J, Qian X, Tang Q, Sun L. Application of machine learning for ancestry inference using multi-InDel markers. Forensic Sci Int Genet 2022; 59:102702. [DOI: 10.1016/j.fsigen.2022.102702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 03/22/2022] [Accepted: 03/27/2022] [Indexed: 01/04/2023]
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18
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Dziech A. Identification of Wolf-Dog Hybrids in Europe – An Overview of Genetic Studies. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.760160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Significant development of genetic tools during the last decades provided opportunities for more detailed analyses and deeper understanding of species hybridization. New genetic markers allowed for reliable identification of admixed individuals deriving from recent hybridization events (a few generations) and those originating from crossings up to 19 generations back. Implementation of microsatellites (STRs) together with Bayesian clustering provided abundant knowledge regarding presence of admixed individuals in numerous populations and helped understand the problematic nature of studying hybridization (i.a., defining a reliable thresholds for recognizing individuals as admixed or obtaining well-grounded results representing actual proportion of hybrids in a population). Nevertheless, their utilization is limited to recent crossbreeding events. Single Nucleotide Polymorphisms (SNPs) proved to be more sensible tools for admixture analyses furnishing more reliable knowledge, especially for older generation backcrosses. Small sets of Ancestry Informative Markers (AIMs) of both types of markers were effective enough to implement in monitoring programs, however, SNPs seem to be more appropriate because of their ability to identify admixed individuals up to 3rd generations. The main aim of this review is to summarize abundant knowledge regarding identification of wolf-dog hybrids in Europe and discuss the most relevant problems relating to the issue, together with advantages and disadvantages of implemented markers and approaches.
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19
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Yougbaré B, Ouédraogo D, Tapsoba ASR, Soudré A, Zoma BL, Orozco-terWengel P, Moumouni S, Ouédraogo-Koné S, Wurzinger M, Tamboura HH, Traoré A, Mwai OA, Sölkner J, Khayatzadeh N, Mészáros G, Burger PA. Local Ancestry to Identify Selection in Response to Trypanosome Infection in Baoulé x Zebu Crossbred Cattle in Burkina Faso. Front Genet 2021; 12:670390. [PMID: 34646296 PMCID: PMC8504455 DOI: 10.3389/fgene.2021.670390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 08/09/2021] [Indexed: 11/15/2022] Open
Abstract
The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or tolerance against pathogens, and for performances in production traits. Using a medium-density genomic marker panel from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5 and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21, and 22. Some candidate genes on chromosome 6 (PDGFRA) and chromosome 19 (CDC6) have been found associated to trypanotolerance in West African taurines. Screening for FST outliers in trypanosome positive/negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative markers for routine admixture testing. The results of this study contribute to a better understanding of the genetic basis of trypanotolerance in Baoulé cattle and their crossbreeds. Furthermore, we provide a small informative marker set to monitor admixture in this valuable indigenous breed. As such, our results are important for conserving the genetic uniqueness and trypanotolerance of Baoulé cattle, as well as for the improvement of Baoulé and Zebu crossbreds in specific community-based breeding programs.
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Affiliation(s)
- Bernadette Yougbaré
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Dominique Ouédraogo
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,Institut du Développement Rural, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Arnaud S R Tapsoba
- Institut du Développement Rural, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Albert Soudré
- Unité de Formation et de Recherche en Sciences et Technologies, Université Norbert Zongo, Koudougou, Burkina Faso
| | - Bienvenue L Zoma
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,Institut du Développement Rural, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | | | - Sanou Moumouni
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | | | - Maria Wurzinger
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Hamidou H Tamboura
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Amadou Traoré
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,SUISAG, Sempach, Switzerland
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, Vienna, Austria
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20
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Neale ZE, Kuo SIC, Dick DM. A systematic review of gene-by-intervention studies of alcohol and other substance use. Dev Psychopathol 2021; 33:1410-1427. [PMID: 32602428 PMCID: PMC7772257 DOI: 10.1017/s0954579420000590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Alcohol and other substance use problems are common, and the efficacy of current prevention and intervention programs is limited. Genetics may contribute to differential effectiveness of psychosocial prevention and intervention programs. This paper reviews gene-by-intervention (G×I) studies of alcohol and other substance use, and implications for integrating genetics into prevention science. Systematic review yielded 17 studies for inclusion. Most studies focused on youth substance prevention, alcohol was the most common outcome, and measures of genotype were heterogeneous. All studies reported at least one significant G×I interaction. We discuss these findings in the context of the history and current state of genetics, and provide recommendations for future G×I research. These include the integration of genome-wide polygenic scores into prevention studies, broad outcome measurement, recruitment of underrepresented populations, testing mediators of G×I effects, and addressing ethical implications. Integrating genetic research into prevention science, and training researchers to work fluidly across these fields, will enhance our ability to determine the best intervention for each individual across development. With growing public interest in obtaining personalized genetic information, we anticipate that the integration of genetics and prevention science will become increasingly important as we move into the era of precision medicine.
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Affiliation(s)
- Zoe E. Neale
- Department of Psychology, Virginia Commonwealth University
| | | | - Danielle M. Dick
- Department of Psychology, Virginia Commonwealth University
- Department of Human and Molecular Genetics, Virginia Commonwealth University
- College Behavioral and Emotional Health Institute, Virginia Commonwealth University
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21
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Yang HC, Chen CW, Lin YT, Chu SK. Genetic ancestry plays a central role in population pharmacogenomics. Commun Biol 2021; 4:171. [PMID: 33547344 PMCID: PMC7864978 DOI: 10.1038/s42003-021-01681-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Recent studies have pointed out the essential role of genetic ancestry in population pharmacogenetics. In this study, we analyzed the whole-genome sequencing data from The 1000 Genomes Project (Phase 3) and the pharmacogenetic information from Drug Bank, PharmGKB, PharmaADME, and Biotransformation. Here we show that ancestry-informative markers are enriched in pharmacogenetic loci, suggesting that trans-ancestry differentiation must be carefully considered in population pharmacogenetics studies. Ancestry-informative pharmacogenetic loci are located in both protein-coding and non-protein-coding regions, illustrating that a whole-genome analysis is necessary for an unbiased examination over pharmacogenetic loci. Finally, those ancestry-informative pharmacogenetic loci that target multiple drugs are often a functional variant, which reflects their importance in biological functions and pathways. In summary, we develop an efficient algorithm for an ultrahigh-dimensional principal component analysis. We create genetic catalogs of ancestry-informative markers and genes. We explore pharmacogenetic patterns and establish a high-accuracy prediction panel of genetic ancestry. Moreover, we construct a genetic ancestry pharmacogenomic database Genetic Ancestry PhD (http://hcyang.stat.sinica.edu.tw/databases/genetic_ancestry_phd/). Hsin-Chou Yang et al. examine population structure in several genomic databases and identify that pharmacogenetic loci are enriched for markers of genetic ancestry. Their results suggest that genetic ancestry must be carefully considered in population pharmacogenetics studies.
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Affiliation(s)
- Hsin-Chou Yang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan. .,Institute of Statistics, National Cheng Kung University, Tainan, Taiwan. .,Institute of Public Health, National Yang-Ming University, Taipei, Taiwan.
| | - Chia-Wei Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Yu-Ting Lin
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Shih-Kai Chu
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
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22
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Massively parallel sequencing of 165 ancestry-informative SNPs and forensic biogeographical ancestry inference in three southern Chinese Sinitic/Tai-Kadai populations. Forensic Sci Int Genet 2021; 52:102475. [PMID: 33561661 DOI: 10.1016/j.fsigen.2021.102475] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 12/06/2020] [Accepted: 01/20/2021] [Indexed: 01/01/2023]
Abstract
Ancestry informative markers (AIMs), which are distributed throughout the human genome, harbor significant allele frequency differences among diverse ethnic groups. The use of sets of AIMs to reconstruct population history and genetic relationships is attracting interest in the forensic community, because biogeographic ancestry information for a casework sample can potentially be predicted and used to guide the investigative process. However, subpopulation ancestry inference within East Asia remains in its infancy due to a lack of population reference data collection and incomplete validation work on newly developed or commercial AIM sets. In the present study, 316 Chinese persons, including 85 Sinitic-speaking Haikou Han, 120 Qiongzhong Hlai and 111 Daozhen Gelao individuals belonging to Tai-Kadai-speaking populations, were analyzed using the Precision ID Ancestry Panel (165 AISNPs). Combined with our previous 165-AISNP data (375 individuals from 6 populations), the 1000 Genomes Project and forensic literature, comprehensive population genetic comparisons and ancestry inference were further performed via ADMIXTURE, TreeMix, PCA, f-statistics and N-J tree. Although several nonpolymorphic loci were identified in the three southern Chinese populations, the forensic parameters of this ancestry inference panel were better than those for the 23 STR-based Huaxia Platinum System, which is suitable for use as a robust tool in forensic individual identification and parentage testing. The results based on the ancestry assignment and admixture proportion evaluation revealed that this panel could be used successfully to assign individuals at a continental scale but also possessed obvious limitations in discriminatory power in intercontinental individuals, especially for European-Asian admixed Uyghurs or in populations lacking reference databases. Population genetic analyses further revealed five continental population clusters and three East Asian-focused population subgroups, which is consistent with linguistic affiliations. Ancestry composition and multiple phylogenetic analysis further demonstrated that the geographically isolated Qiongzhong Hlai harbored a close phylogenetic relationship with Austronesian speakers and possessed a homogenous Tai-Kadai-dominant ancestry, which could be used as the ancestral source proxy in population history reconstruction of Tai-Kadai-speaking populations and as one of the representatives for forensic database establishment. In summary, more population-specific AIM sets focused on East Asian subpopulations, comprehensive algorithms and high-coverage population reference data should be developed and validated in the next step.
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23
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Parfenchyk MS, Kotava SA. The Theoretical Framework for the Panels of DNA Markers Formation in the Forensic Determination of an Individual Ancestral Origin. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421010105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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24
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Colistro V, Mut P, Hidalgo PC, Carracedo A, Quintela I, Rojas-Martínez A, Sans M. Differential admixture in Latin American populations and its impact on the study of colorectal cancer. Genet Mol Biol 2020; 43:e20200143. [PMID: 33306774 PMCID: PMC7783724 DOI: 10.1590/1678-4685-gmb-2020-0143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022] Open
Abstract
Genome-wide association studies focused on searching genes responsible for
several diseases. Admixture mapping studies proposed a more efficient
alternative capable of detecting polymorphisms contributing with a small effect
on the disease risk. This method focuses on the higher values of linkage
disequilibrium in admixed populations. To test this, we analyzed 10 genomic
regions previously defined as related with colorectal cancer among nine
populations and studied the variation pattern of haplotypic structures and
heterozygosity values on seven categories of SNPs. Both analyses showed
differences among chromosomal regions and studied populations. Admixed
Latin-American samples generally show intermediate values. Heterozygosity of the
SNPs grouped in categories varies more in each gene than in each population.
African related populations have more blocks per chromosomal region, coherently
with their antiquity. In sum, some similarities were found among Latin American
populations, but each chromosomal region showed a particular behavior, despite
the fact that the study refers to genes and regions related with one particular
complex disease. This study strongly suggests the necessity of developing
statistical methods to deal with di- or tri-hybrid populations, as well as to
carefully analyze the different historic and demographic scenarios, and the
different characteristics of particular chromosomal regions and evolutionary
forces.
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Affiliation(s)
- Valentina Colistro
- Universidad de la República, Facultad de Medicina, Departamento de Métodos Cuantitativos, Montevideo, Uruguay
| | - Patricia Mut
- Universidad de la República, Facultad de Humanidades y Ciencias de la Educación, Departamento de Antropología Biológica, Montevideo, Uruguay
| | - Pedro C Hidalgo
- Universidad de la República, Centro Universitario de Tacuarembó, Polo de Desarrollo Universitario Diversidad Genética Humana, Tacuarembó, Uruguay
| | - Angel Carracedo
- Universidad de Santiago de Compostela, Centro Nacional de Genotipado (CEGEN), Spain.,Universidade de Santiago de Compostela, CIBER de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Grupo de Medicina Xenómica, Santiago de Compostela, Spain
| | - Inés Quintela
- Universidad de Santiago de Compostela, Centro Nacional de Genotipado (CEGEN), Spain
| | | | - Mónica Sans
- Universidad de la República, Facultad de Humanidades y Ciencias de la Educación, Departamento de Antropología Biológica, Montevideo, Uruguay
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25
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Aouizerat BE, Byun E, Pullinger CR, Gay C, Lerdal A, Lee KA. Sleep disruption and duration are associated with variants in genes involved in energy homeostasis in adults with HIV/AIDS. Sleep Med 2020; 82:84-95. [PMID: 33906044 DOI: 10.1016/j.sleep.2020.08.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 07/21/2020] [Accepted: 08/25/2020] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To determine whether selected genes and plasma markers involved in energy homeostasis are associated with sleep disruption or duration in adults with HIV/AIDS. METHODS A sample of 289 adults with HIV/AIDS wore a wrist actigraph for 72 h to estimate total sleep time (TST) and wake after sleep onset (WASO). Twenty-three single nucleotide polymorphisms (SNP) spanning 5 energy homeostasis genes (adiponectin [ADIPOQ], ghrelin [GHRL], leptin [LEP], peroxisome proliferator-activated receptor-alpha [PPARA], and -gamma [PPARG]) were genotyped using a custom array. Plasma markers of energy homeostasis (adiponectin, ghrelin, leptin) were measured by commercial multiplex assay. RESULTS After adjusting for demographic and clinical characteristics (race/ethnicity, gender, CD4 cell count, waist circumference, medications), both WASO and TST were associated with SNPs in ADIPOQ (rs182052), LEP (rs10244329, rs3828942), PPARA (rs135551, rs4253655), and PPARG (rs709151). Additional SNPs in ADIPOQ were associated with WASO (rs1501299, rs3821799, rs6773957) and TST (rs2241766). TST was also associated with SNPs in GHRL (rs26802), LEP (rs11760956), PPARA (rs135547, rs8138102, rs4253776), and PPARG (rs12490265, rs796313). Many covariate-adjusted associations involved a significant interaction with markers of HIV (viral load, years since diagnosis). Among plasma markers, higher adiponectin was associated with less WASO, higher ghrelin and glucose levels with shorter TST, and higher leptin with longer TST. CONCLUSIONS Replication of SNPs in all five genes and three plasma markers of energy homeostasis were associated with objective sleep measures. HIV disease influenced many of the associations. Findings strengthen evidence for associations between energy homeostasis genetics and poor sleep, and provide direction for pharmacological intervention research.
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Affiliation(s)
- Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, NY, USA; Department of Oral and Maxillofacial Surgery, New York University, NY, USA.
| | - Eeeseung Byun
- Department of Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, WA, USA
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA, USA; Department of Physiological Nursing, University of California at San Francisco, San Francisco, CA, USA
| | - Caryl Gay
- Department of Family Health Care Nursing, University of California at San Francisco, San Francisco, CA, USA; Department of Patient Safety and Research, Lovisenberg Diakonale Hospital, Oslo, Norway
| | - Anners Lerdal
- Department of Patient Safety and Research, Lovisenberg Diakonale Hospital, Oslo, Norway; Department of Interdisciplinary Health Sciences, Institute of Health and Society, Faculty of Medicine, University of Oslo, Norway
| | - Kathryn A Lee
- Department of Family Health Care Nursing, University of California at San Francisco, San Francisco, CA, USA
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Teteh DK, Dawkins-Moultin L, Hooker S, Hernandez W, Bonilla C, Galloway D, LaGroon V, Santos ER, Shriver M, Royal CDM, Kittles RA. Genetic ancestry, skin color and social attainment: The four cities study. PLoS One 2020; 15:e0237041. [PMID: 32813691 PMCID: PMC7446776 DOI: 10.1371/journal.pone.0237041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/17/2020] [Indexed: 12/26/2022] Open
Abstract
Introduction The Black population in the US is heterogeneous but is often treated as monolithic in research, with skin pigmentation being the primary indicator of racial classification. Objective: This paper examines the differences among Blacks by comparing genetic ancestry, skin color and social attainment of 259 residents across four US cities—Norman, Oklahoma; Cincinnati, Ohio; Harlem, New York; and Washington, District of Columbia. Methods Participants were recruited between 2004 and 2006 at community-based forums. Cross-sectional data were analyzed using chi-square tests, correlation analyses and logistic regression. Results There were variations in ancestry, melanin index and social attainment across some cities. Overall, men with darker skin color, and women with lighter skin color were significantly more likely to be married. Darker skin individuals with significantly more West African ancestry reported attainment of graduate degrees, and professional occupations than lighter skin individuals. Conclusions Our findings suggest differences in skin pigmentation by geography and support regional variations in ancestry of US Blacks. Biomedical research should consider genetic ancestry and local historical/social context rather than relying solely on skin pigmentation as a proxy for race.
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Affiliation(s)
- Dede K. Teteh
- Division of Health Equities, Department of Population Sciences, City of Hope Medical Center, Duarte, California, United States of America
| | - Lenna Dawkins-Moultin
- Department of Health Disparities Research, M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Stanley Hooker
- Division of Health Equities, Department of Population Sciences, City of Hope Medical Center, Duarte, California, United States of America
| | - Wenndy Hernandez
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, Illinois, United States of America
| | - Carolina Bonilla
- Departamento de Medicina Preventiva, Faculdade de Medicina, Universidade de São Paulo, Butanta, Brazil
| | - Dorothy Galloway
- Division of Health Equities, Department of Population Sciences, City of Hope Medical Center, Duarte, California, United States of America
| | - Victor LaGroon
- Division of Health Equities, Department of Population Sciences, City of Hope Medical Center, Duarte, California, United States of America
| | | | - Mark Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Charmaine D. M. Royal
- Department of African & African American Studies, Duke University, Durham, North Carolina, United States of America
| | - Rick A. Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope Medical Center, Duarte, California, United States of America
- * E-mail:
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Rotroff DM. A Bioinformatics Crash Course for Interpreting Genomics Data. Chest 2020; 158:S113-S123. [PMID: 32658646 PMCID: PMC8176646 DOI: 10.1016/j.chest.2020.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/11/2019] [Accepted: 03/09/2020] [Indexed: 10/23/2022] Open
Abstract
Reductions in genotyping costs and improvements in computational power have made conducting genome-wide association studies (GWAS) standard practice for many complex diseases. GWAS is the assessment of genetic variants across the genome of many individuals to determine which, if any, genetic variants are associated with a specific trait. As with any analysis, there are evolving best practices that should be followed to ensure scientific rigor and reliability in the conclusions. This article presents a brief summary for many of the key bioinformatics considerations when either planning or evaluating GWAS. This review is meant to serve as a guide to those without deep expertise in bioinformatics and GWAS and give them tools to critically evaluate this popular approach to investigating complex diseases. In addition, a checklist is provided that can be used by investigators to evaluate whether a GWAS has appropriately accounted for the many potential sources of bias and generally followed current best practices.
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Affiliation(s)
- Daniel M Rotroff
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH.
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Identification of Ancestry Informative Marker (AIM) Panels to Assess Hybridisation between Feral and Domestic Sheep. Animals (Basel) 2020; 10:ani10040582. [PMID: 32235592 PMCID: PMC7222383 DOI: 10.3390/ani10040582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/21/2020] [Accepted: 03/25/2020] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Once present in the entirety of Europe, mouflon (wild sheep) became extinct due to intense hunting, but remnant populations survived and became feral on the Mediterranean islands of Corsica and Sardinia. Although now protected by regional laws, Sardinian mouflon is threatened by crossbreeding with domestic sheep causing genetic hybridisation. The spread of domestic genes can be detrimental for wild populations as it dilutes the genetic features that characterise them. This work aimed to identify diagnostic tools that could be applied to monitor the level of hybridisation between mouflon and domestic sheep. Tens of thousands of genetic markers known as single nucleotide polymorphisms (SNPs) were screened and we identified the smallest number of SNPs necessary to discriminate between pure mouflon and sheep. We produced four SNP panels of different sizes which were able to assess the hybridisation level of a mouflon and we verified that the SNP panels efficacy is independent of the domestic sheep breed involved in the hybrid. The implementation of these results into actual diagnostic tools will help the conservation of this unique and irreplaceable mouflon population, and the methodology applied can easily be transferred to other case studies of interest. Abstract Hybridisation of wild populations with their domestic counterparts can lead to the loss of wildtype genetic integrity, outbreeding depression, and loss of adaptive features. The Mediterranean island of Sardinia hosts one of the last extant autochthonous European mouflon (Ovis aries musimon) populations. Although conservation policies, including reintroduction plans, have been enforced to preserve Sardinian mouflon, crossbreeding with domestic sheep has been documented. We identified panels of single nucleotide polymorphisms (SNPs) that could act as ancestry informative markers able to assess admixture in feral x domestic sheep hybrids. The medium-density SNP array genotyping data of Sardinian mouflon and domestic sheep (O. aries aries) showing pure ancestry were used as references. We applied a two-step selection algorithm to this data consisting of preselection via Principal Component Analysis followed by a supervised machine learning classification method based on random forest to develop SNP panels of various sizes. We generated ancestry informative marker (AIM) panels and tested their ability to assess admixture in mouflon x domestic sheep hybrids both in simulated and real populations of known ancestry proportions. All the AIM panels recorded high correlations with the ancestry proportion computed using the full medium-density SNP array. The AIM panels proposed here may be used by conservation practitioners as diagnostic tools to exclude hybrids from reintroduction plans and improve conservation strategies for mouflon populations.
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Shan MA, Refn M, Morling N, Børsting C, Pereira V. GENETIC PORTRAIT OF THE PUNJABI POPULATION FROM PAKISTAN USING THE PRECISION ID ANCESTRY PANEL. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Jin X, Cui W, Chen C, Guo Y, Tao Y, Lan Q, Kong T, Zhu B. Biogeographic origin prediction of three continental populations through 42 ancestry informative SNPs. Electrophoresis 2019; 41:235-245. [DOI: 10.1002/elps.201900241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/04/2019] [Accepted: 11/13/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Xiao‐Ye Jin
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- College of Forensic MedicineXi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Wei Cui
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- College of Forensic MedicineXi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Chong Chen
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- College of Forensic MedicineXi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Yu‐Xin Guo
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- College of Forensic MedicineXi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Yong‐Wei Tao
- Cranio‐Maxillofacial Trauma Plastic SurgeryStomatology Hospital of Xi'an Jiaotong University College of Medicine Xi'an P. R. China
| | - Qiong Lan
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical University Guangzhou P. R. China
| | - Ting‐Ting Kong
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
| | - Bo‐Feng Zhu
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical University Guangzhou P. R. China
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Chhotaray S, Panigrahi M, Pal D, Ahmad SF, Bhushan B, Gaur GK, Mishra BP, Singh RK. Ancestry informative markers derived from discriminant analysis of principal components provide important insights into the composition of crossbred cattle. Genomics 2019; 112:1726-1733. [PMID: 31678154 DOI: 10.1016/j.ygeno.2019.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 07/06/2019] [Accepted: 10/01/2019] [Indexed: 12/19/2022]
Abstract
The cost of SNP genotyping to screen different breeds and to estimate the exact proportion of ancestry level is quite high, which can be compensated through deriving a small panel of ancestry informative markers (AIMs). Hence, we carried out the present study to provide an insight into ancestry level inferred from a panel of informative markers in the crossbred Vrindavani population developed at ICAR-IVRI, India. We have performed a new method i.e., discriminant analysis of principal components (DAPC) for the first time on the dataset of Vrindavani cattle. To confirm our method, we had performed DAPC on two other well-known crossbred cattle, i.e., Frieswal and Beefmaster. Three sets of panels (500, 1000 and 2000 markers) were tested for clustering of individuals. Among all the panels, we found the panel (1000 markers) with DAPC based contribution method was of the smallest size and comparatively of the highest accuracy.
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Affiliation(s)
- Supriya Chhotaray
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Dhan Pal
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - G K Gaur
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - B P Mishra
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - R K Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Graph Theoretical Analysis of Genome-Scale Data: Examination of Gene Activation Occurring in the Setting of Community-Acquired Pneumonia. Shock 2019; 50:53-59. [PMID: 29049138 DOI: 10.1097/shk.0000000000001029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTION We have previously reported evidence that Black individuals appear to have a significantly higher incidence of infection-related hospitalizations compared with White individuals. It is possible that the host immune response is responsible for this vital difference. In support of such a hypothesis, the aim of this study was to determine whether Black and White individuals exhibit differential whole blood gene network activation. METHODS We examined whole blood network activation in a subset of patients (n = 22 pairs, propensity score matched (1:1) Black and White patients) with community-acquired pneumonia (CAP) from the Genetic and Inflammatory Markers of Sepsis study. We employed day one whole blood transcriptomic data generated from this cohort and constructed co-expression graphs for each racial group. Pearson correlation coefficients were used to weight edges. Spectral thresholding was applied to ascribe significance. Innovative graph theoretical methods were then invoked to detect densely connected gene networks and provide differential structural analysis. RESULTS Propensity matching was employed to reduce potential bias due to confounding variables. Although Black and White patients had similar socio- and clinical demographics, we identified novel differences in molecular network activation-dense subgraphs known as paracliques that displayed complete gene connection for both White (three paracliques) and Black patients (one paraclique). Specifically, the genes that comprised the paracliques in the White patients include circadian loop, cell adhesion, mobility, proliferation, tumor suppression, NFκB, and chemokine signaling. However, the genes that comprised the paracliques in the Black patients include DNA and messenger RNA processes, and apoptosis signaling. We investigated the distribution of Black paracliques across White paracliques. Black patients had five paracliques (with almost complete connection) comprised of genes that are critical for host immune response widely distributed across 22 parcliques in the White population. Anchoring the analysis on two critical inflammatory mediators, interleukin (IL)-6 and IL-10 identified further differential network activation among the White and Black patient populations. CONCLUSIONS These results demonstrate that, at the molecular level, Black and White individuals may experience different activation patterns with CAP. Further validation of the gene networks we have identified may help pinpoint genetic factors that increase host susceptibility to community-acquired pneumonia, and may lay the groundwork for personalized management of CAP.
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Knisely MR, Conley YP, Smoot B, Paul SM, Levine JD, Miaskowski C. Associations Between Catecholaminergic and Serotonergic Genes and Persistent Arm Pain Severity Following Breast Cancer Surgery. THE JOURNAL OF PAIN 2019; 20:1100-1111. [PMID: 30904518 PMCID: PMC6736756 DOI: 10.1016/j.jpain.2019.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/17/2019] [Accepted: 03/19/2019] [Indexed: 01/09/2023]
Abstract
Persistent arm pain is a common problem after breast cancer surgery. Little is known about genetic factors that contribute to this type of postsurgical pain. Study purpose was to explore associations between persistent arm pain phenotypes and genetic polymorphisms among 15 genes involved in catecholaminergic and serotonergic neurotransmission. Women (n = 398) rated the presence and intensity of arm pain monthly for 6 months after breast cancer surgery. Three distinct latent classes of patients were identified (ie, no arm pain [41.6%], mild arm pain (23.6%), and moderate arm pain (34.8%). Logistic regression analyses were used to evaluate for differences between genotype or haplotype frequencies and the persistent arm pain classes. Compared with the no arm pain class, 3 single nucleotide polymorphisms and 1 haplotype, in 4 genes, were associated with membership in the mild arm pain class: COMT rs4633, HTR2A haplotype B02 (composed of rs1923886 and rs7330636), HTR3A rs1985242, and TH rs2070762. Compared with the no arm pain class, 4 single nucleotide polymorphisms in 3 genes were associated with membership in the moderate arm pain class: COMT rs165656, HTR2A rs2770298 and rs9534511, and HTR3A rs1985242. Findings suggest that variations in catecholaminergic and serotonergic genes play a role in the development of persistent arm pain. PERSPECTIVE: Limited information is available on genetic factors that contribute to persistent arm pain after breast cancer surgery. Genetic polymorphisms in genes involved in catecholaminergic and serotonergic neurotransmission were associated with 2 persistent arm pain phenotypes. Findings may be used to identify patients are higher risk for this common pain condition.
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Affiliation(s)
| | - Yvette P Conley
- School of Nursing, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Betty Smoot
- Schools of Medicine, University of California, San Francisco, California
| | - Steven M Paul
- Schools of Nursing, University of California, San Francisco, California
| | - Jon D Levine
- Schools of Medicine, University of California, San Francisco, California
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Phillips C, McNevin D, Kidd K, Lagacé R, Wootton S, de la Puente M, Freire-Aradas A, Mosquera-Miguel A, Eduardoff M, Gross T, Dagostino L, Power D, Olson S, Hashiyada M, Oz C, Parson W, Schneider P, Lareu M, Daniel R. MAPlex - A massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations. Forensic Sci Int Genet 2019; 42:213-226. [DOI: 10.1016/j.fsigen.2019.06.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 06/04/2019] [Accepted: 06/26/2019] [Indexed: 11/25/2022]
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Abstract
Using data from the Philadelphia Neurodevelopmental Cohort, we examined whether European ancestry predicted cognitive ability over and above both parental socioeconomic status (SES) and measures of eye, hair, and skin color. First, using multi-group confirmatory factor analysis, we verified that strict factorial invariance held between self-identified African and European-Americans. The differences between these groups, which were equivalent to 14.72 IQ points, were primarily (75.59%) due to difference in general cognitive ability (g), consistent with Spearman’s hypothesis. We found a relationship between European admixture and g. This relationship existed in samples of (a) self-identified monoracial African-Americans (B = 0.78, n = 2,179), (b) monoracial African and biracial African-European-Americans, with controls added for self-identified biracial status (B = 0.85, n = 2407), and (c) combined European, African-European, and African-American participants, with controls for self-identified race/ethnicity (B = 0.75, N = 7,273). Controlling for parental SES modestly attenuated these relationships whereas controlling for measures of skin, hair, and eye color did not. Next, we validated four sets of polygenic scores for educational attainment (eduPGS). MTAG, the multi-trait analysis of genome-wide association study (GWAS) eduPGS (based on 8442 overlapping variants) predicted g in both the monoracial African-American (r = 0.111, n = 2179, p < 0.001), and the European-American (r = 0.227, n = 4914, p < 0.001) subsamples. We also found large race differences for the means of eduPGS (d = 1.89). Using the ancestry-adjusted association between MTAG eduPGS and g from the monoracial African-American sample as an estimate of the transracially unbiased validity of eduPGS (B = 0.124), the results suggest that as much as 20%–25% of the race difference in g can be naïvely explained by known cognitive ability-related variants. Moreover, path analysis showed that the eduPGS substantially mediated associations between cognitive ability and European ancestry in the African-American sample. Subtest differences, together with the effects of both ancestry and eduPGS, had near-identity with subtest g-loadings. This finding confirmed a Jensen effect acting on ancestry-related differences. Finally, we confirmed measurement invariance along the full range of European ancestry in the combined sample using local structural equation modeling. Results converge on genetics as a potential partial explanation for group mean differences in intelligence.
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GRAF-pop: A Fast Distance-Based Method To Infer Subject Ancestry from Multiple Genotype Datasets Without Principal Components Analysis. G3-GENES GENOMES GENETICS 2019; 9:2447-2461. [PMID: 31151998 PMCID: PMC6686921 DOI: 10.1534/g3.118.200925] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Inferring subject ancestry using genetic data is an important step in genetic association studies, required for dealing with population stratification. It has become more challenging to infer subject ancestry quickly and accurately since large amounts of genotype data, collected from millions of subjects by thousands of studies using different methods, are accessible to researchers from repositories such as the database of Genotypes and Phenotypes (dbGaP) at the National Center for Biotechnology Information (NCBI). Study-reported populations submitted to dbGaP are often not harmonized across studies or may be missing. Widely-used methods for ancestry prediction assume that most markers are genotyped in all subjects, but this assumption is unrealistic if one wants to combine studies that used different genotyping platforms. To provide ancestry inference and visualization across studies, we developed a new method, GRAF-pop, of ancestry prediction that is robust to missing genotypes and allows researchers to visualize predicted population structure in color and in three dimensions. When genotypes are dense, GRAF-pop is comparable in quality and running time to existing ancestry inference methods EIGENSTRAT, FastPCA, and FlashPCA2, all of which rely on principal components analysis (PCA). When genotypes are not dense, GRAF-pop gives much better ancestry predictions than the PCA-based methods. GRAF-pop employs basic geometric and probabilistic methods; the visualized ancestry predictions have a natural geometric interpretation, which is lacking in PCA-based methods. Since February 2018, GRAF-pop has been successfully incorporated into the dbGaP quality control process to identify inconsistencies between study-reported and computationally predicted populations and to provide harmonized population values in all new dbGaP submissions amenable to population prediction, based on marker genotypes. Plots, produced by GRAF-pop, of summary population predictions are available on dbGaP study pages, and the software, is available at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/Software.cgi.
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Next-generation sequencing reveals new information about HLA allele and haplotype diversity in a large European American population. Hum Immunol 2019; 80:807-822. [PMID: 31345698 DOI: 10.1016/j.humimm.2019.07.275] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 06/21/2019] [Accepted: 07/06/2019] [Indexed: 12/11/2022]
Abstract
The human leukocyte antigen (HLA) genes are extremely polymorphic and are useful molecular markers to make inferences about human population history. However, the accuracy of the estimation of genetic diversity at HLA loci very much depends on the technology used to characterize HLA alleles; high-resolution genotyping of long-range HLA gene products improves the assessment of HLA population diversity as well as other population parameters compared to lower resolution typing methods. In this study we examined allelic and haplotype HLA diversity in a large healthy European American population sourced from the UCSF-DNA bank. A high-resolution next-generation sequencing method was applied to define non-ambiguous 3- and 4-field alleles at the HLA-A, HLA-C, HLA-B, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1 loci in samples provided by 2248 unrelated individuals. A number of population parameters were examined including balancing selection and various measurements of linkage disequilibrium were calculated. There were no detectable deviations from Hardy-Weinberg proportions at HLA-A, HLA-DRB1, HLA-DQA1 and HLA-DQB1. For the remaining loci moderate and significant deviations were detected at HLA-C, HLA-B, HLA-DRB3/4/5, HLA-DPA1 and HLA-DPB1 loci mostly from population substructures. Unique 4-field associations were observed among alleles at 2 loci and haplotypes extending large intervals that were not apparent in results obtained using testing methodologies with limited sequence coverage and phasing. The high diversity at HLA-DPA1 results from detection of intron variants of otherwise well conserved protein sequences. It may be speculated that divergence in exon sequences may be negatively selected. Our data provides a valuable reference source for future population studies that may allow for precise fine mapping of coding and non-coding sequences determining disease susceptibility and allo-immunogenicity.
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Marshall K, Gibson JP, Mwai O, Mwacharo JM, Haile A, Getachew T, Mrode R, Kemp SJ. Livestock Genomics for Developing Countries – African Examples in Practice. Front Genet 2019. [DOI: 10.10.3389/fgene.2019.00297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Marshall K, Gibson JP, Mwai O, Mwacharo JM, Haile A, Getachew T, Mrode R, Kemp SJ. Livestock Genomics for Developing Countries - African Examples in Practice. Front Genet 2019; 10:297. [PMID: 31105735 PMCID: PMC6491883 DOI: 10.3389/fgene.2019.00297] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/19/2019] [Indexed: 01/17/2023] Open
Abstract
African livestock breeds are numerous and diverse, and typically well adapted to the harsh environment conditions under which they perform. They have been used over centuries to provide livelihoods as well as food and nutritional security. However, African livestock systems are dynamic, with many small- and medium-scale systems transforming, to varying degrees, to become more profitable. In these systems the women and men livestock keepers are often seeking new livestock breeds or genotypes - typically those that increase household income through having enhanced productivity in comparison to traditional breeds while maintaining adaptedness. In recent years genomic approaches have started to be utilized in the identification and development of such breeds, and in this article we describe a number of examples to this end from sub-Saharan Africa. These comprise case studies on: (a) dairy cattle in Kenya and Senegal, as well as sheep in Ethiopia, where genomic approaches aided the identification of the most appropriate breed-type for the local productions systems; (b) a cross-breeding program for dairy cattle in East Africa incorporating genomic selection as well as other applications of genomics; (c) ongoing work toward creating a new cattle breed for East Africa that is both productive and resistant to trypanosomiasis; and (d) the use of African cattle as resource populations to identify genomic variants of economic or ecological significance, including a specific case where the discovery data was from a community based breeding program for small ruminants in Ethiopia. Lessons learnt from the various case studies are highlighted, and the concluding section of the paper gives recommendations for African livestock systems to increasingly capitalize on genomic technologies.
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Affiliation(s)
- Karen Marshall
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
- Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
| | - John P. Gibson
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Okeyo Mwai
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
| | - Joram M. Mwacharo
- Small Ruminant Breeding and Genomics Group, International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Aynalem Haile
- Small Ruminant Breeding and Genomics Group, International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Tesfaye Getachew
- Small Ruminant Breeding and Genomics Group, International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Raphael Mrode
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
- Scotland’s Rural College, Edinburgh, United Kingdom
| | - Stephen J. Kemp
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
- Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
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Burris HH, Hwang SS, Collins JW, Kirpalani H, Wright CJ. Re-conceptualizing Associations between Race and Morbidities of Extreme Prematurity. J Pediatr 2019; 207:10-14.e1. [PMID: 30723017 DOI: 10.1016/j.jpeds.2018.12.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/21/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Heather H Burris
- Division of Neonatology, The Children's Hospital of Philadelphia at the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sunah S Hwang
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado
| | - James W Collins
- Division of Neonatology, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Haresh Kirpalani
- Emeritus, Division of Neonatology, The Children's Hospital of Philadelphia at the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Clyde J Wright
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado.
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Zhao S, Shi CM, Ma L, Liu Q, Liu Y, Wu F, Chi L, Chen H. AIM-SNPtag: A computationally efficient approach for developing ancestry-informative SNP panels. Forensic Sci Int Genet 2019; 38:245-253. [DOI: 10.1016/j.fsigen.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/03/2018] [Accepted: 10/23/2018] [Indexed: 01/13/2023]
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Schlomer GL, Cleveland HH, Deutsch AR, Vandenbergh DJ, Feinberg ME, Greenberg MT, Spoth RL, Redmond C. Developmental Change in Adolescent Delinquency: Modeling Time-Varying Effects of a Preventative Intervention and GABRA2 Halpotype Linked to Alcohol Use. J Youth Adolesc 2019; 48:71-85. [PMID: 30244312 PMCID: PMC10507654 DOI: 10.1007/s10964-018-0929-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/08/2018] [Indexed: 11/24/2022]
Abstract
Better integrating human developmental factors in genomic research is part of a set of next steps for testing gene-by-environment interaction hypotheses. This study adds to this work by extending prior research using time-varying effect modeling (TVEM) to evaluate the longitudinal associations between the PROSPER preventive intervention delivery system, a GABRA2 haplotype linked to alcohol use, and their interaction on adolescent delinquency. Logistic and Poisson analyses on eight waves of data spanning ages 11 to 19 (60% female, 90% Caucasian) showed the intervention reduced delinquency from ages 13 to 16. Moreover, interaction analysis revealed that the effect of the multicomponent intervention was significantly greater for T-allele carriers of the GABRA2 SNP rs279845, but only during the 13 to 16 age period. The results are discussed in terms of adolescent delinquency normativeness, implications for preventive intervention research, and the utility of incorporating development in GxE research.
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Affiliation(s)
- Gabriel L Schlomer
- Division of Educational Psychology and Methodology, University at Albany, State University of New York, Albany, NY, USA.
| | - H Harrington Cleveland
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
| | | | - David J Vandenbergh
- Department of Biobehavioral Health, Huck Institute for the Neurosciences, Molecular Cellular & Integrative Biosciences Program, The Pennsylvania State University, University Park, PA, USA
| | - Mark E Feinberg
- Prevention Research Center, The Pennsylvania State University, University Park, PA, USA
| | - Mark T Greenberg
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
- Prevention Research Center, The Pennsylvania State University, University Park, PA, USA
| | - Richard L Spoth
- Partnerships in Prevention Science Institute, Iowa State University, Ames, IA, USA
| | - Cleve Redmond
- Partnerships in Prevention Science Institute, Iowa State University, Ames, IA, USA
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Toma TT, Dawson JM, Adjeroh DA. Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry? BMC Med Genomics 2018; 11:0. [PMID: 30453954 PMCID: PMC6245491 DOI: 10.1186/s12920-018-0412-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult challenge. METHODS We study the problem of predicting human biogeographical ancestry from genomic data under resource constraints. In particular, we focus on the case where the analysis is constrained to using single nucleotide polymorphisms (SNPs) from just one chromosome. We propose methods to construct such ancestry informative SNP panels using correlation-based and outlier-based methods. RESULTS We accessed the performance of the proposed SNP panels derived from just one chromosome, using data from the 1000 Genome Project, Phase 3. For continental-level ancestry classification, we achieved an overall classification rate of 96.75% using 206 single nucleotide polymorphisms (SNPs). For sub-population level ancestry prediction, we achieved an average pairwise binary classification rates as follows: subpopulations in Europe: 76.6% (58 SNPs); Africa: 87.02% (87 SNPs); East Asia: 73.30% (68 SNPs); South Asia: 81.14% (75 SNPs); America: 85.85% (68 SNPs). CONCLUSION Our results demonstrate that one single chromosome (in particular, Chromosome 1), if carefully analyzed, could hold enough information for accurate prediction of human biogeographical ancestry. This has significant implications in terms of the computational resources required for analysis of ancestry, and in the applications of such analyses, such as in studies of genetic diseases, forensics, and soft biometrics.
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Affiliation(s)
- Tanjin T Toma
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA
| | - Jeremy M Dawson
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA
| | - Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA.
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Socio-technical disagreements as ethical fora: Parabon NanoLab’s forensic DNA Snapshot™ service at the intersection of discourses around robust science, technology validation, and commerce. BIOSOCIETIES 2018. [DOI: 10.1057/s41292-018-0138-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Estimating Asian Contribution to the Brazilian Population: A New Application of a Validated Set of 61 Ancestry Informative Markers. G3-GENES GENOMES GENETICS 2018; 8:3577-3582. [PMID: 30185426 PMCID: PMC6222592 DOI: 10.1534/g3.118.200650] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Estimates of different ancestral proportions in admixed populations are very important in population genetics studies, especially for the detection of population substructure effects in studies of case-control associations. Brazil is one of the most heterogeneous countries in the world, both from a socio-cultural and a genetic point of view. In this work, we investigated a previously developed set of 61 ancestry informative markers (AIM), aiming to estimate the proportions of four different ancestral groups (African, European, Native American and Asian) in Brazilian populations. To the best of our knowledge, this is the first study to use a set of AIM to investigate the genetic contribution of all four main parental populations to the Brazilian population, including Asian contribution. All selected markers were genotyped through multiplex PCR and capillary electrophoresis. The set was able to successfully differentiate the four ancestral populations (represented by 939 individuals) and identify their genetic contributions to the Brazilian population. In addition, it was used to estimate individual interethnic admixture of 1050 individuals from the Southeast region of Brazil and it showed that these individuals present a higher European ancestry contribution, followed by African, Asian and Native American ancestry contributions. Therefore, the 61 AIM set has proved to be a valuable tool to estimate individual and global ancestry proportions in populations mainly formed by these four groups. Our findings highlight the importance of using sets of AIM to evaluate population substructure in studies carried in admixed populations, in order to avoid misinterpretation of results.
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Moriot A, Santos C, Freire-Aradas A, Phillips C, Hall D. Inferring biogeographic ancestry with compound markers of slow and fast evolving polymorphisms. Eur J Hum Genet 2018; 26:1697-1707. [PMID: 29995845 PMCID: PMC6189140 DOI: 10.1038/s41431-018-0215-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/23/2018] [Accepted: 06/12/2018] [Indexed: 11/09/2022] Open
Abstract
Bio-geographic ancestry is an area of considerable interest in the medical genetics, anthropology and forensics. Although genome-wide panels are ideal as they provide dense genotyping data, small sets of ancestry informative marker provide a cost-effective way to investigate genetic ancestry and population structure. Here, we investigate the performance of a reduced marker set that combine different types of autosomal markers through haplotype analysis. In particular, recently described DIP-STR markers should offer the advantage of comprising both, low mutation rate Indels (DIPs), to study human history over longer time scale; and high mutation rate STRs, to trace relatively recent demographic events. In this study, we assessed the ability of an initial set of 23 DIP-STRs to distinguish major population groups using the HGDP-CEPH reference samples. The results obtained applying the STRUCTURE algorithm show that the discrimination capacity of the DIP-STRs is comparable to currently used small-scale ancestry informative markers by approaching seven major demographic groups. Yet, the DIP-STRs show an improved success rate in assigning individuals to populations of Europe and Middle East. These data show a remarkable ability of a preliminary set of 23 DIP-STR markers to infer major biogeographic origins. A novel set of DIP-STRs preselected to contain ancestry information should lead to further improvements.
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Affiliation(s)
- Amandine Moriot
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Lausanne, Switzerland
| | - Carla Santos
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Diana Hall
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Lausanne, Switzerland.
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Current and emerging tools for the recovery of genetic information from post mortem samples: New directions for disaster victim identification. Forensic Sci Int Genet 2018; 37:270-282. [DOI: 10.1016/j.fsigen.2018.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/27/2018] [Accepted: 08/27/2018] [Indexed: 01/14/2023]
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Maróti Z, Boldogkői Z, Tombácz D, Snyder M, Kalmár T. Evaluation of whole exome sequencing as an alternative to BeadChip and whole genome sequencing in human population genetic analysis. BMC Genomics 2018; 19:778. [PMID: 30373510 PMCID: PMC6206721 DOI: 10.1186/s12864-018-5168-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/15/2018] [Indexed: 11/26/2022] Open
Abstract
Background Understanding the underlying genetic structure of human populations is of fundamental interest to both biological and social sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation. The most widely used methods for collecting variant information at the DNA-level include whole genome sequencing, which remains costly, and the more economical solution of array-based techniques, as these are capable of simultaneously genotyping a pre-selected set of variable DNA sites in the human genome. The largest publicly accessible set of human genomic sequence data available today originates from exome sequencing that comprises around 1.2% of the whole genome (approximately 30 million base pairs). Results To unbiasedly compare the effect of SNP selection strategies in population genetic analysis we subsampled the variants of the same highly curated 1 K Genome dataset to mimic genome, exome sequencing and array data in order to eliminate the effect of different chemistry and error profiles of these different approaches. Next we compared the application of the exome dataset to the array-based dataset and to the gold standard whole genome dataset using the same population genetic analysis methods. Conclusions Our results draw attention to some of the inherent problems that arise from using pre-selected SNP sets for population genetic analysis. Additionally, we demonstrate that exome sequencing provides a better alternative to the array-based methods for population genetic analysis. In this study, we propose a strategy for unbiased variant collection from exome data and offer a bioinformatics protocol for proper data processing. Electronic supplementary material The online version of this article (10.1186/s12864-018-5168-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zoltán Maróti
- Department of Pediatrics and Pediatric Health Center, Faculty of Medicine, University of Szeged, Szeged, Hungary.
| | - Zsolt Boldogkői
- Department of Medical Biology, University of Szeged, Faculty of Medicine, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, University of Szeged, Faculty of Medicine, Szeged, Hungary.,Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Tibor Kalmár
- Department of Pediatrics and Pediatric Health Center, Faculty of Medicine, University of Szeged, Szeged, Hungary.
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Bradbury C, Köttgen A, Staubach F. Off-target phenotypes in forensic DNA phenotyping and biogeographic ancestry inference: A resource. Forensic Sci Int Genet 2018; 38:93-104. [PMID: 30391626 DOI: 10.1016/j.fsigen.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/27/2018] [Accepted: 10/13/2018] [Indexed: 01/04/2023]
Abstract
With recent advances in DNA sequencing technologies it has become feasible and cost effective to genotype larger marker sets for forensic purposes. Two technologies that make use of the larger marker sets have come into focus in forensic research and applications; inference of biogeographic ancestry (BGA) and forensic DNA phenotyping (FDP). These methods hold the promise to reveal information about a yet unknown perpetrator from a DNA sample. In contrast, DNA-profiling, that is a standard practice in case work, relies on matching DNA-profiles between crime scene material and suspects on a database of DNA-profiles. Markers for DNA-profiling were developed under the premise to reveal as little additional information about the human source of the profile as possible, the rationale being that personal privacy rights have to be balanced against the public interest in solving a crime. The same argument holds for markers used in BGA and FDP; these markers might also reveal information on off-target phenotypes (OTPs), that go beyond BGA and the phenotypes targeted in FDP. In particular, health related OTPs might shift the balance between privacy protection and public interest. However, to our knowledge, there is currently no convenient resource available to incorporate knowledge on OTPs in BGA and FDP assay design and application. In order to provide such a resource, we performed a systematic search for OTPs associated with a comprehensive set of markers (1766 SNPs) used or suggested to be used for BGA inference and FDP. In this set, we identified a relatively small number of 27 SNPs (1.53%) that convey information on diverse health related OTPs such as cancer risk, induced asthma, or risk of alcoholism. Some of these SNPs are commonly used for FDP and BGA across different marker sets. We conclude that the effects of SNP markers used in FDP and BGA on OTPs are currently limited, with few exceptions that should be considered in a balanced decision on assay design and application.
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Affiliation(s)
- Cedric Bradbury
- University College Freiburg, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Dept. of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Fabian Staubach
- Institute of Biology I, Dept. of Evolutionary Biology and Ecology, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
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Knisely MR, Conley YP, Kober KM, Smoot B, Paul SM, Levine JD, Miaskowski C. Associations Between Catecholaminergic and Serotonergic Genes and Persistent Breast Pain Phenotypes After Breast Cancer Surgery. THE JOURNAL OF PAIN 2018; 19:1130-1146. [DOI: 10.1016/j.jpain.2018.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/04/2018] [Accepted: 04/12/2018] [Indexed: 12/20/2022]
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