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Shui YB, Liu Y, Huang AJW, Siegfried CJ. SDPR expression in human trabecular meshwork and its potential role in racial disparities of glaucoma. Sci Rep 2024; 14:10258. [PMID: 38704467 PMCID: PMC11069504 DOI: 10.1038/s41598-024-61071-w] [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: 10/18/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
In order to identify how differential gene expression in the trabecular meshwork (TM) contributes to racial disparities of caveolar protein expression, TM dysfunction and development of primary open angle glaucoma (POAG), RNA sequencing was performed to compare TM tissue obtained from White and Black POAG surgical (trabeculectomy) specimens. Healthy donor TM tissue from White and Black donors was analyzed by PCR, qPCR, immunohistochemistry staining, and Western blot to evaluate SDPR (serum deprivation protein response; Cavin 2) and CAV1/CAV2 (Caveolin 1/Caveolin 2). Standard transmission electron microscopy (TEM) and immunogold labeled studies were performed. RNA sequencing demonstrated reduced SDPR expression in TM from Black vs White POAG patients' surgical specimens, with no significant expression differences in other caveolae-associated genes, confirmed by qPCR analysis. No racial differences in SDPR gene expression were noted in healthy donor tissue by PCR analysis, but there was greater expression as compared to specimens from patients with glaucoma. Analysis of SDPR protein expression confirmed specific expression in the TM regions, but not in adjacent tissues. TEM studies of TM specimens from healthy donors did not demonstrate any racial differences in caveolar morphology, but a significant reduction of caveolae with normal morphology and immuno-gold staining of SDPR were noted in glaucomatous TM as compared to TM from healthy donors. Linkage of SDPR expression levels in TM, POAG development, and caveolar ultrastructural morphology may provide the basis for a novel pathway of exploration of the pathologic mechanisms of glaucoma. Differential gene expression of SDPR in TM from Black vs White subjects with glaucoma may further our understanding of the important public health implications of the racial disparities of this blinding disease.
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Affiliation(s)
- Ying-Bo Shui
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ying Liu
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Andrew J W Huang
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Carla J Siegfried
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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2
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Lima-Cooper G, Ouma BJ, Datta D, Bond C, Soto AA, Conroy AL, Park GS, Bangirana P, Joloba ML, Opoka RO, Idro R, John CC. Apolipoprotein-E4: risk of severe malaria and mortality and cognitive impairment in pediatric cerebral malaria. Pediatr Res 2023:10.1038/s41390-023-02912-8. [PMID: 38007518 DOI: 10.1038/s41390-023-02912-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/21/2023] [Accepted: 11/02/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND The relationship of apolipoprotein-E4 (APOE4) to mortality and cognition after severe malaria in children is unknown. METHODS APOE genotyping was performed in children with cerebral malaria (CM, n = 261), severe malarial anemia (SMA, n = 224) and community children (CC, n = 213). Cognition was assessed over 2-year follow-up. RESULTS A greater proportion of children with CM or SMA than CC had APOE4 (n = 162, 31.0%; n = 142, 31.7%; n = 103, 24.2%, respectively, p = 0.02), but no difference was seen in APOE3 (n = 310, 59.4%; n = 267, 59.6%; n = 282, 66.2%, respectively, p = 0.06), or APOE2 (n = 50, 9.6%; n = 39, 8.7%; and n = 41, 9.6%, respectively, p = 0.87). APOE4 was associated with increased mortality in CM (odds ratio, 2.28; 95% CI, 1.01, 5.11). However, APOE4 was associated with better long-term cognition (ß, 0.55; 95% CI, 0.04, 1.07, p = 0.04) and attention (ß 0.78; 95% CI, 0.26, 1.30, p = 0.004) in children with CM < 5 years old, but worse attention (ß, -0.90; 95% CI, -1.69, -0.10, p = 0.03) in children with CM ≥ 5 years old. Among children with CM, risk of post-discharge malaria was increased with APOE4 and decreased with APOE3. CONCLUSIONS APOE4 is associated with higher risk of CM or SMA and mortality in children with CM, but better long-term cognition in CM survivors <5 years of age.
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Affiliation(s)
- Giselle Lima-Cooper
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Disease and Global Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Benson J Ouma
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Dibyadyuti Datta
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Disease and Global Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Caitlin Bond
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Disease and Global Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Alejandro A Soto
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Disease and Global Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrea L Conroy
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Disease and Global Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gregory S Park
- Office of the Vice President for Research, University of Minnesota, Minneapolis, MN, USA
| | - Paul Bangirana
- Department of Psychiatry, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses L Joloba
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Robert O Opoka
- Department of Pediatrics and Child Health, Makerere University, Kampala, Uganda
| | - Richard Idro
- Department of Pediatrics and Child Health, Makerere University, Kampala, Uganda
- Nuffield Department of Medicine, Centre of Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Chandy C John
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Disease and Global Health, Indiana University School of Medicine, Indianapolis, IN, USA.
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Alyabyeva PV, Petrova MM, Dmitrenko DV, Garganeeva NP, Chumakova GA, Al-Zamil M, Trefilova VV, Nasyrova RF, Shnayder NA. Association of Single-Nucleotide Polymorphisms Rs2779249 (chr17:26128581 C>A) and Rs rs2297518 (chr17: chr17:27769571 G>A) of the NOS2 Gene with Tension-Type Headache and Arterial Hypertension Overlap Syndrome in Eastern Siberia. Genes (Basel) 2023; 14:513. [PMID: 36833440 PMCID: PMC9957272 DOI: 10.3390/genes14020513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Inducible nitric oxide (NO) synthase (iNOS), encoded by the NOS2 gene, promotes the generation of high levels of NO to combat harmful environmental influences in a wide range of cells. iNOS can cause adverse effects, such as falling blood pressure, if overexpressed. Thus, according to some data, this enzyme is an important precursor of arterial hypertension (AH) and tension-type headache (TTH), which are the most common multifactorial diseases in adults. The purpose of this study was to investigate the association of rs2779249 (chr17:26128581 C>A) and rs2297518 (chr17: chr17:27769571 G>A) of the NOS2 gene with TTH and AH overlap syndrome (OS) in Caucasians in Eastern Siberia. The sample size was 91 participants: the first group-30 patients with OS; the second group-30 patients AH; and the third group-31 healthy volunteers. RT-PCR was used for the determination of alleles and genotypes of the SNPs rs2779249 and rs2297518 of the NOS2 gene in all groups of participants. We showed that the frequency of allele A was significantly higher among patients with AH compared with healthy volunteers (p-value < 0.05). The frequency of the heterozygous genotype CA of rs2779249 was higher in the first group vs. the control (p-value = 0.03), and in the second group vs. the control (p-value = 0.045). The frequency of the heterozygous genotype GA of rs2297518 was higher in the first group vs. the control (p-value = 0.035), and in the second group vs. the control (p-value = 0.001). The allele A of rs2779249 was associated with OS (OR = 3.17 [95% CI: 1.31-7.67], p-value = 0.009) and AH (OR = 2.94 [95% CI: 1.21-7.15], p-value = 0.015) risks compared with the control. The minor allele A of rs2297518 was associated with OS (OR = 4.0 [95% CI: 0.96-16.61], p-value = 0.035) and AH (OR = 8.17 [95% CI: 2.03-32.79], p-value = 0.001) risks compared with the control. Therefore, our pilot study demonstrated that the SNPs rs2779249 and rs229718 of the NOS2 gene could be promising genetic biomarkers for this OS risk in Caucasians from Eastern Siberia.
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Affiliation(s)
- Polina V. Alyabyeva
- Shared Core Facilities Molecular and Cell Technologies, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
| | - Marina M. Petrova
- Shared Core Facilities Molecular and Cell Technologies, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
| | - Diana V. Dmitrenko
- Shared Core Facilities Molecular and Cell Technologies, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
| | - Natalia P. Garganeeva
- Department of General Medical Practice and Outpatient Therapy, Siberian State Medical University, 634050 Tomsk, Russia
| | - Galina A. Chumakova
- Department of Therapy and General Medical Practice with a Course of Postgraduate Professional Education, Altai State Medical University, 656038 Barnaul, Russia
| | - Mustafa Al-Zamil
- Department of Physiotherapy, Faculty of Continuing Medical Education, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
| | - Vera V. Trefilova
- Neurological Department No. 16, Hospital for War Veterans, 193079 St. Petersburg, Russia
| | - Regina F. Nasyrova
- Institute of Personalized Psychiatry and Neurology, V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, 192019 St. Petersburg, Russia
| | - Natalia A. Shnayder
- Shared Core Facilities Molecular and Cell Technologies, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
- Institute of Personalized Psychiatry and Neurology, V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, 192019 St. Petersburg, Russia
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Chapman JA, Stewart CJ. Methodological challenges in neonatal microbiome research. Gut Microbes 2023; 15:2183687. [PMID: 36843005 PMCID: PMC9980642 DOI: 10.1080/19490976.2023.2183687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/16/2023] [Indexed: 02/28/2023] Open
Abstract
Following microbial colonization at birth, the gut microbiome plays a vital role in the healthy development of human neonates and impacts both health and disease in later life. Understanding the development of the neonatal gut microbiome and how it interacts with the neonatal host are therefore important areas of study. However, research within this field must address a range of specific challenges that impact the design and implementation of research methods. If not considered ahead of time, these challenges have the potential to introduce biases into studies, negatively affecting the relevance, reproducibility, and impact of any findings. This review outlines the nature of these challenges and points to current and future solutions, as outlined in the literature, to assist researchers in the early stages of study design.
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Affiliation(s)
- Jonathan A Chapman
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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Shin E, Schwarz KB, Jones-Brando LV, Florea LD, Sabunciyan S, Wood LD, Yolken RH. Expression of HLA and Autoimmune Pathway Genes in Liver Biopsies of Young Subjects With Autoimmune Hepatitis Type 1. J Pediatr Gastroenterol Nutr 2022; 75:269-275. [PMID: 35759748 PMCID: PMC9365252 DOI: 10.1097/mpg.0000000000003538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/18/2022] [Indexed: 12/10/2022]
Abstract
OBJECTIVES To test the hypothesis that autoimmune hepatitis (AIH type I) in young subjects is due to genetic differences in proinflammatory genes responding to viral triggers in patients and controls. METHODS Intrahepatic gene expression was compared between AIH type I (n = 24, age 9-30 years) patients (hereafter referred to as the AIH group) and controls (n = 21, age 4-25 years). RNA sequencing was performed on complementary DNA (cDNA) libraries made from total RNA extracted from formalin-fixed paraffin-embedded (FFPE) liver biopsy samples. Gene expression levels were quantified, and differentially expressed genes were functionally analyzed. Pathway analysis was performed using the databases Kyoto Encyclopedia of Genes and Genomes (KEGG) and PANTHER. The remaining sequences were mapped to the RefSeq complete set of viral genomes. RESULTS Differential gene analysis identified 181 genes that were significantly differentially expressed (136 upregulated in the AIH group). Autoimmune pathway genes such as CD19 and CD20 which are important in B cell regulation and maturation as well as, CD8 and LY9 , which are T-cell related, were upregulated in our AIH group. Genes implicated in AIH pathogenesis including CXCL10 , which is thought to be associated with AIH severity and progression, complement genes ( C1QA, C1QB , and C1QC ), and human leucocyte antigen ( HLA ) genes ( HLA-DRB1, HLA-DRA, HLA-B , and HLA-C ) were upregulated in samples from the AIH group. Specific viral etiologies were not found. CONCLUSIONS Unbiased next-generation sequencing and differential gene expression analysis of the AIH group has not only added support for the role of B cells in the pathogenesis and treatment of AIH but also has introduced potential new therapeutic targets: CXCL10 (anti- CXCL10 ) and several complement system-related genes.
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Affiliation(s)
- Emilia Shin
- From the Pediatrics, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | | | - Liliana D. Florea
- the Genetic Medicine, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Sarven Sabunciyan
- From the Pediatrics, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Robert H. Yolken
- From the Pediatrics, Johns Hopkins Medical Institutions, Baltimore, MD
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6
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Panda G, Mishra N, Sharma D, Kutum R, Bhoyar RC, Jain A, Imran M, Senthilvel V, Divakar MK, Mishra A, Garg P, Banerjee P, Sivasubbu S, Scaria V, Ray A. Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum. Front Pharmacol 2022; 13:858345. [PMID: 35865963 PMCID: PMC9294532 DOI: 10.3389/fphar.2022.858345] [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: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
India confines more than 17% of the world’s population and has a diverse genetic makeup with several clinically relevant rare mutations belonging to many sub-group which are undervalued in global sequencing datasets like the 1000 Genome data (1KG) containing limited samples for Indian ethnicity. Such databases are critical for the pharmaceutical and drug development industry where diversity plays a crucial role in identifying genetic disposition towards adverse drug reactions. A qualitative and comparative sequence and structural study utilizing variant information present in the recently published, largest curated Indian genome database (IndiGen) and the 1000 Genome data was performed for variants belonging to the kinase coding genes, the second most targeted group of drug targets. The sequence-level analysis identified similarities and differences among different populations based on the nsSNVs and amino acid exchange frequencies whereas a comparative structural analysis of IndiGen variants was performed with pathogenic variants reported in UniProtKB Humsavar data. The influence of these variations on structural features of the protein, such as structural stability, solvent accessibility, hydrophobicity, and the hydrogen-bond network was investigated. In-silico screening of the known drugs to these Indian variation-containing proteins reveals critical differences imparted in the strength of binding due to the variations present in the Indian population. In conclusion, this study constitutes a comprehensive investigation into the understanding of common variations present in the second largest population in the world and investigating its implications in the sequence, structural and pharmacogenomic landscape. The preliminary investigation reported in this paper, supporting the screening and detection of ADRs specific to the Indian population could aid in the development of techniques for pre-clinical and post-market screening of drug-related adverse events in the Indian population.
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Affiliation(s)
- Gayatri Panda
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
| | - Neha Mishra
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
| | - Disha Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Rintu Kutum
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Ashoka University, Sonipat, India
| | - Rahul C. Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Abhinav Jain
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mohamed Imran
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Vigneshwar Senthilvel
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mohit Kumar Divakar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Anushree Mishra
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Parth Garg
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
| | - Priyanka Banerjee
- Institute for Physiology, Charité-University Medicine Berlin, Berlin, Germany
| | - Sridhar Sivasubbu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Arjun Ray
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
- *Correspondence: Arjun Ray,
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Siegfried CJ, Shui YB. Racial Disparities in Glaucoma: From Epidemiology to Pathophysiology. MISSOURI MEDICINE 2022; 119:49-54. [PMID: 36033149 PMCID: PMC9312450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Among individuals of African and Latinx descent compared to those of European background, there is a higher prevalence, earlier onset, more rapid progression of primary open angle glaucoma and greater incidence of blindness. Although some suggest that outreach, education and screening programs may expand earlier diagnosis, and attention to access, cost of treatment, and adherence will improve outcomes, there is increasing evidence of genetic and physiologic differences which may be associated with these disease disparities.
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Affiliation(s)
- Carla J Siegfried
- John F. Hardesty MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Ying-Bo Shui
- John F. Hardesty MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
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Pang H, Xia Y, Luo S, Huang G, Li X, Xie Z, Zhou Z. Emerging roles of rare and low-frequency genetic variants in type 1 diabetes mellitus. J Med Genet 2021; 58:289-296. [PMID: 33753534 PMCID: PMC8086251 DOI: 10.1136/jmedgenet-2020-107350] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/06/2021] [Accepted: 01/10/2021] [Indexed: 12/12/2022]
Abstract
Type 1 diabetes mellitus (T1DM) is defined as an autoimmune disorder and has enormous complexity and heterogeneity. Although its precise pathogenic mechanisms are obscure, this disease is widely acknowledged to be precipitated by environmental factors in individuals with genetic susceptibility. To date, the known susceptibility loci, which have mostly been identified by genome-wide association studies, can explain 80%–85% of the heritability of T1DM. Researchers believe that at least a part of its missing genetic component is caused by undetected rare and low-frequency variants. Most common variants have only small to modest effect sizes, which increases the difficulty of dissecting their functions and restricts their potential clinical application. Intriguingly, many studies have indicated that rare and low-frequency variants have larger effect sizes and play more significant roles in susceptibility to common diseases, including T1DM, than common variants do. Therefore, better recognition of rare and low-frequency variants is beneficial for revealing the genetic architecture of T1DM and for providing new and potent therapeutic targets for this disease. Here, we will discuss existing challenges as well as the great significance of this field and review current knowledge of the contributions of rare and low-frequency variants to T1DM.
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Affiliation(s)
- Haipeng Pang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ying Xia
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Margres MJ, Rautsaw RM, Strickland JL, Mason AJ, Schramer TD, Hofmann EP, Stiers E, Ellsworth SA, Nystrom GS, Hogan MP, Bartlett DA, Colston TJ, Gilbert DM, Rokyta DR, Parkinson CL. The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype. Proc Natl Acad Sci U S A 2021; 118:e2014634118. [PMID: 33468678 PMCID: PMC7848695 DOI: 10.1073/pnas.2014634118] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Variation in gene regulation is ubiquitous, yet identifying the mechanisms producing such variation, especially for complex traits, is challenging. Snake venoms provide a model system for studying the phenotypic impacts of regulatory variation in complex traits because of their genetic tractability. Here, we sequence the genome of the Tiger Rattlesnake, which possesses the simplest and most toxic venom of any rattlesnake species, to determine whether the simple venom phenotype is the result of a simple genotype through gene loss or a complex genotype mediated through regulatory mechanisms. We generate the most contiguous snake-genome assembly to date and use this genome to show that gene loss, chromatin accessibility, and methylation levels all contribute to the production of the simplest, most toxic rattlesnake venom. We provide the most complete characterization of the venom gene-regulatory network to date and identify key mechanisms mediating phenotypic variation across a polygenic regulatory network.
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Affiliation(s)
- Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Biology, University of South Alabama, Mobile, AL 36688
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Tristan D Schramer
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erin Stiers
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634
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10
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Gualtieri CT. Genomic Variation, Evolvability, and the Paradox of Mental Illness. Front Psychiatry 2021; 11:593233. [PMID: 33551865 PMCID: PMC7859268 DOI: 10.3389/fpsyt.2020.593233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
Twentieth-century genetics was hard put to explain the irregular behavior of neuropsychiatric disorders. Autism and schizophrenia defy a principle of natural selection; they are highly heritable but associated with low reproductive success. Nevertheless, they persist. The genetic origins of such conditions are confounded by the problem of variable expression, that is, when a given genetic aberration can lead to any one of several distinct disorders. Also, autism and schizophrenia occur on a spectrum of severity, from mild and subclinical cases to the overt and disabling. Such irregularities reflect the problem of missing heritability; although hundreds of genes may be associated with autism or schizophrenia, together they account for only a small proportion of cases. Techniques for higher resolution, genomewide analysis have begun to illuminate the irregular and unpredictable behavior of the human genome. Thus, the origins of neuropsychiatric disorders in particular and complex disease in general have been illuminated. The human genome is characterized by a high degree of structural and behavioral variability: DNA content variation, epistasis, stochasticity in gene expression, and epigenetic changes. These elements have grown more complex as evolution scaled the phylogenetic tree. They are especially pertinent to brain development and function. Genomic variability is a window on the origins of complex disease, neuropsychiatric disorders, and neurodevelopmental disorders in particular. Genomic variability, as it happens, is also the fuel of evolvability. The genomic events that presided over the evolution of the primate and hominid lineages are over-represented in patients with autism and schizophrenia, as well as intellectual disability and epilepsy. That the special qualities of the human genome that drove evolution might, in some way, contribute to neuropsychiatric disorders is a matter of no little interest.
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11
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Abstract
Genome-wide association studies and candidate gene findings suggest that genetic approaches may help in choosing the most appropriate drug and dosage, while preventing adverse drug reactions. This is the field that addresses precision medicine: to evaluate variations in the DNA sequence that could be responsible for different individual analgesic response. We review potential gene biomarkers with best overall convergent functional evidence, for opioid use, in pain management. Polymorphisms can modify pharmacodynamics (i.e., mu opioid receptor, OPRM1) and pharmacokinetics (i.e., CYP2D6 phenotypes) pathways altering opioid effectiveness, consumption, side effects or additionally, prescription opioid use dependence vulnerability. This review provides a summary of these candidate variants for the translation of genotype into clinically useful information in pain medicine.
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Affiliation(s)
- Mongi Benjeddou
- Department of Biotechnology, University of The Western Cape, Robert Sobukwe Road, Bellville 7535, Cape Town, Western Cape, South Africa
| | - Ana M Peiró
- Neuropharmacology on Pain & Functional Diversity (NED), Alicante Institute for Health & Biomedical Research (ISABIAL), Alicante, Spain
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12
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Franca R, Zudeh G, Lucafò M, Rabusin M, Decorti G, Stocco G. Genome wide association studies for treatment-related adverse effects of pediatric acute lymphoblastic leukemia. WIREs Mech Dis 2020; 13:e1509. [PMID: 33016644 DOI: 10.1002/wsbm.1509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 08/01/2020] [Accepted: 09/04/2020] [Indexed: 12/14/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric hematological malignancy; notwithstanding the success of ALL therapy, severe adverse drugs effects represent a serious issue in pediatric oncology, because they could be both an additional life threatening condition for ALL patients per se and a reason to therapy delay or discontinuation with important fallouts on final outcome. Cancer treatment-related toxicities have generated a significant need of finding predictive pharmacogenomic markers for the a priori identification of at risk patients. In the era of precision medicine, high throughput genomic screening such as genome wide association studies (GWAS) might provide useful markers to tailor therapy intensity on patients' genetic profile. Furthermore, these findings could be useful in basic research for better understanding the mechanistic and regulatory pathways of the biological functions associated with ALL treatment toxicities. The purpose of this review is to give an overview of high throughput genomic screening of the last 10 years that had investigated the landscape of ALL treatment-associated toxicities. This article is categorized under: Cancer > Genetics/Genomics/Epigenetics.
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Affiliation(s)
- Raffaella Franca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Giulia Zudeh
- University of Trieste, PhD Course in Reproductive and Developmental Sciences, Trieste, Italy
| | - Marianna Lucafò
- Institute for Maternal and Child Health I.R.C.C.S Burlo Garofolo, Trieste, Italy
| | - Marco Rabusin
- Institute for Maternal and Child Health I.R.C.C.S Burlo Garofolo, Trieste, Italy
| | - Giuliana Decorti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health I.R.C.C.S Burlo Garofolo, Trieste, Italy
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
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13
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Georges A, Albuisson J, Berrandou T, Dupré D, Lorthioir A, D'Escamard V, Di Narzo AF, Kadian-Dodov D, Olin JW, Warchol-Celinska E, Prejbisz A, Januszewicz A, Bruneval P, Baranowska AA, Webb TR, Hamby SE, Samani NJ, Adlam D, Fendrikova-Mahlay N, Hazen S, Wang Y, Yang ML, Hunker K, Combaret N, Motreff P, Chédid A, Fiquet B, Plouin PF, Mousseaux E, Azarine A, Amar L, Azizi M, Gornik HL, Ganesh SK, Kovacic JC, Jeunemaitre X, Bouatia-Naji N. Rare loss-of-function mutations of PTGIR are enriched in fibromuscular dysplasia. Cardiovasc Res 2020; 117:1154-1165. [PMID: 32531060 PMCID: PMC7983006 DOI: 10.1093/cvr/cvaa161] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/14/2020] [Accepted: 06/07/2020] [Indexed: 12/12/2022] Open
Abstract
Aims Fibromuscular dysplasia (FMD) and spontaneous coronary artery dissection (SCAD) are related, non-atherosclerotic arterial diseases mainly affecting middle-aged women. Little is known about their physiopathological mechanisms. We aimed to identify rare genetic causes to elucidate molecular mechanisms implicated in FMD and SCAD. Methods and results We analysed 29 exomes that included familial and sporadic FMD. We identified one rare loss-of-function variant (LoF) (frequencygnomAD = 0.000075) shared by two FMD sisters in the prostaglandin I2 receptor gene (PTGIR), a key player in vascular remodelling. Follow-up was conducted by targeted or Sanger sequencing (1071 FMD and 363 SCAD patients) or lookups in exome (264 FMD) or genome sequences (480 SCAD), all independent and unrelated. It revealed four additional LoF allele carriers, in addition to several rare missense variants, among FMD patients, and two LoF allele carriers among SCAD patients, including one carrying a rare splicing mutation (c.768 + 1C>G). We used burden test to test for enrichment in patients compared to gnomAD controls, which detected a putative enrichment in FMD (PTRAPD = 8 × 10−4), but not a significant enrichment (PTRAPD = 0.12) in SCAD. The biological effects of variants on human prostaclycin receptor (hIP) signalling and protein expression were characterized using transient overexpression in human cells. We confirmed the LoFs (Q163X and P17RfsX6) and one missense (L67P), identified in one FMD and one SCAD patient, to severely impair hIP function in vitro. Conclusions Our study shows that rare genetic mutations in PTGIR are enriched among FMD patients and found in SCAD patients, suggesting a role for prostacyclin signalling in non-atherosclerotic stenosis and dissection.
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Affiliation(s)
- Adrien Georges
- Paris Cardiovascular Research Center, Inserm, Université de Paris, 56 Rue Leblanc, F-75015 Paris, France
| | - Juliette Albuisson
- Paris Cardiovascular Research Center, Inserm, Université de Paris, 56 Rue Leblanc, F-75015 Paris, France.,Department of Genetics, Assistance-publique-hôpitaux de Paris, Hopital Européen Georges Pompidou, F-75015 Paris, France
| | - Takiy Berrandou
- Paris Cardiovascular Research Center, Inserm, Université de Paris, 56 Rue Leblanc, F-75015 Paris, France
| | - Délia Dupré
- Paris Cardiovascular Research Center, Inserm, Université de Paris, 56 Rue Leblanc, F-75015 Paris, France
| | - Aurélien Lorthioir
- Department of Hypertension, Assistance-publique-hôpitaux de Paris, Hopital Européen Georges Pompidou, F-75015 Paris, France
| | - Valentina D'Escamard
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Antonio F Di Narzo
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniella Kadian-Dodov
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey W Olin
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | | | - Patrick Bruneval
- Paris Cardiovascular Research Center, Inserm, Université de Paris, 56 Rue Leblanc, F-75015 Paris, France
| | - Anna A Baranowska
- Department of Cardiovascular Sciences, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE5 4PW, UK
| | - Tom R Webb
- Department of Cardiovascular Sciences, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE5 4PW, UK
| | - Stephen E Hamby
- Department of Cardiovascular Sciences, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE5 4PW, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE5 4PW, UK
| | - David Adlam
- Department of Cardiovascular Sciences, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE5 4PW, UK
| | - Natalia Fendrikova-Mahlay
- Department of Cardiovascular Medicine, Cleveland Clinic Heart and Vascular Institute, Cleveland, OH 44195, USA
| | - Stanley Hazen
- Department of Cardiovascular Medicine, Cleveland Clinic Heart and Vascular Institute, Cleveland, OH 44195, USA
| | - Yu Wang
- Division of Cardiovascular Medicine, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109-5856, USA.,Division of Cardiovascular Medicine, Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Min-Lee Yang
- Division of Cardiovascular Medicine, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109-5856, USA.,Division of Cardiovascular Medicine, Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Kristina Hunker
- Division of Cardiovascular Medicine, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109-5856, USA.,Division of Cardiovascular Medicine, Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Nicolas Combaret
- Department of Cardiology, University Hospital of Clermont-Ferrand, Auvergne University, F-63003 Clermont-Ferrand, France
| | - Pascal Motreff
- Department of Cardiology, University Hospital of Clermont-Ferrand, Auvergne University, F-63003 Clermont-Ferrand, France
| | - Antoine Chédid
- Department of Hypertension, Assistance-publique-hôpitaux de Paris, Hopital Européen Georges Pompidou, F-75015 Paris, France
| | - Béatrice Fiquet
- Department of Hypertension, Assistance-publique-hôpitaux de Paris, Hopital Européen Georges Pompidou, F-75015 Paris, France
| | - Pierre-François Plouin
- Department of Hypertension, Assistance-publique-hôpitaux de Paris, Hopital Européen Georges Pompidou, F-75015 Paris, France
| | - Elie Mousseaux
- Paris Cardiovascular Research Center, Inserm, Université de Paris, 56 Rue Leblanc, F-75015 Paris, France.,Department of Radiology, Assistance-publique-hôpitaux de Paris, Hopital Européen Georges Pompidou, F-75015 Paris, France
| | - Arshid Azarine
- Department of Radiology, Assistance-publique-hôpitaux de Paris, Hopital Européen Georges Pompidou, F-75015 Paris, France
| | - Laurence Amar
- Paris Cardiovascular Research Center, Inserm, Université de Paris, 56 Rue Leblanc, F-75015 Paris, France.,Department of Hypertension, Assistance-publique-hôpitaux de Paris, Hopital Européen Georges Pompidou, F-75015 Paris, France
| | - Michel Azizi
- Department of Hypertension, Assistance-publique-hôpitaux de Paris, Hopital Européen Georges Pompidou, F-75015 Paris, France.,Université de Paris, Inserm CIC1418, F-75015 Paris, France
| | - Heather L Gornik
- University Hospitals Harrington Heart and Vascular Institute, University Hospitals and Case Western Reserve University, Cleveland, OH 44106, USA
| | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109-5856, USA.,Division of Cardiovascular Medicine, Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Jason C Kovacic
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.,St Vincent's Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
| | - Xavier Jeunemaitre
- Paris Cardiovascular Research Center, Inserm, Université de Paris, 56 Rue Leblanc, F-75015 Paris, France.,Department of Genetics, Assistance-publique-hôpitaux de Paris, Hopital Européen Georges Pompidou, F-75015 Paris, France
| | - Nabila Bouatia-Naji
- Paris Cardiovascular Research Center, Inserm, Université de Paris, 56 Rue Leblanc, F-75015 Paris, France
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14
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Guilherme JPLF, Lancha AH. Total genotype score and athletic status: An exploratory cross-sectional study of a Brazilian athlete cohort. Ann Hum Genet 2019; 84:141-150. [PMID: 31571205 DOI: 10.1111/ahg.12353] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 01/14/2023]
Abstract
The purpose of the present study was to explore the ability of the total genotype score (TGS) for evaluation of the polygenic profile of elite athletes. Data from a Brazilian athlete cohort were used in this study, which included 368 athletes and 818 nonathletes. The TGS targeted to power athletes was computed using from two to 10 associated polymorphisms. In all models, the power group showed a higher TGS mean compared to the nonathlete group. In particular, scores using more associated polymorphisms showed stronger differences (P < 0.0001). Moreover, the more polymorphisms included in the score, the greater its discriminatory power. The frequency distribution of individuals according to the TGS computed using 10 associated polymorphisms showed that both the power group and the replication group were overrepresented in scores ≥60.0 (P < 0.0075). Individuals with a score ≥60.0 had an increased odds ratio (OR) of being an elite athlete compared to the nonathlete group (OR > 2.03; P < 0.006), although there were athletes with TGS values ranging from 15.0 to 90.0. By setting 60.0 as the cutoff point, the sensitivity and specificity of the TGS was approximately 30% and 82.5%, respectively. In conclusion, the TGS computed using 10 associated polymorphisms proved to be effective in discriminating the target athlete group, but with limited accuracy as evidenced by its sensitivity rate.
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Affiliation(s)
| | - Antonio Herbert Lancha
- Laboratory of Applied Nutrition and Metabolism, School of Physical Education and Sport, University of São Paulo, São Paulo, SP, Brazil
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15
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François L, Hoskens H, Velie BD, Stinckens A, Tinel S, Lamberigts C, Peeters L, Savelkoul HFJ, Tijhaar E, Lindgren G, Janssens S, Ducro BJ, Buys N, Schurink AA. Genomic Regions Associated with IgE Levels against Culicoides spp. Antigens in Three Horse Breeds. Genes (Basel) 2019; 10:genes10080597. [PMID: 31398914 PMCID: PMC6723964 DOI: 10.3390/genes10080597] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/25/2019] [Accepted: 08/06/2019] [Indexed: 11/16/2022] Open
Abstract
Insect bite hypersensitivity (IBH), which is a cutaneous allergic reaction to antigens from Culicoides spp., is the most prevalent skin disorder in horses. Misdiagnosis is possible, as IBH is usually diagnosed based on clinical signs. Our study is the first to employ IgE levels against several recombinant Culicoides spp. allergens as an objective, independent, and quantitative phenotype to improve the power to detect genetic variants that underlie IBH. Genotypes of 200 Shetland ponies, 127 Icelandic horses, and 223 Belgian Warmblood horses were analyzed while using a mixed model approach. No single-nucleotide polymorphism (SNP) passed the Bonferroni corrected significance threshold, but several regions were identified within and across breeds, which confirmed previously identified regions of interest and, in addition, identifying new regions of interest. Allergen-specific IgE levels are a continuous and objective phenotype that allow for more powerful analyses when compared to a case-control set-up, as more significant associations were obtained. However, the use of a higher density array seems necessary to fully employ the use of IgE levels as a phenotype. While these results still require validation in a large independent dataset, the use of allergen-specific IgE levels showed value as an objective and continuous phenotype that can deepen our understanding of the biology underlying IBH.
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Affiliation(s)
- Liesbeth François
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, B-3000 Leuven, Belgium
| | - Brandon D Velie
- School of Life & Environmental Sciences, B19-603 University of Sydney, Sydney, NSW 2006,Australia
| | - Anneleen Stinckens
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Susanne Tinel
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Chris Lamberigts
- Research Group Livestock Physiology, Department of Biosystems, KU Leuven, Leuven, B-3001 Leuven, Belgium
| | - Liesbet Peeters
- Biomedical Research Institute, Hasselt University, B-3590 Diepenbeek, Belgium
| | - Huub F J Savelkoul
- Cell Biology and Immunology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Edwin Tijhaar
- Cell Biology and Immunology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Gabriella Lindgren
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Steven Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Nadine Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - And Anouk Schurink
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
- Centre for Genetic Resources, The Netherlands (CGN), Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
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16
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Lin W, Xu H, Wu Y, Wang J, Yuan Q. In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis. J Cell Physiol 2019; 235:900-908. [PMID: 31245852 DOI: 10.1002/jcp.29005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/04/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Weimin Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology Sichuan University Chengdu China
| | - Hao Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology Sichuan University Chengdu China
| | - Yunshu Wu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology Sichuan University Chengdu China
| | - Jun Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology Sichuan University Chengdu China
- Department of Periodontics, West China Hospital of Stomatology Sichuan University Chengdu China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology Sichuan University Chengdu China
- Department of Oral Implantology, West China Hospital of Stomatology Sichuan University Chengdu China
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17
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GenePy - a score for estimating gene pathogenicity in individuals using next-generation sequencing data. BMC Bioinformatics 2019; 20:254. [PMID: 31096927 PMCID: PMC6524327 DOI: 10.1186/s12859-019-2877-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 05/06/2019] [Indexed: 12/30/2022] Open
Abstract
Background Next-generation sequencing is revolutionising diagnosis and treatment of rare diseases, however its application to understanding common disease aetiology is limited. Rare disease applications binarily attribute genetic change(s) at a single locus to a specific phenotype. In common diseases, where multiple genetic variants within and across genes contribute to disease, binary modelling cannot capture the burden of pathogenicity harboured by an individual across a given gene/pathway. We present GenePy, a novel gene-level scoring system for integration and analysis of next-generation sequencing data on a per-individual basis that transforms NGS data interpretation from variant-level to gene-level. This simple and flexible scoring system is intuitive and amenable to integration for machine learning, network and topological approaches, facilitating the investigation of complex phenotypes. Results Whole-exome sequencing data from 508 individuals were used to generate GenePy scores. For each variant a score is calculated incorporating: i) population allele frequency estimates; ii) individual zygosity, determined through standard variant calling pipelines and; iii) any user defined deleteriousness metric to inform on functional impact. GenePy then combines scores generated for all variants observed into a single gene score for each individual. We generated a matrix of ~ 14,000 GenePy scores for all individuals for each of sixteen popular deleteriousness metrics. All per-gene scores are corrected for gene length. The majority of genes generate GenePy scores < 0.01 although individuals harbouring multiple rare highly deleterious mutations can accumulate extremely high GenePy scores. In the absence of a comparator metric, we examine GenePy performance in discriminating genes known to be associated with three common, complex diseases. A Mann-Whitney U test conducted on GenePy scores for this positive control gene in cases versus controls demonstrates markedly more significant results (p = 1.37 × 10− 4) compared to the most commonly applied association tool that combines common and rare variation (p = 0.003). Conclusions Per-gene per-individual GenePy scores are intuitive when assessing genetic variation in individual patients or comparing scores between groups. GenePy outperforms the currently accepted best practice tools for combining common and rare variation. GenePy scores are suitable for downstream data integration with transcriptomic and proteomic data that also report at the gene level. Electronic supplementary material The online version of this article (10.1186/s12859-019-2877-3) contains supplementary material, which is available to authorized users.
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18
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Kim H, Lee JK. The effects of combined exercise program on health and physical fitness factors according to a BglI RFLP in renin gene in middle-aged obese women. GAZZETTA MEDICA ITALIANA ARCHIVIO PER LE SCIENZE MEDICHE 2019. [DOI: 10.23736/s0393-3660.18.03853-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Cuna A, George L, Sampath V. Genetic predisposition to necrotizing enterocolitis in premature infants: Current knowledge, challenges, and future directions. Semin Fetal Neonatal Med 2018; 23:387-393. [PMID: 30292709 PMCID: PMC6626706 DOI: 10.1016/j.siny.2018.08.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The role of genetics in the pathogenesis of necrotizing enterocolitis (NEC) was initially informed by epidemiological data indicating differences in prevalence among different ethnic groups as well as concordance in twins. These early observations, together with major advances in genomic research, paved the way for studies that begin to reveal the contribution of genetics to NEC. Using the candidate gene or pathway approach, several potential pathogenic variants for NEC in premature infants have already been identified. More recently, genome-wide association studies and exome-sequencing based studies for NEC have been reported. These advances, however, are tempered by the lack of adequately powered replication cohorts to validate the accuracy of these discoveries. Despite many challenges, genetic research in NEC is expected to increase, providing new insights into its pathogenesis and bringing the promise of personalized care closer to reality. In this review we provide a summary of genetic studies in NEC along with defining the challenges and possible future approaches.
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Affiliation(s)
| | | | - Venkatesh Sampath
- Division of Neonatology, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA.
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20
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Dong L, Wu N, Wang S, Cheng Y, Han L, Zhao J, Long X, Mu K, Li M, Wei L, Wang W, Zhang W, Cao Y, Liu J, Yu J, Hao X. Detection of novel germline mutations in six breast cancer predisposition genes by targeted next-generation sequencing. Hum Mutat 2018; 39:1442-1455. [PMID: 30039884 DOI: 10.1002/humu.23597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 07/13/2018] [Accepted: 07/18/2018] [Indexed: 11/10/2022]
Abstract
In this study, a customized amplicon-based target sequencing panel was designed to enrich the whole exon regions of six genes associated with the risk of breast cancer. Targeted next-generation sequencing (NGS) was performed for 146 breast cancer patients (BC), 71 healthy women with a family history of breast cancer (high risk), and 55 healthy women without a family history of cancer (control). Sixteen possible disease-causing mutations on four genes were identified in 20 samples. The percentages of possible disease-causing mutation carriers in the BC group (8.9%) and in the high-risk group (8.5%) were higher than that in the control group (1.8%). The BRCA1 possible disease-causing mutation group had a higher prevalence in family history and triple-negative breast cancer, while the BRCA2 possible disease-causing mutation group was younger and more likely to develop axillary lymph node metastasis (P < 0.05). Among the 146 patients, 47 with a family history of breast cancer were also sequenced with another 14 moderate-risk genes. Three additional possible disease-causing mutations were found on PALB2, CHEK2, and PMS2 genes, respectively. The results demonstrate that the six-gene targeted NGS panel may provide an approach to assess the genetic risk of breast cancer and predict the clinical prognosis of breast cancer patients.
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Affiliation(s)
- Li Dong
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer , Tianjin, China
| | - Nan Wu
- Cancer Prevention Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | | | - Yanan Cheng
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer , Tianjin, China
| | - Lei Han
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer , Tianjin, China
| | - Jing Zhao
- The Second Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Xinxin Long
- Department of Oncology, Tengzhou Central People's Hospital, Tengzhou, P.R. China
| | - Kun Mu
- Department of Breast Surgery, Hebei Province Cangzhou Hospital of Integrated Traditional and Western Medicine (Cangzhou No. 2 Hospital), Cangzhou, P. R. China
| | - Menghui Li
- Cancer Prevention Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Lijuan Wei
- Cancer Prevention Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | | | - Weijia Zhang
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yandong Cao
- Analyses Technology Co. Ltd., Beijing, China
| | - Juntian Liu
- Cancer Prevention Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China.,The Second Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer , Tianjin, China
| | - Xishan Hao
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer , Tianjin, China
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21
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Hiyari S, Green E, Pan C, Lari S, Davar M, Davis R, Camargo PM, Tetradis S, Lusis AJ, Pirih FQ. Genomewide Association Study Identifies Cxcl Family Members as Partial Mediators of LPS-Induced Periodontitis. J Bone Miner Res 2018; 33:1450-1463. [PMID: 29637625 PMCID: PMC8434897 DOI: 10.1002/jbmr.3440] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 12/21/2022]
Abstract
Periodontitis (PD) is characterized by bacterial infection and inflammation of tooth-supporting structures and can lead to tooth loss. PD affects ∼47% of the US population over age 30 years and has a heritability of about 50%. Although the host immunoinflammatory response and genetic background play a role, little is known of the underlying genetic factors. We examined natural genetic variation in lipopolysaccharide (LPS)-induced PD across a panel of inbred mouse strains, the hybrid mouse diversity panel (HMDP). We observed a strain-dependent sixfold difference in LPS-induced bone loss across the HMDP with a heritability of 53%. We performed a genomewide association study (GWAS) using FAST-LMM, which corrects for population structure, and identified loci significantly associated with PD. We examined candidate genes at a locus on chromosome 5, which suggested a relationship between LPS-induced bone loss and, together with expression data, identified Cxcl family members as associated with PD. We observed an increase in Cxcl10 protein, as well as immune cells and pro-inflammatory cytokines in C57BL/6J (high bone loss strain) but not in A/J (low bone loss strain) after LPS injections. Genetic deletion of CXCR3 (Cxcl9 and10 receptor) demonstrated a ∼50% reduction in bone loss and reduced osteoclasts after LPS injections. Furthermore, WT mice treated with AMG-487 (a CXCR3 antagonist) showed a ∼45% reduction in bone loss and decreased osteoclasts after LPS injections. We conclude that CXCR3 is a strong candidate for modulating the host response in individuals susceptible to PD. © 2018 American Society for Bone and Mineral Research.
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Affiliation(s)
- Sarah Hiyari
- Section of Periodontics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Elissa Green
- Section of Periodontics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Calvin Pan
- Departments of Medicine, Cardiology, and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Soma Lari
- Section of Periodontics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mina Davar
- Section of Periodontics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Richard Davis
- Departments of Medicine, Cardiology, and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Paulo M Camargo
- Section of Periodontics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sotirios Tetradis
- Section of Oral Radiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aldons J Lusis
- Departments of Medicine, Cardiology, and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Flavia Q Pirih
- Section of Periodontics, University of California, Los Angeles, Los Angeles, CA, USA
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22
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O'Donoghue MC, Murphy SE, Zamboni G, Nobre AC, Mackay CE. APOE genotype and cognition in healthy individuals at risk of Alzheimer's disease: A review. Cortex 2018; 104:103-123. [DOI: 10.1016/j.cortex.2018.03.025] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/02/2018] [Accepted: 03/19/2018] [Indexed: 01/22/2023]
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23
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Heritability of Hwabyung Symptoms in South Korean Adolescent and Young Adult Twins. Twin Res Hum Genet 2018; 21:378-383. [PMID: 29929564 DOI: 10.1017/thg.2018.40] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The present study aimed to estimate heritability of Hwabyung (HB) symptoms in adolescent and young adult twins in South Korea. The sample included 1,601 twins consisting of 143 pairs of monozygotic male (MZM), 67 pairs of dizygotic male (DZM), 295 pairs of monozygotic female (MZF), 114 pairs of dizygotic female (DZF), and 117 pairs of opposite-sex dizygotic (OSDZ) twins and 129 twins with non-participating co-twins (mean age = 19.1 ± 3.1 years; range: 12-29 years). An HB symptom questionnaire was given to twins via a telephone interview. Consistent with the literature of HB, the mean level of HB was significantly higher in females than in males. Maximum likelihood twin correlations for HB were 0.31 (95% CI [0.16, 0.45]) for MZM, 0.19 (95% CI [-0.05, 0.41]) for DZM, 0.50 (95% CI [0.41, 0.58]) for MZF, 0.28 (95% CI [0.11, 0.44]) for DZF, and 0.23 (95% CI [0.05, 0.40]) for OSDZ twins. These patterns of twin correlations suggested the presence of additive genetic influences on HB. Model-fitting analysis showed that additive genetic and individual-specific environmental influences on HB were 44% (95% CI [37, 51]) and 56% (95% CI [49, 63]), respectively. Shared environmental influences were not significant. These parameter estimates were not significantly different between two sexes, and did not change significantly with age in the present sample, suggesting that genetic and environmental influences on HB in both sexes are stable across adolescence and young adulthood.
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24
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Geets E, Meuwissen MEC, Van Hul W. Clinical, molecular genetics and therapeutic aspects of syndromic obesity. Clin Genet 2018; 95:23-40. [PMID: 29700824 DOI: 10.1111/cge.13367] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/05/2018] [Accepted: 04/16/2018] [Indexed: 12/13/2022]
Abstract
Obesity has become a major health problem worldwide. To date, more than 25 different syndromic forms of obesity are known in which one (monogenic) or multiple (polygenic) genes are involved. This review gives an overview of these forms and focuses more in detail on 6 syndromes: Prader Willi Syndrome and Prader Willi like phenotype, Bardet Biedl Syndrome, Alström Syndrome, Wilms tumor, Aniridia, Genitourinary malformations and mental Retardation syndrome and 16p11.2 (micro)deletions. Years of research provided plenty of information on the molecular genetics of these disorders and the obesity phenotype leading to a more individualized treatment of the symptoms, however, many questions still remain unanswered. As these obesity syndromes have different signs and symptoms in common, it makes it difficult to accurately diagnose patients which may result in inappropriate treatment of the disease. Therefore, the big challenge for clinicians and scientists is to more clearly differentiate all syndromic forms of obesity to provide conclusive genetic explanations and eventually deliver accurate genetic counseling and treatment. In addition, further delineation of the (functions of the) underlying genes with the use of array- or next-generation sequencing-based technology will be helpful to unravel the mechanisms of energy metabolism in the general population.
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Affiliation(s)
- E Geets
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - M E C Meuwissen
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - W Van Hul
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
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25
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Wright F, Fessele K. Primer in Genetics and Genomics, Article 5-Further Defining the Concepts of Genotype and Phenotype and Exploring Genotype-Phenotype Associations. Biol Res Nurs 2018; 19:576-585. [PMID: 28920489 DOI: 10.1177/1099800417725190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
As nurses begin to incorporate genetic and genomic sciences into clinical practice, education, and research, it is essential that they have a working knowledge of the terms foundational to the science. The first article in this primer series provided brief definitions of the basic terms (e.g., genetics and genomics) and introduced the concept of phenotype during the discussion of Mendelian inheritance. These terms, however, are inconsistently used in publications and conversations, and the linkage between genotype and phenotype requires clarification. The goal of this fifth article in the series is to elucidate these terms, provide an overview of the research methods used to determine genotype-phenotype associations, and discuss their significance to nursing through examples from the current nursing literature.
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Affiliation(s)
- Fay Wright
- 1 Yale School of Nursing, Orange CT, USA
| | - Kristen Fessele
- 2 Scientific Project Leader, Flatiron Health, New York, NY, USA.,3 Post-doctoral Research Fellow, University of Utah College of Nursing, Salt Lake City, UT, USA
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26
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Guilherme JPLF, Bertuzzi R, Lima-Silva AE, Pereira ADC, Lancha Junior AH. Analysis of sports-relevant polymorphisms in a large Brazilian cohort of top-level athletes. Ann Hum Genet 2018; 82:254-264. [PMID: 29603120 DOI: 10.1111/ahg.12248] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/10/2018] [Accepted: 02/16/2018] [Indexed: 12/13/2022]
Abstract
In recent years, there have been an increasing number of genetic variants associated with athletic phenotypes. Here, we selected a set of sports-relevant polymorphisms that have been previously suggested as genetic markers for human physical performance, and we examined their association with athletic status in a large cohort of Brazilians. We evaluated a sample of 1,622 individuals, in which 966 were nonathletes, and 656 were athletes: 328 endurance athletes and 328 power athletes. Only the AGT M268T minor allele was nominally associated with the endurance status. Conversely, we found that seven polymorphisms are more frequent in power athletes (MCT1 D490E, AGT M268T, PPARG P12A, PGC1A G482S, VEGFR2 Q472H, NOS3 C/T, and ACTN3 R577X). For all of these polymorphisms, power athletes were more likely than nonathletes or endurance athletes to carry the major allele or the homozygous genotype for the major allele. In particular, MCT1 D490E, AGT M268T, NOS3 C/T, and ACTN3 R577X showed stronger associations. Our findings support a role for these variants in the achievement of power athletic status in Brazilians: MCT1 D490E (T allele), AGT M268T (G allele), PPARG (C allele), PGC1A G482S (C allele), VEGFR2 Q472H (T allele), NOS3 C/T (T allele), and ACTN3 R577X (R allele).
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Affiliation(s)
| | - Rômulo Bertuzzi
- Endurance Performance Research Group, School of Physical Education and Sport, University of São Paulo, São Paulo, SP, Brazil
| | | | - Alexandre da Costa Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School of University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Antonio Herbert Lancha Junior
- Laboratory of Applied Nutrition and Metabolism, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo, SP, Brazil
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27
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Guilherme JPLF, Silva MS, Bertuzzi R, Lancha Junior AH. TheAGTR2rs11091046 (A>C) polymorphism and power athletic status in top-level Brazilian athletes. J Sports Sci 2018; 36:2327-2332. [DOI: 10.1080/02640414.2018.1455260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | - Mariana Sussi Silva
- Laboratory of Applied Nutrition and Metabolism, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo, Brazil
| | - Rômulo Bertuzzi
- Endurance Performance Research Group, School of Physical Education and Sport, University of São Paulo, Sao Paulo, Brazil
| | - Antonio Herbert Lancha Junior
- Laboratory of Applied Nutrition and Metabolism, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo, Brazil
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28
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Complex Segregation Analysis Provides Evidence for Autosomal Dominant Transmission in the Chinese Han Families with Ankylosing Spondylitis. BIOMED RESEARCH INTERNATIONAL 2018; 2017:4515701. [PMID: 29349072 PMCID: PMC5733618 DOI: 10.1155/2017/4515701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 09/17/2017] [Indexed: 11/17/2022]
Abstract
Introduction Familial aggregation of ankylosing spondylitis (AS) has been frequently noticed. However, the mode of inheritance in AS remains poorly understood. Our aim was to determine the mode of inheritance best fitting the observed transmission pattern of AS families. Methods Families with 5 or more AS patients diagnosed with 1984 modified New York criteria were recruited. We performed complex segregation analysis for a binary trait in regressive multivariate logistic models. The inheritance models, including sporadic, major gene, environmental, general, and other 9 models, were compared by likelihood ratio tests and Akaike's Information Criterion. Results This research included 9 Chinese Han AS families with a total number of 315 persons, including 74 patients. First, familial association was determined. Sporadic with familial association model was rejected when compared with either the general model or the homogeneous general model (p < 0.001). The environmental model was also rejected when compared with general models (p < 0.02). Mendelian dominate mode fitted best in 5 AS families, while Tau AB free model best explained the mode of inheritance in these AS families. Conclusion This study provided evidence in support of Mendelian dominant mode and firstly discovered a non-Mendelian mode called tau AB free inheritance mode in AS.
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29
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Tombácz D, Maróti Z, Kalmár T, Csabai Z, Balázs Z, Takahashi S, Palkovits M, Snyder M, Boldogkői Z. High-Coverage Whole-Exome Sequencing Identifies Candidate Genes for Suicide in Victims with Major Depressive Disorder. Sci Rep 2017; 7:7106. [PMID: 28769055 PMCID: PMC5541090 DOI: 10.1038/s41598-017-06522-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/14/2017] [Indexed: 01/06/2023] Open
Abstract
We carried out whole-exome ultra-high throughput sequencing in brain samples of suicide victims who had suffered from major depressive disorder and control subjects who had died from other causes. This study aimed to reveal the selective accumulation of rare variants in the coding and the UTR sequences within the genes of suicide victims. We also analysed the potential effect of STR and CNV variations, as well as the infection of the brain with neurovirulent viruses in this behavioural disorder. As a result, we have identified several candidate genes, among others three calcium channel genes that may potentially contribute to completed suicide. We also explored the potential implication of the TGF-β signalling pathway in the pathogenesis of suicidal behaviour. To our best knowledge, this is the first study that uses whole-exome sequencing for the investigation of suicide.
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Affiliation(s)
- Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, H-6720, Hungary.,Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr., Stanford, CA, 94305-5120, USA
| | - Zoltán Maróti
- Department of Paediatrics, Faculty of Medicine, University of Szeged, Korányi fasor 14-15., Szeged, H-6720, Hungary
| | - Tibor Kalmár
- Department of Paediatrics, Faculty of Medicine, University of Szeged, Korányi fasor 14-15., Szeged, H-6720, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, H-6720, Hungary
| | - Zsolt Balázs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, H-6720, Hungary
| | - Shinichi Takahashi
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr., Stanford, CA, 94305-5120, USA
| | - Miklós Palkovits
- Neuromorphological and Neuroendocrine Research Laboratory, Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Üllői u. 26., H-1085, Hungary
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr., Stanford, CA, 94305-5120, USA.
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, H-6720, Hungary.
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30
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Blue GM, Kirk EP, Giannoulatou E, Sholler GF, Dunwoodie SL, Harvey RP, Winlaw DS. Advances in the Genetics of Congenital Heart Disease: A Clinician's Guide. J Am Coll Cardiol 2017; 69:859-870. [PMID: 28209227 DOI: 10.1016/j.jacc.2016.11.060] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/15/2016] [Accepted: 11/17/2016] [Indexed: 11/18/2022]
Abstract
Our understanding of the genetics of congenital heart disease (CHD) is rapidly expanding; however, many questions, particularly those relating to sporadic forms of disease, remain unanswered. Massively parallel sequencing technology has made significant contributions to the field, both from a diagnostic perspective for patients and, importantly, also from the perspective of disease mechanism. The importance of de novo variation in sporadic disease is a recent highlight, and the genetic link between heart and brain development has been established. Furthermore, evidence of an underlying burden of genetic variation contributing to sporadic and familial forms of CHD has been identified. Although we are still unable to identify the cause of CHD for most patients, recent findings have provided us with a much clearer understanding of the types of variants and their individual contributions and collectively mark an important milestone in our understanding of both familial and sporadic forms of disease.
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Affiliation(s)
- Gillian M Blue
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia
| | - Edwin P Kirk
- Department of Medical Genetics, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney
| | - Gary F Sholler
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney
| | - David S Winlaw
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia.
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Abstract
An underlying genetic predisposition to necrotizing enterocolitis (NEC) is increasingly being recognized. Candidate gene or pathway approaches as well as genome-wide approaches are beginning to identify potential pathogenic variants for NEC in premature infants. However, a majority of these studies have not yielded definitive results because of limited sample size and lack of validation. Despite these challenges, understanding the contribution of genetic variation to NEC is important for providing new insights into the pathogenesis of NEC as well as allowing for targeted care of infants with inherent susceptibility. In this review we provide a summary of published genetic association studies in NEC along with defining the challenges and possible future approaches.
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Affiliation(s)
- Alain Cuna
- Division of Neonatology, Department of Pediatrics, Children's Mercy Hospital, University of Missouri-Kansas City, 2401 Gillham Rd, Kansas City, MO 64108
| | - Venkatesh Sampath
- Division of Neonatology, Department of Pediatrics, Children's Mercy Hospital, University of Missouri-Kansas City, 2401 Gillham Rd, Kansas City, MO 64108.
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32
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Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium. J Genet 2016; 94:731-40. [PMID: 26690529 DOI: 10.1007/s12041-015-0588-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) determined based on SNP arrays from the international HapMap consortium (HapMap) and the genetic variants detected in the 1000 genomes project (1KGP) can serve as two references for genomewide association studies (GWAS). We conducted comparative analyses to provide a means for assessing concerns regarding SNP array-based GWAS findings as well as for realistically bounding expectations for next generation sequencing (NGS)-based GWAS. We calculated and compared base composition, transitions to transversions ratio, minor allele frequency and heterozygous rate for SNPs from HapMap and 1KGP for the 622 common individuals. We analysed the genotype discordance between HapMap and 1KGP to assess consistency in the SNPs from the two references. In 1KGP, 90.58% of 36,817,799 SNPs detected were not measured in HapMap. More SNPs with minor allele frequencies less than 0.01 were found in 1KGP than HapMap. The two references have low disc ordance (generally smaller than 0.02) in genotypes of common SNPs, with most discordance from heterozygous SNPs. Our study demonstrated that SNP array-based GWAS findings were reliable and useful, although only a small portion of genetic variances were explained. NGS can detect not only common but also rare variants, supporting the expectation that NGS-based GWAS will be able to incorporate a much larger portion of genetic variance than SNP arrays-based GWAS.
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33
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Gasc C, Peyretaillade E, Peyret P. Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms. Nucleic Acids Res 2016; 44:4504-18. [PMID: 27105841 PMCID: PMC4889952 DOI: 10.1093/nar/gkw309] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/07/2016] [Accepted: 04/12/2016] [Indexed: 12/25/2022] Open
Abstract
The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology.
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Affiliation(s)
- Cyrielle Gasc
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
| | | | - Pierre Peyret
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
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34
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Marian AJ. Genetic Causality in Complex Traits: The Case of Uric Acid. J Am Coll Cardiol 2016; 67:417-419. [PMID: 26821630 DOI: 10.1016/j.jacc.2015.09.109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/29/2015] [Indexed: 12/09/2022]
Affiliation(s)
- A J Marian
- Center for Cardiovascular Genetics, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center and Texas Heart Institute, Houston, Texas.
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35
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A Quantitative Genomic Approach for Analysis of Fitness and Stress Related Traits in a Drosophila melanogaster Model Population. Int J Genomics 2016; 2016:2157494. [PMID: 27274984 PMCID: PMC4853962 DOI: 10.1155/2016/2157494] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/29/2016] [Indexed: 12/27/2022] Open
Abstract
The ability of natural populations to withstand environmental stresses relies partly on their adaptive ability. In this study, we used a subset of the Drosophila Genetic Reference Panel, a population of inbred, genome-sequenced lines derived from a natural population of Drosophila melanogaster, to investigate whether this population harbors genetic variation for a set of stress resistance and life history traits. Using a genomic approach, we found substantial genetic variation for metabolic rate, heat stress resistance, expression of a major heat shock protein, and egg-to-adult viability investigated at a benign and a higher stressful temperature. This suggests that these traits will be able to evolve. In addition, we outline an approach to conduct pathway associations based on genomic linear models, which has potential to identify adaptive genes and pathways, and therefore can be a valuable tool in conservation genomics.
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36
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Lacour A, Ellinghaus D, Schreiber S, Franke A, Becker T. Haplotype synthesis analysis reveals functional variants underlying known genome-wide associated susceptibility loci. Bioinformatics 2016; 32:2136-42. [PMID: 27153721 DOI: 10.1093/bioinformatics/btw125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/01/2016] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION The functional mechanisms underlying disease association remain unknown for Genome-wide Association Studies (GWAS) susceptibility variants located outside coding regions. Synthesis of effects from multiple surrounding functional variants has been suggested as an explanation of hard-to-interpret findings. We define filter criteria based on linkage disequilibrium measures and allele frequencies which reflect expected properties of synthesizing variant sets. For eligible candidate sets, we search for haplotype markers that are highly correlated with associated variants. RESULTS Via simulations we assess the performance of our approach and suggest parameter settings which guarantee 95% sensitivity at 20-fold reduced computational cost. We apply our method to 1000 Genomes data and confirmed Crohn's Disease (CD) and Type 2 Diabetes (T2D) variants. A proportion of 36.9% allowed explanation by three-variant-haplotypes carrying at least two functional variants, as compared to 16.4% for random variants ([Formula: see text]). Association could be explained by missense variants for MUC19, PER3 (CD) and HMG20A (T2D). In a CD GWAS-imputed using haplotype reference consortium data (64 976 haplotypes)-we could confirm the syntheses of MUC19 and PER3 and identified synthesis by missense variants for 6 further genes (ZGPAZ, GPR65, CLN3/NPIPB8, LOC102723878, rs2872507, GCKR). In all instances, the odds ratios of the synthesizing haplotypes were virtually identical to that of the index SNP. In summary, we demonstrate the potential of synthesis analysis to guide functional follow-up of GWAS findings. AVAILABILITY AND IMPLEMENTATION All methods are implemented in the C/C ++ toolkit GetSynth, available at http://sourceforge.net/projects/getsynth/ CONTACT tim.becker@uni-greifswald.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- André Lacour
- German Center for Neurodegenerative Diseases (DZNE), Bonn 53127, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Tim Becker
- Institute for Community Medicine, Ernst Moritz Arndt University Greifswald, Greifswald 17475, Germany
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Fallin MD, Duggal P, Beaty TH. Genetic Epidemiology and Public Health: The Evolution From Theory to Technology. Am J Epidemiol 2016; 183:387-93. [PMID: 26905340 DOI: 10.1093/aje/kww001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 01/04/2016] [Indexed: 12/28/2022] Open
Abstract
Genetic epidemiology represents a hybrid of epidemiologic designs and statistical models that explicitly consider both genetic and environmental risk factors for disease. It is a relatively new field in public health; the term was first coined only 35 years ago. In this short time, the field has been through a major evolution, changing from a field driven by theory, without the technology for genetic measurement or computational capacity to apply much of the designs and methods developed, to a field driven by rapidly expanding technology in genomic measurement and computational analyses while epidemiologic theory struggles to keep up. In this commentary, we describe 4 different eras of genetic epidemiology, spanning this evolution from theory to technology, what we have learned, what we have added to the broader field of public health, and what remains to be done.
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Marian AJ. Clinical applications of molecular genetic discoveries. Transl Res 2016; 168:6-14. [PMID: 26548329 PMCID: PMC4718781 DOI: 10.1016/j.trsl.2015.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/13/2015] [Accepted: 10/17/2015] [Indexed: 01/08/2023]
Abstract
Genome-wide association studies of complex traits have mapped >15,000 common single nucleotide variants (SNVs). Likewise, applications of massively parallel nucleic acid sequencing technologies often referred to as next-generation sequencing to molecular genetic studies of complex traits have catalogued a large number of rare variants (population frequency of <0.01) in cases with complex traits. Moreover, high-throughput nucleic acid sequencing, variant burden analysis, and linkage studies are illuminating the presence of large number of SNVs in cases and families with single-gene disorders. The plethora of the genetic variants has exposed the formidable challenge of identifying the causal and pathogenic variants from the enormous number of innocuous common and rare variants that exist in the population and in an individual genome. The arduous task of identifying the causal and pathogenic variants is further compounded by the pleiotropic effects of the variants, complexity of cis and trans interactions in the genome, variability in phenotypic expression of the disease, as well as phenotypic plasticity, and the multifarious determinants of the phenotype. Population genetic studies offer the initial roadmaps and have the potential to elucidate novel pathways involved in the pathogenesis of the disease. However, the genome of an individual is unique, rendering unambiguous identification of the causal or pathogenic variant in a single individual exceedingly challenging. Yet, the focus of the practice of medicine is on the individual, as Sir William Osler elegantly expressed in his insightful quotation: "The good physician treats the disease; the great physician treats the patient who has the disease." The daunting task facing physicians, patients, and researchers alike is to apply the modern genetic discoveries to care of the individual with or at risk of the disease.
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Affiliation(s)
- Ali J Marian
- Center for Cardiovascular Genetics, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Tex; Center for Cardiovascular Genetics, Texas Heart Institute, Houston, Tex.
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Shen L, Jia J. An Overview of Genome-Wide Association Studies in Alzheimer's Disease. Neurosci Bull 2016; 32:183-90. [PMID: 26810783 DOI: 10.1007/s12264-016-0011-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/09/2015] [Indexed: 12/25/2022] Open
Abstract
Genome-wide association studies (GWASs) have revealed a plethora of putative susceptibility genes for Alzheimer's disease (AD). With the sole exception of the APOE gene, these AD susceptibility genes have not been unequivocally validated in independent studies. No single novel functional risk genetic variant has been identified. In this review, we evaluate recent GWASs of AD, and discuss their significance, limitations, and challenges in the investigation of the genetic spectrum of AD.
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Affiliation(s)
- Luxi Shen
- Department of Neurology, Xuan Wu Hospital of the Capital Medical University, Beijing, 100053, China
| | - Jianping Jia
- Department of Neurology, Xuan Wu Hospital of the Capital Medical University, Beijing, 100053, China.
- Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, 100053, China.
- Beijing Key Laboratory of Geriatric Cognitive Disorders, Beijing, 100053, China.
- Neurodegenerative Laboratory of Ministry of Education of the People's Republic of China, Beijing, 100053, China.
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Carrera P, Di Resta C, Volonteri C, Castiglioni E, Bonfiglio S, Lazarevic D, Cittaro D, Stupka E, Ferrari M, Somaschini M. Exome sequencing and pathway analysis for identification of genetic variability relevant for bronchopulmonary dysplasia (BPD) in preterm newborns: A pilot study. Clin Chim Acta 2015; 451:39-45. [PMID: 25578394 DOI: 10.1016/j.cca.2015.01.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/30/2014] [Accepted: 01/02/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Paola Carrera
- Unit of Genomics for Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy; Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milano, Italy.
| | - Chiara Di Resta
- Unit of Genomics for Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy
| | | | - Emanuela Castiglioni
- Unit of Genomics for Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Silvia Bonfiglio
- Centre for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Dejan Lazarevic
- Centre for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Davide Cittaro
- Centre for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Elia Stupka
- Centre for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Maurizio Ferrari
- Unit of Genomics for Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy; Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milano, Italy; Vita-Salute San Raffaele University, Milano, Italy
| | - Marco Somaschini
- Unit of Genomics for Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy
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Visvikis-Siest S, Stathopoulou MG. Beyond genome-wide association studies: identifying variants using -omics approaches. Per Med 2015; 12:529-531. [PMID: 29750611 DOI: 10.2217/pme.15.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Sophie Visvikis-Siest
- INSERM UMR U1122; IGE-PCV "Interactions Gène-Environnement en Physiopathologie CardioVasculaire", Université de Lorraine, Faculté de Pharmacie, 30 Rue Lionnois, 54000 Nancy, France
| | - Maria G Stathopoulou
- INSERM UMR U1122; IGE-PCV "Interactions Gène-Environnement en Physiopathologie CardioVasculaire", Université de Lorraine, Faculté de Pharmacie, 30 Rue Lionnois, 54000 Nancy, France
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A review of genome-wide association studies for multiple sclerosis: classical and hypothesis-driven approaches. Hum Genet 2015; 134:1143-62. [DOI: 10.1007/s00439-015-1601-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/10/2015] [Indexed: 12/17/2022]
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Bouchiat C, Moreau K, Devillard S, Rasigade JP, Mosnier A, Geissmann T, Bes M, Tristan A, Lina G, Laurent F, Piroth L, Aissa N, Duval X, Le Moing V, Vandenesch F. Staphylococcus aureus infective endocarditis versus bacteremia strains: Subtle genetic differences at stake. INFECTION GENETICS AND EVOLUTION 2015; 36:524-530. [PMID: 26318542 DOI: 10.1016/j.meegid.2015.08.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/03/2015] [Accepted: 08/23/2015] [Indexed: 11/25/2022]
Abstract
Infective endocarditis (IE)((1)) is a severe condition complicating 10-25% of Staphylococcus aureus bacteremia. Although host-related IE risk factors have been identified, the involvement of bacterial features in IE complication is still unclear. We characterized strictly defined IE and bacteremia isolates and searched for discriminant features. S. aureus isolates causing community-acquired, definite native-valve IE (n=72) and bacteremia (n=54) were collected prospectively as part of a French multicenter cohort. Phenotypic traits previously reported or hypothesized to be involved in staphylococcal IE pathogenesis were tested. In parallel, the genotypic profiles of all isolates, obtained by microarray, were analyzed by discriminant analysis of principal components (DAPC)((2)). No significant difference was observed between IE and bacteremia strains, regarding either phenotypic or genotypic univariate analyses. However, the multivariate statistical tool DAPC, applied on microarray data, segregated IE and bacteremia isolates: IE isolates were correctly reassigned as such in 80.6% of the cases (C-statistic 0.83, P<0.001). The performance of this model was confirmed with an independent French collection IE and bacteremia isolates (78.8% reassignment, C-statistic 0.65, P<0.01). Finally, a simple linear discriminant function based on a subset of 8 genetic markers retained valuable performance both in study collection (86.1%, P<0.001) and in the independent validation collection (81.8%, P<0.01). We here show that community-acquired IE and bacteremia S. aureus isolates are genetically distinct based on subtle combinations of genetic markers. This finding provides the proof of concept that bacterial characteristics may contribute to the occurrence of IE in patients with S. aureus bacteremia.
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Affiliation(s)
- Coralie Bouchiat
- Laboratoire de Bactériologie, Centre de Biologie Est, Hospices Civils de Lyon, 59 Boulevard Louis Pinel, 69677 Bron Cedex, France; CIRI, International Center for Infectiology Research, Inserm U1111, Université Lyon 1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, 7 rue Guillaume Paradin, 69008 Lyon, France; Centre National de Référence des Staphylocoques, 59 Boulevard Louis Pinel, 69677 Bron Cedex, France
| | - Karen Moreau
- CIRI, International Center for Infectiology Research, Inserm U1111, Université Lyon 1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, 7 rue Guillaume Paradin, 69008 Lyon, France
| | - Sébastien Devillard
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Jean-Philippe Rasigade
- CIRI, International Center for Infectiology Research, Inserm U1111, Université Lyon 1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, 7 rue Guillaume Paradin, 69008 Lyon, France; Centre National de Référence des Staphylocoques, 59 Boulevard Louis Pinel, 69677 Bron Cedex, France
| | - Amandine Mosnier
- CIRI, International Center for Infectiology Research, Inserm U1111, Université Lyon 1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, 7 rue Guillaume Paradin, 69008 Lyon, France
| | - Tom Geissmann
- CIRI, International Center for Infectiology Research, Inserm U1111, Université Lyon 1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, 7 rue Guillaume Paradin, 69008 Lyon, France
| | - Michèle Bes
- Laboratoire de Bactériologie, Centre de Biologie Est, Hospices Civils de Lyon, 59 Boulevard Louis Pinel, 69677 Bron Cedex, France; CIRI, International Center for Infectiology Research, Inserm U1111, Université Lyon 1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, 7 rue Guillaume Paradin, 69008 Lyon, France; Centre National de Référence des Staphylocoques, 59 Boulevard Louis Pinel, 69677 Bron Cedex, France
| | - Anne Tristan
- Laboratoire de Bactériologie, Centre de Biologie Est, Hospices Civils de Lyon, 59 Boulevard Louis Pinel, 69677 Bron Cedex, France; CIRI, International Center for Infectiology Research, Inserm U1111, Université Lyon 1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, 7 rue Guillaume Paradin, 69008 Lyon, France; Centre National de Référence des Staphylocoques, 59 Boulevard Louis Pinel, 69677 Bron Cedex, France
| | - Gérard Lina
- CIRI, International Center for Infectiology Research, Inserm U1111, Université Lyon 1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, 7 rue Guillaume Paradin, 69008 Lyon, France; Centre National de Référence des Staphylocoques, 59 Boulevard Louis Pinel, 69677 Bron Cedex, France
| | - Frédéric Laurent
- CIRI, International Center for Infectiology Research, Inserm U1111, Université Lyon 1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, 7 rue Guillaume Paradin, 69008 Lyon, France; Centre National de Référence des Staphylocoques, 59 Boulevard Louis Pinel, 69677 Bron Cedex, France
| | - Lionel Piroth
- Service de Maladies Infectieuses, CHU de Dijon, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Nejla Aissa
- Laboratoire de Bactériologie, CHU de Nancy, 29 avenue du Maréchal de Lattre de Tassigny, 54035 Nancy, France
| | - Xavier Duval
- Centre d'Investigation Clinique, Inserm CIC 1425, IAME, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018 Paris, France
| | - Vincent Le Moing
- Service des Maladies Infectieuses et Tropicales, CHU de Montpellier, Hôpital Gui de Chauliac, 34000 Montpellier, France
| | - François Vandenesch
- Laboratoire de Bactériologie, Centre de Biologie Est, Hospices Civils de Lyon, 59 Boulevard Louis Pinel, 69677 Bron Cedex, France; CIRI, International Center for Infectiology Research, Inserm U1111, Université Lyon 1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, 7 rue Guillaume Paradin, 69008 Lyon, France; Centre National de Référence des Staphylocoques, 59 Boulevard Louis Pinel, 69677 Bron Cedex, France.
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Verification of the Chromosome Region 9q21 Association with Pelvic Organ Prolapse Using RegulomeDB Annotations. BIOMED RESEARCH INTERNATIONAL 2015; 2015:837904. [PMID: 26347886 PMCID: PMC4546950 DOI: 10.1155/2015/837904] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/28/2015] [Indexed: 12/16/2022]
Abstract
Pelvic organ prolapse (POP) is a common highly disabling disorder with a large hereditary component. It is characterized by a loss of pelvic floor support that leads to the herniation of the uterus in or outside the vagina. Genome-wide linkage studies have shown an evidence of POP association with the region 9q21 and six other loci in European pedigrees. The aim of our study was to test the above associations in a case-control study in Russian population. Twelve SNPs including SNPs cited in the above studies and those selected using the RegulomeDB annotations for the region 9q21 were genotyped in 210 patients with POP (stages III-IV) and 292 controls with no even minimal POP. Genotyping was performed using the polymerase chain reaction with confronting two-pair primers (PCR–CTPP). Association analyses were conducted for individual SNPs, 9q21 haplotypes, and SNP-SNP interactions. SNP rs12237222 with the highest RegulomeDB score 1a appeared to be the key SNP in haplotypes associated with POP. Other RegulomeDB Category 1 SNPs, rs12551710 and rs2236479 (scores 1d and 1f, resp.), exhibited epistatic effects. In this study, we verified the region 9q21 association with POP in Russians, using RegulomeDB annotations.
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Singh R, Ghoshal UC, Misra A, Mittal B. Achalasia Is Associated With eNOS4a4a, iNOS22GA, and nNOS29TT Genotypes: A Case-control Study. J Neurogastroenterol Motil 2015; 21:380-9. [PMID: 26088023 PMCID: PMC4496906 DOI: 10.5056/jnm14123] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 01/25/2015] [Accepted: 01/25/2015] [Indexed: 12/16/2022] Open
Abstract
Background/Aims Achalasia is known to result from degeneration of inhibitory neurons, which are mostly nitrinergic. Characteristic features of achalasia include incomplete lower esophageal sphincter (LES) relaxation and esophageal aperistalsis. Nitric oxide (NO), produced by NO synthase (NOS), plays an important role in peristalsis and LES relaxation. Therefore, we evaluated genetic polymorphisms of NOS gene isoforms (endothelial NOS [eNOS], inducible NOS [iNOS], and neuronal NOS [nNOS]) in patients with achalasia and healthy subjects (HS). Methods Consecutive patients with achalasia (diagnosed using esophageal manometry) and HS were genotyped for 27-base pair (bp) eNOS variable number of tandem repeats (VNTR), iNOS22G/A (rs1060826), nNOS C/T (rs2682826) polymorphisms by polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (RFLP), respectively. Results Among 183 patients (118 [64.5%] male, age 39.5 ± 13.0 years) with achalasia and 366 HS (254 [69.4%] male, age 40.8 ± 11.0 years), eNOS4a4a genotype of 27-bp VNTR was more common among achalasia than HS (20 [10.9%] vs 13 [3.6%]; P < 0.001; OR, 3.72; 95% CI, 1.8–7.7). Patients with achalasia had iNOS22GA genotypes more often than HS (95 [51.9%] vs 93 [25.4%]; P < 0.001; OR, 3.0; 95% CI, 2.1–4.4). Frequency of genotypes GA + AA was higher in patients than HS (97 [53%] vs 107 [29.2%]; P < 0.001; OR, 2.7; 95% CI, 1.8–3.9). Also, nNOS29TT variant genotype in rs2682826 was more common among patients compared to HS (14 [7.7%] vs 6 [1.6%]; P < 0.001; OR, 5.91; 95% CI, 2.2–15.8). Conclusions Achalasia is associated with eNOS4a4a, iNOS22GA, and nNOS29TT genotypes. This may suggest that polymorphisms of eNOS, iNOS, and nNOS genes are risk factors for achalasia.
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Affiliation(s)
- Rajan Singh
- Departments of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Uday C Ghoshal
- Departments of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Asha Misra
- Departments of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Balraj Mittal
- Departments of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
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Jansen RJ, Tan XL, Petersen GM. Gene-by-Environment Interactions in Pancreatic Cancer: Implications for Prevention. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2015; 88:115-26. [PMID: 26029010 PMCID: PMC4445433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Pancreatic cancer (PC) has been estimated to have higher incidence and correspondingly higher mortality rates in more developed regions worldwide. Overall, the age-adjusted incidence rate is 4.9/10(5) and age-adjusted mortality rate is at 4.8/10(5). We review here our current knowledge of modifiable risk factors (cigarette smoking, obesity, diet, and alcohol) for PC, genetic variants implicated by genome-wide association studies, possible genetic interactions with risk factors, and prevention strategies to provide future research directions that may further our understanding of this complex disease. Cigarette smoking is consistently associated with a two-fold increased PC risk. PC associations with dietary intake have been largely inconsistent, with the potential exception of certain unsaturated fatty acids decreasing risk and well-done red meat or meat mutagens increasing risk. There is strong evidence to support that obesity (and related measures) increase risk of PC. Only the heaviest alcohol drinkers seem to be at an increased risk of PC. Currently, key prevention strategies include avoiding tobacco and excessive alcohol consumption and adopting a healthy lifestyle. Screening technologies and PC chemoprevention are likely to become more sophisticated, but may only apply to those at high risk. Risk stratification may be improved by taking into account gene environment interactions. Research on these modifiable risk factors is key to reducing the incidence of PC and understanding who in the population can be considered high risk.
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Affiliation(s)
- Rick J. Jansen
- Department of Public Health Sciences, University of Chicago Biological Sciences, Chicago, Illinois,To whom all correspondence should be addressed: Rick Jansen, PhD, Department of Public Health Sciences, University of Chicago Biological Sciences, 5841 S. Maryland Ave., Rm N101D, MC2000, Chicago, IL 60637;
| | - Xiang-Lin Tan
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey,Department of Epidemiology, School of Public Health, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Gloria M. Petersen
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
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Horita N, Kaneko T. Genetic model selection for a case-control study and a meta-analysis. Meta Gene 2015; 5:1-8. [PMID: 26042205 PMCID: PMC4443430 DOI: 10.1016/j.mgene.2015.04.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 04/29/2015] [Accepted: 04/29/2015] [Indexed: 12/04/2022] Open
Abstract
A case–control study often compares the prevalence of a specific disease among persons with normal alleles and persons with variant alleles, which generates an odds ratio (OR). The most common type of allele variation, single-nucleotide polymorphism, consists of a major allele (M) and a minor allele (m). Thus, the genotype can be a major allele homozygote (MM), a heterozygote (Mm) or a minor allele homozygote (mm). Odds are given for each genotype, and a pair of odds generates an OR. Summarizing data using two-by-two contingency is the simplest method of estimating an OR. Thus, dominant, multiplicative, recessive, and over-dominant models are often used. Traditionally, researchers used to calculate ORs using many models and then select the best model from among these calculated ORs. This may cause problems due to multiple comparisons. Therefore, we should choose the best model before calculating the OR for each model. In this article, we will discuss how to choose the best model among many subject-level models when evaluating the impact of the MM/Mm/mm genotype on the disease prevalence. A case-control study often compares the prevalence of a specific disease among persons with normal alleles and persons with variant alleles, which generates an odds ratio (OR). Traditionally, researchers used to calculate ORs using many models and then select the best model from among these calculated ORs. In this article, we will discuss how to choose the best model among many subject-level models before calculating ORs using some models.
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Affiliation(s)
- Nobuyuki Horita
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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Weber S. Erhöhtes Risiko einer terminalen Niereninsuffizienz bei Verwandten ersten Grades mit Nierenersatztherapie. Urologe A 2015. [DOI: 10.1007/s00120-015-3850-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Albuquerque D, Stice E, Rodríguez-López R, Manco L, Nóbrega C. Current review of genetics of human obesity: from molecular mechanisms to an evolutionary perspective. Mol Genet Genomics 2015; 290:1191-221. [DOI: 10.1007/s00438-015-1015-9] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 02/11/2015] [Indexed: 12/18/2022]
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Abstract
The human genome contains approximately 3.2 billion nucleotides and about 23,500 genes. Each gene has protein-coding regions that are referred to as exons. The human genome contains about 180,000 exons, which are collectively called an exome. An exome comprises about 1% of the human genome and hence is about 30 million nucleotides in size. Today's technologies afford the opportunity to sequence all nucleotides in the human exome and even in the human genome. Given that more than three-quarters of the known disease-causing variants are located in the exome, and considering the cost and technical challenges in analyzing the whole genome sequence data, the focus of present research is primarily on whole exome sequencing (WES). While WES at the medical sequencing level is still expensive, it is becoming more affordable. Cost will not likely be a major barrier in the near future, and the data analysis is becoming less tedious. The most difficult challenge at the heart of medical sequencing is interpreting the findings. Each exome contains about 13,500 single nucleotide variants (SNVs) that affect the amino acid sequence, and a large number are expected to be functional variants. The daunting task is to distinguish the variants that are pathogenic from those that have minimal or no discernible clinical effects. While various algorithms exist, none are sufficiently robust. Thus, in-depth knowledge in genetics and medicine is essential for the proper interpretation of the WES findings. This review will discuss the potential applications of the WES data in the practice of cardiovascular medicine.
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Affiliation(s)
- A J Marian
- The University of Texas Health Science Center, Houston, Texas; Texas Heart Institute, Houston, Texas
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