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Peng J, Rajeevan H, Kubatko L, RoyChoudhury A. A fast likelihood approach for estimation of large phylogenies from continuous trait data. Mol Phylogenet Evol 2021; 161:107142. [PMID: 33713799 DOI: 10.1016/j.ympev.2021.107142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/15/2020] [Accepted: 03/03/2021] [Indexed: 11/28/2022]
Abstract
Despite the recent availability of large-scale genomic data for many individuals, few methods for phylogenetic inference are both computationally efficient and highly accurate for trees with hundreds of taxa. Model-based methods such as those developed in the maximum likelihood and Bayesian frameworks are especially time-consuming, as they involve both computationally intensive calculations on fixed phylogenies and searches through the space of possible phylogenies, and they are known to scale poorly with the addition of taxa. Here, we propose a fast approximation to the maximum likelihood estimator that directly uses continuous trait data, such as allele frequency data. The approximation works by first computing the maximum likelihood estimates of some internal branch lengths, and then inferring the tree-topology using these estimates. Our approach is more computationally efficient than existing methods for such data while still achieving comparable accuracy. This method is innovative in its use of the mathematical properties of tree-topologies for inference, and thus serves as a useful addition to the collection of methods available for estimating phylogenies from continuous trait data.
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Affiliation(s)
- Jing Peng
- Division of Biostatistics, College of Public Health, The Ohio State University, United States; Department of Statistics, The Ohio State University, United States
| | | | - Laura Kubatko
- Department of Statistics, The Ohio State University, United States; Department of Evolution, Ecology and Organismal Biology, The Ohio State University, United States.
| | - Arindam RoyChoudhury
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, United States
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2
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Skadrić I, Stojković O. Defining screening panel of functional variants of CYP1A1, CYP2C9, CYP2C19, CYP2D6, and CYP3A4 genes in Serbian population. Int J Legal Med 2019; 134:433-439. [PMID: 31858263 DOI: 10.1007/s00414-019-02234-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/11/2019] [Indexed: 12/18/2022]
Abstract
Plethora of drugs and toxic substances is metabolized by cytochrome P450 enzymes (CYP450). These enzymes are coded by highly variable genes abundant with single nucleotide variants (SNVs) and small insertions/deletions (indels) that affect the functionality of the enzymes, increasing or decreasing their activity. CYP genes genotyping, followed by haplotype inference, provides substrate specific metabolic phenotype prediction. This is crucial in pharmacogenetics and applicable in molecular autopsy. However, high number of alleles in CYP450 superfamily and interethnic variability in frequency distribution require precise gene panel customization. To estimate informativeness of SNVs and alleles in CYP gene families 1, 2, and 3, associated with metabolic alterations, 500 unrelated individuals from 5 regions of Serbia were genotyped using TaqMan assays to determine frequencies of CYP2C9 *2 and *3, CYP2C19 *2 and *17 alleles, four variants in CYP2D6 (rs3892097, rs1065852, rs28371725, rs28371706) gene, and CYP3A4*1B allele. In addition, CYP1A1 rs4646903 and rs1048943 (m1 and m2) variants were genotyped by RFLP. Our results showed that frequencies of tested variants in Serbian population corresponded to general European population and somewhat differed from neighboring populations. SNV rs1065852, the main contributor to non-functional CYP2D6 *4, significantly departed from Hardy-Weinberg equilibrium. With the exception of rs28371706 in CYP2D6 and rs2740574 in CYP3A4, which were very rare in our sample, all other tested variants in CYP2 family are informative and appropriate for pharmacogenetic testing, molecular autopsy, and medico-legal genetic analyses.
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Affiliation(s)
- Ivan Skadrić
- Institute for Forensic Medicine, Faculty of Medicine, University of Belgrade, Belgrade, 11000, Serbia
| | - Oliver Stojković
- Institute for Forensic Medicine, Faculty of Medicine, University of Belgrade, Belgrade, 11000, Serbia.
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Chetaille P, Preuss C, Burkhard S, Côté JM, Houde C, Castilloux J, Piché J, Gosset N, Leclerc S, Wünnemann F, Thibeault M, Gagnon C, Galli A, Tuck E, Hickson GR, El Amine N, Boufaied I, Lemyre E, de Santa Barbara P, Faure S, Jonzon A, Cameron M, Dietz HC, Gallo-McFarlane E, Benson DW, Moreau C, Labuda D, Zhan SH, Shen Y, Jomphe M, Jones SJM, Bakkers J, Andelfinger G. Mutations in SGOL1 cause a novel cohesinopathy affecting heart and gut rhythm. Nat Genet 2014; 46:1245-9. [PMID: 25282101 DOI: 10.1038/ng.3113] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 09/11/2014] [Indexed: 12/17/2022]
Abstract
The pacemaking activity of specialized tissues in the heart and gut results in lifelong rhythmic contractions. Here we describe a new syndrome characterized by Chronic Atrial and Intestinal Dysrhythmia, termed CAID syndrome, in 16 French Canadians and 1 Swede. We show that a single shared homozygous founder mutation in SGOL1, a component of the cohesin complex, causes CAID syndrome. Cultured dermal fibroblasts from affected individuals showed accelerated cell cycle progression, a higher rate of senescence and enhanced activation of TGF-β signaling. Karyotypes showed the typical railroad appearance of a centromeric cohesion defect. Tissues derived from affected individuals displayed pathological changes in both the enteric nervous system and smooth muscle. Morpholino-induced knockdown of sgol1 in zebrafish recapitulated the abnormalities seen in humans with CAID syndrome. Our findings identify CAID syndrome as a novel generalized dysrhythmia, suggesting a new role for SGOL1 and the cohesin complex in mediating the integrity of human cardiac and gut rhythm.
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Affiliation(s)
- Philippe Chetaille
- Department of Pediatrics, Centre Mère Enfants Soleil, Centre Hospitalier de l'Université (CHU) de Québec, Quebec City, Quebec, Canada
| | - Christoph Preuss
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, Université de Montréal, Montreal, Quebec, Canada
| | - Silja Burkhard
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jean-Marc Côté
- Department of Pediatrics, Centre Mère Enfants Soleil, Centre Hospitalier de l'Université (CHU) de Québec, Quebec City, Quebec, Canada
| | - Christine Houde
- Department of Pediatrics, Centre Mère Enfants Soleil, Centre Hospitalier de l'Université (CHU) de Québec, Quebec City, Quebec, Canada
| | - Julie Castilloux
- Department of Pediatrics, Centre Mère Enfants Soleil, Centre Hospitalier de l'Université (CHU) de Québec, Quebec City, Quebec, Canada
| | - Jessica Piché
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, Université de Montréal, Montreal, Quebec, Canada
| | - Natacha Gosset
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, Université de Montréal, Montreal, Quebec, Canada
| | - Séverine Leclerc
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, Université de Montréal, Montreal, Quebec, Canada
| | - Florian Wünnemann
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, Université de Montréal, Montreal, Quebec, Canada
| | - Maryse Thibeault
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, Université de Montréal, Montreal, Quebec, Canada
| | - Carmen Gagnon
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, Université de Montréal, Montreal, Quebec, Canada
| | - Antonella Galli
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Elizabeth Tuck
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Gilles R Hickson
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada
| | - Nour El Amine
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada
| | - Ines Boufaied
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada
| | - Emmanuelle Lemyre
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada
| | | | | | - Anders Jonzon
- Department of Women's and Children's Health, Section for Pediatrics, Astrid Lindgren's Children's Hospital, Uppsala University, Uppsala, Sweden
| | - Michel Cameron
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, Université de Montréal, Montreal, Quebec, Canada
| | - Harry C Dietz
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elena Gallo-McFarlane
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - D Woodrow Benson
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Claudia Moreau
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada
| | - Damian Labuda
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada
| | - Shing H Zhan
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Yaoqing Shen
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Michèle Jomphe
- Projet BALSAC, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jeroen Bakkers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gregor Andelfinger
- 1] Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, Université de Montréal, Montreal, Quebec, Canada. [2] Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada. [3] Department of Biochemistry, Université de Montréal, Montreal, Quebec, Canada
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Ngamruengphong S, Patel T. Molecular evolution of genetic susceptibility to hepatocellular carcinoma. Dig Dis Sci 2014; 59:986-91. [PMID: 24357186 PMCID: PMC3995842 DOI: 10.1007/s10620-013-2984-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/04/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a leading cancer-related cause of death worldwide. There are widespread global differences in HCC risk. Although the impact of geographic prevalence of specific causes of chronic liver disease on HCC is recognized, the contribution of the underlying genetic architecture to the risk of HCC remains undefined. Our aim was to characterize evolutionary trends in genetic susceptibility to HCC. METHODS We examined the genetic risk associated with HCC risk alleles identified from genome-wide association studies and correlated these with geographic location and temporal and spatial patterns of human migration. RESULTS A moderate increase in differentiation was noted for rs2596542 (F st = 0.106) and rs17401966 (F st = 0.116), single nucleotide polymorphisms (SNPs) associated with an increased risk of HCC in patients with chronic HCV and HBV, respectively. Both of these SNPs show a recent increase in allelic frequency with the most recent human migrations into East Asia, Oceania and the Americas. In contrast another SNP associated with an increased risk of HCC, rs9275572, showed a lack of differentiation (F st = 0.09) with stable allelic expression across populations. The genetic risk score for HCC, based on the allelic frequency and risk odds ratio of five SNPs associated with increased risk of HCC, was greatest in populations from Africa and decreased with subsequent migration into Europe and Asia. However, a major increase was noted with the most recent migrations into Oceania and the Americas. CONCLUSIONS There are differences in directional differentiation of HCC risk alleles across human populations that can contribute to population-based differences in HCC prevalence.
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Affiliation(s)
- Saowanee Ngamruengphong
- Gastroenterology and Hepatology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
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Gontijo CC, Guerra Amorim CE, Godinho NMO, Toledo RCP, Nunes A, Silva W, Da Fonseca Moura MM, De Oliveira JCC, Pagotto RC, De Nazaré Klautau-Guimarães M, De Oliveira SF. Brazilian quilombos: A repository of Amerindian alleles. Am J Hum Biol 2014; 26:142-50. [DOI: 10.1002/ajhb.22501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/05/2013] [Accepted: 12/15/2013] [Indexed: 11/05/2022] Open
Affiliation(s)
- Carolina Carvalho Gontijo
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
| | - Carlos Eduardo Guerra Amorim
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
| | - Neide Maria Oliveira Godinho
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
- Instituto de Criminalística Leonardo Rodrigues; 74425-030 Goiânia GO Brazil
| | - Rafaela Cesare Parmezan Toledo
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
| | - Adriana Nunes
- Departamento de Arqueologia; Universidade Federal de Rondônia; 76801-059 Porto Velho RO Brazil
| | - Wellington Silva
- Faculdade Adventista da Bahia; Caixa Postal 18 44300-000 Cachoeira BA Brazil
| | | | | | - Rubiani C. Pagotto
- Departamento de Biologia; Universidade Federal de Rondônia; 76801-059 Porto Velho RO Brazil
| | - Maria De Nazaré Klautau-Guimarães
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
| | - Silviene Fabiana De Oliveira
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de Ciências Biológicas, Universidade de Brasília; 70910-900 Brasília DF Brazil
- Jackson Laboratory for Genomic Medicine; University of Connecticut Health Center; 06032 Farmington CT, USA
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Fazeli Z, Vallian S. Molecular phylogenetic study of the Iranians based on polymorphic markers. Gene 2013; 512:123-6. [PMID: 23073556 DOI: 10.1016/j.gene.2012.09.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 06/05/2012] [Accepted: 09/11/2012] [Indexed: 11/25/2022]
Abstract
The application of polymorphic markers in construction of phylogenetic trees has been documented. Five polymorphic markers located in the PAH gene region including PAH-BglII, PAH-PvuII(A), PAH-EcoRI, PAH-MspI and PAH-STR were selected for analysis of phylogenetic relationships of the Iranians with 15 other populations of the world. The lowest genetic distance was observed between the Iranians and populations residing in Adygei (an ethnic group of the Russian Caucasus), Russia and Druze (a Middle Eastern group). However, East Asian populations including Han, Japanese and Cambodians, Khmer or the Oceanians (Melanesian, Nasioi) showed high genetic distance with the Iranians. The data suggested that the Iranians might have relatively close evolutionary history with the populations residing in Russia rather than East Asian populations. This study provided the first new molecular insight into the evolutionary history of the Iranian population.
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Affiliation(s)
- Zahra Fazeli
- Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Islamic Republic of Iran; Department of Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran
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7
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Parczewski M, Bander D, Leszczyszyn-Pynka M, Urbańska A, Socha Ł, Boroń-Kaczmarska A. IL28B CC genotype is associated with higher all-cause mortality in antiretroviral-treated HIV-infected patients. AIDS Res Hum Retroviruses 2012; 28:1640-6. [PMID: 22545770 DOI: 10.1089/aid.2011.0354] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Il28B single nucleotide polymorphisms were found to influence interferon λ expression, resulting in changes in hepatitis C virus (HCV)-RNA serum levels as well as the HIV-RNA set point prior to combined antiretroviral therapy (cART). To date, there is limited information on the influence of this polymorphism on survival in HIV-infected, treatment-naïve, and antiretroviral-treated patients. Longitudinal data from 484 patients diagnosed with HIV infection (including 406 on cART) were analyzed to investigate the association between Il28B rs 1979860 variants and all-cause mortality. Kaplan-Meyer and Cox models were used to calculate the hazard ratio associated with IL28B genotypes predictive of a greater likelihood of survival for patients prior to the introduction of cART and for patients on cART. The IL28B genotype frequencies were 41.7% (n=202) for CC, 46.5% (n=225) for CT, and 11.7% (n=57) for TT patients. The CC variant was associated with higher mortality (46 cases, 22.8%) compared to other genotypes [n=31 (13.8%) and n=7 (12.3%) for CT and TT, respectively, p=0.02]. IL28 genotypes did not influence the survival probability prior to treatment initiation (HR 1.04, 95% CI: 0.84-1.24, p=0.68). In antiretroviral-treated patients, after adjustment for gender, baseline CD4 count, CDC category at HIV diagnosis, and age (multivariate HR 1.75, 95% CI: 1.20-2.30, p=0.047), the CC genotype was associated with a decreased probability of survival when compared to the non-CC genotype (univariate HR 1.8, 95% CI: 1.28-2.34, p=0.029). IL28B rs12979860 genotypes influence mortality risk in HIV-infected, antiretroviral-treated patients. The effect may be related to higher baseline plasma HIV viremia and possibly altered immune reconstitution associated with interferon λ expression.
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Affiliation(s)
- Miłosz Parczewski
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland.
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Fazeli Z, Vallian S. Phylogenetic relationship analysis of Iranians and other world populations using allele frequencies at 12 polymorphic markers. Mol Biol Rep 2012; 39:11187-99. [PMID: 23065267 DOI: 10.1007/s11033-012-2028-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 10/02/2012] [Indexed: 11/29/2022]
Abstract
The estimation of genetic distance between populations could improve our viewpoint about human migration and its genetic origin. In this study, we used allele frequency data of 12 polymorphic markers on 250 individuals (500 alleles) from the Iranian population to estimate genetic distance between the Iranians and other world populations. The phylogenetic trees for three different sets of allele frequency data were constructed. Our results revealed the genetic similarity between the Iranians and European populations. The lowest genetic distance was observed between the Iranians and some populations reside in Russia. Furthermore, the high genetic distance was observed between the Iranians and East Asian populations. The data suggested that the Iranians might have relatively close evolutionary history with Europeans, but historically independent from East Asian populations. The evaluation of genetic distance between Indians populations and Iranians was also performed. The Indian groups showed low genetic distance with others, but high genetic distance with the Iranians. This study could provide a new insight into the evolutionary history of the Iranian population.
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Affiliation(s)
- Zahra Fazeli
- Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Islamic Republic of Iran
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Kee BP, Chua KH, Lee PC, Lian LH. Population data of six Alu insertions in indigenous groups from Sabah, Malaysia. Ann Hum Biol 2012; 39:505-10. [PMID: 22989108 DOI: 10.3109/03014460.2012.719548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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The endothelial protein C receptor (PROCR) Ser219Gly variant and risk of common thrombotic disorders: a HuGE review and meta-analysis of evidence from observational studies. Blood 2012; 119:2392-400. [PMID: 22251481 DOI: 10.1182/blood-2011-10-383448] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The endothelial protein C receptor (EPCR) limits thrombus formation by enhancing activation of the protein C anticoagulant pathway, and therefore may play a role in the etiology of thrombotic disorders. The rs867186 single-nucleotide polymorphism in the PROCR gene (g.6936A > G, c.4600A > G), resulting in a serine-to-glycine substitution at codon 219, has been associated with reduced activation of the protein C pathway, although its association with thrombosis risk remains unclear. The present study is a highly comprehensive systematic review and meta-analysis, including unpublished genome-wide association study results, conducted to evaluate the evidence for an association between rs867186 and 2 common thrombotic outcomes, venous thromboembolism (VTE) and myocardial infarction (MI), which are hypothesized to share some etiologic pathways. MEDLINE, EMBASE, and HuGE Navigator were searched through July 2011 to identify relevant epidemiologic studies, and data were summarized using random-effects meta-analysis. Twelve candidate genes and 13 genome-wide association studies were analyzed (11 VTE and 14 MI, including 37,415 cases and 84,406 noncases). Under the additive genetic model, the odds of VTE increased by a factor of 1.22 (95% confidence interval, 1.11-1.33, P < .001) for every additional copy of the G allele. No evidence for association with MI was observed.
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Godshalk SE, Paranjape T, Nallur S, Speed W, Chan E, Molinaro AM, Bacchiocchi A, Hoyt K, Tworkoski K, Stern DF, Sznol M, Ariyan S, Lazova R, Halaban R, Kidd KK, Weidhaas J, Slack FJ. A Variant in a MicroRNA complementary site in the 3' UTR of the KIT oncogene increases risk of acral melanoma. Oncogene 2011; 30:1542-50. [PMID: 21119596 PMCID: PMC3069149 DOI: 10.1038/onc.2010.536] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 09/15/2010] [Accepted: 10/07/2010] [Indexed: 01/14/2023]
Abstract
MicroRNAs (miRNAs) are small ∼22nt single stranded RNAs that negatively regulate protein expression by binding to partially complementary sequences in the 3' untranslated region (3' UTRs) of target gene messenger RNAs (mRNA). Recently, mutations have been identified in both miRNAs and target genes that disrupt regulatory relationships, contribute to oncogenesis and serve as biomarkers for cancer risk. KIT, an established oncogene with a multifaceted role in melanogenesis and melanoma pathogenesis, has recently been shown to be upregulated in some melanomas, and is also a target of the miRNA miR-221. Here, we describe a genetic variant in the 3' UTR of the KIT oncogene that correlates with a greater than fourfold increased risk of acral melanoma. This KIT variant results in a mismatch in the seed region of a miR-221 complementary site and reporter data suggests that this mismatch can result in increased expression of the KIT oncogene. Consistent with the hypothesis that this is a functional variant, KIT mRNA and protein levels are both increased in the majority of samples harboring the KIT variant. This work identifies a novel genetic marker for increased heritable risk of melanoma.
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Affiliation(s)
- Sirie E. Godshalk
- Department of Molecular, Cellular and Developmental Biology, Yale University
| | - Trupti Paranjape
- Department of Therapeutic Radiology, Yale University School of Medicine
| | - Sunitha Nallur
- Department of Therapeutic Radiology, Yale University School of Medicine
| | - William Speed
- Department of Genetics, Yale University School of Medicine
| | - Elcie Chan
- Department of Therapeutic Radiology, Yale University School of Medicine
| | | | | | - Kathleen Hoyt
- Department of Dermatology, Yale University School of Medicine
| | | | - David F. Stern
- Department of Pathology, Yale University School of Medicine
| | - Mario Sznol
- Section of Medical Oncology, Yale University School of Medicine
| | - Stephan Ariyan
- Department of Surgery, Yale University School of Medicine
| | - Rossitza Lazova
- Department of Dermatology, Yale University School of Medicine
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine
| | | | - Joanne Weidhaas
- Department of Therapeutic Radiology, Yale University School of Medicine
| | - Frank J. Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University
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12
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Myles S, Lea RA, Ohashi J, Chambers GK, Weiss JG, Hardouin E, Engelken J, Macartney-Coxson DP, Eccles DA, Naka I, Kimura R, Inaoka T, Matsumura Y, Stoneking M. Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans. BMC MEDICAL GENETICS 2011; 12:10. [PMID: 21244673 PMCID: PMC3025936 DOI: 10.1186/1471-2350-12-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 01/18/2011] [Indexed: 12/03/2022]
Abstract
Background The thrifty gene hypothesis posits that, in populations that experienced periods of feast and famine, natural selection favoured individuals carrying thrifty alleles that promote the storage of fat and energy. Polynesians likely experienced long periods of cold stress and starvation during their settlement of the Pacific and today have high rates of obesity and type 2 diabetes (T2DM), possibly due to past positive selection for thrifty alleles. Alternatively, T2DM risk alleles may simply have drifted to high frequency in Polynesians. To identify thrifty alleles in Polynesians, we previously examined evidence of positive selection on T2DM-associated SNPs and identified a T2DM risk allele at unusually high frequency in Polynesians. We suggested that the risk allele of the Gly482Ser variant in the PPARGC1A gene was driven to high frequency in Polynesians by positive selection and therefore possibly represented a thrifty allele in the Pacific. Methods Here we examine whether PPARGC1A is a thrifty gene in Pacific populations by testing for an association between Gly482Ser genotypes and BMI in two Pacific populations (Maori and Tongans) and by evaluating the frequency of the risk allele of the Gly482Ser variant in a sample of worldwide populations. Results We find that the Gly482Ser variant is associated with BMI in Tongans but not in Maori. In a sample of 58 populations worldwide, we also show that the 482Ser risk allele reaches its highest frequency in the Pacific. Conclusion The association between Gly482Ser genotypes and BMI in Tongans together with the worldwide frequency distribution of the Gly482Ser risk allele suggests that PPARGC1A remains a candidate thrifty gene in Pacific populations.
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Affiliation(s)
- Sean Myles
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA.
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