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Saif-Ali R, Al-Hamodi Z, Salem SD, AL-Habori M, Al-Dubai SA, Ismail IS. Association of Protein Tyrosine Phosphatase Receptor Type D and Serine Racemase Genetic Variants with Type 2 Diabetes in Malaysian Indians. Indian J Endocrinol Metab 2024; 28:55-59. [PMID: 38533286 PMCID: PMC10962774 DOI: 10.4103/ijem.ijem_209_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/24/2023] [Indexed: 03/28/2024] Open
Abstract
Introduction Type 2 diabetes (T2D) candidate genes, protein tyrosine phosphatase receptor type D (PTPRD), and serine racemase (SRR) were suggested by a genome-wide association study (GWAS) in the Chinese population. Association studies have been replicated among East Asian populations. The association of PTPRD and SRR genetic variants with T2D in Southeast Asian populations still needs to be studied. This study aimed to investigate the association of PTPRD and SSR genetic variants with T2D in Malaysian Indian subjects. Methods The single nucleotide polymorphisms (SNPs) of PTPRD (rs649891 and rs17584499) and SRR (rs4523957, rs391300, and rs8081273) were genotyped in 397 T2D and 285 normal Malaysian Indian subjects. Results The homozygous dominant genotype of rs17584499 is frequent in diabetic patients (56.5%) compared to normal subjects (47.3%). In contrast, the homozygous recessive genotype of rs8081273 is more frequent among normal subjects (12.5%) than diabetic patients (5.6%). The dominant genetic model showed that PTPRD rs17584499 (CC) is a risk factor for T2D (OR = 1.42, P = 0.029), whereas the recessive genetic model showed that SRS SNP rs8081273 was protective for T2D (OR = 0.42, P = 0.003). Conclusion This study confirmed the association of PTPRD rs17584499 genetic variations with T2D in Malaysian Indians. While the SRR rs8081273 (TT) genotype showed protection against T2D, more investigation in different populations is required to confirm this protection.
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Affiliation(s)
- Riyadh Saif-Ali
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sana’a University, Sana’a, Yemen
| | - Zaid Al-Hamodi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sana’a University, Sana’a, Yemen
| | - Sameer D. Salem
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sana’a University, Sana’a, Yemen
| | - Molham AL-Habori
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sana’a University, Sana’a, Yemen
| | - Sami A. Al-Dubai
- Joint Program of Preventive Medicine, Post Graduate Studies, Medina, Saudi Arabia
| | - Ikram S. Ismail
- Department of Medicine, Faculty of Medicine, UM, Kuala Lumpur, Malaysia
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Mohammed NI, Alzubaidi ZF, Khudhair M. THE RELEVANCE OF RS6777038 AND RS6444082 OF IGF2BP2 GENE POLYMORPHISM AND TYPE 2 DIABETES MELLITUS: A CASE CONTROL STUDY. WIADOMOSCI LEKARSKIE (WARSAW, POLAND : 1960) 2022; 75:2811-2816. [PMID: 36591772 DOI: 10.36740/wlek202211215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVE The aim: We investigate IGF2BP2 gene polymorphisms (rs6777038 and rs6444082) association with T2DM of Iraqi sample. PATIENTS AND METHODS Materials and methods: The study involves 800 participants that divided to a healthy control group (400) and T2DM patients (400). Fasting blood sugar (FBS), triglycerides (Tgs), high-density lipoprotein cholesterol (HDL-Ch), total cholesterol (T-Ch), low-density lipoprotein cholesterol (LDL-Ch), and fasting insulin measured for both participant groups. IGF2BP2 gene has been genotyped for polymorphisms, rs6777038 and rs6444082 using the PCR-RFLP technique. RESULTS Results: Logistic regression analysis testing for rs6777038 revealed that the genotype and allele frequency differ significantly (p=0.009) between T2DM and control group. In codominant model, TT genotype carriers had higher risks for diabetes than control also in the recessive model TT genotype significantly had higher risk for diabetes than control group. The other models of rs6777038 failed to reveal significant differences. The rs6777038 genotypes as codominant model showed significant differences with phenotypic characters of BMI, insulin and HOMA-IR. As well as, this SNP as dominant model showed significant differences with fasting insulin and HOMA-IR. However, rs6444082 genotypes only as dominant model reveal significant variation with HOMA-IR. CONCLUSION Conclusions: This study confirmed the variant rs6777038 of IGF2BP2 possibly associated with T2DM risks and some anthropometric parameters such as lower fasting insulin, HOMA-IR and BMI in Iraqi T2DM participants.
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Affiliation(s)
- Noaman Ibadi Mohammed
- DEPARTMENT OF PHYSIOLOGY, BIOCHEMISTRY AND PHARMACOLOGY, FACULTY OF VETERINARY MEDICINE, UNIVERSITY OF KUFA, NAJAF, IRAQ
| | - Zubaida Falih Alzubaidi
- DEPARTMENT OF CLINICAL AND LABORATORY SCIENCES, FACULTY OF PHARMACY, UNIVERSITY OF KUFA, NAJAF, IRAQ
| | - Muneer Khudhair
- DEPARTMENT OF LAB INVESTIGATIONS, FACULTY OF SCIENCES, UNIVERSITY OF KUFA, NAJAF, IRAQ
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Secolin R, Gonsales MC, Rocha CS, Naslavsky M, De Marco L, Bicalho MAC, Vazquez VL, Zatz M, Silva WA, Lopes-Cendes I. Exploring a Region on Chromosome 8p23.1 Displaying Positive Selection Signals in Brazilian Admixed Populations: Additional Insights Into Predisposition to Obesity and Related Disorders. Front Genet 2021; 12:636542. [PMID: 33841501 PMCID: PMC8027303 DOI: 10.3389/fgene.2021.636542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/04/2021] [Indexed: 11/13/2022] Open
Abstract
We recently reported a deviation of local ancestry on the chromosome (ch) 8p23.1, which led to positive selection signals in a Brazilian population sample. The deviation suggested that the genetic variability of candidate genes located on ch 8p23.1 may have been evolutionarily advantageous in the early stages of the admixture process. In the present work, we aim to extend the previous work by studying additional Brazilian admixed individuals and examining DNA sequencing data from the ch 8p23.1 candidate region. Thus, we inferred the local ancestry of 125 exomes from individuals born in five towns within the Southeast region of Brazil (São Paulo, Campinas, Barretos, and Ribeirão Preto located in the state of São Paulo and Belo Horizonte, the capital of the state of Minas Gerais), and compared to data from two public Brazilian reference genomic databases, BIPMed and ABraOM, and with information from the 1000 Genomes Project phase 3 and gnomAD databases. Our results revealed that ancestry is similar among individuals born in the five Brazilian towns assessed; however, an increased proportion of sub-Saharan African ancestry was observed in individuals from Belo Horizonte. In addition, individuals from the five towns considered, as well as those from the ABRAOM dataset, had the same overrepresentation of Native-American ancestry on the ch 8p23.1 locus that was previously reported for the BIPMed reference sample. Sequencing analysis of ch 8p23.1 revealed the presence of 442 non-synonymous variants, including frameshift, inframe deletion, start loss, stop gain, stop loss, and splicing site variants, which occurred in 24 genes. Among these genes, 13 were associated with obesity, type II diabetes, lipid levels, and waist circumference (PRAG1, MFHAS1, PPP1R3B, TNKS, MSRA, PRSS55, RP1L1, PINX1, MTMR9, FAM167A, BLK, GATA4, and CTSB). These results strengthen the hypothesis that a set of variants located on ch 8p23.1 that result from positive selection during early admixture events may influence obesity-related disease predisposition in admixed individuals of the Brazilian population. Furthermore, we present evidence that the exploration of local ancestry deviation in admixed individuals may provide information with the potential to be translated into health care improvement.
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Affiliation(s)
- Rodrigo Secolin
- Department of Medical Genetics and Genomic Medicine, Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), University of Campinas - UNICAMP, Campinas, Brazil
| | - Marina C Gonsales
- Department of Medical Genetics and Genomic Medicine, Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), University of Campinas - UNICAMP, Campinas, Brazil
| | - Cristiane S Rocha
- Department of Medical Genetics and Genomic Medicine, Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), University of Campinas - UNICAMP, Campinas, Brazil
| | - Michel Naslavsky
- Departament of Genetics and Evolutive Biology, Human Genome and Stem Cell Research Center, Institute of Bioscience, University of São Paulo (USP), São Paulo, Brazil
| | - Luiz De Marco
- Department of Surgery, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Maria A C Bicalho
- Department of Clinical Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Vinicius L Vazquez
- Molecular Oncology Research Center (CPOM) - Barretos Cancer Hospital, Barretos, Brazil
| | - Mayana Zatz
- Departament of Genetics and Evolutive Biology, Human Genome and Stem Cell Research Center, Institute of Bioscience, University of São Paulo (USP), São Paulo, Brazil
| | - Wilson A Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo at Ribeirão Preto (USP), Ribeirão Preto, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics and Genomic Medicine, Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), University of Campinas - UNICAMP, Campinas, Brazil
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4
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The Brazilian Initiative on Precision Medicine (BIPMed): fostering genomic data-sharing of underrepresented populations. NPJ Genom Med 2020; 5:42. [PMID: 33083011 PMCID: PMC7532430 DOI: 10.1038/s41525-020-00149-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 08/24/2020] [Indexed: 12/19/2022] Open
Abstract
The development of precision medicine strategies requires prior knowledge of the genetic background of the target population. However, despite the availability of data from admixed Americans within large reference population databases, we cannot use these data as a surrogate for that of the Brazilian population. This lack of transferability is mainly due to differences between ancestry proportions of Brazilian and other admixed American populations. To address the issue, a coalition of research centres created the Brazilian Initiative on Precision Medicine (BIPMed). In this study, we aim to characterise two datasets obtained from 358 individuals from the BIPMed using two different platforms: whole-exome sequencing (WES) and a single nucleotide polymorphism (SNP) array. We estimated allele frequencies and variant pathogenicity values from the two datasets and compared our results using the BIPMed dataset with other public databases. Here, we show that the BIPMed WES dataset contains variants not included in dbSNP, including 6480 variants that have alternative allele frequencies (AAFs) >1%. Furthermore, after merging BIPMed WES and SNP array data, we identified 809,589 variants (47.5%) not present within the 1000 Genomes dataset. Our results demonstrate that, through the incorporation of Brazilian individuals into public genomic databases, BIPMed not only was able to provide valuable knowledge needed for the implementation of precision medicine but may also enhance our understanding of human genome variability and the relationship between genetic variation and disease predisposition.
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5
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Secolin R, Mas-Sandoval A, Arauna LR, Torres FR, de Araujo TK, Santos ML, Rocha CS, Carvalho BS, Cendes F, Lopes-Cendes I, Comas D. Distribution of local ancestry and evidence of adaptation in admixed populations. Sci Rep 2019; 9:13900. [PMID: 31554886 PMCID: PMC6761108 DOI: 10.1038/s41598-019-50362-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/11/2019] [Indexed: 12/14/2022] Open
Abstract
Admixed American populations have different global proportions of European, Sub-Saharan African, and Native-American ancestry. However, individuals who display the same global ancestry could exhibit remarkable differences in the distribution of local ancestry blocks. We studied for the first time the distribution of local ancestry across the genome of 264 Brazilian admixed individuals, ascertained within the scope of the Brazilian Initiative on Precision Medicine. We found a decreased proportion of European ancestry together with an excess of Native-American ancestry on chromosome 8p23.1 and showed that this is due to haplotypes created by chromosomal inversion events. Furthermore, Brazilian non-inverted haplotypes were more similar to Native-American haplotypes than to European haplotypes, in contrast to what was found in other American admixed populations. We also identified signals of recent positive selection on chromosome 8p23.1, and one gene within this locus, PPP1R3B, is related to glycogenesis and has been associated with an increased risk of type 2 diabetes and obesity. These findings point to a selection event after admixture, which is still not entirely understood in recent admixture events.
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Affiliation(s)
- Rodrigo Secolin
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Alex Mas-Sandoval
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.,Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Fábio R Torres
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Tânia K de Araujo
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Marilza L Santos
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Cristiane S Rocha
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Benilton S Carvalho
- Department of Statistics, Institute of Mathematics, Statistics and Scientific Computing, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Fernando Cendes
- Department of Neurology, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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6
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Torres JB. Race, Rare Genetic Variants, and the Science of Human Difference in the Post‐Genomic Age. TRANSFORMING ANTHROPOLOGY 2019. [DOI: 10.1111/traa.12144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jada Benn Torres
- Genetic Anthropology and Biocultural Studies Laboratory Department of Anthropology Vanderbilt University Nashville TN 37235
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7
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Wang T, Hosgood HD, Lan Q, Xue X. The Relationship Between Population Attributable Fraction and Heritability in Genetic Studies. Front Genet 2018; 9:352. [PMID: 30327663 PMCID: PMC6174220 DOI: 10.3389/fgene.2018.00352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/09/2018] [Indexed: 01/03/2023] Open
Abstract
Population attributable fraction (PAF) has been widely used to quantify the proportion of disease risk in a population that can be attributed to risk factors in epidemiological studies. However, the use of PAF has been limited in assessing the contribution of genetic variants. Most notably, the PAF estimate is typically much larger than other commonly used measures, such as heritability, thereby raising the concern that PAF may overestimate the genetic contribution. In this paper, we show that PAF is a one-to-one function of heritability, and explain why PAF is larger than heritability. Further, we present an estimation procedure based on the summary statistics from genome-wide association studies (GWAS) to estimate the PAF of multiple correlated genetic variants for a binary outcome. Currently available estimation procedures only apply to a single variant or to multiple genetic variants that are independent from each other. Our simulation studies verified the relationship between PAF and heritability, and showed that the proposed estimation procedure for these two measures performed well. Finally, we applied the proposed method to the published data of two lung cancer GWAS to estimate the PAF and heritability of several newly identified variants. Our results demonstrate that the PAF estimate is a useful measure of the genetic contribution to the development of the disease. We hope this paper serves as an advocate for a wider use of PAF in genetic studies.
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Affiliation(s)
- Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, The Bronx, NY, United States
| | - H Dean Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, The Bronx, NY, United States
| | - Qing Lan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, The Bronx, NY, United States
| | - Xiaonan Xue
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, The Bronx, NY, United States
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8
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Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ. Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. PLoS Genet 2018; 14:e1007329. [PMID: 29795570 PMCID: PMC5967709 DOI: 10.1371/journal.pgen.1007329] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/22/2018] [Indexed: 02/05/2023] Open
Abstract
As part of a broader collaborative network of exome sequencing studies, we developed a jointly called data set of 5,685 Ashkenazi Jewish exomes. We make publicly available a resource of site and allele frequencies, which should serve as a reference for medical genetics in the Ashkenazim (hosted in part at https://ibd.broadinstitute.org, also available in gnomAD at http://gnomad.broadinstitute.org). We estimate that 34% of protein-coding alleles present in the Ashkenazi Jewish population at frequencies greater than 0.2% are significantly more frequent (mean 15-fold) than their maximum frequency observed in other reference populations. Arising via a well-described founder effect approximately 30 generations ago, this catalog of enriched alleles can contribute to differences in genetic risk and overall prevalence of diseases between populations. As validation we document 148 AJ enriched protein-altering alleles that overlap with "pathogenic" ClinVar alleles (table available at https://github.com/macarthur-lab/clinvar/blob/master/output/clinvar.tsv), including those that account for 10-100 fold differences in prevalence between AJ and non-AJ populations of some rare diseases, especially recessive conditions, including Gaucher disease (GBA, p.Asn409Ser, 8-fold enrichment); Canavan disease (ASPA, p.Glu285Ala, 12-fold enrichment); and Tay-Sachs disease (HEXA, c.1421+1G>C, 27-fold enrichment; p.Tyr427IlefsTer5, 12-fold enrichment). We next sought to use this catalog, of well-established relevance to Mendelian disease, to explore Crohn's disease, a common disease with an estimated two to four-fold excess prevalence in AJ. We specifically attempt to evaluate whether strong acting rare alleles, particularly protein-truncating or otherwise large effect-size alleles, enriched by the same founder-effect, contribute excess genetic risk to Crohn's disease in AJ, and find that ten rare genetic risk factors in NOD2 and LRRK2 are enriched in AJ (p < 0.005), including several novel contributing alleles, show evidence of association to CD. Independently, we find that genomewide common variant risk defined by GWAS shows a strong difference between AJ and non-AJ European control population samples (0.97 s.d. higher, p<10-16). Taken together, the results suggest coordinated selection in AJ population for higher CD risk alleles in general. The results and approach illustrate the value of exome sequencing data in case-control studies along with reference data sets like ExAC (sites VCF available via FTP at ftp.broadinstitute.org/pub/ExAC_release/release0.3/) to pinpoint genetic variation that contributes to variable disease predisposition across populations.
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Affiliation(s)
- Manuel A. Rivas
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Department of Biomedical Data Science, Stanford University, Stanford, CA, United States of America
| | - Brandon E. Avila
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Jukka Koskela
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Hailiang Huang
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Christine Stevens
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Talin Haritunians
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Benjamin M. Neale
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Mitja Kurki
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Andrea Ganna
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Daniel Graham
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Benjamin Glaser
- Hadassah-Hebrew University Medical Center, Endocrinology and Metabolism Service Department of Internal Medicine, Jerusalem, Israel
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Gil Atzmon
- Department of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Nir Barzilai
- Department of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Adam P. Levine
- Division of Medicine, University College London, London, United Kingdom
| | - Elena Schiff
- Division of Medicine, University College London, London, United Kingdom
| | - Nikolas Pontikos
- Division of Medicine, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Ben Weisburd
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Monkol Lek
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Konrad J. Karczewski
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Jonathan Bloom
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Eric V. Minikel
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Britt-Sabina Petersen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Laurent Beaugerie
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Philippe Seksik
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Jacques Cosnes
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Stefan Schreiber
- Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Johannes Bethge
- Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | | | | | - Graham Heap
- IBD Pharmacogenetics, Royal Devon and Exeter NHS Trust, Exeter, United Kingdom
| | - Tariq Ahmad
- Peninsula College of Medicine and Dentistry, Exeter, United Kingdom
| | - Vincent Plagnol
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Anthony W. Segal
- Division of Medicine, University College London, London, United Kingdom
| | - Stephan Targan
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Dan Turner
- Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Paivi Saavalainen
- Research Programs Unit, Immunobiology, and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Martti Farkkila
- Department of Medicine, Division of Gastroenterology, Helsinki University Hospital, Helsinki, Finland
| | - Kimmo Kontula
- Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Aarno Palotie
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States of America
| | - Steven R. Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States of America
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States of America
| | - Mark S. Silverberg
- Inflammatory Bowel Disease Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - John D. Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom
| | - Carl A. Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Jeffrey C. Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Daniel G. MacArthur
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Chaim Jalas
- Bonei Olam, Center for Rare Jewish Genetic Disorders, Brooklyn, NY, United States of America
| | - Harry Sokol
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Ramnik J. Xavier
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease and Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Ann Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Judy H. Cho
- Icahn School of Medicine at Mount Sinai, Dr Henry D. Janowitz Division of Gastroenterology, New York, NY, United States of America
| | - Dermot P. B. McGovern
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Mark J. Daly
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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9
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Liu G, Liu S, Lin M, Li X, Chen W, Zuo Y, Liu J, Niu Y, Zhao S, Long B, Wu Z, Wu N, Qiu G. Genetic polymorphisms of GPR126 are functionally associated with PUMC classifications of adolescent idiopathic scoliosis in a Northern Han population. J Cell Mol Med 2018; 22:1964-1971. [PMID: 29363878 PMCID: PMC5824397 DOI: 10.1111/jcmm.13486] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 10/31/2017] [Indexed: 12/15/2022] Open
Abstract
GPR126 has been identified to be associated with AIS (Adolescent Idiopathic Scoliosis) in different populations, but data on the northern Chinese population are unavailable. Additionally, it is important to know the exact clinical phenotypes associated with specific genetic polymorphisms. Fourteen SNP (single nucleotide polymorphism) loci in GPR126 were genotyped in 480 northern Chinese Han AIS patients and 841 controls. These patients were classified into three types based on the PUMC classification system. Luciferase assays were used to investigate their regulation of GPR126 transcription activity. Combined and stratified genotype-phenotype association analyses were conducted. The alleles rs225694, rs7774095 and rs2294773 were significantly associated with AIS (P = 0.021, 0.048 and 0.023, respectively). rs225694 and rs7774095 potentially have regulatory functions for the GRP126 gene. Correlation analysis revealed that allele A of rs225694 was a risk allele only for PUMC type II AIS (P = 0.036) and allele G of rs2294773 was a risk allele only for PUMC type I AIS (P = 0.018). In summary, rs225694, rs7774095 and rs2294773 are significantly associated with disease in northern Chinese Han AIS patients. The SNPs rs225694 and rs2294773 are associated with different AIS PUMC classifications.
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Affiliation(s)
- Gang Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Sen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Mao Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yuzhi Zuo
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Jiaqi Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Bo Long
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
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10
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Niu ZS, Niu XJ, Wang WH. Genetic alterations in hepatocellular carcinoma: An update. World J Gastroenterol 2016; 22:9069-9095. [PMID: 27895396 PMCID: PMC5107590 DOI: 10.3748/wjg.v22.i41.9069] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/20/2016] [Accepted: 10/19/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Although recent advances in therapeutic approaches for treating HCC have improved the prognoses of patients with HCC, this cancer is still associated with a poor survival rate mainly due to late diagnosis. Therefore, a diagnosis must be made sufficiently early to perform curative and effective treatments. There is a need for a deeper understanding of the molecular mechanisms underlying the initiation and progression of HCC because these mechanisms are critical for making early diagnoses and developing novel therapeutic strategies. Over the past decade, much progress has been made in elucidating the molecular mechanisms underlying hepatocarcinogenesis. In particular, recent advances in next-generation sequencing technologies have revealed numerous genetic alterations, including recurrently mutated genes and dysregulated signaling pathways in HCC. A better understanding of the genetic alterations in HCC could contribute to identifying potential driver mutations and discovering novel therapeutic targets in the future. In this article, we summarize the current advances in research on the genetic alterations, including genomic instability, single-nucleotide polymorphisms, somatic mutations and deregulated signaling pathways, implicated in the initiation and progression of HCC. We also attempt to elucidate some of the genetic mechanisms that contribute to making early diagnoses of and developing molecularly targeted therapies for HCC.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Genomic Instability
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Molecular Diagnostic Techniques
- Molecular Targeted Therapy
- Mutation
- Patient Selection
- Phenotype
- Polymorphism, Single Nucleotide
- Precision Medicine
- Predictive Value of Tests
- Signal Transduction
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11
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Ahmed RH, Huri HZ, Al-Hamodi Z, Salem SD, Al-absi B, Muniandy S. Association of DPP4 Gene Polymorphisms with Type 2 Diabetes Mellitus in Malaysian Subjects. PLoS One 2016; 11:e0154369. [PMID: 27111895 PMCID: PMC4844141 DOI: 10.1371/journal.pone.0154369] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/12/2016] [Indexed: 12/15/2022] Open
Abstract
Background Genetic polymorphisms of the Dipeptidyl Peptidase 4 (DPP4) gene may play a role in the etiology of type 2 diabetes mellitus (T2DM). This study aimed to investigate the possible association of single nucleotide polymorphisms (SNPs) of the DPP4 gene in Malaysian subjects with T2DM and evaluated whether they had an effect on the serum levels of soluble dipeptidyl peptidase 4 (sDPP-IV). Method Ten DPP4 SNPs were genotyped by TaqMan genotyping assays in 314 subjects with T2DM and 235 controls. Of these, 71 metabolic syndrome (MetS) subjects were excluded from subsequent analysis. The odds ratios (ORs) and their 95% confidence interval (CIs) were calculated using multiple logistic regression for the association between the SNPs of DPP4 and T2DM. In addition, the serum levels of sDPP-IV were investigated to evaluate the association of the SNPs of DPP4 with the sDPP-IV levels. Results Dominant, recessive, and additive genetic models were employed to test the association of DPP4 polymorphisms with T2DM, after adjusting for age, race, gender and BMI. The rs12617656 was associated with T2DM in Malaysian subjects in the recessive genetic model (OR = 1.98, p = 0.006), dominant model (OR = 1.95, p = 0.008), and additive model (OR = 1.63, p = 0.001). This association was more pronounced among Malaysian Indians, recessive (OR = 3.21, p = 0.019), dominant OR = 3.72, p = 0.003) and additive model (OR = 2.29, p = 0.0009). The additive genetic model showed that DPP4 rs4664443 and rs7633162 polymorphisms were associated with T2DM (OR = 1.53, p = 0.039), and (OR = 1.42, p = 0.020), respectively. In addition, the rs4664443 G>A polymorphism was associated with increased sDPP-IV levels (p = 0.042) in T2DM subjects. Conclusions DPP4 polymorphisms were associated with T2DM in Malaysian subjects, and linked to variations in sDPP-IV levels. In addition, these associations were more pronounced among Malaysian Indian subjects.
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Affiliation(s)
- Radwan H. Ahmed
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail: (RHA); (SM)
| | - Hasniza Zaman Huri
- Department of Pharmacy, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Clinical Investigation Centre, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Zaid Al-Hamodi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sana’a University, Sana’a, Yemen
| | - Sameer D. Salem
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sana’a University, Sana’a, Yemen
| | - Boshra Al-absi
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sekaran Muniandy
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail: (RHA); (SM)
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12
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Parolo S, Lisa A, Gentilini D, Di Blasio AM, Barlera S, Nicolis EB, Boncoraglio GB, Parati EA, Bione S. Characterization of the biological processes shaping the genetic structure of the Italian population. BMC Genet 2015; 16:132. [PMID: 26553317 PMCID: PMC4640365 DOI: 10.1186/s12863-015-0293-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/03/2015] [Indexed: 12/11/2022] Open
Abstract
Background The genetic structure of human populations is the outcome of the combined action of different processes such as demographic dynamics and natural selection. Several efforts toward the characterization of population genetic architectures and the identification of adaptation signatures were recently made. In this study, we provide a genome-wide depiction of the Italian population structure and the analysis of the major determinants of the current existing genetic variation. Results We defined and characterized 210 genomic loci associated with the first Principal Component calculated on the Italian genotypic data and correlated to the North–south genetic gradient. Using a gene-enrichment approach we identified the immune function as primarily involved in the Italian population differentiation and we described a locus on chromosome 13 showing combined evidence of North–south diversification in allele frequencies and signs of recent positive selection. In this region our bioinformatics analysis pinpointed an uncharacterized long intergenic non-coding (lincRNA), whose expression appeared specific for immune-related tissues suggesting its relevance for the immune function. Conclusions Our study, combining population genetic analyses with biological insights provides a description of the Italian genetic structure that in future could contribute to the evaluation of complex diseases risk in the population context. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0293-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvia Parolo
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
| | - Antonella Lisa
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
| | - Davide Gentilini
- Molecular Biology Laboratory, Istituto Auxologico Italiano, Milan, Italy.
| | | | - Simona Barlera
- Department of Cardiovascular Research, IRCCS Mario Negri Institute for Pharmacological Research, Milan, Italy.
| | - Enrico B Nicolis
- Department of Cardiovascular Research, IRCCS Mario Negri Institute for Pharmacological Research, Milan, Italy.
| | - Giorgio B Boncoraglio
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - Eugenio A Parati
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - Silvia Bione
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
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13
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Kaufman JS, Dolman L, Rushani D, Cooper RS. The contribution of genomic research to explaining racial disparities in cardiovascular disease: a systematic review. Am J Epidemiol 2015; 181:464-72. [PMID: 25731887 DOI: 10.1093/aje/kwu319] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
After nearly a decade of genome-wide association studies, no assessment has yet been made of their contribution toward an explanation of the most prominent racial health disparities observed at the population level. We examined populations of African and European ancestry and focused on cardiovascular diseases, which are collectively the largest contributor to the racial mortality gap. We conducted a systematic search for review articles and meta-analyses published in 2007-2013 in which genetic data from both populations were available. We identified 68 articles relevant to this question; however, few reported significant associations in both racial groups, with just 3 variants meeting study-specific significance criteria. For most outcomes, there were too few estimates for quantitative summarization, but when summarization was possible, racial group did not contribute to heterogeneity. Most associations reported from genome-wide searches were small, difficult to replicate, and in no consistent direction that favored one racial group or another. Although the substantial investment in this technology might have produced clinical advances, it has thus far made little or no contribution to our understanding of population-level racial health disparities in cardiovascular disease.
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14
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Zhang J, Yang Z, Xiao J, Xing X, Lu J, Weng J, Jia W, Ji L, Shan Z, Liu J, Tian H, Ji Q, Zhu D, Ge J, Chen L, Guo X, Zhao Z, Li Q, Zhou Z, Lin L, Wang N, Yang W. Association between family history risk categories and prevalence of diabetes in Chinese population. PLoS One 2015; 10:e0117044. [PMID: 25664814 PMCID: PMC4321835 DOI: 10.1371/journal.pone.0117044] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 12/17/2014] [Indexed: 02/05/2023] Open
Abstract
AIM To investigate the association between different family history risk categories and prevalence of diabetes in the Chinese population. METHODS The family history of diabetes was obtained from each subject, and an oral glucose tolerance test was performed for measuring the fasting and postload glucose and insulin levels based on a national representative cross-sectional survey of 46,239 individuals (age ≥ 20 years) in the 2007-2008 China National Diabetes and Metabolism Disorders Study. The family history risk categories of diabetes were high, moderate, and average (FH2 and FH1: at least two generations and one generation of first-degree relatives with diabetes, respectively; FH0: no first-degree relatives with diabetes). RESULTS The age- and gender-adjusted prevalence rates of diabetes were 32.7% (95% confidence interval (CI): 26.4-39.7%) in FH2, 20.1% (95% CI: 18.2-22.1%) in FH1, and 8.4% (95% CI: 7.9-8.9%) in FH0 (P < 0.0001). The calculated homeostatic model assessment-estimated insulin resistance (HOMA-IR), Matsuda insulin sensitivity index (ISI), and insulinogenic index (ΔI30/ΔG30) values showed significant trending changes among the three risk categories, with the most negative effects in FH2. Multivariate logistic regression analysis showed that the odds ratios of having diabetes were 6.16 (95% CI: 4.46-8.50) and 2.86 (95% CI: 2.41-3.39) times higher in FH2 and FH1, respectively, than in FH0 after adjustment for classical risk factors for diabetes. CONCLUSIONS Family history risk categories of diabetes have a significant, independent, and graded association with the prevalence of this disease in the Chinese population.
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Affiliation(s)
- Jinping Zhang
- Department of Endocrinology, China–Japan Friendship Hospital, Beijing, China
| | - Zhaojun Yang
- Department of Endocrinology, China–Japan Friendship Hospital, Beijing, China
- * E-mail: (ZY); (WY)
| | - Jianzhong Xiao
- Department of Endocrinology, China–Japan Friendship Hospital, Beijing, China
| | - Xiaoyan Xing
- Department of Endocrinology, China–Japan Friendship Hospital, Beijing, China
| | - Juming Lu
- Department of Endocrinology, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Jianping Weng
- Department of Endocrinology, Sun Yat-sen University Third Hospital, Guangzhou, China
| | - Weiping Jia
- Department of Endocrinology, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Linong Ji
- Department of Endocrinology, Peking University People's Hospital, Beijing, China
| | - Zhongyan Shan
- Department of Endocrinology, First Affiliated Hospital, Chinese Medical University, Liaoling, China
| | - Jie Liu
- Department of Endocrinology, Shanxi Province People's Hospital, Taiyuan, Shanxi, China
| | - Haoming Tian
- Department of Endocrinology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qiuhe Ji
- Department of Endocrinology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, China
| | - Dalong Zhu
- Department of Endocrinology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Jiapu Ge
- Department of Endocrinology, Xinjiang Uygur Autonomous Region's Hospital, Urmqi, Xinjiang, China
| | - Li Chen
- Department of Endocrinology, Qilu Hospital, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xiaohui Guo
- Department of Endocrinology, Peking University First Hospital, Beijing, China
| | - Zhigang Zhao
- Department of Endocrinology, Henan Province People's Hospital, Zhengzhou, Henan, China
| | - Qiang Li
- Department of Endocrinology, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhiguang Zhou
- Department of Endocrinology, Xiangya Second Hospital, Changsha, Hunan, China
| | - Lixiang Lin
- Department of Endocrinology, Fujian Provincial Hospital, Fuzhou, Fujiang, China
| | - Na Wang
- Department of Endocrinology, China–Japan Friendship Hospital, Beijing, China
| | - Wenying Yang
- Department of Endocrinology, China–Japan Friendship Hospital, Beijing, China
- * E-mail: (ZY); (WY)
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15
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Difference in health inequity between two population groups due to a social determinant of health. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2014; 11:13074-83. [PMID: 25522048 PMCID: PMC4276663 DOI: 10.3390/ijerph111213074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/21/2014] [Accepted: 12/09/2014] [Indexed: 11/17/2022]
Abstract
The World Health Organization defines social determinants of health as "complex, integrated, and overlapping social structures and economic systems" that are responsible for most health inequities. Similar to the individual-level risk factors such as behavioral and biological risk factors that influence disease, we consider social determinants of health such as the distribution of income, wealth, influence and power as risk factors for risk of disease. We operationally define health inequity in a disease within a population due to a risk factor that is unfair and avoidable as the difference between the disease outcome with and without the risk factor in the population. We derive expressions for difference in health inequity between two populations due to a risk factor that is unfair and avoidable for a given disease. The difference in heath inequity between two population groups due to a risk factor increases with increasing difference in relative risks and the difference in prevalence of the risk factor in the two populations. The difference in health inequity could be larger than the difference in health outcomes between the two populations in some situations. Compared to health disparities which are typically measured and monitored using absolute or relative disparities of health outcomes, the methods presented in this manuscript provide a different, yet complementary, picture because they parse out the contributions of unfair and avoidable risk factors.
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16
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Common vitamin D pathway gene variants reveal contrasting effects on serum vitamin D levels in African Americans and European Americans. Hum Genet 2014; 133:1395-405. [PMID: 25085266 PMCID: PMC4185105 DOI: 10.1007/s00439-014-1472-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/18/2014] [Indexed: 01/06/2023]
Abstract
Vitamin D deficiency is more common among African Americans (AAs) than among European Americans (EAs), and epidemiologic evidence links vitamin D status to many health outcomes. Two genome-wide association studies (GWAS) in European populations identified vitamin D pathway gene single-nucleotide polymorphisms (SNPs) associated with serum vitamin D [25(OH)D] levels, but a few of these SNPs have been replicated in AAs. Here, we investigated the associations of 39 SNPs in vitamin D pathway genes, including 19 GWAS-identified SNPs, with serum 25(OH)D concentrations in 652 AAs and 405 EAs. Linear and logistic regression analyses were performed adjusting for relevant environmental and biological factors. The pattern of SNP associations was distinct between AAs and EAs. In AAs, six GWAS-identified SNPs in GC, CYP2R1, and DHCR7/NADSYN1 were replicated, while nine GWAS SNPs in GC and CYP2R1 were replicated in EAs. A CYP2R1 SNP, rs12794714, exhibited the strongest signal of association in AAs. In EAs, however, a different CYP2R1 SNP, rs1993116, was the most strongly associated. Our models, which take into account genetic and environmental variables, accounted for 20 and 28 % of the variance in serum vitamin D levels in AAs and EAs, respectively.
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17
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Xu H, Yang W, Perez-Andreu V, Devidas M, Fan Y, Cheng C, Pei D, Scheet P, Burchard EG, Eng C, Huntsman S, Torgerson DG, Dean M, Winick NJ, Martin PL, Camitta BM, Bowman WP, Willman CL, Carroll WL, Mullighan CG, Bhojwani D, Hunger SP, Pui CH, Evans WE, Relling MV, Loh ML, Yang JJ. Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations. J Natl Cancer Inst 2013; 105:733-42. [PMID: 23512250 DOI: 10.1093/jnci/djt042] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is the most common cancer in children and the incidence of ALL varies by ethnicity. Although accumulating evidence indicates inherited predisposition to ALL, the genetic basis of ALL susceptibility in diverse ancestry has not been comprehensively examined. METHODS We performed a multiethnic genome-wide association study in 1605 children with ALL and 6661 control subjects after adjusting for population structure, with validation in three replication series of 845 case subjects and 4316 control subjects. Association was tested by two-sided logistic regression. RESULTS A novel ALL susceptibility locus at 10p12.31-12.2 (BMI1-PIP4K2A, rs7088318, P = 1.1 × 10(-11)) was identified in the genome-wide association study, with independent replication in European Americans, African Americans, and Hispanic Americans (P = .001, .009, and .04, respectively). Association was also validated at four known ALL susceptibility loci: ARID5B, IKZF1, CEBPE, and CDKN2A/2B. Associations at ARID5B, IKZF1, and BMI1-PIP4K2A variants were consistent across ethnicity, with multiple independent signals at IKZF1 and BMI1-PIP4K2A loci. The frequency of ARID5B and BMI1-PIP4K2A variants differed by ethnicity, in parallel with ethnic differences in ALL incidence. Suggestive evidence for modifying effects of age on genetic predisposition to ALL was also observed. ARID5B, IKZF1, CEBPE, and BMI1-PIP4K2A variants cumulatively conferred strong predisposition to ALL, with children carrying six to eight copies of risk alleles at a ninefold (95% confidence interval = 6.9 to 11.8) higher ALL risk relative to those carrying zero to one risk allele at these four single nucleotide polymorphisms. CONCLUSIONS These findings indicate strong associations between inherited genetic variation and ALL susceptibility in children and shed new light on ALL molecular etiology in diverse ancestry.
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Affiliation(s)
- Heng Xu
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
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18
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Salem SD, Saif-Ali R, Ismail IS, Al-Hamodi Z, Poh R, Muniandy S. IGF2BP2 alternative variants associated with glutamic acid decarboxylase antibodies negative diabetes in Malaysian subjects. PLoS One 2012; 7:e45573. [PMID: 23029108 PMCID: PMC3446917 DOI: 10.1371/journal.pone.0045573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Accepted: 08/22/2012] [Indexed: 01/19/2023] Open
Abstract
Background The association of Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) common variants (rs4402960 and rs1470579) with type 2 diabetes (T2D) has been performed in different populations. The aim of this study was to evaluate the association of alternative variants of IGF2BP2; rs6777038, rs16860234 and rs7651090 with glutamic acid decarboxylase antibodies (GADA) negative diabetes in Malaysian Subjects. Methods/Principal Findings IGF2BP2; rs6777038, rs16860234 and rs7651090 single nucleotide polymorphisms (SNPs) were genotyped in 1107 GADA negative diabetic patients and 620 control subjects of Asian from Malaysia. The additive genetic model adjusted for age, race, gender and BMI showed that alternative variants; rs6777038, rs16860234 and rs7651090 of IGF2BP2 associated with GADA negative diabetes (OR = 1.21; 1.36; 1.35, P = 0.03; 0.0004; 0.0002, respectively). In addition, the CCG haplotype and diplotype CCG-TCG increased the risk of diabetes (OR = 1.51, P = 0.01; OR = 2.36, P = 0.009, respectively). Conclusions/Significance IGF2BP2 alternative variants were associated with GADA negative diabetes. The IGF2BP2 haplotypes and diplotypes increased the risk of diabetes in Malaysian subject.
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Affiliation(s)
- Sameer D. Salem
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail: (SDS); (SM)
| | - Riyadh Saif-Ali
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Department of Biochemistry, Faculty of Medicine, Sana’a University, Sana’a, Yemen
| | - Ikram S. Ismail
- Department of Medicine, Faculty of Medicine, University of Malaya Medical Centre, University of Malaya, Kuala Lumpur, Malaysia
| | - Zaid Al-Hamodi
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Rozaida Poh
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sekaran Muniandy
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail: (SDS); (SM)
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