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de Jesús Ascencio-Montiel I, Pinto D, Parra EJ, Valladares-Salgado A, Cruz M, Scherer SW. Characterization of Large Copy Number Variation in Mexican Type 2 Diabetes subjects. Sci Rep 2017; 7:17105. [PMID: 29213072 PMCID: PMC5719030 DOI: 10.1038/s41598-017-17361-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/20/2017] [Indexed: 01/26/2023] Open
Abstract
The effect of Copy Number Variants (CNVs) on Type 2 Diabetes (T2D) remains little explored. The present study characterized large rare CNVs in 686 T2D and 194 non-T2D subjects of Mexican ancestry genotyped using the Affymetrix Genome-Wide Human SNP array 5.0. Rare CNVs with ≥ 100 kb length were identified using a stringent strategy based on merging CNVs calls generated using Birdsuit, iPattern and PennCNV algorithms. We applied three different strategies to evaluate the distribution of CNVs in the T2D and non-T2D samples: 1) Burden analysis, 2) Identification of CNVs in loci previously associated to T2D, and 3) Identification of CNVs observed only in the T2D group. In the CNV burden analysis, the T2D group showed a higher proportion of CNVs, and also a higher proportion of CNVs overlapping at least one gene than the non T2D group. Five of the six loci previously associated with T2D had duplications or deletions in the T2D sample, but not the non-T2D sample. A gene-set analysis including genes with CNVs observed only in the T2D group highlighted gene-sets related with sensory perception (olfactory receptors, OR) and phenylpyruvate tautomerase/dopachrome isomerase activity (MIF and DDT genes).
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Affiliation(s)
- Iván de Jesús Ascencio-Montiel
- Instituto Mexicano del Seguro Social, Coordinación de Vigilancia Epidemiológica, Mier y Pesado 120, Col. del Valle, Benito Juárez, 03100, Mexico City, Mexico.
| | - Dalila Pinto
- Departments of Psychiatry, Genetics and Genomic Sciences, The Mindich Child Health & Development Institute, Seaver Autism Center, Institute for Genomics and Multiscale Biology, at the Icahn School of Medicine at Mount Sinai, New York, 1470 Madison Avenue, S8-115, New York, NY, 10029, USA
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, 3359 Mississauga Road, room 352, Health Sciences Complex, Mississauga, ON L5L 1C6, Canada
| | - Adán Valladares-Salgado
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. del Doctores, 06720, Mexico City, Mexico
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. del Doctores, 06720, Mexico City, Mexico
| | - Stephen W Scherer
- The Centre for Applied Genomics. The Hospital for Sick Children. Peter Gilgan Centre for Research and Learning, 686 Bay Street, Room 139800, Toronto, Ontario, M5G 0A4, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, 686 Bay Street, 13th Floor, Toronto, Ontario, M5G 0A4, Canada
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Hanson RL, Leti F, Tsinajinnie D, Kobes S, Puppala S, Curran JE, Almasy L, Lehman DM, Blangero J, Duggirala R, DiStefano JK. The Arg59Trp variant in ANGPTL8 (betatrophin) is associated with total and HDL-cholesterol in American Indians and Mexican Americans and differentially affects cleavage of ANGPTL3. Mol Genet Metab 2016; 118:128-37. [PMID: 27117576 PMCID: PMC4880492 DOI: 10.1016/j.ymgme.2016.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/15/2016] [Accepted: 04/15/2016] [Indexed: 11/19/2022]
Abstract
We previously identified a locus linked to total cholesterol (TC) concentration in Pima Indians on chromosome 19p. To characterize this locus, we genotyped >2000 SNPs in 1838 Pimas and assessed association with log(TC). We observed evidence for association with log(TC) with rs2278426 (3.5% decrease/copy of the T allele; P=5.045×10(-6)) in the ANGPTL8 (angiopoietin-like 8) gene. We replicated this association in 2413 participants of the San Antonio Mexican American Family Study (SAMAFS: 2.0% decrease per copy of the T allele; P=0.005842). In a meta-analysis of the combined data, we found the strongest estimated effect with rs2278426 (P=2.563×10(-7)). The variant T allele at rs2278426 predicts an Arg59Trp substitution and has previously been associated with LDL-C and HDL-C. In Pimas and SAMAFS participants, the T allele of rs2278426 was associated with reduced HDL-C levels (P=0.000741 and 0.00002, respectively), and the combined estimated effect for the two cohorts was -3.8% (P=8.526×10(-8)). ANGPTL8 transcript and protein levels increased in response to both glucose and insulin. The variant allele was associated with increased levels of cleaved ANGPTL3. We conclude that individuals with the variant allele may have lower TC and HDL-C levels due to increased activation of ANGPTL3 by ANGPTL8.
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MESH Headings
- Adult
- Alleles
- Amino Acid Substitution
- Angiopoietin-Like Protein 3
- Angiopoietin-Like Protein 8
- Angiopoietin-like Proteins/genetics
- Angiopoietin-like Proteins/metabolism
- Arginine/genetics
- Blood Glucose/metabolism
- Cholesterol, HDL/blood
- Cholesterol, HDL/genetics
- Cholesterol, HDL/metabolism
- Cholesterol, LDL/blood
- Cholesterol, LDL/genetics
- Cholesterol, LDL/metabolism
- Chromosomes, Human, Pair 19/genetics
- Cohort Studies
- Coronary Disease/blood
- Coronary Disease/genetics
- Diabetes Mellitus/genetics
- Female
- Genome-Wide Association Study
- Hep G2 Cells
- Humans
- Indians, North American/genetics
- Insulin/metabolism
- Male
- Mexican Americans/genetics
- Middle Aged
- Peptide Hormones/genetics
- Peptide Hormones/metabolism
- Polymorphism, Single Nucleotide
- Tryptophan/genetics
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Affiliation(s)
- Robert L Hanson
- Diabetes Epidemiology and Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 1550 East Indian School Road, Phoenix, AZ 85014, United States
| | - Fatjon Leti
- Center for Genes, Environment, and Health, Department of Biomedical Research, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, United States
| | - Darwin Tsinajinnie
- Diabetes, Cardiovascular and Metabolic Diseases Division, Translational Genomics Research Institute, 445 Fifth Street, Phoenix, AZ 85004, United States
| | - Sayuko Kobes
- Diabetes Epidemiology and Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 1550 East Indian School Road, Phoenix, AZ 85014, United States
| | - Sobha Puppala
- South Texas Diabetes and Obesity Institute (STDOI), University of Texas Rio Grande Valley (UTRGV) School of Medicine, 2700 E. Jackson St. Brownsville, TX 78520; 1214 W. Schunior Street, Edinburgh, TX 78541; 3463 Magic Drive San Antonio, TX 78229, United States
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute (STDOI), University of Texas Rio Grande Valley (UTRGV) School of Medicine, 2700 E. Jackson St. Brownsville, TX 78520; 1214 W. Schunior Street, Edinburgh, TX 78541; 3463 Magic Drive San Antonio, TX 78229, United States
| | - Laura Almasy
- South Texas Diabetes and Obesity Institute (STDOI), University of Texas Rio Grande Valley (UTRGV) School of Medicine, 2700 E. Jackson St. Brownsville, TX 78520; 1214 W. Schunior Street, Edinburgh, TX 78541; 3463 Magic Drive San Antonio, TX 78229, United States
| | - Donna M Lehman
- Departments of Medicine and Cellular & Structural Biology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, United States
| | - John Blangero
- South Texas Diabetes and Obesity Institute (STDOI), University of Texas Rio Grande Valley (UTRGV) School of Medicine, 2700 E. Jackson St. Brownsville, TX 78520; 1214 W. Schunior Street, Edinburgh, TX 78541; 3463 Magic Drive San Antonio, TX 78229, United States
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute (STDOI), University of Texas Rio Grande Valley (UTRGV) School of Medicine, 2700 E. Jackson St. Brownsville, TX 78520; 1214 W. Schunior Street, Edinburgh, TX 78541; 3463 Magic Drive San Antonio, TX 78229, United States
| | - Johanna K DiStefano
- Center for Genes, Environment, and Health, Department of Biomedical Research, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, United States; Diabetes, Cardiovascular and Metabolic Diseases Division, Translational Genomics Research Institute, 445 Fifth Street, Phoenix, AZ 85004, United States.
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Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans. Eur J Hum Genet 2015; 23:1229-35. [PMID: 25585699 PMCID: PMC4538210 DOI: 10.1038/ejhg.2014.280] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 09/25/2014] [Accepted: 11/26/2014] [Indexed: 11/23/2022] Open
Abstract
Only few systematic studies on the contribution of copy number variation to gene expression variation have been published to date. Here we identify effects of copy number variable regions (CNVRs) on nearby gene expression by investigating 909 CNVRs and expression levels of 12059 nearby genes in white blood cells from Mexican-American participants of the San Antonio Family Heart Study. We empirically evaluate our ability to detect the contribution of CNVs to proximal gene expression (presumably in cis) at various window sizes (up to a 10 Mb distance) between the gene and CNV. We found a ~1-Mb window size to be optimal for capturing cis effects of CNVs. Up to 10% of the CNVs in this study were found to be significantly associated with the expression of at least one gene within their vicinity. As expected, we find that CNVs that directly overlap gene sequences have the largest effects on gene expression (compared with non-overlapping CNVRs located nearby), with positive correlation (except for a few exceptions) between estimated genomic dosage and expression level. We find that genes whose expression level is significantly influenced by nearby CNVRs are enriched for immunity and autoimmunity related genes. These findings add to the currently limited catalog of CNVRs that are recognized as expression quantitative trait loci, and have implications for future study designs as well as for prioritizing candidate causal variants in genomic regions associated with disease.
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Fanciulli M, Pasini E, Malacrida S, Striano P, Striano S, Michelucci R, Ottman R, Nobile C. Copy number variations and susceptibility to lateral temporal epilepsy: A study of 21 pedigrees. Epilepsia 2014; 55:1651-8. [DOI: 10.1111/epi.12767] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2014] [Indexed: 11/28/2022]
Affiliation(s)
| | - Elena Pasini
- Unit of Neurology; Bellaria Hospital; IRCCS of Neurological Sciences; Bologna Italy
| | | | - Pasquale Striano
- Pediatric Neurology and Neuromuscular Disease Unit; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health; “G. Gaslini” Institute; University of Genoa; Genova Italy
| | - Salvatore Striano
- Department of Neurological Sciences; Federico II University; Napoli Italy
| | - Roberto Michelucci
- Unit of Neurology; Bellaria Hospital; IRCCS of Neurological Sciences; Bologna Italy
| | - Ruth Ottman
- Departments of Epidemiology and Neurology and the G.H. Sergievsky Center; Columbia University; New York New York U.S.A
- Division of Epidemiology; New York State Psychiatric Institute; New York New York U.S.A
| | - Carlo Nobile
- CNR-Neuroscience Institute; Section of Padua; Padova Italy
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Abstract
Whole genome sequencing (WGS) remains prohibitively expensive, which has encouraged the development of methods to impute WGS data into nonsequenced individuals using a framework of single nucleotide polymorphisms genotyped for genome-wide association studies (GWAS). Although successful methods have been developed for cohorts of unrelated individuals, current imputation methods in related individuals are limited by pedigree size, by the distance of relationships, or by computation time. In this article, we describe a method for imputation in arbitrarily shaped multigenerational pedigrees that can impute genotypes across distantly related individuals based on identity by descent. We evaluate this approach using GWAS data and apply this approach to WGS data distributed for Genetic Analysis Workshop 18.
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Affiliation(s)
- August N Blackburn
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, 7702 Floyd Curl Road, San Antonio, TX 78229, USA
| | - Angela K Dean
- Department of Medicine/Clinical Epidemiology, University of Texas Health Science Center at San Antonio, 7702 Floyd Curl Road, San Antonio, TX 78229, USA
| | - Donna M Lehman
- Department of Medicine/Clinical Epidemiology, University of Texas Health Science Center at San Antonio, 7702 Floyd Curl Road, San Antonio, TX 78229, USA
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