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Pradas N, Jurado-Ruiz F, Onielfa C, Arús P, Aranzana MJ. PERSEUS: an interactive and intuitive web-based tool for pedigree visualization. Bioinformatics 2024; 40:btae060. [PMID: 38310342 PMCID: PMC10898331 DOI: 10.1093/bioinformatics/btae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 02/05/2024] Open
Abstract
SUMMARY Pedigree-based analyses' prime role is to unravel relationships between individuals in breeding programs and germplasms. This is critical information for decoding the genetics underlying main inherited traits of relevance, and unlocking the genotypic variability of a species to carry out genomic selections and predictions. Despite the great interest, current lineage visualizations become quite limiting in terms of public display, exploration, and tracing of traits up to ancestral donors. PERSEUS is a user-friendly, intuitive, and interactive web-based tool for pedigree visualizations represented as directed graph networks distributed using a force-repulsion method. The visualizations do not only showcase individual relationships among accessions, but also facilitate a seamless search and download of phenotypic traits along the pedigrees. PERSEUS is a promising tool for breeders and scientists, advantageous for evolutionary, genealogy, and diversity analyses among related accessions and species. AVAILABILITY AND IMPLEMENTATION PERSEUS is freely accessible at https://bioinformatics.cragenomica.es/perseus and GitHub code is available at https://github.com/aranzana-lab/PERSEUS.
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Affiliation(s)
- Nicole Pradas
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Federico Jurado-Ruiz
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Carles Onielfa
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 0814 Barcelona, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 0814 Barcelona, Spain
| | - Maria José Aranzana
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 0814 Barcelona, Spain
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Finke K, Kourakos M, Brown G, Dang HT, Tan SJS, Simons YB, Ramdas S, Schäffer AA, Kember RL, Bućan M, Mathieson S. Ancestral haplotype reconstruction in endogamous populations using identity-by-descent. PLoS Comput Biol 2021; 17:e1008638. [PMID: 33635861 PMCID: PMC7946327 DOI: 10.1371/journal.pcbi.1008638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 03/10/2021] [Accepted: 12/15/2020] [Indexed: 12/24/2022] Open
Abstract
In this work we develop a novel algorithm for reconstructing the genomes of ancestral individuals, given genotype or sequence data from contemporary individuals and an extended pedigree of family relationships. A pedigree with complete genomes for every individual enables the study of allele frequency dynamics and haplotype diversity across generations, including deviations from neutrality such as transmission distortion. When studying heritable diseases, ancestral haplotypes can be used to augment genome-wide association studies and track disease inheritance patterns. The building blocks of our reconstruction algorithm are segments of Identity-By-Descent (IBD) shared between two or more genotyped individuals. The method alternates between identifying a source for each IBD segment and assembling IBD segments placed within each ancestral individual. Unlike previous approaches, our method is able to accommodate complex pedigree structures with hundreds of individuals genotyped at millions of SNPs. We apply our method to an Old Order Amish pedigree from Lancaster, Pennsylvania, whose founders came to North America from Europe during the early 18th century. The pedigree includes 1338 individuals from the past 12 generations, 394 with genotype data. The motivation for reconstruction is to understand the genetic basis of diseases segregating in the family through tracking haplotype transmission over time. Using our algorithm thread, we are able to reconstruct an average of 224 ancestral individuals per chromosome. For these ancestral individuals, on average we reconstruct 79% of their haplotypes. We also identify a region on chromosome 16 that is difficult to reconstruct—we find that this region harbors a short Amish-specific copy number variation and the gene HYDIN. thread was developed for endogamous populations, but can be applied to any extensive pedigree with the recent generations genotyped. We anticipate that this type of practical ancestral reconstruction will become more common and necessary to understand rare and complex heritable diseases in extended families. When analyzing complex heritable traits, genomic data from many generations of an extended family increases the amount of information available for statistical inference. However, typically only genomic data from the recent generations of a pedigree are available, as ancestral individuals are deceased. In this work we present an algorithm, called thread, for reconstructing the genomes of ancestral individuals, given a complex pedigree and genomic data from the recent generations. Previous approaches have not been able to accommodate large datasets (both in terms of sites and individuals), made simplifying assumptions about pedigree structure, or did not tie reconstructed sequences back to specific individuals. We apply thread to a complex Old Order Amish pedigree of 1338 individuals, 394 with genotype data.
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Affiliation(s)
- Kelly Finke
- Department of Computer Science, Swarthmore College, Swarthmore, Pennsylvania, United States of America
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Michael Kourakos
- Department of Computer Science, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Gabriela Brown
- Department of Computer Science, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Huyen Trang Dang
- Department of Computer Science, Bryn Mawr College, Bryn Mawr, Pennsylvania, United States of America
| | - Shi Jie Samuel Tan
- Department of Computer Science, Haverford College, Haverford, Pennsylvania, United States of America
| | - Yuval B. Simons
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Shweta Ramdas
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alejandro A. Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rachel L. Kember
- Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Maja Bućan
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sara Mathieson
- Department of Computer Science, Haverford College, Haverford, Pennsylvania, United States of America
- * E-mail:
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Anderson C, Potts L. The Amish health culture and culturally sensitive health services: An exhaustive narrative review. Soc Sci Med 2020; 265:113466. [PMID: 33153874 PMCID: PMC8431948 DOI: 10.1016/j.socscimed.2020.113466] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/17/2020] [Accepted: 10/18/2020] [Indexed: 01/31/2023]
Abstract
As the Amish population is growing, researcher and practitioner interest in the Amish health culture is also growing. This is largely due to demand from practitioners for population-specific cultural guidance. Once a small area of study, health-themed publications in Amish studies (n = 246) now account for approximately one-fourth of all peer-reviewed publications, and a sizeable percentage address the health culture, i.e. Amish beliefs, practices, attitudes, decision-making processes, financing, and values. In this article, we provide a first-ever exhaustive narrative review of the Amish health culture literature (addressing Amish health conditions elsewhere). Specifically, we address Amish use of modern medicine, complementary & alternative medicine, cultural norms for birthing and intercourse, support and care for the sick and aged, health knowledge, payment for services, barriers to service access, service provider effectiveness, health programming, and ethical conflicts. Our goal is to organize the literature, synthesize findings, identify orienting perspectives, and clarify research questions and directions. Following our synthesis, we reflect on the current state of Amish health culture research, drawing particular attention to strengths and limitations of the oft-used cultural competency paradigm, and recommending more rigorous social scientific theorization of the Amish health culture.
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Affiliation(s)
- Cory Anderson
- Population Research Institute, Pennsylvania State University, State College, PA, 717-330-1766, USA.
| | - Lindsey Potts
- Truman State University, 100 E. Normal Ave, Kirksville, MO, 63501, USA
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Kessler MD, Loesch DP, Perry JA, Heard-Costa NL, Taliun D, Cade BE, Wang H, Daya M, Ziniti J, Datta S, Celedón JC, Soto-Quiros ME, Avila L, Weiss ST, Barnes K, Redline SS, Vasan RS, Johnson AD, Mathias RA, Hernandez R, Wilson JG, Nickerson DA, Abecasis G, Browning SR, Zöllner S, O'Connell JR, Mitchell BD, O'Connor TD. De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population. Proc Natl Acad Sci U S A 2020; 117:2560-2569. [PMID: 31964835 PMCID: PMC7007577 DOI: 10.1073/pnas.1902766117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains <1% of variation. While we are underpowered to see small differences, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, we did find significantly fewer DNMs in Amish individuals, even when compared with other Europeans, and even after accounting for parental age and sequencing center. Specifically, we found significant reductions in the number of C→A and T→C mutations in the Amish, which seem to underpin their overall reduction in DNMs. Finally, we calculated near-zero estimates of narrow sense heritability (h2), which suggest that variation in DNM rate is significantly shaped by nonadditive genetic effects and the environment.
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Affiliation(s)
- Michael D Kessler
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Douglas P Loesch
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - James A Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Nancy L Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118
- Framingham Heart Study, Framingham, MA 01702
| | - Daniel Taliun
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142
| | - Michelle Daya
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045
| | - John Ziniti
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Soma Datta
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Manuel E Soto-Quiros
- Department of Pediatrics, Hospital Nacional de Niños, 10103 San José, Costa Rica
| | - Lydiana Avila
- Department of Pediatrics, Hospital Nacional de Niños, 10103 San José, Costa Rica
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Kathleen Barnes
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045
| | - Susan S Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115
- Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215
| | | | - Andrew D Johnson
- Framingham Heart Study, Framingham, MA 01702
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, The Johns Hopkins School of Medicine, Baltimore, MD 21224
- Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD 21218
| | - Ryan Hernandez
- Quantitative Life Sciences, McGill University, Montreal, QC H3A OG4, Canada
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216
| | | | - Goncalo Abecasis
- School of Public Health, University of Michigan, Ann Arbor, MI 48109
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201;
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
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5
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Cognitive profiles and heritability estimates in the Old Order Amish. Psychiatr Genet 2016; 26:178-83. [PMID: 27105171 DOI: 10.1097/ypg.0000000000000134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE This study aimed to establish the applicability of the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) in the Old Order Amish (OOA) and to assess the genetic contribution toward the RBANS total score and its cognitive domains using a large family-based sample of OOA. PARTICIPANTS AND METHODS RBANS data were collected in 103 OOA individuals from Lancaster County, Pennsylvania, including 85 individuals without psychiatric illness and 18 individuals with current psychiatric diagnoses. RESULTS The RBANS total score and all five cognitive domains of in nonpsychiatric OOA were within half a SD of the normative data of the general population. The RBANS total score was highly heritable (h=0.51, P=0.019). OOA with psychiatric diagnoses had a numerically lower RBANS total score and domain scores compared with the nonpsychiatric participants. CONCLUSION The RBANS appears to be a suitable cognitive battery for the OOA population as measurements obtained from the OOA are comparable with normative data in the US population. The heritability estimated from the OOA is in line with heritabilities of other cognitive batteries estimated in other populations. These results support the use of RBANS in cognitive assessment, clinical care, and behavioral genetic studies of neuropsychological functioning in this population.
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Kochunov P, Fu M, Nugent K, Wright SN, Du X, Muellerklein F, Morrissey M, Eskandar G, Shukla DK, Jahanshad N, Thompson PM, Patel B, Postolache TT, Strauss KA, Shuldiner AR, Mitchell BD, Hong LE. Heritability of complex white matter diffusion traits assessed in a population isolate. Hum Brain Mapp 2015; 37:525-35. [PMID: 26538488 DOI: 10.1002/hbm.23047] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/07/2015] [Accepted: 10/22/2015] [Indexed: 11/09/2022] Open
Abstract
INTRODUCTION Diffusion weighted imaging (DWI) methods can noninvasively ascertain cerebral microstructure by examining pattern and directions of water diffusion in the brain. We calculated heritability for DWI parameters in cerebral white (WM) and gray matter (GM) to study the genetic contribution to the diffusion signals across tissue boundaries. METHODS Using Old Order Amish (OOA) population isolate with large family pedigrees and high environmental homogeneity, we compared the heritability of measures derived from three representative DWI methods targeting the corpus callosum WM and cingulate gyrus GM: diffusion tensor imaging (DTI), the permeability-diffusivity (PD) model, and the neurite orientation dispersion and density imaging (NODDI) model. These successively more complex models represent the diffusion signal modeling using one, two, and three diffusion compartments, respectively. RESULTS We replicated the high heritability of the DTI-based fractional anisotropy (h(2) = 0.67) and radial diffusivity (h(2) = 0.72) in WM. High heritability in both WM and GM tissues were observed for the permeability-diffusivity index from the PD model (h(2) = 0.64 and 0.84), and the neurite density from the NODDI model (h(2) = 0.70 and 0.55). The orientation dispersion index from the NODDI model was only significantly heritable in GM (h(2) = 0.68). CONCLUSION DWI measures from multicompartmental models were significantly heritable in WM and GM. DWI can offer valuable phenotypes for genetic research; and genes thus identified may reveal mechanisms contributing to mental and neurological disorders in which diffusion imaging anomalies are consistently found. Hum Brain Mapp 37:525-535, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Peter Kochunov
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Mao Fu
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - Katie Nugent
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Susan N Wright
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Xiaoming Du
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Florian Muellerklein
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Mary Morrissey
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - George Eskandar
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Dinesh K Shukla
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Neda Jahanshad
- Keck School of Medicine of USC, Imaging Genetics Center, Marina Del Rey, California
| | - Paul M Thompson
- Keck School of Medicine of USC, Imaging Genetics Center, Marina Del Rey, California
| | - Binish Patel
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Teodor T Postolache
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland
| | | | - Alan R Shuldiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland.,Veterans Affairs Maryland Health Care System, Geriatric Research and Education Clinical Center, Baltimore, Maryland
| | - L Elliot Hong
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland
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Wojczynski MK, Parnell LD, Pollin TI, Lai CQ, Feitosa MF, O'Connell JR, Frazier-Wood AC, Gibson Q, Aslibekyan S, Ryan KA, Province MA, Tiwari HK, Ordovas JM, Shuldiner AR, Arnett DK, Borecki IB. Genome-wide association study of triglyceride response to a high-fat meal among participants of the NHLBI Genetics of Lipid Lowering Drugs and Diet Network (GOLDN). Metabolism 2015; 64:1359-71. [PMID: 26256467 PMCID: PMC4573277 DOI: 10.1016/j.metabol.2015.07.001] [Citation(s) in RCA: 30] [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: 12/04/2014] [Revised: 05/19/2015] [Accepted: 07/01/2015] [Indexed: 12/21/2022]
Abstract
OBJECTIVE The triglyceride (TG) response to a high-fat meal (postprandial lipemia, PPL) affects cardiovascular disease risk and is influenced by genes and environment. Genes involved in lipid metabolism have dominated genetic studies of PPL TG response. We sought to elucidate common genetic variants through a genome-wide association (GWA) study in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN). METHODS The GOLDN GWAS discovery sample consisted of 872 participants within families of European ancestry. Genotypes for 2,543,887 variants were measured or imputed from HapMap. Replication of our top results was performed in the Heredity and Phenotype Intervention (HAPI) Heart Study (n = 843). PPL TG response phenotypes were constructed from plasma TG measured at baseline (fasting, 0 hour), 3.5 and 6 hours after a high-fat meal, using a random coefficient regression model. Association analyses were adjusted for covariates and principal components, as necessary, in a linear mixed model using the kinship matrix; additional models further adjusted for fasting TG were also performed. Meta-analysis of the discovery and replication studies (n = 1715) was performed on the top SNPs from GOLDN. RESULTS GOLDN revealed 111 suggestive (p < 1E-05) associations, with two SNPs meeting GWA significance level (p < 5E-08). Of the two significant SNPs, rs964184 demonstrated evidence of replication (p = 1.20E-03) in the HAPI Heart Study and in a joint analysis, was GWA significant (p = 1.26E-09). Rs964184 has been associated with fasting lipids (TG and HDL) and is near ZPR1 (formerly ZNF259), close to the APOA1/C3/A4/A5 cluster. This association was attenuated upon additional adjustment for fasting TG. CONCLUSION This is the first report of a genome-wide significant association with replication for a novel phenotype, namely PPL TG response. Future investigation into response phenotypes is warranted using pathway analyses, or newer genetic technologies such as metabolomics.
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Affiliation(s)
- Mary K Wojczynski
- Department of Genetics, Washington University School of Medicine, St. Louis, MO.
| | - Laurence D Parnell
- Nutrition and Genomics Laboratory, Jean Mayer-US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA
| | - Toni I Pollin
- Program in Personalized and Genomic Medicine, and Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD
| | - Chao Q Lai
- Nutrition and Genomics Laboratory, Jean Mayer-US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA
| | - Mary F Feitosa
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Jeff R O'Connell
- Program in Personalized and Genomic Medicine, and Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD
| | | | - Quince Gibson
- Program in Personalized and Genomic Medicine, and Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD
| | - Stella Aslibekyan
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Kathy A Ryan
- Program in Personalized and Genomic Medicine, and Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD
| | - Michael A Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Hemant K Tiwari
- Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Jose M Ordovas
- Nutrition and Genomics Laboratory, Jean Mayer-US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA
| | - Alan R Shuldiner
- Program in Personalized and Genomic Medicine, and Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD; Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, MD
| | - Donna K Arnett
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Ingrid B Borecki
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
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Fisch AS, Yerges-Armstrong LM, Backman JD, Wang H, Donnelly P, Ryan KA, Parihar A, Pavlovich MA, Mitchell BD, O’Connell JR, Herzog W, Harman CR, Wren JD, Lewis JP. Genetic Variation in the Platelet Endothelial Aggregation Receptor 1 Gene Results in Endothelial Dysfunction. PLoS One 2015; 10:e0138795. [PMID: 26406321 PMCID: PMC4583223 DOI: 10.1371/journal.pone.0138795] [Citation(s) in RCA: 23] [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: 06/26/2015] [Accepted: 09/03/2015] [Indexed: 12/22/2022] Open
Abstract
Platelet Endothelial Aggregation Receptor 1 (PEAR1) is a newly identified membrane protein reported to be involved in multiple vascular and thrombotic processes. While most studies to date have focused on the effects of this receptor in platelets, PEAR1 is located in multiple tissues including the endothelium, where it is most highly expressed. Our first objective was to evaluate the role of PEAR1 in endothelial function by examining flow-mediated dilation of the brachial artery in 641 participants from the Heredity and Phenotype Intervention Heart Study. Our second objective was to further define the impact of PEAR1 on cardiovascular disease computationally through meta-analysis of 75,000 microarrays, yielding insights regarding PEAR1 function, and predictions of phenotypes and diseases affected by PEAR1 dysregulation. Based on the results of this meta-analysis we examined whether genetic variation in PEAR1 influences endothelial function using an ex vivo assay of endothelial cell migration. We observed a significant association between rs12041331 and flow-mediated dilation in participants of the Heredity and Phenotype Intervention Heart Study (P = 0.02). Meta-analysis results revealed that PEAR1 expression is highly correlated with several genes (e.g. ANG2, ACVRL1, ENG) and phenotypes (e.g. endothelial cell migration, angiogenesis) that are integral to endothelial function. Functional validation of these results revealed that PEAR1 rs12041331 is significantly associated with endothelial migration (P = 0.04). Our results suggest for the first time that genetic variation of PEAR1 is a significant determinant of endothelial function through pathways implicated in cardiovascular disease.
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Affiliation(s)
- Adam S. Fisch
- Division of Endocrinology, Diabetes, and Nutrition, and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Laura M. Yerges-Armstrong
- Division of Endocrinology, Diabetes, and Nutrition, and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Joshua D. Backman
- Division of Endocrinology, Diabetes, and Nutrition, and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hong Wang
- Division of Endocrinology, Diabetes, and Nutrition, and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Patrick Donnelly
- Division of Endocrinology, Diabetes, and Nutrition, and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Kathleen A. Ryan
- Division of Endocrinology, Diabetes, and Nutrition, and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Ankita Parihar
- Division of Endocrinology, Diabetes, and Nutrition, and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Mary A. Pavlovich
- Division of Endocrinology, Diabetes, and Nutrition, and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Braxton D. Mitchell
- Division of Endocrinology, Diabetes, and Nutrition, and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jeffrey R. O’Connell
- Division of Endocrinology, Diabetes, and Nutrition, and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - William Herzog
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Christopher R. Harman
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jonathan D. Wren
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, United States of America
- Program in Arthritis & Clinical Immunology Research, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Joshua P. Lewis
- Division of Endocrinology, Diabetes, and Nutrition, and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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9
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Bui DK, Jiang Y, Wei X, Ortube MC, Weeks DE, Conley YP, Gorin MB. Genetic ME-a visualization application for merging and editing pedigrees for genetic studies. BMC Res Notes 2015; 8:241. [PMID: 26076732 PMCID: PMC4478623 DOI: 10.1186/s13104-015-1131-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 04/21/2015] [Indexed: 11/23/2022] Open
Abstract
Background In order to study the genetics of diseases more accurately and effectively, one often collects large families. Different members of a large family may provide differing information about the structure and make-up of their pedigree. Thus, software is needed to facilitate reconciliation of pedigrees collected independently from multiple informants from a single large family to create a unified pedigree that is based on the best composite information available. Findings Our implementation demonstrates that Genetic ME performs merging in terms of adding, replacing and combining information from two pedigrees. Through a tracking process, all of the changes made to the data set for the individuals can be traced back to their original source material. A new pedigree structure can be easily visualized while reconciling disparate information from multiple pedigrees. Methods We developed the Genetic Merging & Editing (Genetic ME) program, an open source Java application built on top of CraneFoot and Ghostscript, to support comparing, editing and merging of pedigrees collected from multiple sources in a visually-oriented manner. Conclusions Genetic ME constitutes an ideal addition to software packages for reconciling pedigree information from multiple sources. Genetic ME provides a friendly graphical user interface, traces the changes made by users, and produces viewable merged pedigree structures able to be further used by other popular analysis programs. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1131-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diem K Bui
- Department of Ophthalmology, David Geffen School of Medicine-UCLA, Los Angeles, CA, 90095, USA.
| | - Yingda Jiang
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Xin Wei
- Department of Ophthalmology, David Geffen School of Medicine-UCLA, Los Angeles, CA, 90095, USA.
| | - Maria C Ortube
- Department of Ophthalmology, David Geffen School of Medicine-UCLA, Los Angeles, CA, 90095, USA.
| | - Daniel E Weeks
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA. .,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Yvette P Conley
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA. .,Department of Health Promotion and Development, School of Nursing, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Michael B Gorin
- Department of Ophthalmology, David Geffen School of Medicine-UCLA, Los Angeles, CA, 90095, USA. .,Department of Human Genetics, David Geffen School of Medicine-UCLA, Los Angeles, CA, 90095, USA.
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Gauvin H, Lefebvre JF, Moreau C, Lavoie EM, Labuda D, Vézina H, Roy-Gagnon MH. GENLIB: an R package for the analysis of genealogical data. BMC Bioinformatics 2015; 16:160. [PMID: 25971991 PMCID: PMC4431039 DOI: 10.1186/s12859-015-0581-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/22/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Founder populations have an important role in the study of genetic diseases. Access to detailed genealogical records is often one of their advantages. These genealogical data provide unique information for researchers in evolutionary and population genetics, demography and genetic epidemiology. However, analyzing large genealogical datasets requires specialized methods and software. The GENLIB software was developed to study the large genealogies of the French Canadian population of Quebec, Canada. These genealogies are accessible through the BALSAC database, which contains over 3 million records covering the whole province of Quebec over four centuries. Using this resource, extended pedigrees of up to 17 generations can be constructed from a sample of present-day individuals. RESULTS We have extended and implemented GENLIB as a package in the R environment for statistical computing and graphics, thus allowing optimal flexibility for users. The GENLIB package includes basic functions to manage genealogical data allowing, for example, extraction of a part of a genealogy or selection of specific individuals. There are also many functions providing information to describe the size and complexity of genealogies as well as functions to compute standard measures such as kinship, inbreeding and genetic contribution. GENLIB also includes functions for gene-dropping simulations. The goal of this paper is to present the full functionalities of GENLIB. We used a sample of 140 individuals from the province of Quebec (Canada) to demonstrate GENLIB's functions. Ascending genealogies for these individuals were reconstructed using BALSAC, yielding a large pedigree of 41,523 individuals. Using GENLIB's functions, we provide a detailed description of these genealogical data in terms of completeness, genetic contribution of founders, relatedness, inbreeding and the overall complexity of the genealogical tree. We also present gene-dropping simulations based on the whole genealogy to investigate identical-by-descent sharing of alleles and chromosomal segments of different lengths and estimate probabilities of identical-by-descent sharing. CONCLUSIONS The R package GENLIB provides a user friendly and flexible environment to analyze extensive genealogical data, allowing an efficient and easy integration of different types of data, analytical methods and additional developments and making this tool ideal for genealogical analysis.
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Affiliation(s)
- Héloïse Gauvin
- Département de médecine sociale et préventive, Université de Montréal, Montréal, Québec, Canada.
- Centre de recherche, Centre hospitalier universitaire Sainte-Justine, Montréal, Québec, Canada.
| | - Jean-François Lefebvre
- Centre de recherche, Centre hospitalier universitaire Sainte-Justine, Montréal, Québec, Canada.
| | - Claudia Moreau
- Centre de recherche, Centre hospitalier universitaire Sainte-Justine, Montréal, Québec, Canada.
| | - Eve-Marie Lavoie
- BALSAC Project, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada.
| | - Damian Labuda
- Centre de recherche, Centre hospitalier universitaire Sainte-Justine, Montréal, Québec, Canada.
- Département de pédiatrie, Université de Montréal, Montréal, Québec, Canada.
| | - Hélène Vézina
- BALSAC Project, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada.
| | - Marie-Hélène Roy-Gagnon
- Centre de recherche, Centre hospitalier universitaire Sainte-Justine, Montréal, Québec, Canada.
- School of Epidemiology, Public Health and Preventive Medicine, Faculty of Medicine, University of Ottawa, 600 Peter Morand Cres, Room 101E, Ottawa, ON, K1G 5Z3, Canada.
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11
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Lu W, Cheng YC, Chen K, Wang H, Gerhard GS, Still CD, Chu X, Yang R, Parihar A, O'Connell JR, Pollin TI, Angles-Cano E, Quon MJ, Mitchell BD, Shuldiner AR, Fu M. Evidence for several independent genetic variants affecting lipoprotein (a) cholesterol levels. Hum Mol Genet 2015; 24:2390-400. [PMID: 25575512 PMCID: PMC4380064 DOI: 10.1093/hmg/ddu731] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 12/05/2014] [Accepted: 12/22/2014] [Indexed: 01/06/2023] Open
Abstract
Lipoprotein (a) [Lp(a)] is an independent risk factor for atherosclerosis-related events that is under strong genetic control (heritability = 0.68-0.98). However, causal mutations and functional validation of biological pathways modulating Lp(a) metabolism are lacking. We performed a genome-wide association scan to identify genetic variants associated with Lp(a)-cholesterol levels in the Old Order Amish. We confirmed a previously known locus on chromosome 6q25-26 and found Lp(a) levels also to be significantly associated with a SNP near the APOA5-APOA4-APOC3-APOA1 gene cluster on chromosome 11q23 linked in the Amish to the APOC3 R19X null mutation. On 6q locus, we detected associations of Lp(a)-cholesterol with 118 common variants (P = 5 × 10(-8) to 3.91 × 10(-19)) spanning a ∼5.3 Mb region that included the LPA gene. To further elucidate variation within LPA, we sequenced LPA and identified two variants most strongly associated with Lp(a)-cholesterol, rs3798220 (P = 1.07 × 10(-14)) and rs10455872 (P = 1.85 × 10(-12)). We also measured copy numbers of kringle IV-2 (KIV-2) in LPA using qPCR. KIV-2 numbers were significantly associated with Lp(a)-cholesterol (P = 2.28 × 10(-9)). Conditional analyses revealed that rs3798220 and rs10455872 were associated with Lp(a)-cholesterol levels independent of each other and KIV-2 copy number. Furthermore, we determined for the first time that levels of LPA mRNA were higher in the carriers than non-carriers of rs10455872 (P = 0.0001) and were not different between carriers and non-carriers of rs3798220. Protein levels of apo(a) were higher in the carriers than non-carriers of both rs10455872 and rs3798220. In summary, we identified multiple independent genetic determinants for Lp(a)-cholesterol. These findings provide new insights into Lp(a) regulation.
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Affiliation(s)
- Wensheng Lu
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Department of Endocrinology, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, China
| | - Yu-Ching Cheng
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Veterans Affairs Maryland Health Care System, Baltimore, MD 21201, USA
| | - Keping Chen
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hong Wang
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Glenn S Gerhard
- Geisinger Obesity Institute, Geisinger Clinic, Danville, PA 17822, USA, Penn State Institute for Personalized Medicine, Penn State College of Medicine, Hershey, PA 17033, USA
| | | | - Xin Chu
- Geisinger Obesity Institute, Geisinger Clinic, Danville, PA 17822, USA
| | - Rongze Yang
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ankita Parihar
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jeffrey R O'Connell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Toni I Pollin
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Eduardo Angles-Cano
- Inserm U1140, Institut National de la Santé et de la Recherche Médicale, Paris, France and Faculty of Pharmaceutical and Biological Sciences, University Paris Descartes, Paris F-75006, France
| | - Michael J Quon
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alan R Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Veterans Affairs Maryland Health Care System, Baltimore, MD 21201, USA
| | - Mao Fu
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA,
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12
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David VA, Menotti-Raymond M, Wallace AC, Roelke M, Kehler J, Leighty R, Eizirik E, Hannah SS, Nelson G, Schäffer AA, Connelly CJ, O'Brien SJ, Ryugo DK. Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic cats. G3 (BETHESDA, MD.) 2014; 4:1881-91. [PMID: 25085922 PMCID: PMC4199695 DOI: 10.1534/g3.114.013425] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/26/2014] [Indexed: 01/06/2023]
Abstract
The Dominant White locus (W) in the domestic cat demonstrates pleiotropic effects exhibiting complete penetrance for absence of coat pigmentation and incomplete penetrance for deafness and iris hypopigmentation. We performed linkage analysis using a pedigree segregating White to identify KIT (Chr. B1) as the feline W locus. Segregation and sequence analysis of the KIT gene in two pedigrees (P1 and P2) revealed the remarkable retrotransposition and evolution of a feline endogenous retrovirus (FERV1) as responsible for two distinct phenotypes of the W locus, Dominant White, and white spotting. A full-length (7125 bp) FERV1 element is associated with white spotting, whereas a FERV1 long terminal repeat (LTR) is associated with all Dominant White individuals. For purposes of statistical analysis, the alternatives of wild-type sequence, FERV1 element, and LTR-only define a triallelic marker. Taking into account pedigree relationships, deafness is genetically linked and associated with this marker; estimated P values for association are in the range of 0.007 to 0.10. The retrotransposition interrupts a DNAase I hypersensitive site in KIT intron 1 that is highly conserved across mammals and was previously demonstrated to regulate temporal and tissue-specific expression of KIT in murine hematopoietic and melanocytic cells. A large-population genetic survey of cats (n = 270), representing 30 cat breeds, supports our findings and demonstrates statistical significance of the FERV1 LTR and full-length element with Dominant White/blue iris (P < 0.0001) and white spotting (P < 0.0001), respectively.
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Affiliation(s)
- Victor A David
- Laboratory of Genomic Diversity, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702
| | - Marilyn Menotti-Raymond
- Laboratory of Genomic Diversity, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702
| | - Andrea Coots Wallace
- Laboratory of Genomic Diversity, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702
| | - Melody Roelke
- Leidos Biomedical Research Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702 Labooratory Animal Sciences Program (LASP) Bethesda Leidos Biomedical Research, Bethesda, Maryland 20892-2471
| | - James Kehler
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20814
| | - Robert Leighty
- Data Management Services, Inc., National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Eduardo Eizirik
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90619-900, Brazil Instituto Pró-Carnívoros, Atibaia, Sao Paulo 12945-010, Brazil
| | | | - George Nelson
- BSP-CCR Genetics Core, Frederick National Laboratory, Frederick, Maryland 21702
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894
| | | | - Stephen J O'Brien
- Laboratory of Genomic Diversity, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - David K Ryugo
- Department of Otolaryngology, Head and Neck Surgery, Center for Hearing Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Garvan Institute of Medical Research, Sydney, New South Wales, Australia
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Abstract
This is a guide for fieldwork in Population Medical Genetics research projects. Data collection, handling, and analysis from large pedigrees require the use of specific tools and methods not widely familiar to human geneticists, unfortunately leading to ineffective graphic pedigrees. Initially, the objective of the pedigree must be decided, and the available information sources need to be identified and validated. Data collection and recording by the tabulated method is advocated, and the involved techniques are presented. Genealogical and personal information are the two main components of pedigree data. While the latter is unique to each investigation project, the former is solely represented by gametic links between persons. The triad of a given pedigree member and its two parents constitutes the building unit of a genealogy. Likewise, three ID numbers representing those three elements of the triad is the record field required for any pedigree analysis. Pedigree construction, as well as pedigree and population data analysis, varies according to the pre-established objectives, the existing information, and the available resources.
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Affiliation(s)
- Fernando A Poletta
- Estudio Colaborativo Latinoamericano de Malformaciones Congénitas, Instituto Nacional de Genética Médica Populacional, Rio de Janeiro, RJ, Brazil . ; Latin American Collaborative Study of Congenital Malformations, Center for Medical Education and Clinical Research, Buenos Aires, Argentina
| | - Ieda M Orioli
- Estudio Colaborativo Latinoamericano de Malformaciones Congénitas, Instituto Nacional de Genética Médica Populacional, Rio de Janeiro, RJ, Brazil . ; Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Eduardo E Castilla
- Estudio Colaborativo Latinoamericano de Malformaciones Congénitas, Instituto Nacional de Genética Médica Populacional, Rio de Janeiro, RJ, Brazil . ; Latin American Collaborative Study of Congenital Malformations, Center for Medical Education and Clinical Research, Buenos Aires, Argentina
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Genome-wide association studies identified novel loci for non-high-density lipoprotein cholesterol and its postprandial lipemic response. Hum Genet 2014; 133:919-30. [PMID: 24604477 DOI: 10.1007/s00439-014-1435-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/24/2014] [Indexed: 12/27/2022]
Abstract
Non-high-density lipoprotein cholesterol(NHDL) is an independent and superior predictor of CVD risk as compared to low-density lipoprotein alone. It represents a spectrum of atherogenic lipid fractions with possibly a distinct genomic signature. We performed genome-wide association studies (GWAS) to identify loci influencing baseline NHDL and its postprandial lipemic (PPL) response. We carried out GWAS in 4,241 participants of European descent. Our discovery cohort included 928 subjects from the Genetics of Lipid-Lowering Drugs and Diet Network Study. Our replication cohorts included 3,313 subjects from the Heredity and Phenotype Intervention Heart Study and Family Heart Study. A linear mixed model using the kinship matrix was used for association tests. The best association signal was found in a tri-genic region at RHOQ-PIGF-CRIPT for baseline NHDL (lead SNP rs6544903, discovery p = 7e-7, MAF = 2 %; validation p = 6e-4 at 0.1 kb upstream neighboring SNP rs3768725, and 5e-4 at 0.7 kb downstream neighboring SNP rs6733143, MAF = 10 %). The lead and neighboring SNPs were not perfect surrogate proxies to each other (D' = 1, r (2) = 0.003) but they seemed to be partially dependent (likelihood ration test p = 0.04). Other suggestive loci (discovery p < 1e-6) included LOC100419812 and LOC100288337 for baseline NHDL, and LOC100420502 and CDH13 for NHDL PPL response that were not replicated (p > 0.01). The current and first GWAS of NHDL yielded an interesting common variant in RHOQ-PIGF-CRIPT influencing baseline NHDL levels. Another common variant in CDH13 for NHDL response to dietary high-fat intake challenge was also suggested. Further validations for both loci from large independent studies, especially interventional studies, are warranted.
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Seifter A, Singh S, McArdle PF, Ryan KA, Shuldiner AR, Mitchell BD, Schäffer AA. Analysis of the bereavement effect after the death of a spouse in the Amish: a population-based retrospective cohort study. BMJ Open 2014; 4:e003670. [PMID: 24435888 PMCID: PMC3902313 DOI: 10.1136/bmjopen-2013-003670] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE This study investigates the association between bereavement and the mortality of a surviving spouse among Amish couples. We hypothesised that the bereavement effect would be relatively small in the Amish due to the unusually cohesive social structure of the Amish that might attenuate the loss of spousal support. DESIGN Population-based cohort study. SETTING The USA. PARTICIPANTS 10,892 Amish couples born during 1725-1900 located in Pennsylvania, Ohio and Indiana. All the participants are deceased. OUTCOME MEASURES The survival time is 'age'; event is 'death'. Hazard ratios (HRs) of widowed individuals with respect to gender, age at widowhood, remarriage, the number of surviving children and time since bereavement. RESULTS We observed HRs for widowhood ranging from 1.06 to 1.26 over the study period (nearly all differences significant at p<0.05). Mortality risks tended to be higher in men than in women and in younger compared with older bereaved spouses. There were significantly increased mortality risks in widows and widowers who did not remarry. We observed a higher number of surviving children to be associated with increased mortality in men and women. Mortality risk following bereavement was higher in the first 6 months among men and women. CONCLUSIONS We conclude that bereavement effects remain apparent even in this socially cohesive Amish community. Remarriage is associated with a significant decrease in the mortality risk among Amish individuals. Contrary to results from previous studies, an increase in the number of surviving children was associated with decreased survival rate.
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Affiliation(s)
- Ari Seifter
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sarabdeep Singh
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, DHHS, Bethesda, Maryland, USA
| | - Patrick F McArdle
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kathleen A Ryan
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Alan R Shuldiner
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, Maryland, USA
| | - Braxton D Mitchell
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, Maryland, USA
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, DHHS, Bethesda, Maryland, USA
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Polymorphisms in the SOCS7 gene and glucose homeostasis traits. BMC Res Notes 2013; 6:235. [PMID: 23767996 PMCID: PMC3686602 DOI: 10.1186/1756-0500-6-235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 06/07/2013] [Indexed: 11/15/2022] Open
Abstract
Background SOCS7 is a member of the suppressor of cytokine signaling family of proteins and is expressed in skeletal muscle and islets. SOCS7 deficient mice develop islet hyperplasia in the setting of increased insulin sensitivity and normal glucose tolerance. The objective of this study was to determine if variants in SOCS7 play a role in variation of glucose and insulin levels and the development of type 2 diabetes (T2DM). Results Five SOCS7 tagging SNPs were genotyped in diabetic and nondiabetic Old Order Amish. A case–control study was performed in T2DM (n = 145) and normal glucose tolerant (n = 358) subjects. Nominal associations were observed with T2DM and the minor alleles for rs8068600 (P = 0.01) and rs8074124 (P = 0.04); however, only rs8068600 remained significant after Bonferroni adjustment for multiple comparisons (P = 0.01). Among nondiabetic Amish (n = 765), no significant associations with glucose or insulin traits including fasting or 2 hour glucose and insulin from the oral glucose tolerance test, insulin or glucose area under the curve, Matsuda Index or HOMA-IR were found for any of the SNPs. Conclusion In conclusion, genetic variants in the SOCS7 gene do not impact variation in glucose homeostasis traits and only minimally impact risk of T2DM in the Old Order Amish. Our study was not able to address whether rare variants that potentially impact gene function might influence T2DM risk.
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The functional G143E variant of carboxylesterase 1 is associated with increased clopidogrel active metabolite levels and greater clopidogrel response. Pharmacogenet Genomics 2013; 23:1-8. [PMID: 23111421 DOI: 10.1097/fpc.0b013e32835aa8a2] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Carboxylesterase 1 (CES1) is the primary enzyme responsible for converting clopidogrel into biologically inactive carboxylic acid metabolites. METHODS We genotyped a functional variant in CES1, G143E, in participants of the Pharmacogenomics of Anti-Platelet Intervention (PAPI) study (n=566) and in 350 patients with coronary heart disease treated with clopidogrel, and carried out an association analysis of bioactive metabolite levels, on-clopidogrel ADP-stimulated platelet aggregation, and cardiovascular outcomes. RESULTS The levels of clopidogrel active metabolite were significantly greater in CES1 143E-allele carriers (P=0.001). Consistent with these findings, individuals who carried the CES1 143E-allele showed a better clopidogrel response as measured by ADP-stimulated platelet aggregation in both participants of the PAPI study (P=0.003) and clopidogrel-treated coronary heart disease patients (P=0.03). No association was found between this single nucleotide polymorphism and baseline measures of platelet aggregation in either cohort. CONCLUSION Taken together, these findings suggest, for the first time, that genetic variation in CES1 may be an important determinant of the efficacy of clopidogrel.
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Shah KP, Douglas JA. A method to prioritize quantitative traits and individuals for sequencing in family-based studies. PLoS One 2013; 8:e62545. [PMID: 23626830 PMCID: PMC3633859 DOI: 10.1371/journal.pone.0062545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 03/21/2013] [Indexed: 11/18/2022] Open
Abstract
Owing to recent advances in DNA sequencing, it is now technically feasible to evaluate the contribution of rare variation to complex traits and diseases. However, it is still cost prohibitive to sequence the whole genome (or exome) of all individuals in each study. For quantitative traits, one strategy to reduce cost is to sequence individuals in the tails of the trait distribution. However, the next challenge becomes how to prioritize traits and individuals for sequencing since individuals are often characterized for dozens of medically relevant traits. In this article, we describe a new method, the Rare Variant Kinship Test (RVKT), which leverages relationship information in family-based studies to identify quantitative traits that are likely influenced by rare variants. Conditional on nuclear families and extended pedigrees, we evaluate the power of the RVKT via simulation. Not unexpectedly, the power of our method depends strongly on effect size, and to a lesser extent, on the frequency of the rare variant and the number and type of relationships in the sample. As an illustration, we also apply our method to data from two genetic studies in the Old Order Amish, a founder population with extensive genealogical records. Remarkably, we implicate the presence of a rare variant that lowers fasting triglyceride levels in the Heredity and Phenotype Intervention (HAPI) Heart study (p = 0.044), consistent with the presence of a previously identified null mutation in the APOC3 gene that lowers fasting triglyceride levels in HAPI Heart study participants.
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Affiliation(s)
- Kaanan P. Shah
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Julie A. Douglas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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Lewis JP, Ryan K, O'Connell JR, Horenstein RB, Damcott CM, Gibson Q, Pollin TI, Mitchell BD, Beitelshees AL, Pakzy R, Tanner K, Parsa A, Tantry US, Bliden KP, Post WS, Faraday N, Herzog W, Gong Y, Pepine CJ, Johnson JA, Gurbel PA, Shuldiner AR. Genetic variation in PEAR1 is associated with platelet aggregation and cardiovascular outcomes. ACTA ACUST UNITED AC 2013; 6:184-92. [PMID: 23392654 DOI: 10.1161/circgenetics.111.964627] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND- Aspirin or dual antiplatelet therapy with aspirin and clopidogrel is a standard therapy for patients who are at increased risk for cardiovascular events. However, the genetic determinants of variable response to aspirin (alone and in combination with clopidogrel) are not known. METHODS AND RESULTS- We measured ex vivo platelet aggregation before and after dual antiplatelet therapy in individuals (n=565) from the Pharmacogenomics of Anti-Platelet Intervention (PAPI) Study and conducted a genome-wide association study of drug response. Significant findings were extended by examining genotype and cardiovascular outcomes in 2 independent aspirin-treated cohorts: 227 percutaneous coronary intervention patients and 1000 patients of the International Verapamil SR/Trandolapril Study (INVEST) Genetic Substudy (INVEST-GENES). Results from the genome-wide association study revealed a strong association between single-nucleotide polymorphisms on chromosome 1q23 and post-dual antiplatelet therapyplatelet aggregation. Further genotyping revealed rs12041331 in the platelet endothelial aggregation receptor-1 (PEAR1) gene to be most strongly associated with dual antiplatelet therapy response (P=7.66×10(-9)). In white and black patients undergoing percutaneous coronary intervention, A-allele carriers of rs12041331 were more likely to experience a cardiovascular event or death compared with GG homozygotes (hazard ratio, 2.62; 95% confidence interval, 0.96-7.10; P=0.059; and hazard ratio, 3.97; 95% confidence interval, 1.10-14.31; P=0.035, respectively). In aspirin-treated INVEST-GENES patients, rs12041331 A-allele carriers had significantly increased risk of myocardial infarction compared with GG homozygotes (odds ratio, 2.03; 95% confidence interval, 1.01-4.09; P=0.048). CONCLUSION- Common genetic variation in PEAR1 may be a determinant of platelet response and cardiovascular events in patients on aspirin alone or in combination with clopidogrel. Clinical Trial Registration- URL: http://www.clinicaltrials.gov. Unique identifiers: NCT00799396 and NCT00370045.
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Affiliation(s)
- Joshua P Lewis
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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20
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Mitchell BD, Lee WJ, Tolea MI, Shields K, Ashktorab Z, Magder LS, Ryan KA, Pollin TI, McArdle PF, Shuldiner AR, Schäffer AA. Living the good life? Mortality and hospital utilization patterns in the Old Order Amish. PLoS One 2012; 7:e51560. [PMID: 23284714 PMCID: PMC3526600 DOI: 10.1371/journal.pone.0051560] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 11/02/2012] [Indexed: 01/08/2023] Open
Abstract
Lifespan increases observed in the United States and elsewhere throughout the developed world, have been attributed in part to improvements in medical care access and technology and to healthier lifestyles. To differentiate the relative contributions of these two factors, we have compared lifespan in the Old Order Amish (OOA), a population with historically low use of medical care, with that of Caucasian participants from the Framingham Heart Study (FHS), focusing on individuals who have reached at least age 30 years. Analyses were based on 2,108 OOA individuals from the Lancaster County, PA community born between 1890 and 1921 and 5,079 FHS participants born approximately the same time. Vital status was ascertained on 96.9% of the OOA cohort through 2011 and through systematic follow-up of the FHS cohort. The lifespan part of the study included an enlargement of the Anabaptist Genealogy Database to 539,822 individuals, which will be of use in other studies of the Amish. Mortality comparisons revealed that OOA men experienced better longevity (p<0.001) and OOA women comparable longevity than their FHS counterparts. We further documented all OOA hospital discharges in Lancaster County, PA during 2002–2004 and compared OOA discharge rates to Caucasian national rates obtained from the National Hospital Discharge Survey for the same time period. Both OOA men and women experienced markedly lower rates of hospital discharges than their non-Amish counterparts, despite the increased lifespan. We speculate that lifestyle factors may predispose the OOA to greater longevity and perhaps to lesser hospital use. Identifying these factors, which might include behaviors such as lesser tobacco use, greater physical activity, and/or enhanced community assimilation, and assessing their transferability to non-Amish communities may produce significant gains to the public health.
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Affiliation(s)
- Braxton D Mitchell
- Department of Medicine, Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
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Voorrips RE, Bink MCAM, van de Weg WE. Pedimap: software for the visualization of genetic and phenotypic data in pedigrees. J Hered 2012; 103:903-7. [PMID: 23087384 PMCID: PMC3510005 DOI: 10.1093/jhered/ess060] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Pedimap is a user-friendly software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees. Genetic data can include marker scores, Identity-by-Descent probabilities, and marker linkage map positions, allowing the visualization of haplotypes through lineages. The pedigrees can accommodate all types of inheritance, including selfing, cloning, and repeated backcrossing, and all ploidy levels are supported. Visual association of the genetic data with phenotypic data simplifies the exploration of large data sets, thereby improving breeding decision making. Data are imported from text files; in addition data exchange with other software packages (FlexQTLTM and GenomeStudioTM) is possible. Instructions for use and an executable version compatible with the Windows platform are available for free from http://www.plantbreeding.wur.nl/UK/software_pedimap.html.
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Affiliation(s)
- Roeland E Voorrips
- Wageningen University & Research Centre, Plant Breeding, PO Box 16, 6700 AA Wageningen, The Netherlands.
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22
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Aschebrook-Kilfoy B, Heltshe SL, Nuckols JR, Sabra MM, Shuldiner AR, Mitchell BD, Airola M, Holford TR, Zhang Y, Ward MH. Modeled nitrate levels in well water supplies and prevalence of abnormal thyroid conditions among the Old Order Amish in Pennsylvania. Environ Health 2012; 11:6. [PMID: 22339761 PMCID: PMC3305600 DOI: 10.1186/1476-069x-11-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 02/17/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Nitrate is a widespread contaminant of drinking water supplies, especially in agricultural areas. Nitrate intake from drinking water and dietary sources can interfere with the uptake of iodide by the thyroid, thus potentially impacting thyroid function. METHODS We assessed the relation of estimated nitrate levels in well water supplies with thyroid health in a cohort of 2,543 Old Order Amish residing in Lancaster, Chester, and Lebanon counties in Pennsylvania for whom thyroid stimulating hormone (TSH) levels were measured during 1995-2008. Nitrate measurement data (1976-2006) for 3,613 wells in the study area were obtained from the U.S. Geological Survey and we used these data to estimate concentrations at study participants' residences using a standard linear mixed effects model that included hydrogeological covariates and kriging of the wells' residuals. Nitrate levels estimated by the model ranged from 0.35 mg/L to 16.4 mg/L N-NO3(-), with a median value of 6.5 mg/L, which was used as the cutpoint to define high and low nitrate exposure. In a validation analysis of the model, we calculated that the sensitivity of the model was 67% and the specificity was 93%. TSH levels were used to define the following outcomes: clinical hyperthyroidism (n = 10), clinical hypothyroidism (n = 56), subclinical hyperthyroidism (n = 25), and subclinical hypothyroidism (n = 228). RESULTS In women, high nitrate exposure was significantly associated with subclinical hypothyroidism (OR = 1.60; 95% CI: 1.11-2.32). Nitrate was not associated with subclinical thyroid disease in men or with clinical thyroid disease in men or women. CONCLUSIONS Although these data do not provide strong support for an association between nitrate in drinking water and thyroid health, our results do suggest that further exploration of this hypothesis is warranted using studies that incorporate individual measures of both dietary and drinking water nitrate intake.
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Affiliation(s)
- Briseis Aschebrook-Kilfoy
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
- Yale School of Public Health, Yale University, New Haven, Connecticut, USA
- Department of Health Studies, University of Chicago, Chicago, IL, USA
| | - Sonya L Heltshe
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
| | - John R Nuckols
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Mona M Sabra
- Endocrine Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Alan R Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, MD, USA
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Theodore R Holford
- Yale School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Yawei Zhang
- Yale School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Mary H Ward
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
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Liu J, Hoppman N, O'Connell JR, Wang H, Streeten EA, McLenithan JC, Mitchell BD, Shuldiner AR. A functional haplotype in EIF2AK3, an ER stress sensor, is associated with lower bone mineral density. J Bone Miner Res 2012; 27:331-41. [PMID: 22028037 PMCID: PMC3319695 DOI: 10.1002/jbmr.549] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
EIF2AK3 is a type I transmembrane protein that functions as an endoplasmic reticulum (ER) stress sensor to regulate global protein synthesis. Rare mutations in EIF2AK3 cause Wolcott-Rallison syndrome (OMIM 226980), an autosomal recessive disorder characterized by diabetes, epiphyseal dysplasia, osteoporosis, and growth retardation. To investigate the role of common genetic variation in EIF2AK3 as a determinant of bone mineral density (BMD) and osteoporosis, we sequenced all exons and flanking regions, then genotyped six potentially functional single nucleotide polymorphisms (SNPs) in this gene in 997 Amish subjects for association analysis, and attempted replication in 887 Mexican Americans. We found that the minor allele of a nonsynonymous SNP rs13045 had borderline associations with decreased forearm BMD in both discovery and replication cohorts (unadjusted p = 0.036 and β = -0.007 for the Amish; unadjusted p = 0.031 and β = -0.008 for Mexican Americans). A meta-analysis indicated this association achieved statistical significance in the combined sample (unadjusted p = 0.003; Bonferroni corrected p = 0.009). Rs13045 and three other potentially functional SNPs, a promoter SNP (rs6547787) and two nonsynonymous SNPs (rs867529 and rs1805165), formed two haplotypes: a low-BMD associated haplotype, denoted haplotype B [minor allele frequency (MAF) = 0.311] and a common haplotype A (MAF = 0.676). There were no differences in mRNA expression in lymphoblastoid cell lines between the two haplotypes. However, after treating lymphoblastoid cell lines with thapsigargin to induce ER stress, cell lines with haplotype B showed increased sensitivity to ER stress (p = 0.014) compared with cell lines with haplotype A. Taken together, our results suggest that common nonsynonymous sequence variants in EIF2AK3 have a modest effect on ER stress response and may contribute to the risk for low BMD through this mechanism.
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Affiliation(s)
- Jie Liu
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nicole Hoppman
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jeffrey R O'Connell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hong Wang
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Elizabeth A Streeten
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - John C McLenithan
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alan R Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Geriatric Research Education and Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
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Computer-based genealogy reconstruction in founder populations. J Biomed Inform 2011; 44:997-1003. [PMID: 21884821 DOI: 10.1016/j.jbi.2011.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 06/21/2011] [Accepted: 08/04/2011] [Indexed: 11/22/2022]
Abstract
This paper describes a software tool that reconstructs entire genealogies from data collected from different and heterogeneous sources, including municipal and parish records archived over centuries. The tool exploits a record linkage algorithm relying on a rule-based data matching approach. It applies a general strategy for managing the ambiguities due to missing, imprecise or erroneous input data. The process follows an iterative approach that combines automatic pedigree reconstruction with software-empowered human data revision to improve the quality and the accuracy of the results and to optimize the matching rules. The paper discusses the results obtained by reconstructing the entire genealogy of the population of the Val Borbera, a geographically isolated valley in Northern Italy. The genealogy could be reconstructed from data going back as far as the XVI century. The resulting pedigree includes 75,994 trios, 58.9% of which belonging to a unique big family, reconstructed over 13 generations.
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Njajou OT, Blackburn EH, Pawlikowska L, Mangino M, Damcott CM, Kwok PY, Spector TD, Newman AB, Harris TB, Cummings SR, Cawthon RM, Shuldiner AR, Valdes AM, Hsueh WC. A common variant in the telomerase RNA component is associated with short telomere length. PLoS One 2010; 5:e13048. [PMID: 20885959 PMCID: PMC2946401 DOI: 10.1371/journal.pone.0013048] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 08/04/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Telomeres shorten as cells divide. This shortening is compensated by the enzyme telomerase. We evaluated the effect of common variants in the telomerase RNA component (TERC) gene on telomere length (TL) in the population-based Health Aging and Body Composition (Health ABC) Study and in two replication samples (the TwinsUK Study and the Amish Family Osteoporosis Study, AFOS). METHODOLOGY Five variants were identified in the TERC region by sequence analysis and only one SNP was common (rs2293607, G/A). The frequency of the G allele was 0.26 and 0.07 in white and black, respectively. Testing for association between TL and rs2293607 was performed using linear regression models or variance component analysis conditioning on relatedness among subjects. RESULTS The adjusted mean TL was significantly shorter in 665 white carriers of the G allele compared to 887 non-carriers from the Health ABC Study (4.69±0.05 kbp vs. 4.86±0.04 kbp, measured by quantitative PCR, p = 0.005). This association was replicated in another white sample from the TwinsUK Study (6.90±0.03 kbp in 301 carriers compared to 7.06±0.03 kbp in 395 non-carriers, measured by Southern blots, p = 0.009). A similar pattern of association was observed in whites from the family-based AFOS and blacks from the Health ABC cohort, although not statistically significant, possibly due to the lower allele frequency in these populations. Combined analysis using 2,953 white subjects from 3 studies showed a significant association between TL and rs2293607 (β = -0.19±0.04 kbp, p = 0.001). CONCLUSION Our study shows a significant association between a common variant in TERC and TL in humans, suggesting that TERC may play a role in telomere homeostasis.
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Affiliation(s)
- Omer T. Njajou
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Elizabeth H. Blackburn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Ludmila Pawlikowska
- Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
| | - Massimo Mangino
- Twin Research and Genetic Epidemiology Unit, King's College London, St Thomas Hospital, London, United Kingdom
| | - Coleen M. Damcott
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Timothy D. Spector
- Twin Research and Genetic Epidemiology Unit, King's College London, St Thomas Hospital, London, United Kingdom
| | - Anne B. Newman
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Bethesda, Maryland, United States of America
| | - Steven R. Cummings
- Research Institute, California Pacific Medical Center, San Francisco, California, United States of America
| | - Richard M. Cawthon
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Alan R. Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Ana M. Valdes
- Twin Research and Genetic Epidemiology Unit, King's College London, St Thomas Hospital, London, United Kingdom
| | - Wen-Chi Hsueh
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Aguirre-Hernández J, Polton G, Kennedy LJ, Sargan DR. Association between anal sac gland carcinoma and dog leukocyte antigen-DQB1 in the English Cocker Spaniel. ACTA ACUST UNITED AC 2010; 76:476-81. [PMID: 20727114 DOI: 10.1111/j.1399-0039.2010.01554.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Anal sac gland carcinomas occur frequently in English Cocker Spaniels and, to a lesser extent, in other spaniel breeds. The disease typically presents in dogs aged 8 years or older and frequently metastasises to the local lymph nodes. The association between anal sac gland carcinoma in English Cocker Spaniels and the major histocompatibility complex class II loci (the dog leukocyte antigen loci DLA-DRB1, -DQA1, -DQB1) was investigated in 42 cases and 75 controls. Based on a corrected error rate of 0.017 for each test, the allele distribution in DLA-DRB1 showed no significant difference between cases and controls (P value = 0.019), while a significant difference was obtained for DLA-DQA1 and -DQB1 alleles (P values are 0.010 and 3.3 × 10⁻⁵). The DLA-DQB1*00701 allele was the most common in both cases and controls, but it had a higher frequency among the former (0.89) than in the latter (0.61), while the second most common allele had a higher frequency in the controls (0.23) than in the cases (0.07). Haplotype distributions were also significantly different between the two groups (P value = 1.61 × 10⁻⁴). This is the second disease in English Cocker Spaniels for which the most common DLA-DQB1 allele in the breed has been shown to have a higher frequency in cases than controls, while the second most common allele in the breed (*02001) has a significantly higher frequency in the controls, compared with the cases.
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Affiliation(s)
- J Aguirre-Hernández
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK.
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27
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Cheng YC, Kao WHL, Mitchell BD, Sharrett AR, Ryan KA, Vogel RA, Shuldiner AR, Pollin TI. Genetic effects on postprandial variations of inflammatory markers in healthy individuals. Obesity (Silver Spring) 2010; 18:1417-22. [PMID: 19910936 PMCID: PMC3066005 DOI: 10.1038/oby.2009.416] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Circulating levels of inflammatory markers predict the risk of cardiovascular disease (CVD), mediated perhaps in part by dietary fat intake, through mechanisms only partially understood. To evaluate post-fat load changes in inflammatory markers and genetic influences on these changes, we administered a standardized high-fat meal to 838 related Amish subjects as part of the Heredity and Phenotype Intervention (HAPI) Heart Study and measured a panel of inflammatory markers, including C-reactive protein (CRP), interleukin-1beta (IL-1beta), matrix metalloproteinase-1 and -9 (MMP-1 and MMP-9), and white blood cell (WBC) count, before and 4 h after fat challenge (CRP prechallenge only). Heritabilities (h(2) +/- s.d.) of basal inflammatory levels ranged from 16 +/- 8% for MMP-9 (P = 0.02) to 90 +/- 7% for MMP-1 (P < 0.0001). Post-fat load, circulating levels of WBC, MMP-1, and MMP-9 increased by 16, 32, and 43% (all P < 0.0001), with no significant changes in IL-1beta. Postprandial changes over the 4-h period were modestly heritable for WBC (age- and sex-adjusted h(2) = 14 +/- 9%, P = 0.04), but the larger MMP-1 and MMP-9 changes appeared to be independent of additive genetic effects. These results reveal that a high-fat meal induces a considerable inflammatory response. Genetic factors appear to play a significant role influencing basal inflammatory levels but to have minimal influence on post-fat intake inflammatory changes.
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Affiliation(s)
- Yu-Ching Cheng
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, USA.
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Lee WJ, Pollin TI, O'Connell JR, Agarwala R, Schäffer AA. PedHunter 2.0 and its usage to characterize the founder structure of the Old Order Amish of Lancaster County. BMC MEDICAL GENETICS 2010; 11:68. [PMID: 20433770 PMCID: PMC2880975 DOI: 10.1186/1471-2350-11-68] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 05/02/2010] [Indexed: 01/11/2023]
Abstract
BACKGROUND Because they are a closed founder population, the Old Order Amish (OOA) of Lancaster County have been the subject of many medical genetics studies. We constructed four versions of Anabaptist Genealogy Database (AGDB) using three sources of genealogies and multiple updates. In addition, we developed PedHunter, a suite of query software that can solve pedigree-related problems automatically and systematically. METHODS We report on how we have used new features in PedHunter to quantify the number and expected genetic contribution of founders to the OOA. The queries and utility of PedHunter programs are illustrated by examples using AGDB in this paper. For example, we calculated the number of founders expected to be contributing genetic material to the present-day living OOA and estimated the mean relative founder representation for each founder. New features in PedHunter also include pedigree trimming and pedigree renumbering, which should prove useful for studying large pedigrees. RESULTS With PedHunter version 2.0 querying AGDB version 4.0, we identified 34,160 presumed living OOA individuals and connected them into a 14-generation pedigree descending from 554 founders (332 females and 222 males) after trimming. From the analysis of cumulative mean relative founder representation, 128 founders (78 females and 50 males) accounted for over 95% of the mean relative founder contribution among living OOA descendants. DISCUSSION/CONCLUSIONS The OOA are a closed founder population in which a modest number of founders account for the genetic variation present in the current OOA population. Improvements to the PedHunter software will be useful in future studies of both the OOA and other populations with large and computerized genealogies.
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Affiliation(s)
- Woei-Jyh Lee
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
| | - Toni I Pollin
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, 660 W. Redwood Street, Baltimore, Maryland 21201, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, 660 W. Redwood Street, Baltimore, Maryland 21201, USA
- Animal Improvement Programs Laboratory, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA
| | - Richa Agarwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
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Abstract
Osteogenesis imperfecta (OI) is a heritable form of bone fragility typically associated with a dominant COL1A1 or COL1A2 mutation. Variable phenotype for OI patients with identical collagen mutations is well established, but phenotype variability is described using the qualitative Sillence classification. Patterning a new OI mouse model on a specific collagen mutation therefore has been hindered by the absence of an appropriate kindred with extensive quantitative phenotype data. We benefited from the large sibships of the Old Order Amish (OOA) to define a wide range of OI phenotypes in 64 individuals with the identical COL1A2 mutation. Stratification of carrier spine (L1-4) areal bone mineral density (aBMD) Z-scores demonstrated that 73% had moderate to severe disease (less than -2), 23% had mild disease (-1 to -2), and 4% were in the unaffected range (greater than -1). A line of knock-in mice was patterned on the OOA mutation. Bone phenotype was evaluated in four F(1) lines of knock-in mice that each shared approximately 50% of their genetic background. Consistent with the human pedigree, these mice had reduced body mass, aBMD, and bone strength. Whole-bone fracture susceptibility was influenced by individual genomic factors that were reflected in size, shape, and possibly bone metabolic regulation. The results indicate that the G610C OI (Amish) knock-in mouse is a novel translational model to identify modifying genes that influence phenotype and for testing potential therapies for OI.
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30
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Aguirre-Hernández J, Sargan DR. Multifocal retinal dysplasia in the German Spitz (Klein and Mittel) is not caused by mutations in BEST1. Anim Genet 2009; 41:333-4. [PMID: 19968643 DOI: 10.1111/j.1365-2052.2009.02005.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J Aguirre-Hernández
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
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Nuzzo A, Riva A, Bellazzi R. Phenotypic and genotypic data integration and exploration through a web-service architecture. BMC Bioinformatics 2009; 10 Suppl 12:S5. [PMID: 19828081 PMCID: PMC2762070 DOI: 10.1186/1471-2105-10-s12-s5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Linking genotypic and phenotypic information is one of the greatest challenges of current genetics research. The definition of an Information Technology infrastructure to support this kind of studies, and in particular studies aimed at the analysis of complex traits, which require the definition of multifaceted phenotypes and the integration genotypic information to discover the most prevalent diseases, is a paradigmatic goal of Biomedical Informatics. This paper describes the use of Information Technology methods and tools to develop a system for the management, inspection and integration of phenotypic and genotypic data. Results We present the design and architecture of the Phenotype Miner, a software system able to flexibly manage phenotypic information, and its extended functionalities to retrieve genotype information from external repositories and to relate it to phenotypic data. For this purpose we developed a module to allow customized data upload by the user and a SOAP-based communications layer to retrieve data from existing biomedical knowledge management tools. In this paper we also demonstrate the system functionality by an example application of the system in which we analyze two related genomic datasets. Conclusion In this paper we show how a comprehensive, integrated and automated workbench for genotype and phenotype integration can facilitate and improve the hypothesis generation process underlying modern genetic studies.
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Affiliation(s)
- Angelo Nuzzo
- Department of Computer Engineering and Systems Science, University of Pavia, Via Ferrata 1, Pavia, Italy.
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Elliott B, Cheng E, Mayes S, Ozsoyoglu ZM. Efficiently calculating inbreeding on large pedigrees databases. INFORM SYST 2009. [DOI: 10.1016/j.is.2009.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Shuldiner AR, O'Connell JR, Bliden KP, Gandhi A, Ryan K, Horenstein RB, Damcott CM, Pakyz R, Tantry US, Gibson Q, Pollin TI, Post W, Parsa A, Mitchell BD, Faraday N, Herzog W, Gurbel PA. Association of cytochrome P450 2C19 genotype with the antiplatelet effect and clinical efficacy of clopidogrel therapy. JAMA 2009; 302:849-57. [PMID: 19706858 PMCID: PMC3641569 DOI: 10.1001/jama.2009.1232] [Citation(s) in RCA: 1092] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
CONTEXT Clopidogrel therapy improves cardiovascular outcomes in patients with acute coronary syndromes and following percutaneous coronary intervention by inhibiting adenosine diphosphate (ADP)-dependent platelet activation. However, nonresponsiveness is widely recognized and is related to recurrent ischemic events. OBJECTIVE To identify gene variants that influence clopidogrel response. DESIGN, SETTING, AND PARTICIPANTS In the Pharmacogenomics of Antiplatelet Intervention (PAPI) Study (2006-2008), we administered clopidogrel for 7 days to 429 healthy Amish persons and measured response by ex vivo platelet aggregometry. A genome-wide association study was performed followed by genotyping the loss-of-function cytochrome P450 (CYP) 2C19*2 variant (rs4244285). Findings in the PAPI Study were extended by examining the relation of CYP2C19*2 genotype to platelet function and cardiovascular outcomes in an independent sample of 227 patients undergoing percutaneous coronary intervention. MAIN OUTCOME MEASURE ADP-stimulated platelet aggregation in response to clopidogrel treatment and cardiovascular events. RESULTS Platelet response to clopidogrel was highly heritable (h(2) = 0.73; P < .001). Thirteen single-nucleotide polymorphisms on chromosome 10q24 within the CYP2C18-CYP2C19-CYP2C9-CYP2C8 cluster were associated with diminished clopidogrel response, with a high degree of statistical significance (P = 1.5 x 10(-13) for rs12777823, additive model). The rs12777823 polymorphism was in strong linkage disequilibrium with the CYP2C19*2 variant, and was associated with diminished clopidogrel response, accounting for 12% of the variation in platelet aggregation to ADP (P = 4.3 x 10(-11)). The relation between CYP2C19*2 genotype and platelet aggregation was replicated in clopidogrel-treated patients undergoing coronary intervention (P = .02). Furthermore, patients with the CYP2C19*2 variant were more likely (20.9% vs 10.0%) to have a cardiovascular ischemic event or death during 1 year of follow-up (hazard ratio, 2.42; 95% confidence interval, 1.18-4.99; P = .02). CONCLUSION CYP2C19*2 genotype was associated with diminished platelet response to clopidogrel treatment and poorer cardiovascular outcomes.
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Affiliation(s)
- Alan R Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, 660 W Redwood St, Room 494, Baltimore, MD 21201, USA.
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Racette BA, Good LM, Kissel AM, Criswell SR, Perlmutter JS. A population-based study of parkinsonism in an Amish community. Neuroepidemiology 2009; 33:225-30. [PMID: 19641327 DOI: 10.1159/000229776] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Accepted: 03/12/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a neurodegenerative disorder with unknown cause. Genetic mutations account for a minority of cases but the role of environmental factors is unclear. METHODS We performed a population-based screening for PD in subjects in an Amish community over age 60. PD was diagnosed using standard clinical criteria and the Unified Parkinson Disease Rating Scale motor subsection 3 (UPDRS3). Community prevalence was calculated. We constructed a community pedigree and calculated kinship coefficients, a measure of relatedness between 2 subjects, for every pair of subjects in diagnostic categories: clinically definite PD, UPDRS3 score >9, Mini-Mental State Exam (MMSE) score <25, and normal. RESULTS Of 262 eligible subjects, 213 agreed to participate, 15 had PD, 43 had MMSE <25, 73 had UPDRS3 >9. The prevalence of PD was 5,703/100,000 with increasing prevalence in every decade of age. Excluding first-degree relatives, normal subjects were more related to each other (0.0102, SD = 0.0266) than subjects with clinically definite PD (0.0054, SD = 0.0100; p = 0.00003), subjects with UPDRS >9 (0.0076, SD = 0.0155; p = 0.00001), and subjects with MMSE <25 (0.0090, SD = 0.0180; p = 0.00003). CONCLUSIONS PD and parkinsonian signs are common in this population and the prevalence increases with age. The finding that subjects with PD were not more related than normal subjects suggests that environmental factors may contribute to the parkinsonian phenotype in this community.
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Affiliation(s)
- Brad A Racette
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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The immunoglobulin gene repertoire of low-count chronic lymphocytic leukemia (CLL)-like monoclonal B lymphocytosis is different from CLL: diagnostic implications for clinical monitoring. Blood 2008; 114:26-32. [PMID: 19029437 DOI: 10.1182/blood-2008-09-176933] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the revised National Cancer Institute Working Group (NCI-WG)/International Workshop on Chronic Lymphocytic Leukemia (IWCLL) guidelines for CLL, CLL-like monoclonal B lymphocytosis (MBL) is defined as the presence of less than 5 x 10(9)/L B lymphocytes in the peripheral blood. However, the concentration of MBL in the blood is extremely variable. MBL in subjects with lymphocytosis require treatment at a rate of 1.1% per year and present immunoglobulin (IG) gene features and similar to good prognosis CLL. Little is known about low-count MBL cases, accidentally found in the general population. We analyzed IGHV-D-J rearrangements in 51 CLL-like MBL cases from healthy individuals, characterized by few clonal B cells. Seventy percent of the IGHV genes were mutated. The most frequent IGHV gene was IGHV4-59/61, rarely used in CLL, whereas the IGHV1-69 gene was lacking and the IGHV4-34 gene was infrequent. Only 2 of 51 (3.9%) MBL cases expressed a CLL-specific stereotyped HCDR3. Therefore, the IG gene repertoire in low-count MBL differs from both mutated and unmutated CLL, suggesting that the detection of MBL in an otherwise healthy subject is not always equivalent to a preleukemic state. Detailed IG analysis of individual MBL may help to identify cases that necessitate continuous clinical monitoring to anticipate disease progression.
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Pinto JM, Hayes MG, Schneider D, Naclerio RM, Ober C. A genomewide screen for chronic rhinosinusitis genes identifies a locus on chromosome 7q. Laryngoscope 2008; 118:2067-72. [PMID: 18622306 DOI: 10.1097/mlg.0b013e3181805147] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE/HYPOTHESIS Chronic rhinosinusitis (CRS) is an important public health problem with substantial impact on patient quality of life and health care costs. We hypothesized that genetic variation may be one factor that affects this disease. STUDY DESIGN Identification of genetic variation underlying susceptibility to CRS using linkage analysis in a founder population. METHODS We studied a religious isolate that practices a communal lifestyle and shares common environmental exposures. Using physical examination, medical interviews, and a review of medical records, we identified eight individuals with CRS of 291 screened. These eight individuals were related to each other in a single 60 member, nine generation pedigree. A genome-wide screen for loci influencing susceptibility to CRS using 1123 genome-wide markers was conducted. RESULTS The largest linkage peak (P = .0023; 127.15 cM, equivalent to limit of detection = 2.01) was on chromosome 7q31.1-7q32.1, 7q31 (127.15 cM; 1-limit of detection support region: 115-135 cM) and included the CFTR locus. Genotyping of 38 mutations in the CFTR gene did not reveal variation accounting for this linkage signal. CONCLUSIONS Understanding the genes involved in CRS may lead to improvements in its diagnosis and treatment. Our results represent the first genome-wide screen for CRS and suggest that a locus on 7q31.1-7q32.1 influences disease susceptibility. This may be the CFTR gene or another nearby locus.
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Affiliation(s)
- Jayant M Pinto
- Section of Otolaryngology-Head and Neck Surgery, Department of Surgery, The University of Chicago, Chicago, Illinois 60637, USA.
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Abstract
Dogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breed-specific selective breeding patterns. To address the lack of such studies we have exploited one of the world's most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, >90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index Psi for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare.
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Mitchell BD, McArdle PF, Shen H, Rampersaud E, Pollin TI, Bielak LF, Jaquish C, Douglas JA, Roy-Gagnon MH, Sack P, Naglieri R, Hines S, Horenstein RB, Chang YPC, Post W, Ryan KA, Brereton NH, Pakyz RE, Sorkin J, Damcott CM, O'Connell JR, Mangano C, Corretti M, Vogel R, Herzog W, Weir MR, Peyser PA, Shuldiner AR. The genetic response to short-term interventions affecting cardiovascular function: rationale and design of the Heredity and Phenotype Intervention (HAPI) Heart Study. Am Heart J 2008; 155:823-8. [PMID: 18440328 PMCID: PMC2443415 DOI: 10.1016/j.ahj.2008.01.019] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 01/08/2008] [Indexed: 11/17/2022]
Abstract
BACKGROUND The etiology of cardiovascular disease (CVD) is multifactorial. Efforts to identify genes influencing CVD risk have met with limited success to date, likely because of the small effect sizes of common CVD risk alleles and the presence of gene by gene and gene by environment interactions. METHODS The HAPI Heart Study was initiated in 2002 to measure the cardiovascular response to 4 short-term interventions affecting cardiovascular risk factors and to identify the genetic and environmental determinants of these responses. The measurements included blood pressure responses to the cold pressor stress test and to a high salt diet, triglyceride excursion in response to a high-fat challenge, and response in platelet aggregation to aspirin therapy. RESULTS The interventions were carried out in 868 relatively healthy Amish adults from large families. The heritabilities of selected response traits for each intervention ranged from 8% to 38%, suggesting that some of the variation associated with response to each intervention can be attributed to the additive effects of genes. CONCLUSIONS Identifying these response genes may identify new mechanisms influencing CVD and may lead to individualized preventive strategies and improved early detection of high-risk individuals.
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Affiliation(s)
- Braxton D Mitchell
- Division of Endocrinology, Department of Medicine, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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Douglas JA, Sandefur CI. PedMine--a simulated annealing algorithm to identify maximally unrelated individuals in population isolates. Bioinformatics 2008; 24:1106-8. [PMID: 18321883 DOI: 10.1093/bioinformatics/btn087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED In family-based genetic studies, it is often useful to identify a subset of unrelated individuals. When such studies are conducted in population isolates, however, most if not all individuals are often detectably related to each other. To identify a set of maximally unrelated (or equivalently, minimally related) individuals, we have implemented simulated annealing, a general-purpose algorithm for solving difficult combinatorial optimization problems. We illustrate our method on data from a genetic study in the Old Order Amish of Lancaster County, Pennsylvania, a population isolate derived from a modest number of founders. Given one or more pedigrees, our program automatically and rapidly extracts a fixed number of maximally unrelated individuals. AVAILABILITY http://www.hg.med.umich.edu/labs/douglaslab/software.html (version 1.0.0).
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Affiliation(s)
- Julie A Douglas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
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Liu F, Kirichenko A, Axenovich TI, van Duijn CM, Aulchenko YS. An approach for cutting large and complex pedigrees for linkage analysis. Eur J Hum Genet 2008; 16:854-60. [PMID: 18301450 DOI: 10.1038/ejhg.2008.24] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Utilizing large pedigrees in linkage analysis is a computationally challenging task. The pedigree size limits applicability of the Lander-Green-Kruglyak algorithm for linkage analysis. A common solution is to split large pedigrees into smaller computable subunits. We present a pedigree-splitting method that, within a user supplied bit-size limit, identifies subpedigrees having the maximal number of subjects of interest (eg patients) who share a common ancestor. We compare our method with the maximum clique partitioning method using a large and complex human pedigree consisting of 50 patients with Alzheimer's disease ascertained from genetically isolated Dutch population. We show that under a bit-size limit our method can assign more patients to subpedigrees than the clique partitioning method, particularly when splitting deep pedigrees where the subjects of interest are scattered in recent generations and are relatively distantly related via multiple genealogic connections. Our pedigree-splitting algorithm and associated software can facilitate genome-wide linkage scans searching for rare mutations in large pedigrees coming from genetically isolated populations. The software package PedCut implementing our approach is available at http://mga.bionet.nsc.ru/soft/index.html.
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Affiliation(s)
- Fan Liu
- Department of Epidemiology & Biostatistics, Erasmus MC, Rotterdam, The Netherlands
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Pinto JM, Thanaviratananich S, Hayes MG, Naclerio RM, Ober C. A Genome-Wide Screen for Hyposmia Susceptibility Loci. Chem Senses 2008; 33:319-29. [DOI: 10.1093/chemse/bjm092] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Saunders-Pullman R, Raymond D, Senthil G, Kramer P, Ohmann E, Deligtisch A, Shanker V, Greene P, Tabamo R, Huang N, Tagliati M, Kavanagh P, Soto-Valencia J, Aguiar PDC, Risch N, Ozelius L, Bressman S. Narrowing the DYT6 dystonia region and evidence for locus heterogeneity in the Amish-Mennonites. Am J Med Genet A 2007; 143A:2098-105. [PMID: 17702011 DOI: 10.1002/ajmg.a.31887] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The DYT6 gene for primary torsion dystonia (PTD) was mapped to chromosome 8p21-q22 in two Amish-Mennonite families who shared a haplotype of marker alleles across a 40 cM linked region. The objective of this study was to narrow the DYT6 region, clinically characterize DYT6 dystonia in a larger cohort, and to determine whether DYT6 is associated with dystonia in newly ascertained multiplex families. We systematically examined familial Amish-Mennonite dystonia cases, identifying five additional members from the original families, as well as three other multiplex Amish-Mennonite families, and evaluated the known DYT6 haplotype and recombination events. One of the three new families carried the shared haplotype, whereas the region was excluded in the two other families, suggesting genetic heterogeneity for PTD in the Amish-Mennonites. Clinical features in the five newly identified DYT6 carriers were similar to those initially described. In contrast, affected individuals from the excluded families had a later age of onset (46.9 years vs. 16.1 years in the DYT6), and the dystonia was both more likely to be of focal distribution and begin in the cervical muscles. Typing of additional markers in the DYT6-linked families revealed recombinations that now place the gene in a 23 cM region surrounding the centromere. In summary, the DYT6 gene is in a 23 cM region on chromosome 8q21-22 and does not account for all familial PTD in Amish-Mennonites.
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Pollin TI, McBride DJ, Agarwala R, Schäffer AA, Shuldiner AR, Mitchell BD, O'Connell JR. Investigations of the Y chromosome, male founder structure and YSTR mutation rates in the Old Order Amish. Hum Hered 2007; 65:91-104. [PMID: 17898540 PMCID: PMC2857628 DOI: 10.1159/000108941] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2007] [Accepted: 06/06/2007] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Using Y chromosome short tandem repeat (YSTR) genotypes, (1) evaluate the accuracy and completeness of the Lancaster County Old Order Amish (OOA) genealogical records and (2) estimate YSTR mutation rates. METHODS Nine YSTR markers were genotyped in 739 Old Order Amish males who participated in several ongoing genetic studies of complex traits and could be connected into one of 28 all-male lineage pedigrees constructed using the Anabaptist Genealogy Database and the query software Ped-Hunter. A putative founder YSTR haplotype was constructed for each pedigree, and observed and inferred father-son transmissions were used to estimate YSTR mutation rates. RESULTS We inferred 27 distinct founder Y chromosome haplotypes in the 28 male lineages, which encompassed 27 surnames accounting for 98% of Lancaster OOA households. Nearly all deviations from founder haplotypes were consistent with mutation events rather than errors. The estimated marker-specific mutation rates ranged from 0 to 1.09% (average 0.33% using up to 283 observed meioses only and 0.28% using up to 1,232 observed and inferred meioses combined). CONCLUSIONS These data confirm the accuracy and completeness of the male lineage portion of the Anabaptist Genealogy Database and contribute mutation rate estimates for several commonly used Y chromosome STR markers.
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Affiliation(s)
- Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
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Aguirre-Hernández J, Wickström K, Sargan DR. The Finnish lapphund retinal atrophy locus maps to the centromeric region of CFA9. BMC Vet Res 2007; 3:14. [PMID: 17623091 PMCID: PMC1933534 DOI: 10.1186/1746-6148-3-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Accepted: 07/10/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dogs have the second largest number of genetic diseases, after humans. Among the diseases present in dogs, progressive retinal atrophy has been reported in more than a hundred breeds. In some of them, the mutation has been identified and genetic tests have allowed the identification of carriers, thus enabling a drastic reduction in the incidence of the disease. The Finnish lapphund is a dog breed presenting late-onset progressive retinal atrophy for which the disease locus remains unknown. RESULTS In this study we mapped the progressive retinal atrophy locus in the Finnish lapphund using a DNA pooling approach, assuming that all affected dogs within the breed share the same identical-by descent-mutation as the cause of the disease (genetic homogeneity). Autosomal recessive inheritance was also assumed, after ruling out, from pedigree analysis, dominant and X-linked inheritance. DNA from 12 Finnish lapphund cases was mixed in one pool, and DNA from 12 first-degree relatives of these cases was mixed to serve as the control pool. The 2 pools were tested with 133 microsatellite markers, 3 of which showed a shift towards homozygosity in the cases. Individual genotyping with these 3 markers confirmed homozygosity for the GALK1 microsatellite only (chromosome 9). Further individual genotyping with additional samples (4 cases and 59 controls) confirmed the association between this marker and the disease locus (p < 0.001). Closely related to this breed are the Swedish lapphund and the Lapponian herder for which a small number of retinal atrophy cases have been reported. Swedish lapphund cases, but not Lapponian herder cases, had the same GALK1 microsatellite genotype as Finnish lapphund cases. CONCLUSION The locus for progressive rod-cone degeneration is known to be close to the GALK1 locus, on the telomeric region of chromosome 9, where the retinal atrophy locus of the Finnish lapphund has been mapped. This suggests that the disease in this breed, as well as in the Swedish lapphund, may correspond to progressive rod-cone degeneration. This would increase the number of known dog breeds having this particular form of progressive retinal atrophy.
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Affiliation(s)
- Jesús Aguirre-Hernández
- Centre for Veterinary Science, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Kaisa Wickström
- Elainlääkäriasema Akuutti, Kansankatu 47, 90100 Oulu, Finland
| | - David R Sargan
- Centre for Veterinary Science, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
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Njajou OT, Cawthon RM, Damcott CM, Wu SH, Ott S, Garant MJ, Blackburn EH, Mitchell BD, Shuldiner AR, Hsueh WC. Telomere length is paternally inherited and is associated with parental lifespan. Proc Natl Acad Sci U S A 2007; 104:12135-9. [PMID: 17623782 PMCID: PMC1924539 DOI: 10.1073/pnas.0702703104] [Citation(s) in RCA: 284] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Telomere length (TL) is emerging as a biomarker for aging and survival. To evaluate factors influencing this trait, we measured TL in a large homogeneous population, estimated the heritability (h(2)), and tested for parental effects on TL variation. Our sample included 356 men and 551 women, aged 18-92 years, from large Amish families. Mean TL in leukocytes was measured by quantitative PCR (mean: 6,198 +/- 1,696 bp). The h(2) of TL was 0.44 +/- 0.06 (P < 0.001), after adjusting for age, sex, and TL assay batch. As expected, TL was negatively correlated with age (r = -0.40; P < 0.001). There was no significant difference in TL between men and women, consistent with our previous findings that Amish men lived as long as Amish women. There was a stronger and positive correlation and association between TL in the offspring and paternal TL (r = 0.46, P < 0.001; beta = 0.22, P = 0.006) than offspring and maternal TL (r = 0.18, P = 0.04; beta = -0.02, P = 0.4). Furthermore, we observed a positive correlation and association between daughter's TL and paternal lifespan (r = 0.20, P < 0.001; beta = 0.21, P = 0.04), but not between daughter's TL and maternal lifespan (r = -0.01, beta = 0.04; both P = not significant). Our data, which are based on one of the largest family studies of human TL, support a link between TL and aging and lifespan and suggest a strong genetic influence, possibly via an imprinting mechanism, on TL regulation.
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Affiliation(s)
- Omer T. Njajou
- *Department of Medicine and Institute of Human Genetics, and
| | - Richard M. Cawthon
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112
| | - Coleen M. Damcott
- Department of Medicine, University of Maryland, Baltimore, MD 21201; and
| | - Shih-Hsuan Wu
- *Department of Medicine and Institute of Human Genetics, and
| | - Sandy Ott
- Department of Medicine, University of Maryland, Baltimore, MD 21201; and
| | - Michael J. Garant
- Department of Medicine, University of Maryland, Baltimore, MD 21201; and
| | - Elizabeth H. Blackburn
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
| | | | - Alan R. Shuldiner
- Department of Medicine, University of Maryland, Baltimore, MD 21201; and
- Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, MD 21201
| | - Wen-Chi Hsueh
- *Department of Medicine and Institute of Human Genetics, and
- To whom correspondence should be addressed. E-mail:
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Wittke-Thompson JK, Ambrose N, Yairi E, Roe C, Cook EH, Ober C, Cox NJ. Genetic studies of stuttering in a founder population. JOURNAL OF FLUENCY DISORDERS 2007; 32:33-50. [PMID: 17276504 PMCID: PMC2128723 DOI: 10.1016/j.jfludis.2006.12.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2006] [Revised: 12/21/2006] [Accepted: 12/21/2006] [Indexed: 05/11/2023]
Abstract
UNLABELLED Genome-wide linkage and association analyses were conducted to identify genetic determinants of stuttering in a founder population in which 48 individuals affected with stuttering are connected in a single 232-person genealogy. A novel approach was devised to account for all necessary relationships to enable multipoint linkage analysis. Regions with nominal evidence for linkage were found on chromosomes 3 (P=0.013, 208.8 centiMorgans (cM)), 13 (P=0.012, 52.6 cM), and 15 (P=0.02, 100 cM). Regions with nominal evidence for association with stuttering that overlapped with a linkage signal are located on chromosomes 3 (P=0.0047, 195 cM), 9 (P=0.0067, 46.5 cM), and 13 (P=0.0055, 52.6 cM). We also conducted the first meta-analysis for stuttering using results from linkage studies in the Hutterites and The Illinois International Genetics of Stuttering Project and identified regions with nominal evidence for linkage on chromosomes 2 (P=0.013, 180-195 cM) and 5 (P=0.0051, 105-120 cM; P=0.015, 120-135 cM). None of the linkage signals detected in the Hutterite sample alone, or in the meta-analysis, meet genome-wide criteria for significance, although some of the stronger signals overlap linkage mapping signals previously reported for other speech and language disorders. EDUCATIONAL OBJECTIVES After reading this article, the reader will be able to: (1) summarize information about the background of common disorders and methodology of genetic studies; (2) evaluate the role of genetics in stuttering; (3) discuss the value of using founder populations in genetic studies; (4) articulate the importance of combining several studies in a meta-analysis; (5) discuss the overlap of genetic signals identified in stuttering with other speech and language disorders.
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Affiliation(s)
| | - Nicoline Ambrose
- Department of Speech and Hearing Science, University of Illinois Urbana-Champaign, Champaign, IL 61820
| | - Ehud Yairi
- Department of Speech and Hearing Science, University of Illinois Urbana-Champaign, Champaign, IL 61820
| | - Cheryl Roe
- Department of Medicine, The University of Chicago, Chicago, IL 60637
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637
| | - Nancy J. Cox
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637
- Department of Medicine, The University of Chicago, Chicago, IL 60637
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Streeten EA, McBride DJ, Pollin TI, Ryan K, Shapiro J, Ott S, Mitchell BD, Shuldiner AR, O'Connell JR. Quantitative trait loci for BMD identified by autosome-wide linkage scan to chromosomes 7q and 21q in men from the Amish Family Osteoporosis Study. J Bone Miner Res 2006; 21:1433-42. [PMID: 16939402 DOI: 10.1359/jbmr.060602] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
UNLABELLED Using autosome-wide linkage analysis in 964 Amish, strong evidence was found for the presence of genes affecting hip and spine BMD in men on chromosomes 7q31 and 21q22 (LOD = 4.15 and 3.36, respectively). INTRODUCTION BMD is highly heritable, with genetic factors accounting for 60-88% of variation. The goal of this study was to localize genes contributing to BMD variation. MATERIALS AND METHODS The Amish Family Osteoporosis Study was designed to identify genes affecting bone health. The Amish are a genetically closed population with a homogeneous lifestyle. BMD was measured at the spine, hip, and radius using DXA in 964 participants (mean age, 50.2 +/- 16.3 [SD] years; range, 18-99 years) from large multigenerational families. Genotyping of 731 highly polymorphic microsatellite markers (average spacing of 5.4 cM) and autosome-wide multipoint linkage analysis were performed. RESULTS In the overall study population, no strong evidence for linkage was detected to any chromosomal region (peak LOD: 2.11 for radius BMD on chromosome 3q26). In a subgroup analysis of men (n = 371), strong evidence was detected for a quantitative trait locus (QTL) influencing BMD variation on chromosome 7q31 at the total hip (LOD = 4.15) and femoral neck (LOD = 3.09) and for a second QTL influencing spine BMD at 21q22 (LOD = 3.36). Suggestive evidence of linkage was found in men for a QTL at 12q24 affecting total hip BMD (LOD = 2.60) and at 18p11 for femoral neck (LOD = 2.07), and in women (n = 593) at 1p36 for femoral neck BMD (LOD = 2.02) and at 1q21 for spine BMD (LOD = 2.11). In age subgroup analyses, suggestive evidence for linkage was found for those <50 years of age (n = 521) on chromosomes 11q22 and 14q23 (LODs = 2.11 and 2.16, respectively) and for those >50 years of age (n = 443) on 3p25.2 (LOD = 2.32). CONCLUSIONS These results strongly suggest the presence of genes affecting hip and spine BMD in men on chromosomes 7q31 and 21q22. Modest evidence was found for genes affecting BMD in women on chromosomes 1p36 and 1q21 and in men at 12q24, replicating results from other populations.
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Affiliation(s)
- Elizabeth A Streeten
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
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49
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Silberstein M, Tzemach A, Dovgolevsky N, Fishelson M, Schuster A, Geiger D. Online system for faster multipoint linkage analysis via parallel execution on thousands of personal computers. Am J Hum Genet 2006; 78:922-35. [PMID: 16685644 PMCID: PMC1474109 DOI: 10.1086/504158] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Accepted: 03/08/2006] [Indexed: 11/03/2022] Open
Abstract
Computation of LOD scores is a valuable tool for mapping disease-susceptibility genes in the study of Mendelian and complex diseases. However, computation of exact multipoint likelihoods of large inbred pedigrees with extensive missing data is often beyond the capabilities of a single computer. We present a distributed system called "SUPERLINK-ONLINE," for the computation of multipoint LOD scores of large inbred pedigrees. It achieves high performance via the efficient parallelization of the algorithms in SUPERLINK, a state-of-the-art serial program for these tasks, and through the use of the idle cycles of thousands of personal computers. The main algorithmic challenge has been to efficiently split a large task for distributed execution in a highly dynamic, nondedicated running environment. Notably, the system is available online, which allows computationally intensive analyses to be performed with no need for either the installation of software or the maintenance of a complicated distributed environment. As the system was being developed, it was extensively tested by collaborating medical centers worldwide on a variety of real data sets, some of which are presented in this article.
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Affiliation(s)
- M Silberstein
- Computer Science Department, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
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50
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McArdle PF, Pollin TI, O'Connell JR, Sorkin JD, Agarwala R, Schäffer AA, Streeten EA, King TM, Shuldiner AR, Mitchell BD. Does having children extend life span? A genealogical study of parity and longevity in the Amish. J Gerontol A Biol Sci Med Sci 2006; 61:190-5. [PMID: 16510865 DOI: 10.1093/gerona/61.2.190] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The relationship between parity and life span is uncertain, with evidence of both positive and negative relationships being reported previously. We evaluated this issue by using genealogical data from an Old Order Amish community in Lancaster, Pennsylvania, a population characterized by large nuclear families, homogeneous lifestyle, and extensive genealogical records. METHODS The analysis was restricted to the set of 2,015 individuals who had children, were born between 1749 and 1912, and survived until at least age 50 years. Pedigree structures and birth and death dates were extracted from Amish genealogies, and the relationship between parity and longevity was examined using a variance component framework. RESULTS Life span of fathers increased in linear fashion with increasing number of children (0.23 years per additional child; p =.01), while life span of mothers increased linearly up to 14 children (0.32 years per additional child; p =.004) but decreased with each additional child beyond 14 (p =.0004). Among women, but not men, a later age at last birth was associated with longer life span (p =.001). Adjusting for age at last birth obliterated the correlation between maternal life span and number of children, except among mothers with ultrahigh (>14 children) parity. CONCLUSIONS We conclude that high parity among men and later menopause among women may be markers for increased life span. Understanding the biological and/or social factors mediating these relationships may provide insights into mechanisms underlying successful aging.
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Affiliation(s)
- Patrick F McArdle
- Department of Epidemiology and Preventive Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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