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Zajac GJM, Gagliano Taliun SA, Sidore C, Graham SE, Åsvold BO, Brumpton B, Nielsen JB, Zhou W, Gabrielsen M, Skogholt AH, Fritsche LG, Schlessinger D, Cucca F, Hveem K, Willer CJ, Abecasis GR. A fast linkage method for population GWAS cohorts with related individuals. Genet Epidemiol 2023; 47:231-248. [PMID: 36739617 PMCID: PMC10027464 DOI: 10.1002/gepi.22516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/27/2022] [Accepted: 01/24/2023] [Indexed: 02/07/2023]
Abstract
Linkage analysis, a class of methods for detecting co-segregation of genomic segments and traits in families, was used to map disease-causing genes for decades before genotyping arrays and dense SNP genotyping enabled genome-wide association studies in population samples. Population samples often contain related individuals, but the segregation of alleles within families is rarely used because traditional linkage methods are computationally inefficient for larger datasets. Here, we describe Population Linkage, a novel application of Haseman-Elston regression as a method of moments estimator of variance components and their standard errors. We achieve additional computational efficiency by using modern methods for detection of IBD segments and variance component estimation, efficient preprocessing of input data, and minimizing redundant numerical calculations. We also refined variance component models to account for the biases in population-scale methods for IBD segment detection. We ran Population Linkage on four blood lipid traits in over 70,000 individuals from the HUNT and SardiNIA studies, successfully detecting 25 known genetic signals. One notable linkage signal that appeared in both was for low-density lipoprotein (LDL) cholesterol levels in the region near the gene APOE (LOD = 29.3, variance explained = 4.1%). This is the region where the missense variants rs7412 and rs429358, which together make up the ε2, ε3, and ε4 alleles each account for 2.4% and 0.8% of variation in circulating LDL cholesterol. Our results show the potential for linkage analysis and other large-scale applications of method of moments variance components estimation.
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Affiliation(s)
- Gregory JM Zajac
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI
| | - Sarah A Gagliano Taliun
- Department of Medicine and Department of Neurosciences, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Montréal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Sarah E Graham
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger 7600, Norway
| | - Ben Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger 7600, Norway
- Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jonas B Nielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Maiken Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anne Heidi Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars G Fritsche
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI
| | | | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger 7600, Norway
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger 7600, Norway
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Gonçalo R Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI
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Delio M, Guo T, McDonald-McGinn D, Zackai E, Herman S, Kaminetzky M, Higgins A, Coleman K, Chow C, Jarlbrzkowski M, Bearden C, Bailey A, Vangkilde A, Olsen L, Olesen C, Skovby F, Werge T, Templin L, Busa T, Philip N, Swillen A, Vermeesch J, Devriendt K, Schneider M, Dahoun S, Eliez S, Schoch K, Hooper S, Shashi V, Samanich J, Marion R, van Amelsvoort T, Boot E, Klaassen P, Duijff S, Vorstman J, Yuen T, Silversides C, Chow E, Bassett A, Frisch A, Weizman A, Gothelf D, Niarchou M, van den Bree M, Owen M, Suñer D, Andreo J, Armando M, Vicari S, Digilio M, Auton A, Kates W, Wang T, Shprintzen R, Emanuel B, Morrow B. Enhanced maternal origin of the 22q11.2 deletion in velocardiofacial and DiGeorge syndromes. Am J Hum Genet 2013; 92:439-47. [PMID: 23453669 PMCID: PMC3591861 DOI: 10.1016/j.ajhg.2013.01.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/19/2012] [Accepted: 01/31/2013] [Indexed: 11/29/2022] Open
Abstract
Velocardiofacial and DiGeorge syndromes, also known as 22q11.2 deletion syndrome (22q11DS), are congenital-anomaly disorders caused by a de novo hemizygous 22q11.2 deletion mediated by meiotic nonallelic homologous recombination events between low-copy repeats, also known as segmental duplications. Although previous studies exist, each was of small size, and it remains to be determined whether there are parent-of-origin biases for the de novo 22q11.2 deletion. To address this question, we genotyped a total of 389 DNA samples from 22q11DS-affected families. A total of 219 (56%) individuals with 22q11DS had maternal origin and 170 (44%) had paternal origin of the de novo deletion, which represents a statistically significant bias for maternal origin (p = 0.0151). Combined with many smaller, previous studies, 465 (57%) individuals had maternal origin and 345 (43%) had paternal origin, amounting to a ratio of 1.35 or a 35% increase in maternal compared to paternal origin (p = 0.000028). Among 1,892 probands with the de novo 22q11.2 deletion, the average maternal age at time of conception was 29.5, and this is similar to data for the general population in individual countries. Of interest, the female recombination rate in the 22q11.2 region was about 1.6-1.7 times greater than that for males, suggesting that for this region in the genome, enhanced meiotic recombination rates, as well as other as-of-yet undefined 22q11.2-specific features, could be responsible for the observed excess in maternal origin.
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Affiliation(s)
- Maria Delio
- Departments of Genetics, Pediatrics, and Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tingwei Guo
- Departments of Genetics, Pediatrics, and Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Donna M. McDonald-McGinn
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Elaine Zackai
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sean Herman
- Departments of Genetics, Pediatrics, and Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Mark Kaminetzky
- Departments of Genetics, Pediatrics, and Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Anne Marie Higgins
- The Virtual Center for Velo-Cardio-Facial Syndrome, Manlius, NY 13104, USA
| | - Karlene Coleman
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA 30322, USA
| | - Carolyn Chow
- Department of Psychiatry and Biobehavioral Sciences and Department of Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Maria Jarlbrzkowski
- Department of Psychiatry and Biobehavioral Sciences and Department of Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carrie E. Bearden
- Department of Psychiatry and Biobehavioral Sciences and Department of Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alice Bailey
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Anders Vangkilde
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, University of Copenhagen, Copenhagen 4000, Denmark
| | - Line Olsen
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, University of Copenhagen, Copenhagen 4000, Denmark
| | - Charlotte Olesen
- Department of Pediatrics, Aarhus University Hospital, Aarhus 8000, Denmark
| | - Flemming Skovby
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Thomas M. Werge
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, University of Copenhagen, Copenhagen 4000, Denmark
| | - Ludivine Templin
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Tiffany Busa
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Nicole Philip
- Hôpital de la Timone, Assistance Publique – Hôpitaux de Marseille, Marseille 13005, France
| | - Ann Swillen
- Center for Human Genetics, University Hospital Gasthuisberg, University of Leuven, Leuven 03000, Belgium
| | - Joris R. Vermeesch
- Center for Human Genetics, University Hospital Gasthuisberg, University of Leuven, Leuven 03000, Belgium
| | - Koen Devriendt
- Center for Human Genetics, University Hospital Gasthuisberg, University of Leuven, Leuven 03000, Belgium
| | - Maude Schneider
- Office Médico-Pédagogique Research Unit, Department of Psychiatry, University of Geneva School of Medicine, Geneva 1211, Switzerland
| | - Sophie Dahoun
- Office Médico-Pédagogique Research Unit, Department of Psychiatry, University of Geneva School of Medicine, Geneva 1211, Switzerland
| | - Stephan Eliez
- Office Médico-Pédagogique Research Unit, Department of Psychiatry, University of Geneva School of Medicine, Geneva 1211, Switzerland
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC 27705, USA
| | - Stephen R. Hooper
- Department of Psychiatry and The Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC 27514, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27705, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC 27705, USA
| | - Joy Samanich
- Department of Pediatrics, Montefiore Medical Center, Bronx, NY 10461, USA
| | - Robert Marion
- Department of Pediatrics, Montefiore Medical Center, Bronx, NY 10461, USA
| | - Therese van Amelsvoort
- Department of Psychiatry and Psychology, University of Maastricht, Maastricht 6211, the Netherlands
| | - Erik Boot
- Department of Psychiatry, Academic Medical Centre, Amsterdam 1100, the Netherlands
| | - Petra Klaassen
- Department of Pediatric Psychology, University Medical Center Utrecht, Utrecht 3584, the Netherlands
| | - Sasja N. Duijff
- Department of Pediatric Psychology, University Medical Center Utrecht, Utrecht 3584, the Netherlands
| | - Jacob Vorstman
- Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Utrecht 3584, the Netherlands
| | - Tracy Yuen
- Center for Addiction and Mental Health, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Candice Silversides
- Center for Addiction and Mental Health, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Eva Chow
- Center for Addiction and Mental Health, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Anne Bassett
- Center for Addiction and Mental Health, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Amos Frisch
- The Felsenstein Medical Research Center, Petah Tikva 49100, Israel
| | - Abraham Weizman
- The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Doron Gothelf
- The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Maria Niarchou
- Medical Research Council Centre for Neuropsychiatric Genetics & Genomics and the Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff CF14 4XN, UK
| | - Marianne van den Bree
- Medical Research Council Centre for Neuropsychiatric Genetics & Genomics and the Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff CF14 4XN, UK
| | - Michael J. Owen
- Medical Research Council Centre for Neuropsychiatric Genetics & Genomics and the Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff CF14 4XN, UK
| | - Damian Heine Suñer
- Laboratory of Molecular Genetics, Department of Genetics, University Hospital Son Espases, Palma de Mallorca 07020, Spain
| | - Jordi Rosell Andreo
- Laboratory of Molecular Genetics, Department of Genetics, University Hospital Son Espases, Palma de Mallorca 07020, Spain
| | - Marco Armando
- Child Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome 00165, Italy
| | - Stefano Vicari
- Child Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome 00165, Italy
| | - Maria Cristina Digilio
- Medical Genetic Unit, Department of Pediatrics, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome 00165, Italy
| | - Adam Auton
- Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wendy R. Kates
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Beverly S. Emanuel
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bernice E. Morrow
- Departments of Genetics, Pediatrics, and Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Bioinformatic perspectives in the neuronal ceroid lipofuscinoses. Biochim Biophys Acta Mol Basis Dis 2012; 1832:1831-41. [PMID: 23274885 DOI: 10.1016/j.bbadis.2012.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/16/2012] [Accepted: 12/19/2012] [Indexed: 02/06/2023]
Abstract
The neuronal ceroid lipofuscinoses (NCLs) are a group of rare genetic diseases characterised clinically by the progressive deterioration of mental, motor and visual functions and histopathologically by the intracellular accumulation of autofluorescent lipopigment - ceroid - in affected tissues. The NCLs are clinically and genetically heterogeneous and more than 14 genetically distinct NCL subtypes have been described to date (CLN1-CLN14) (Haltia and Goebel, 2012 [1]). In this review we will chronologically summarise work which has led over the years to identification of NCL genes, and outline the potential of novel genomic techniques and related bioinformatic approaches for further genetic dissection and diagnosis of NCLs. This article is part of a Special Issue entitled: The Neuronal Ceroid Lipofuscinoses or Batten Disease.
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Attar H, Bedard K, Migliavacca E, Gagnebin M, Dupré Y, Descombes P, Borel C, Deutsch S, Prokisch H, Meitinger T, Mehta D, Wichmann E, Delabar JM, Dermitzakis ET, Krause KH, Antonarakis SE. Extensive natural variation for cellular hydrogen peroxide release is genetically controlled. PLoS One 2012; 7:e43566. [PMID: 22952707 PMCID: PMC3430705 DOI: 10.1371/journal.pone.0043566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 07/26/2012] [Indexed: 02/07/2023] Open
Abstract
Natural variation in DNA sequence contributes to individual differences in quantitative traits. While multiple studies have shown genetic control over gene expression variation, few additional cellular traits have been investigated. Here, we investigated the natural variation of NADPH oxidase-dependent hydrogen peroxide (H2O2 release), which is the joint effect of reactive oxygen species (ROS) production, superoxide metabolism and degradation, and is related to a number of human disorders. We assessed the normal variation of H2O2 release in lymphoblastoid cell lines (LCL) in a family-based 3-generation cohort (CEPH-HapMap), and in 3 population-based cohorts (KORA, GenCord, HapMap). Substantial individual variation was observed, 45% of which were associated with heritability in the CEPH-HapMap cohort. We identified 2 genome-wide significant loci of Hsa12 and Hsa15 in genome-wide linkage analysis. Next, we performed genome-wide association study (GWAS) for the combined KORA-GenCord cohorts (n = 279) using enhanced marker resolution by imputation (>1.4 million SNPs). We found 5 significant associations (p<5.00×10−8) and 54 suggestive associations (p<1.00×10−5), one of which confirmed the linked region on Hsa15. To replicate our findings, we performed GWAS using 58 HapMap individuals and ∼2.1 million SNPs. We identified 40 genome-wide significant and 302 suggestive SNPs, and confirmed genome signals on Hsa1, Hsa12, and Hsa15. Genetic loci within 900 kb from the known candidate gene p67phox on Hsa1 were identified in GWAS in both cohorts. We did not find replication of SNPs across all cohorts, but replication within the same genomic region. Finally, a highly significant decrease in H2O2 release was observed in Down Syndrome (DS) individuals (p<2.88×10−12). Taken together, our results show strong evidence of genetic control of H2O2 in LCL of healthy and DS cohorts and suggest that cellular phenotypes, which themselves are also complex, may be used as proxies for dissection of complex disorders.
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Affiliation(s)
- Homa Attar
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- * E-mail: (HA); (SA)
| | - Karen Bedard
- Department of Pathology and Immunology, University of Geneva Medical School and University Hospitals, Geneva, Switzerland
| | - Eugenia Migliavacca
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Dorigny, Switzerland
| | - Maryline Gagnebin
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Yann Dupré
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Patrick Descombes
- Genomics Platform, NCCR Frontiers in Genetics, University of Geneva Medical School, Geneva, Switzerland
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Samuel Deutsch
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Holger Prokisch
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Divya Mehta
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Klinikum Grosshadern, Munich, Germany
| | - Jean Maurice Delabar
- Functional and Adaptive Biology, Université Paris Diderot-Paris7 and CNRS, Paris, France
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, University of Geneva Medical School and University Hospitals, Geneva, Switzerland
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- * E-mail: (HA); (SA)
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Cavalleri GL, Delanty N. Opportunities and challenges for genome sequencing in the clinic. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 89:65-83. [PMID: 23046882 DOI: 10.1016/b978-0-12-394287-6.00003-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human genome sequencing technology is developing rapidly. These developments are providing exciting opportunities for genetic mapping of human traits, ranging from accelerated discovery of mutations underlying relatively simple Mendelian disorders to more genetically complex human diseases. This chapter outlines the development of whole-genome sequencing in a historical context of genetic mapping and explores the impact that sequencing is having on gene discovery study design. Using the example of epilepsy, the authors outline the opportunities and barriers for the translation of genetic predictors from discovery to the clinic. Finally, the authors discuss the practical challenges of actual implementation of whole-genome sequencing to the clinic.
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Affiliation(s)
- Gianpiero L Cavalleri
- Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland.
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Lee YS, Chao A, Chen CH, Chou T, Wang SYM, Wang TH. Analysis of human meiotic recombination events with a parent-sibling tracing approach. BMC Genomics 2011; 12:434. [PMID: 21867557 PMCID: PMC3186786 DOI: 10.1186/1471-2164-12-434] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 08/26/2011] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Meiotic recombination ensures that each child inherits distinct genetic materials from each parent, but the distribution of crossovers along meiotic chromosomes remains difficult to identify. In this study, we developed a parent-sibling tracing (PST) approach from previously reported methods to identify meiotic crossover sites of GEO GSE6754 data set. This approach requires only the single nucleotide polymorphism (SNP) data of the pedigrees of both parents and at least two of children. RESULTS Compared to other SNP-based algorithms (identity by descent or pediSNP), fewer uninformative SNPs were derived with the use of PST. Analysis of a GEO GSE6754 data set containing 2,145 maternal and paternal meiotic events revealed that the pattern and distribution of paternal and maternal recombination sites vary along the chromosomes. Lower crossover rates near the centromeres were more prominent in males than in females. Based on analysis of repetitive sequences, we also showed that recombination hotspots are positively correlated with SINE/MIR repetitive elements and negatively correlated with LINE/L1 elements. The number of meiotic recombination events was positively correlated with the number of shorter tandem repeat sequences. CONCLUSIONS The advantages of the PST approach include the ability to use only two-generation pedigrees with two siblings and the ability to perform gender-specific analyses of repetitive elements and tandem repeat sequences while including fewer uninformative SNP regions in the results.
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Affiliation(s)
- Yun-Shien Lee
- Department of Biotechnology, Ming Chuan University, Tao-Yuan, Taiwan
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Luo Y, Hermetz KE, Jackson JM, Mulle JG, Dodd A, Tsuchiya KD, Ballif BC, Shaffer LG, Cody JD, Ledbetter DH, Martin CL, Rudd MK. Diverse mutational mechanisms cause pathogenic subtelomeric rearrangements. Hum Mol Genet 2011; 20:3769-78. [PMID: 21729882 DOI: 10.1093/hmg/ddr293] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chromosome rearrangements are a significant cause of intellectual disability and birth defects. Subtelomeric rearrangements, including deletions, duplications and translocations of chromosome ends, were first discovered over 40 years ago and are now recognized as being responsible for several genetic syndromes. Unlike the deletions and duplications that cause some genomic disorders, subtelomeric rearrangements do not typically have recurrent breakpoints and involve many different chromosome ends. To capture the molecular mechanisms responsible for this heterogeneous class of chromosome abnormality, we coupled high-resolution array CGH with breakpoint junction sequencing of a diverse collection of subtelomeric rearrangements. We analyzed 102 breakpoints corresponding to 78 rearrangements involving 28 chromosome ends. Sequencing 21 breakpoint junctions revealed signatures of non-homologous end-joining, non-allelic homologous recombination between interspersed repeats and DNA replication processes. Thus, subtelomeric rearrangements arise from diverse mutational mechanisms. In addition, we find hotspots of subtelomeric breakage at the end of chromosomes 9q and 22q; these sites may correspond to genomic regions that are particularly susceptible to double-strand breaks. Finally, fine-mapping the smallest subtelomeric rearrangements has narrowed the critical regions for some chromosomal disorders.
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Affiliation(s)
- Yue Luo
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
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Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG. Widespread RNA and DNA sequence differences in the human transcriptome. Science 2011; 333:53-8. [PMID: 21596952 PMCID: PMC3204392 DOI: 10.1126/science.1207018] [Citation(s) in RCA: 315] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The transmission of information from DNA to RNA is a critical process. We compared RNA sequences from human B cells of 27 individuals to the corresponding DNA sequences from the same individuals and uncovered more than 10,000 exonic sites where the RNA sequences do not match that of the DNA. All 12 possible categories of discordances were observed. These differences were nonrandom as many sites were found in multiple individuals and in different cell types, including primary skin cells and brain tissues. Using mass spectrometry, we detected peptides that are translated from the discordant RNA sequences and thus do not correspond exactly to the DNA sequences. These widespread RNA-DNA differences in the human transcriptome provide a yet unexplored aspect of genome variation.
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Affiliation(s)
- Mingyao Li
- Departments of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Isabel X. Wang
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Yun Li
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Alan Bruzel
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Allison L. Richards
- Cell and Molecular Biology Graduate Program, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Jonathan M. Toung
- Genomics and Computational Biology Graduate Program, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Vivian G. Cheung
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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9
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Parent-of-origin differences of mutant HTT CAG repeat instability in Huntington’s disease. Eur J Med Genet 2011; 54:e413-8. [DOI: 10.1016/j.ejmg.2011.04.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 04/12/2011] [Indexed: 11/24/2022]
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10
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Abstract
The identification of genomic loci linked to or associated with human disease has been greatly facilitated by the evolution of genotyping strategies and techniques. The success of these strategies continues to be based upon clear clinical assessment, accurate sample handling, and careful data management, but also increasingly upon experimental design. Technological advances in the field of genotyping have permitted increasingly complex and large population studies to be performed. An understanding of publicly available genetic variation databases, including an awareness of the limitations of these data, and an appreciation of the strategic approaches that should be used to exploit this information will provide tremendous insight for researchers are aiming to utilize this accessible technology. As genome-wide association studies (GWAS) and Next Generation (NextGen) sequencing become the mainstays of genetic analyses, it is important that their technical strengths and limitations, as well as their impact on study design, be understood before use in a linkage or genetic association study.
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Affiliation(s)
- Dana C Crawford
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
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11
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Lee E, Kim K, Park T. Genome-wide search for genetic modulators in gene regulatory pathways: weighted window-based peak identification algorithm. Genomics 2011; 97:386-93. [PMID: 21419843 DOI: 10.1016/j.ygeno.2011.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 03/01/2011] [Accepted: 03/11/2011] [Indexed: 10/18/2022]
Abstract
Genome-wide gene expression and genotype data have been integratively analyzed in expression quantitative trait loci (eQTL) studies to elucidate the genetics of gene transcription. Most eQTL analyses have focused on identifying polymorphic genetic variants that influence the expression levels of individual genes, and such analyses may have limitations in explaining gene regulatory pathways that are likely to involve multiple genes and their genetic and/or non-genetic modulators. We have developed a novel two-step method for identifying potential genetic modulators of transcription processes for multiple genes in a biological pathway. We proposed a new weighted window-based peak identification algorithm to improve the detection of genetic modulators for individual genes and employed a Poisson-based test to search for master genetic modulators of multiple genes. Here, we have illustrated this two-step approach by analyzing the gene expression data in the Centre d'Etude du Polymorphisme Humain (CEPH) lymphoblast cells and single nucleotide polymorphism chip data.
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Affiliation(s)
- Eunjee Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Republic of Korea.
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12
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Elferink MG, van As P, Veenendaal T, Crooijmans RPMA, Groenen MAM. Regional differences in recombination hotspots between two chicken populations. BMC Genet 2010; 11:11. [PMID: 20141624 PMCID: PMC2834597 DOI: 10.1186/1471-2156-11-11] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 02/08/2010] [Indexed: 12/17/2022] Open
Abstract
Background Although several genetic linkage maps of the chicken genome have been published, the resolution of these maps is limited and does not allow the precise identification of recombination hotspots. The availability of more than 3.2 million SNPs in the chicken genome and the recent advances in high throughput genotyping techniques enabled us to increase marker density for the construction of a high-resolution linkage map of the chicken genome. This high-resolution linkage map allowed us to study recombination hotspots across the genome between two chicken populations: a purebred broiler line and a broiler × broiler cross. In total, 1,619 animals from the two different broiler populations were genotyped with 17,790 SNPs. Results The resulting linkage map comprises 13,340 SNPs. Although 360 polymorphic SNPs that had not been assigned to a known chromosome on chicken genome build WASHUC2 were included in this study, no new linkage groups were found. The resulting linkage map is composed of 31 linkage groups, with a total length of 3,054 cM for the sex-average map of the combined population. The sex-average linkage map of the purebred broiler line is 686 cM smaller than the linkage map of the broiler × broiler cross. Conclusions In this study, we present a linkage map of the chicken genome at a substantially higher resolution than previously published linkage maps. Regional differences in recombination hotspots between the two mapping populations were observed in several chromosomes near the telomere of the p arm; the sex-specific analysis revealed that these regional differences were mainly caused by female-specific recombination hotspots in the broiler × broiler cross.
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Affiliation(s)
- Martin G Elferink
- Animal Breeding and Genomics Centre, Wageningen University and Research Centre, Wageningen, the Netherlands.
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13
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Abstract
PURPOSE OF REVIEW The relationship between increasing maternal age and trisomy has been recognized for over 50 years and is one of the most important etiological factors associated with any human genetic disorder. Specifically, the risk of trisomy in a clinically recognized pregnancy rises from about 2-3% for women in their twenties to an astounding 30% or more for women in their forties. Thus, as women approach the end of their child-bearing years, errors of chromosome segregation represent the most important impediment to a successful pregnancy. RECENT FINDINGS Despite the clinical importance of this relationship, we do not understand how age affects the likelihood of producing a normal egg. Errors that affect chromosome segregation could occur at several stages during the development of the oocyte: in the fetal ovary, either during the mitotic proliferation of oogonia or the early stages of meiosis; in the 'dictyate' oocyte, during the 10-50-year period of meiotic arrest; or during the final stages of oocyte growth and maturation, when meiosis resumes and the meiotic divisions take place. Recent evidence from studies of human oocytes and trisomic conceptions and from studies in model organisms implicates errors at each of these stages. SUMMARY It seems likely that there are multiple causes of human age-related nondisjunction, complicating our efforts to understand - and, ultimately, to provide preventive measures for - errors associated with increasing maternal age.
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Affiliation(s)
- Terry Hassold
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington 99164, USA.
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14
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Cheng EY, Hunt PA, Naluai-Cecchini TA, Fligner CL, Fujimoto VY, Pasternack TL, Schwartz JM, Steinauer JE, Woodruff TJ, Cherry SM, Hansen TA, Vallente RU, Broman KW, Hassold TJ. Meiotic recombination in human oocytes. PLoS Genet 2009; 5:e1000661. [PMID: 19763179 PMCID: PMC2735652 DOI: 10.1371/journal.pgen.1000661] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 08/24/2009] [Indexed: 11/19/2022] Open
Abstract
Studies of human trisomies indicate a remarkable relationship between abnormal meiotic recombination and subsequent nondisjunction at maternal meiosis I or II. Specifically, failure to recombine or recombination events located either too near to or too far from the centromere have been linked to the origin of human trisomies. It should be possible to identify these abnormal crossover configurations by using immunofluorescence methodology to directly examine the meiotic recombination process in the human female. Accordingly, we initiated studies of crossover-associated proteins (e.g., MLH1) in human fetal oocytes to analyze their number and distribution on nondisjunction-prone human chromosomes and, more generally, to characterize genome-wide levels of recombination in the human female. Our analyses indicate that the number of MLH1 foci is lower than predicted from genetic linkage analysis, but its localization pattern conforms to that expected for a crossover-associated protein. In studies of individual chromosomes, our observations provide evidence for the presence of "vulnerable" crossover configurations in the fetal oocyte, consistent with the idea that these are subsequently translated into nondisjunctional events in the adult oocyte.
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Affiliation(s)
- Edith Y. Cheng
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Patricia A. Hunt
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Theresa A. Naluai-Cecchini
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Corrine L. Fligner
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Victor Y. Fujimoto
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Tanya L. Pasternack
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Jackie M. Schwartz
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Jody E. Steinauer
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Tracey J. Woodruff
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Sheila M. Cherry
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Terah A. Hansen
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Rhea U. Vallente
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Karl W. Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Terry J. Hassold
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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15
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McKnight AJ, O'Donoghue D, Peter Maxwell A. Annotated chromosome maps for renal disease. Hum Mutat 2009; 30:314-20. [PMID: 19085929 DOI: 10.1002/humu.20885] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A combination of linkage analyses and association studies are currently employed to promote the identification of genetic factors contributing to inherited renal disease. We have standardized and merged complex genetic data from disparate sources, creating unique chromosomal maps to enhance genetic epidemiological investigations. This database and novel renal maps effectively summarize genomic regions of suggested linkage, association, or chromosomal abnormalities implicated in renal disease. Chromosomal regions associated with potential intermediate clinical phenotypes have been integrated, adding support for particular genomic intervals. More than 500 reports from medical databases, published scientific literature, and the World Wide Web were interrogated for relevant renal-related information. Chromosomal regions highlighted for prioritized investigation of renal complications include 3q13-26, 6q22-27, 10p11-15, 16p11-13, and 18q22. Combined genetic and physical maps are effective tools to organize genetic data for complex diseases. These renal chromosome maps provide insights into renal phenotype-genotype relationships and act as a template for future genetic investigations into complex renal diseases. New data from individual researchers and/or future publications can be readily incorporated to this resource via a user-friendly web-form accessed from the website: www.qub.ac.uk/neph-res/CORGI/index.php.
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Affiliation(s)
- Amy Jayne McKnight
- Nephrology Research Group, Queen's University of Belfast, United Kingdom.
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16
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Hassold T, Hansen T, Hunt P, VandeVoort C. Cytological studies of recombination in rhesus males. Cytogenet Genome Res 2009; 124:132-8. [PMID: 19420925 DOI: 10.1159/000207519] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2008] [Indexed: 01/04/2023] Open
Abstract
An immunofluorescence approach was used to directly examine meiotic recombination events in 483 pachytene spermatocytes from 11 male rhesus monkeys. Specifically, we examined the nuclear localization patterns of the DNA mismatch repair protein MLH1, known from analyses of other mammalian species to be a useful marker of meiotic cross-overs. Our results indicated that rhesus pachytene spermatocytes contain approximately 40 cross-overs per cell, corresponding to about one cross-over per chromosome. The chromosomal distribution of these exchanges was consistent with data from human and mouse males but, surprisingly, the overall number of foci was lower, and the number of 'exchangeless' bivalents higher, than reported for either humans or mice.
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Affiliation(s)
- T Hassold
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA.
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17
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Fukuda Y, Nakahara Y, Date H, Takahashi Y, Goto J, Miyashita A, Kuwano R, Adachi H, Nakamura E, Tsuji S. SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data. BMC Bioinformatics 2009; 10:121. [PMID: 19393044 PMCID: PMC2680848 DOI: 10.1186/1471-2105-10-121] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Accepted: 04/24/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During this recent decade, microarray-based single nucleotide polymorphism (SNP) data are becoming more widely used as markers for linkage analysis in the identification of loci for disease-associated genes. Although microarray-based SNP analyses have markedly reduced genotyping time and cost compared with microsatellite-based analyses, applying these enormous data to linkage analysis programs is a time-consuming step, thus, necessitating a high-throughput platform. RESULTS We have developed SNP HiTLink (SNP High Throughput Linkage analysis system). In this system, SNP chip data of the Affymetrix Mapping 100 k/500 k array set and Genome-Wide Human SNP array 5.0/6.0 can be directly imported and passed to parametric or model-free linkage analysis programs; MLINK, Superlink, Merlin and Allegro. Various marker-selecting functions are implemented to avoid the effect of typing-error data, markers in linkage equilibrium or to select informative data. CONCLUSION The results using the 100 k SNP dataset were comparable or even superior to those obtained from analyses using microsatellite markers in terms of LOD scores obtained. General personal computers are sufficient to execute the process, as runtime for whole-genome analysis was less than a few hours. This system can be widely applied to linkage analysis using microarray-based SNP data and with which one can expect high-throughput and reliable linkage analysis.
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Affiliation(s)
- Yoko Fukuda
- Department of Neurology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.
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18
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Kurbasic A, Hössjer O. A general method for linkage disequilibrium correction for multipoint linkage and association. Genet Epidemiol 2009; 32:647-57. [PMID: 18481794 DOI: 10.1002/gepi.20339] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lately, many different methods of linkage, association or joint analysis for family data have been invented and refined. Common to most of those is that they require a map of markers that are in linkage equilibrium. However, at the present day, high-density single nucleotide polymorphisms (SNPs) maps are both more inexpensive to create and they have lower genotyping error. When marker data is incomplete, the crucial and computationally most demanding moment in the analysis is to calculate the inheritance distribution at a certain position on the chromosome. Recently, different ways of adjusting traditional methods of linkage analysis to denser maps of SNPs in linkage disequilibrium (LD) have been proposed. We describe a hidden Markov model which generalizes the Lander-Green algorithm. It combines Markov chain for inheritance vectors with a Markov chain modelling founder haplotypes and in this way takes account for LD between SNPs. It can be applied to association, linkage or combined association and linkage analysis, general phenotypes and arbitrary score functions. We also define a joint likelihood for linkage and association that extends an idea of Kong and Cox (1997 Am. J. Hum. Genet. 61: 1179-1188) for pure linkage analysis.
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Affiliation(s)
- Azra Kurbasic
- Centre for Mathematical Sciences, Department of Mathematical Statistics, Lund University, Box 118, SE-211 Lund, Sweden.
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19
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Gelineau-van Waes J, Voss KA, Stevens VL, Speer MC, Riley RT. Maternal fumonisin exposure as a risk factor for neural tube defects. ADVANCES IN FOOD AND NUTRITION RESEARCH 2009; 56:145-181. [PMID: 19389609 DOI: 10.1016/s1043-4526(08)00605-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fumonisins are mycotoxins produced by the fungus F. verticillioides, a common contaminant of maize (corn) worldwide. Maternal consumption of fumonisin B(1)-contaminated maize during early pregnancy has recently been associated with increased risk for neural tube defects (NTDs) in human populations that rely heavily on maize as a dietary staple. Experimental administration of purified fumonisin to mice early in gestation also results in an increased incidence of NTDs in exposed offspring. Fumonisin inhibits the enzyme ceramide synthase in de novo sphingolipid biosynthesis, resulting in an elevation of free sphingoid bases and depletion of downstream glycosphingolipids. Increased sphingoid base metabolites (i.e., sphinganine-1-phosphate) may perturb signaling cascades involved in embryonic morphogenesis by functioning as ligands for sphingosine-1-P (S1P) receptors, a family of G-protein-coupled receptors that regulate key biological processes such as cell survival/proliferation, differentiation and migration. Fumonisin-induced depletion of glycosphingolipids impairs expression and function of the GPI-anchored folate receptor (Folr1), which may also contribute to adverse pregnancy outcomes. NTDs appear to be multifactorial in origin, involving complex gene-nutrient-environment interactions. Vitamin supplements containing folic acid have been shown to reduce the occurrence of NTDs, and may help protect the developing fetus from environmental teratogens. Fumonisins appear to be an environmental risk factor for birth defects, although other aspects of maternal nutrition and genetics play interactive roles in determining pregnancy outcome. Minimizing exposures to mycotoxins through enhanced agricultural practices, identifying biomarkers of exposure, characterizing mechanisms of toxicity, and improving maternal nutrition are all important strategies for reducing the NTD burden in susceptible human populations.
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Affiliation(s)
- J Gelineau-van Waes
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
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20
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Kazadi K, Loeuillet C, Deutsch S, Ciuffi A, Muñoz M, Beckmann JS, Moradpour D, Antonarakis SE, Telenti A. Genomic determinants of the efficiency of internal ribosomal entry sites of viral and cellular origin. Nucleic Acids Res 2008; 36:6918-25. [PMID: 18978018 PMCID: PMC2588522 DOI: 10.1093/nar/gkn812] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Variation in cellular gene expression levels has been shown to be inherited. Expression is controlled at transcriptional and post-transcriptional levels. Internal ribosome entry sites (IRES) are used by viruses to bypass inhibition of cap-dependent translation, and by eukaryotic cells to control translation under conditions when protein synthesis is inhibited. We aimed at identifying genomic determinants of variability in IRES-mediated translation of viral [Encephalomyocarditis virus (EMCV)] and cellular IRES [X-linked inhibitor-of-apoptosis (XIAP) and c-myc]. Bicistronic lentiviral constructs expressing two fluorescent reporters were used to transduce laboratory and B lymphoblastoid cell lines [15 CEPH pedigrees (n = 205) and 50 unrelated individuals]. IRES efficiency varied according to cell type and among individuals. Control of IRES activity has a significant genetic component (h2 of 0.47 and 0.36 for EMCV and XIAP, respectively). Quantitative linkage analysis identified a suggestive locus (LOD 2.35) on chromosome 18q21.2, and genome-wide association analysis revealed of a cluster of SNPs on chromosome 3, intronic to the FHIT gene, marginally associated (P = 5.9E-7) with XIAP IRES function. This study illustrates the in vitro generation of intermediate phenotypes by using cell lines for the evaluation of genetic determinants of control of elements such as IRES.
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Affiliation(s)
- Kayole Kazadi
- Institute of Microbiology, University Hospital Center, University of Lausanne, Switzerland
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21
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Prescott SM, Lalouel JM, Leppert M. From Linkage Maps to Quantitative Trait Loci: The History and Science of the Utah Genetic Reference Project. Annu Rev Genomics Hum Genet 2008; 9:347-58. [DOI: 10.1146/annurev.genom.9.081307.164441] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Jean Marc Lalouel
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112;
| | - Mark Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112;
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22
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Shojaee S, Sina F, Banihosseini SS, Kazemi MH, Kalhor R, Shahidi GA, Fakhrai-Rad H, Ronaghi M, Elahi E. Genome-wide linkage analysis of a Parkinsonian-pyramidal syndrome pedigree by 500 K SNP arrays. Am J Hum Genet 2008; 82:1375-84. [PMID: 18513678 DOI: 10.1016/j.ajhg.2008.05.005] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 04/27/2008] [Accepted: 05/09/2008] [Indexed: 12/12/2022] Open
Abstract
Robust SNP genotyping technologies and data analysis programs have encouraged researchers in recent years to use SNPs for linkage studies. Platforms used to date have been 10 K chip arrays, but the possible value of interrogating SNPs at higher densities has been considered. Here, we present a genome-wide linkage analysis by means of a 500 K SNP platform. The analysis was done on a large pedigree affected with Parkinsonian-pyramidal syndrome (PPS), and the results showed linkage to chromosome 22. Sequencing of candidate genes revealed a disease-associated homozygous variation (R378G) in FBXO7. FBXO7 codes for a member of the F-box family of proteins, all of which may have a role in the ubiquitin-proteosome protein-degradation pathway. This pathway has been implicated in various neurodegenerative diseases, and identification of FBXO7 as the causative gene of PPS is expected to shed new light on its role. The performance of the array was assessed and systematic analysis of effects of SNP density reduction was performed with the real experimental data. Our results suggest that linkage in our pedigree may have been missed had we used chips containing less than 100,000 SNPs across the genome.
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23
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Linardopoulou EV, Parghi SS, Friedman C, Osborn GE, Parkhurst SM, Trask BJ. Human subtelomeric WASH genes encode a new subclass of the WASP family. PLoS Genet 2008; 3:e237. [PMID: 18159949 PMCID: PMC2151093 DOI: 10.1371/journal.pgen.0030237] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 10/19/2007] [Indexed: 12/17/2022] Open
Abstract
Subtelomeres are duplication-rich, structurally variable regions of the human genome situated just proximal of telomeres. We report here that the most terminally located human subtelomeric genes encode a previously unrecognized third subclass of the Wiskott-Aldrich Syndrome Protein family, whose known members reorganize the actin cytoskeleton in response to extracellular stimuli. This new subclass, which we call WASH, is evolutionarily conserved in species as diverged as Entamoeba. We demonstrate that WASH is essential in Drosophila. WASH is widely expressed in human tissues, and human WASH protein colocalizes with actin in filopodia and lamellipodia. The VCA domain of human WASH promotes actin polymerization by the Arp2/3 complex in vitro. WASH duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires vary. Thus, human subtelomeres are not genetic junkyards, and WASH's location in these dynamic regions could have advantageous as well as pathologic consequences. Human subtelomeres are rearrangement-prone regions near chromosome ends. They are concentrations of large, recent interchromosomal duplications. Over half of subtelomeric sequences changed copy number or location since humans and chimpanzee diverged, and subtelomeric content varies greatly among humans. Despite this dynamic activity, subtelomeres contain genes. We report the discovery of genes defining a previously unrecognized third subclass of the Wiskott-Aldrich Syndrome protein (WASP) family within human subtelomeres. The known WASP family members reorganize actin structures in cells in response to various signals, thereby causing cells to change shape and/or move. Representatives of this newly identified subclass, called WASH, exist in many other species, even in Entamoeba and slime mold. Like other WASP family members, WASH colocalizes with actin at the cell periphery and promotes actin polymerization in vitro. Flies lacking WASH die before becoming adults, demonstrating that WASH is critical for survival, and its function is distinct from that of the two other WASP subclasses, Wasp and Scar. Identification of the WASH subclass opens the way for future elucidation of WASH's role in the life cycles of diverse organisms, the implications of human variation in WASH copy number, and the consequences of WASH's location in dynamic telomere-adjacent regions.
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Affiliation(s)
- Elena V Linardopoulou
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Sean S Parghi
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Cynthia Friedman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Gregory E Osborn
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Susan M Parkhurst
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Barbara J Trask
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * To whom correspondence should be addressed. E-mail:
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24
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Loeuillet C, Deutsch S, Ciuffi A, Robyr D, Taffé P, Muñoz M, Beckmann JS, Antonarakis SE, Telenti A. In vitro whole-genome analysis identifies a susceptibility locus for HIV-1. PLoS Biol 2008; 6:e32. [PMID: 18288889 PMCID: PMC2245987 DOI: 10.1371/journal.pbio.0060032] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 01/03/2008] [Indexed: 12/13/2022] Open
Abstract
Advances in large-scale analysis of human genomic variability provide unprecedented opportunities to study the genetic basis of susceptibility to infectious agents. We report here the use of an in vitro system for the identification of a locus on HSA8q24.3 associated with cellular susceptibility to HIV-1. This locus was mapped through quantitative linkage analysis using cell lines from multigeneration families, validated in vitro, and followed up by two independent association studies in HIV-positive individuals. Single nucleotide polymorphism rs2572886, which is associated with cellular susceptibility to HIV-1 in lymphoblastoid B cells and in primary T cells, was also associated with accelerated disease progression in one of two cohorts of HIV-1-infected patients. Biological analysis suggests a role of the rs2572886 region in the regulation of the LY6 family of glycosyl-phosphatidyl-inositol (GPI)-anchored proteins. Genetic analysis of in vitro cellular phenotypes provides an attractive approach for the discovery of susceptibility loci to infectious agents.
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Affiliation(s)
- Corinne Loeuillet
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Samuel Deutsch
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospital of Geneva, Geneva, Switzerland
| | - Angela Ciuffi
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Daniel Robyr
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospital of Geneva, Geneva, Switzerland
| | | | - Miguel Muñoz
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Jacques S Beckmann
- Department of Medical Genetics, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospital of Geneva, Geneva, Switzerland
| | - Amalio Telenti
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
- Swiss HIV Cohort Study, Lausanne, Switzerland
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Xing J, Witherspoon DJ, Ray DA, Batzer MA, Jorde LB. Mobile DNA elements in primate and human evolution. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; Suppl 45:2-19. [PMID: 18046749 DOI: 10.1002/ajpa.20722] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Roughly 50% of the primate genome consists of mobile, repetitive DNA sequences such as Alu and LINE1 elements. The causes and evolutionary consequences of mobile element insertion, which have received considerable attention during the past decade, are reviewed in this article. Because of their unique mutational mechanisms, these elements are highly useful for answering phylogenetic questions. We demonstrate how they have been used to help resolve a number of questions in primate phylogeny, including the human-chimpanzee-gorilla trichotomy and New World primate phylogeny. Alu and LINE1 element insertion polymorphisms have also been analyzed in human populations to test hypotheses about human evolution and population affinities and to address forensic issues. Finally, these elements have had impacts on the genome itself. We review how they have influenced fundamental ongoing processes like nonhomologous recombination, genomic deletion, and X chromosome inactivation.
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Affiliation(s)
- Jinchuan Xing
- Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
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Bray NJ, Holmans PA, van den Bree MB, Jones L, Elliston LA, Hughes G, Richards AL, Williams NM, Craddock N, Owen MJ, O'Donovan MC. Cis- and trans- loci influence expression of the schizophrenia susceptibility gene DTNBP1. Hum Mol Genet 2008; 17:1169-74. [DOI: 10.1093/hmg/ddn006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Data for Genetic Analysis Workshop (GAW) 15, Problem 1: genetics of gene expression variation in humans. BMC Proc 2007; 1 Suppl 1:S2. [PMID: 18466516 PMCID: PMC2367458 DOI: 10.1186/1753-6561-1-s1-s2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Here we describe the data provided for Problem 1 of Genetic Analysis Workshop 15. The data provided for Problem 1 were unusual in two ways. First, the phenotype was the level of gene expression for each gene, not a conventional phenotype like height or disease, and second, there were more than 3500 such phenotypes. Natural variation in gene expression was a new idea in 2004 when these data were collected and published. Because the phenotypes were measured in members of 14 Centre d'Etude du Polymorphisme Humain (CEPH) families, there was an opportunity for linkage mapping on a very large scale. For this purpose, 2882 single-nucleotide polymorphism genotypes were also provided for each family member.
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Abstract
Background Genomic imprinting is a mechanism in which the expression of a gene copy depends upon the sex of the parent from which it was inherited. This mechanism is now well recognized in humans, and the deregulation of imprinted genes has been implicated in a number of diseases. In this study, we performed a genome-wide joint linkage and imprinting scan using two data sets provided by Genetic Analysis Workshop 15 (GAW15). Results The first data set was high-risk rheumatoid arthritis families collected by the North American Rheumatoid Arthritis Consortium. We used both model-based and model-free methods of joint linkage and imprinting analyses. Although a genome scan of rheumatoid arthritis families using GENEHUNTER-MODSCORE suggested regions that might be imprinted, further analyses using variance-components method failed to obtain significant signals of imprinting. The second data set was Problem 1 of GAW15, which included single-nucleotide polymorphism genotypes and gene expression data for Centre d'Etude du Polymorphisme Humain pedigrees. A previous genome-wide linkage scan identified loci that may be regulators of gene expression: our genome-wide joint linkage and imprinting scan using a variance-components approach found significant signals for linkage. Conclusion Our linkage scan results suggest that imprinted genes are unlikely to be involved in susceptibility to rheumatoid arthritis. However, for expression level of TGFBR3 gene, we found a point-wise p-value of 0.03 for imprinting, but increase in the LOD score did not meet the required threshold to reliably identify imprinting as the correct mode of inheritance in genome-wide linkage scans.
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Xing C, Torres-Caban M, Wang T, Lu Q, Xing G, Elston RC. Linkage studies of catechol-O-methyltransferase (COMT) and dopamine-beta-hydroxylase (DBH) cDNA expression levels. BMC Proc 2007; 1 Suppl 1:S95. [PMID: 18466599 PMCID: PMC2367604 DOI: 10.1186/1753-6561-1-s1-s95] [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: 12/19/2022] Open
Abstract
The COMT and DBH genes are physically located at chromosomes 22q11 and 9q34, respectively, and both COMT and DBH are involved in catecholamine metabolism and are strong candidates for certain psychiatric and neurological disorders. Although the genetic determinants for both enzymes' activities have been widely studied, their genetic involvement on gene mRNA expression levels remains unclear. In this study we performed quantitative linkage analysis of COMT and DBH cDNA expression levels, identifying transcriptional regulatory regions for both genes. Multiple Haseman-Elston regression was used to detect both additive and interactive effects between two loci. We found that the master transcriptional regulatory region 20q13 had an additive effect on the COMT expression level. We also found that chromosome 19p13 showed both additive and interactive effects with 9q34 on DBH expression level. Furthermore, a potential interaction between COMT and DBH was indicated.
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Affiliation(s)
- Chao Xing
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Wolstein Research Building 2103, Cornell Drive, Cleveland, Ohio 44106, USA.
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Artificial neural networks for linkage analysis of quantitative gene expression phenotypes and evaluation of gene x gene interactions. BMC Proc 2007; 1 Suppl 1:S47. [PMID: 18466546 PMCID: PMC2367483 DOI: 10.1186/1753-6561-1-s1-s47] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background Using single-nucleotide polymorphism (SNP) genotypes and selected gene expression phenotypes from 14 CEPH (Centre d'Etude du Polymorphisme Humain) pedigrees provided for Genetic Analysis Workshop 15 (GAW15), we analyzed quantitative traits with artificial neural networks (ANNs). Our goals were to identify individual linkage signals and examine gene × gene interactions. First, we used classical multipoint methods to identify phenotypes having nominal linkage evidence at two or more loci. ANNs were then applied to sib-pair identity-by-descent (IBD) allele sharing across the genome as input variables and squared trait sums and differences for the sib pairs as output variables. The weights of the trained networks were analyzed to assess the linkage evidence at each locus as well as potential interactions between them. Results Loci identified by classical linkage analysis could also be identified by our ANN analysis. However some ANN results were noisy, and our attempts to use cross-validated training to avoid overtraining and thereby improve results were only partially successful. Potential interactions between loci with high-ranked weight measures were also evaluated, with the resulting patterns suggesting existence of both synergistic and antagonistic effects between loci. Conclusion Our results suggest that ANNs can serve as a useful method to analyze quantitative traits and are a potential tool for detecting gene × gene interactions. However, for the approach implemented here, optimizing the ANNs and obtaining stable results remains challenging.
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Linkage disequilibrium maps and location databases. Methods Mol Biol 2007. [PMID: 17984536 DOI: 10.1007/978-1-59745-389-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Effective application of association mapping for complex traits requires characterization of linkage disequilibrium (LD) patterns that reflect the dominant process of recombination and its duration in addition to the more subtle influences of mutation, selection, and genetic drift. Maps expressed in linkage disequilibrium units (LDUs) reflect the influences of these factors with the use of a modified version of Malecot's isolation-by-distance model. As a result, LDU maps are analogous to linkage maps in so far as their provision of an additive metric that is related to recombination and facilitates association-mapping studies. However, unlike linkage maps, LDUs also reflect the partly cumulative effects of multiple historical bottlenecks that account for substantial variations in LD patterns between populations. This chapter provides an overview of the data requirements and methodology used to construct LDU maps, their applications outside association mapping, and their integration into location databases.
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Abstract
In many instances, there are large sex differences in mutation rates, recombination rates, selection, rates of gene flow, and genetic drift. Mutation rates are often higher in males, a difference that has been estimated both directly and indirectly. The higher male mutation rate appears related to the larger number of cell divisions in male lineages but mutation rates also appear gene- and organism-specific. When there is recombination in only one sex, it is always the homogametic sex. When there is recombination in both sexes, females often have higher recombination but there are many exceptions. There are a number of hypotheses to explain the sex differences in recombination. Sex-specific differences in selection may result in stable polymorphisms or for sex chromosomes, faster evolutionary change. In addition, sex-dependent selection may result in antagonistic pleiotropy or sexually antagonistic genes. There are many examples of sex-specific differences in gene flow (dispersal) and a number of adaptive explanations for these differences. The overall effective population size (genetic drift) is dominated by the lower sex-specific effective population size. The mean of the mutation, recombination, and gene flow rates over the two sexes can be used in a population genetics context unless there are sex-specific differences in selection or genetic drift. Sex-specific differences in these evolutionary factors appear to be unrelated to each other. The evolutionary explanations for sex-specific differences for each factor are multifaceted and, in addition, explanations may include chance, nonadaptive differences, or mechanistic, nonevolutionary factors.
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Affiliation(s)
- Philip W Hedrick
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA.
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Chen WM, Abecasis GR. Family-based association tests for genomewide association scans. Am J Hum Genet 2007; 81:913-26. [PMID: 17924335 PMCID: PMC2265659 DOI: 10.1086/521580] [Citation(s) in RCA: 345] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 07/11/2007] [Indexed: 01/20/2023] Open
Abstract
With millions of single-nucleotide polymorphisms (SNPs) identified and characterized, genomewide association studies have begun to identify susceptibility genes for complex traits and diseases. These studies involve the characterization and analysis of very-high-resolution SNP genotype data for hundreds or thousands of individuals. We describe a computationally efficient approach to testing association between SNPs and quantitative phenotypes, which can be applied to whole-genome association scans. In addition to observed genotypes, our approach allows estimation of missing genotypes, resulting in substantial increases in power when genotyping resources are limited. We estimate missing genotypes probabilistically using the Lander-Green or Elston-Stewart algorithms and combine high-resolution SNP genotypes for a subset of individuals in each pedigree with sparser marker data for the remaining individuals. We show that power is increased whenever phenotype information for ungenotyped individuals is included in analyses and that high-density genotyping of just three carefully selected individuals in a nuclear family can recover >90% of the information available if every individual were genotyped, for a fraction of the cost and experimental effort. To aid in study design, we evaluate the power of strategies that genotype different subsets of individuals in each pedigree and make recommendations about which individuals should be genotyped at a high density. To illustrate our method, we performed genomewide association analysis for 27 gene-expression phenotypes in 3-generation families (Centre d'Etude du Polymorphisme Humain pedigrees), in which genotypes for ~860,000 SNPs in 90 grandparents and parents are complemented by genotypes for ~6,700 SNPs in a total of 168 individuals. In addition to increasing the evidence of association at 15 previously identified cis-acting associated alleles, our genotype-inference algorithm allowed us to identify associated alleles at 4 cis-acting loci that were missed when analysis was restricted to individuals with the high-density SNP data. Our genotype-inference algorithm and the proposed association tests are implemented in software that is available for free.
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Affiliation(s)
- Wei-Min Chen
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA.
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Abstract
PURPOSE OF REVIEW Essential hypertension affects more than 20% of the adult population, and has a multifactorial origin arising from an interaction between susceptibility genes and environmental factors. Several strategies have been used to identify hypertension susceptibility genes. This review highlights recent efforts in genetic dissection of essential hypertension. RECENT FINDINGS Recently, further chromosomal regions harboring blood pressure loci have emerged in genome-wide linkage studies. Findings from a new systematic two-dimensional genome scan are presented, as well as sex-specific loci linked to hypertension in inbred rodent models. Many case-control association studies have been carried out, but results so far have been equivocal. This review discusses some interesting studies combining linkage and association strategies using gene-gene interactions, and studies the use of haplotypes instead of SNPs. Two novel hypertension susceptibility genes are presented, and a short summary on new insights into genes of the renin-angiotensin and adrenergic systems is given. SUMMARY To date, linkage and association studies have not been convincing. Genome-wide association studies may prove to be an effective approach to the problems posed by complex traits. Combined with candidate gene approaches, it is hoped this strategy will yield convincing evidence for genes associated with essential hypertension.
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Affiliation(s)
- Alexander Binder
- Department of General Pediatrics, Medical University of Graz, Graz, Austria.
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35
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Abstract
Inaccurate genetic (or linkage) maps can reduce the power to detect linkage, increase type I error, and distort haplotype and relationship inference. To improve the accuracy of existing maps, I propose a meta-analysis-based method that combines independent map estimates into a single estimate of the linkage map. The method uses the variance of each independent map estimate to combine them efficiently, whether the map estimates use the same set of markers or not. As compared with a joint analysis of the pooled genotype data, the proposed method is attractive for three reasons: (1) it has comparable efficiency to the maximum likelihood map estimate when the pooled data are homogeneous; (2) relative to existing map estimation methods, it can have increased efficiency when the pooled data are heterogeneous; and (3) it avoids the practical difficulties of pooling human subjects data. On the basis of simulated data modeled after two real data sets, the proposed method can reduce the sampling variation of linkage maps commonly used in whole-genome linkage scans. Furthermore, when the independent map estimates are also maximum likelihood estimates, the proposed method performs as well as or better than when they are estimated by the program CRIMAP. Since variance estimates of maps may not always be available, I demonstrate the feasibility of three different variance estimators. Overall, the method should prove useful to investigators who need map positions for markers not contained in publicly available maps, and to those who wish to minimize the negative effects of inaccurate maps.
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Affiliation(s)
- William C L Stewart
- Department of Biostatistics, Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109-2029, USA.
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36
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Toni C, Domenici R, Presciuttini S. Genotype probabilities of pairs of individuals for X-chromosome markers. Transfusion 2007; 47:1276-80. [PMID: 17581164 DOI: 10.1111/j.1537-2995.2007.01270.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND The usual set of autosomal markers (A-STRs) available in commercial kits is often insufficient to discriminate between close relationships when only two subjects are available for analysis. X-chromosome markers (X-STRs) provide higher statistical power in special cases. STUDY DESIGN AND METHODS Formulas are derived for the probabilities of all possible genotype pairs for X-STRs of any sex combination for seven common relationships. The power of exclusion (PE) of X-STRs in parentage analysis is compared with that of A-STRs of equivalent distribution of allele frequency. RESULTS Seventy-three equations were obtained, from which the likelihood ratio of any two alternative hypotheses about the relationship between two individuals can be obtained by division and simplification. For father-daughter and mother-son duos, the PE of X-STRs is almost twice the corresponding value of A-STRs for moderately low values of heterozygosity (0.6-0.75); for alleged pairs of sisters and pairs of half-sisters the PE is equivalent to that of A-STRs in parent-child duos. Considering four real unlinked X-STRs, the cumulative PE for father-daughter and mother-son duos was 99 percent, compared with 94 percent if they were autosomal. CONCLUSIONS X-STRs can substantially increase the discrimination capacity of standard A-STRs in parentage analyses involving pairs of individuals. Up to four unlinked X-STRs may be treated as independent loci. When linked loci are included, computer programs that calculate pedigree likelihoods can be used.
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Affiliation(s)
- Chiara Toni
- Unit of Legal Medicine, School of Medicine, University of Pisa, Italy
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37
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Abstract
I derive a covariance structure model for pairwise linkage disequilibrium (LD) between binary markers in a recently admixed population and use a generalized least-squares method to fit the model to two different data sets. Both linked and unlinked marker pairs are incorporated in the model. Under the model, a pairwise LD matrix is decomposed into two component matrices, one containing LD attributable to admixture, and another containing, in an aggregate form, LD specific to the populations forming the mixture. I use population genetics theory to show that the latter matrix has block-diagonal structure. For the data sets considered here, I show that the number of source populations can be determined by statistical inference on the canonical correlations of the sample LD matrix.
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Affiliation(s)
- Mark N Grote
- Department of Anthropology, University of California-Davis, 1 Shields Avenue, Davis, CA 95616, USA.
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Wettstein PJ, Borson ND. Distributions of single nucleotide polymorphisms in differential chromosome segments of congenic resistant strains that define minor histocompatibility antigens. Immunogenetics 2007; 59:631-9. [PMID: 17541577 DOI: 10.1007/s00251-007-0231-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 05/08/2007] [Indexed: 01/25/2023]
Abstract
Minor histocompatibility antigens (MiHAs) stimulate the rejection of allografts when donors and recipients are matched at the major histocompatibility complex (MHC). The majority of identified autosomal MiHAs were generated by non-synonymous (NS) substitutions that alter MHC class I-binding peptides. The mosaic distribution of single nucleotide polymorphisms (SNPs) that distinguish inbred mouse strains led us to hypothesize that MiHA genes defined by congenic strains on C57BL/6 and C57BL/10 backgrounds map to chromosomal regions with relatively high numbers of NS SNPs that distinguish C57 strains from other common inbred strains. To test this hypothesis, we mapped the ends of differential chromosome segments of congenic strains, which define 12 MiHAs, relative to microsatellites and SNPs. The lengths of differential segments ranged from 9.7 to 105.9 Mbp in congenic strains where no attempts were made to select recombinants within these segments. There was no apparent correlation between differential segment length and number of backcrosses, suggesting that factors other than the number of opportunities for recombination affected the differential segment lengths in these congenics. These differential segments included higher numbers of NS SNPs that distinguish C57BL/6J from A/J, DBA/2J, and 129S1/J than would be predicted if these SNPs were uniformly distributed along the chromosomes. The most extreme case was the H8 congenic that included 74% of the SNPs on chromosome 14 within its 9.7-11.1 Mbp differential segment. These results point toward a direct relationship between the level of genomic divergence, as indicated by numbers of NS SNPs, and numbers of MiHAs that collectively determine the magnitude of allograft rejection.
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Affiliation(s)
- Peter J Wettstein
- Department of Surgery, Mayo Clinic College of Medicine, Rochester, MN, USA.
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Rudd MK, Friedman C, Parghi SS, Linardopoulou EV, Hsu L, Trask BJ. Elevated rates of sister chromatid exchange at chromosome ends. PLoS Genet 2007; 3:e32. [PMID: 17319749 PMCID: PMC1802831 DOI: 10.1371/journal.pgen.0030032] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Accepted: 01/04/2007] [Indexed: 12/19/2022] Open
Abstract
Chromosome ends are known hotspots of meiotic recombination and double-strand breaks. We monitored mitotic sister chromatid exchange (SCE) in telomeres and subtelomeres and found that 17% of all SCE occurs in the terminal 0.1% of the chromosome. Telomeres and subtelomeres are significantly enriched for SCEs, exhibiting rates of SCE per basepair that are at least 1,600 and 160 times greater, respectively, than elsewhere in the genome.
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Affiliation(s)
- M. Katharine Rudd
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Cynthia Friedman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Sean S Parghi
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Elena V Linardopoulou
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Barbara J Trask
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * To whom correspondence should be addressed. E-mail:
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Cheung VG, Burdick JT, Hirschmann D, Morley M. Polymorphic variation in human meiotic recombination. Am J Hum Genet 2007; 80:526-30. [PMID: 17273974 PMCID: PMC1821106 DOI: 10.1086/512131] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Accepted: 12/19/2006] [Indexed: 02/04/2023] Open
Abstract
In this study, our phenotype of interest is meiotic recombination. Using genotypes of approximately 6,000 SNP markers in members of the Centre d'Etude du Polymorphisme Humain Utah pedigrees, we found extensive individual variation in the number of female and male recombination events. The locations and frequencies of these recombination events vary along the genome. In both female and male meiosis, the regions with the most recombination events are found at the ends of the chromosomes. Our analysis also shows that there are polymorphic differences among individuals in the activity of the recombination "jungles"; these preferred sites of meiotic recombination differ greatly among individuals. These findings have important implications for understanding genetic disorders that result from improper chromosome segregation.
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Affiliation(s)
- Vivian G Cheung
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Sieh W, Yu CE, Bird TD, Schellenberg GD, Wijsman EM. Accounting for linkage disequilibrium among markers in linkage analysis: impact of haplotype frequency estimation and molecular haplotypes for a gene in a candidate region for Alzheimer's disease. Hum Hered 2007; 63:26-34. [PMID: 17215579 DOI: 10.1159/000098459] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Accepted: 11/02/2006] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVES Linkage disequilibrium (LD) between closely spaced SNPs can be accommodated in linkage analysis by specifying the multi-SNP haplotype frequencies, if known. Phased haplotypes in candidate regions can provide gold standard haplotype frequency estimates, and may be of inherent interest as markers. We evaluated the effects of different methods of haplotype frequency estimation, and the use of marker phase information, on linkage analysis of a multi-SNP cluster in a candidate region for Alzheimer's disease (AD). METHODS We performed parametric linkage analysis of a five-SNP cluster in extended pedigrees to compare the use of: (1) haplotype frequencies estimated by molecular phase determination, maximum likelihood estimation, or by assuming linkage equilibrium (LE); (2) AD families or controls as the frequency source; and (3) unphased or molecularly phased SNP data. RESULTS There was moderate to strong pairwise LD among the five SNPs. Falsely assuming LE substantially inflated the LOD score, but the method of haplotype frequency estimation and particular sample used made little difference provided that LD was accommodated. Use of phased haplotypes produced a modest increase in the LOD score over unphased SNPs. CONCLUSIONS Ignoring LD between markers can lead to substantially inflated evidence for linkage in LOD score analysis of extended pedigrees with missing data. Use of marker phase information in linkage analysis may be important in disease studies where the costs of family recruitment and phenotyping greatly exceed the costs of phase determination.
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Affiliation(s)
- Weiva Sieh
- Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
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Abstract
As a result of previous large, multipoint linkage studies there is a substantial amount of existing marker data. Due to the increased sample size, genetic maps estimated from these data could be more accurate than publicly available maps. However, current methods for map estimation are restricted to data sets containing pedigrees with a small number of individuals, or cannot make full use of marker data that are observed at several loci on members of large, extended pedigrees. In this article, a maximum likelihood (ML) method for map estimation that can make full use of the marker data in a large, multipoint linkage study is described. The method is applied to replicate sets of simulated marker data involving seven linked loci, and pedigree structures based on the real multipoint linkage study of Abkevich et al. (2003, American Journal of Human Genetics 73, 1271-1281). The variance of the ML estimate is accurately estimated, and tests of both simple and composite null hypotheses are performed. An efficient procedure for combining map estimates over data sets is also suggested.
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Affiliation(s)
- William C L Stewart
- Department of Statistics, University of Washington, Seattle, Washington 98195, USA.
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Lyrakou S, Mantas D, Msaouel P, Baathalah S, Shrivastav P, Chrisostomou M, Mihalopoulos Y, Hasiakos D, Baka S. Crossover analysis using immunofluorescent detection of MLH1 foci in frozen–thawed testicular tissue. Reprod Biomed Online 2007; 15:99-105. [PMID: 17623546 DOI: 10.1016/s1472-6483(10)60698-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To date, the effects of freezing on spermatogenesis have not yet been fully investigated at a molecular level. Antibody localization studies have identified the MutL homolog 1 (MLH1) protein, a mis-match repair protein, at the prophase I stage of meiosis, which allows the detection of recombination foci during pachytene. This study investigated the effect of long-term testicular tissue cryopreservation on meiotic prophase I, identified by recombination foci frequency and synaptonemal complex (SC) integrity. Frozen-thawed testicular tissues from 12 males who had each fathered a child were used. Because vasectomy or reverse vasectomy procedures are rare in the locale of the investigation, it was not possible to obtain fresh testicular tissue and use the males as their own controls. Immunocytogenetic analysis of 612 spermatocytes at the pachytene stage was performed. The results indicated a mean number of MLH1 foci of 49.2 (SD +/- 5.9), and no correlation was found between the freezing period, the MLH1 frequency and the SC integrity. The results suggest that freezing of testicular tissue taken post-puberty does not appear to be detrimental to the crossover process as identified by occurrence of MLH1 loci.
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Affiliation(s)
- S Lyrakou
- EuroGene Ltd, 21-23 Gounari, Postcode 185-31, Piraeus, Greece.
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Wijsman EM, Sung YJ, Buil A. Summary of Genetic Analysis Workshop 15: Group 9 linkage analysis of the CEPH expression data. Genet Epidemiol 2007; 31 Suppl 1:S75-85. [DOI: 10.1002/gepi.20283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Fairhurst AM, Wandstrat AE, Wakeland EK. Systemic lupus erythematosus: multiple immunological phenotypes in a complex genetic disease. Adv Immunol 2006; 92:1-69. [PMID: 17145301 DOI: 10.1016/s0065-2776(06)92001-x] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex polygenic autoimmune disease characterized by the presence of anti-nuclear autoantibodies (ANAs) that are often detectable years prior to the onset of clinical disease. The disease is associated with a chronic activation of the immune system, with the most severe forms progressing to inflammatory damage that can impact multiple organ systems in afflicted individuals. Current therapeutic strategies poorly control disease manifestations and are generally immunosuppressive. Recent studies in human patient populations and animal models have associated elements of the innate immune system and abnormalities in the immature B lymphocyte receptor repertoires with disease initiation. A variety of cytokines, most notably type I interferons, play important roles in disease pathogenesis and effector mechanisms. The genetic basis for disease susceptibility is complex, and analyses in humans and mice have identified multiple susceptibility loci, several of which are located in genomic regions that are syntenic between humans and mice. The complexities of the genetic interactions that mediate lupus have been investigated in murine model systems by characterizing the progressive development of disease in strains expressing various combinations of susceptibility alleles. These analyses indicate that genetic epistasis dramatically impact disease development and support the feasibility of identifying molecular pathways that can suppress disease progression without completely impairing normal immune function.
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Affiliation(s)
- Anna-Marie Fairhurst
- Center for Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Wijsman EM, Rothstein JH, Thompson EA. Multipoint linkage analysis with many multiallelic or dense diallelic markers: Markov chain-Monte Carlo provides practical approaches for genome scans on general pedigrees. Am J Hum Genet 2006; 79:846-58. [PMID: 17033961 PMCID: PMC1698573 DOI: 10.1086/508472] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 08/11/2006] [Indexed: 11/03/2022] Open
Abstract
Computations for genome scans need to adapt to the increasing use of dense diallelic markers as well as of full-chromosome multipoint linkage analysis with either diallelic or multiallelic markers. Whereas suitable exact-computation tools are available for use with small pedigrees, equivalent exact computation for larger pedigrees remains infeasible. Markov chain-Monte Carlo (MCMC)-based methods currently provide the only computationally practical option. To date, no systematic comparison of the performance of MCMC-based programs is available, nor have these programs been systematically evaluated for use with dense diallelic markers. Using simulated data, we evaluate the performance of two MCMC-based linkage-analysis programs--lm_markers from the MORGAN package and SimWalk2--under a variety of analysis conditions. Pedigrees consisted of 14, 52, or 98 individuals in 3, 5, or 6 generations, respectively, with increasing amounts of missing data in larger pedigrees. One hundred replicates of markers and trait data were simulated on a 100-cM chromosome, with up to 10 multiallelic and up to 200 diallelic markers used simultaneously for computation of multipoint LOD scores. Exact computation was available for comparison in most situations, and comparison with a perfectly informative marker or interprogram comparison was available in the remaining situations. Our results confirm the accuracy of both programs in multipoint analysis with multiallelic markers on pedigrees of varied sizes and missing-data patterns, but there are some computational differences. In contrast, for large numbers of dense diallelic markers, only the lm_markers program was able to provide accurate results within a computationally practical time. Thus, programs in the MORGAN package are the first available to provide a computationally practical option for accurate linkage analyses in genome scans with both large numbers of diallelic markers and large pedigrees.
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Affiliation(s)
- Ellen M Wijsman
- Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA.
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Abstract
By comparison with other species, the meiotic process in the human female is extraordinarily error-prone. In addition to the well-known effect of advancing maternal age, recent studies have demonstrated that the number and location of meiotic recombination events influences the likelihood of meiotic non-disjunction in our species. Although this association extends to many other organisms, the factors that influence the number and placement of exchanges within a cell remain poorly understood. Like other aspects of meiosis, the control of recombination is likely to be subject to variation among species. In this review we summarize data from recent studies in mammals; the combined data suggest that both genetic and environmental factors influence recombination in mammals and, importantly, that control mechanisms probably differ between males and females.
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Affiliation(s)
- P A Hunt
- School of Molecular Biosciences and Center for Reproduction, Fulmer Hall 539, Washington State University, P.O. Box 644660, Pullman, WA 99164-4660, USA.
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Burdick JT, Chen WM, Abecasis GR, Cheung VG. In silico method for inferring genotypes in pedigrees. Nat Genet 2006; 38:1002-4. [PMID: 16921375 PMCID: PMC3005330 DOI: 10.1038/ng1863] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Accepted: 07/20/2006] [Indexed: 01/19/2023]
Abstract
Our genotype inference method combines sparse marker data from a linkage scan and high-resolution SNP genotypes for several individuals to infer genotypes for related individuals. We illustrate the method's utility by inferring over 53 million SNP genotypes for 78 children in the Centre d'Etude du Polymorphisme Humain families. The method can be used to obtain high-density genotypes in different family structures, including nuclear families commonly used in complex disease gene mapping studies.
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Affiliation(s)
- Joshua T Burdick
- Department of Pediatrics, University of Pennsylvania, 3516 Civic Center Blvd., Philadelphia, Pennsylvania 19104, USA
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Pavy N, Parsons LS, Paule C, MacKay J, Bousquet J. Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics 2006; 7:174. [PMID: 16824208 PMCID: PMC1557672 DOI: 10.1186/1471-2164-7-174] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2006] [Accepted: 07/06/2006] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND High-throughput genotyping technologies represent a highly efficient way to accelerate genetic mapping and enable association studies. As a first step toward this goal, we aimed to develop a resource of candidate Single Nucleotide Polymorphisms (SNP) in white spruce (Picea glauca [Moench] Voss), a softwood tree of major economic importance. RESULTS A white spruce SNP resource encompassing 12,264 SNPs was constructed from a set of 6,459 contigs derived from Expressed Sequence Tags (EST) and by using the bayesian-based statistical software PolyBayes. Several parameters influencing the SNP prediction were analysed including the a priori expected polymorphism, the probability score (PSNP), and the contig depth and length. SNP detection in 3' and 5' reads from the same clones revealed a level of inconsistency between overlapping sequences as low as 1%. A subset of 245 predicted SNPs were verified through the independent resequencing of genomic DNA of a genotype also used to prepare cDNA libraries. The validation rate reached a maximum of 85% for SNPs predicted with either PSNP > or = 0.95 or > or = 0.99. A total of 9,310 SNPs were detected by using PSNP > or = 0.95 as a criterion. The SNPs were distributed among 3,590 contigs encompassing an array of broad functional categories, with an overall frequency of 1 SNP per 700 nucleotide sites. Experimental and statistical approaches were used to evaluate the proportion of paralogous SNPs, with estimates in the range of 8 to 12%. The 3,789 coding SNPs identified through coding region annotation and ORF prediction, were distributed into 39% nonsynonymous and 61% synonymous substitutions. Overall, there were 0.9 SNP per 1,000 nonsynonymous sites and 5.2 SNPs per 1,000 synonymous sites, for a genome-wide nonsynonymous to synonymous substitution rate ratio (Ka/Ks) of 0.17. CONCLUSION We integrated the SNP data in the ForestTreeDB database along with functional annotations to provide a tool facilitating the choice of candidate genes for mapping purposes or association studies.
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Affiliation(s)
- Nathalie Pavy
- ARBOREA and Canada Research Chair in Forest Genomics, Pavillon Charles-Eugène-Marchand, Université Laval, Ste.Foy, Québec G1K 7P4, Canada
| | - Lee S Parsons
- Center for Computational Genomics and Bioinformatics, University of Minnesota, 420 Delaware St. S.E., MMC 43, Minneapolis, MN 55455, USA
| | - Charles Paule
- Center for Computational Genomics and Bioinformatics, University of Minnesota, 420 Delaware St. S.E., MMC 43, Minneapolis, MN 55455, USA
| | - John MacKay
- ARBOREA and Canada Research Chair in Forest Genomics, Pavillon Charles-Eugène-Marchand, Université Laval, Ste.Foy, Québec G1K 7P4, Canada
| | - Jean Bousquet
- ARBOREA and Canada Research Chair in Forest Genomics, Pavillon Charles-Eugène-Marchand, Université Laval, Ste.Foy, Québec G1K 7P4, Canada
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50
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Vallente RU, Cheng EY, Hassold TJ. The synaptonemal complex and meiotic recombination in humans: new approaches to old questions. Chromosoma 2006; 115:241-9. [PMID: 16547726 DOI: 10.1007/s00412-006-0058-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 02/07/2006] [Accepted: 02/08/2006] [Indexed: 11/25/2022]
Abstract
Meiotic prophase serves as an arena for the interplay of two important cellular activities, meiotic recombination and synapsis of homologous chromosomes. Synapsis is mediated by the synaptonemal complex (SC), originally characterized as a structure linked to pairing of meiotic chromosomes (Moses (1958) J Biophys Biochem Cytol 4:633-638). In 1975, the first electron micrographs of human pachytene stage SCs were presented (Moses et al. (1975) Science 187:363-365) and over the next 15 years the importance of the SC to normal meiotic progression in human males and females was established (Jhanwar and Chaganti (1980) Hum Genet 54:405-408; Pathak and Elder (1980) Hum Genet 54:171-175; Solari (1980) Chromosoma 81:315-337; Speed (1984) Hum Genet 66:176-180; Wallace and Hulten (1985) Ann Hum Genet 49(Pt 3):215-226). Further, these studies made it clear that abnormalities in the assembly or maintenance of the SC were an important contributor to human infertility (Chaganti et al. (1980) Am J Hum Genet 32:833-848; Vidal et al. (1982) Hum Genet 60:301-304; Bojko (1983) Carlsberg Res Commun 48:285-305; Bojko (1985) Carlsberg Res Commun 50:43-72; Templado et al. (1984) Hum Genet 67:162-165; Navarro et al. (1986) Hum Reprod 1:523-527; Garcia et al. (1989) Hum Genet 2:147-53). However, the utility of these early studies was limited by lack of information on the structural composition of the SC and the identity of other SC-associated proteins. Fortunately, studies of the past 15 years have gone a long way toward remedying this problem. In this minireview, we highlight the most important of these advances as they pertain to human meiosis, focusing on temporal aspects of SC assembly, the relationship between the SC and meiotic recombination, and the contribution of SC abnormalities to human infertility.
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Affiliation(s)
- Rhea U Vallente
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA.
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