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Lin D, Qiu Y, Zhou F, Li X, Deng S, Yang J, Chen Q, Cai G, Yang J, Wu Z, Zheng E. Genome-wide detection of multiple variants associated with teat number in French Yorkshire pigs. BMC Genomics 2024; 25:722. [PMID: 39054457 PMCID: PMC11271213 DOI: 10.1186/s12864-024-10611-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Teat number is a vital reproductive trait in sows, crucial for providing immunity and nutrition to piglets during lactation. However, "missing heritability" in Single Nucleotide Polymorphism (SNP)-based Genome-Wide Association Studies (GWAS) has led to an increasing focus on structural variations in the genetic analysis of complex biological traits. RESULTS In this study, we generated a comprehensive CNV map in a population of French Yorkshire pigs (n = 644) and identified 429 CNVRs. Notably, 44% (189 CNVRs) of these were detected for the first time. Subsequently, we conducted GWAS for teat number in the French Yorkshire pig population using both 80K chip and its imputed data, as well as a GWAS analysis based on CNV regions (CNVR). Interestingly, 80K chip GWAS identified two SNPs located on Sus scrofa chromosome 5 (SSC5) that were simultaneously associated with Total Teat Number (TTN), Left Teat Number (LTN), and Right Teat Number (RTN). The leading SNP (WU_10.2_5_76130558) explained 3.33%, 2.69%, and 2.67% of the phenotypic variance for TTN, LTN, and RTN, respectively. Moreover, through imputed GWAS, we successfully identified 30 genetic variants associated with TTN located within the 73.22 -73.30 Mb region on SSC5. The two SNPs identified in the 80K chip GWAS were also located in this region. In addition, CNVR-based GWAS revealed three significant CNVRs associated with TTN. Finally, through gene annotation, we pinpointed two candidate genes, TRIM66 and PRICKLE1, which are related to diverse processes such as breast cancer and abnormal vertebral development. CONCLUSIONS Our research provides an in-depth analysis of the complex genetic structure underlying teat number, contributing to the genetic enhancement of sows with improved reproductive performance and, ultimately, bolstering the economic benefits of swine production enterprises.
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Affiliation(s)
- Danyang Lin
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China
| | - Fuchen Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China
| | - Xuehua Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China
| | - Shaoxiong Deng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China
| | - Jisheng Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China
| | - Qiaoer Chen
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, China.
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
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Audain E, Wilsdon A, Breckpot J, Izarzugaza JMG, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett AS, Benson WD, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney PEF, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney BD, Klaassen S, Kramer HH, Marshall CR, Milewicz DM, Lemaire S, Coselli JS, Mitchell ME, Tomita-Mitchell A, Prakash SK, Stamm K, Stewart AFR, Silversides CK, Siebert R, Stiller B, Rosenfeld JA, Vater I, Postma AV, Caliebe A, Brook JD, Andelfinger G, Hurles ME, Thienpont B, Larsen LA, Hitz MP. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease. PLoS Genet 2021; 17:e1009679. [PMID: 34324492 PMCID: PMC8354477 DOI: 10.1371/journal.pgen.1009679] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/10/2021] [Accepted: 06/23/2021] [Indexed: 11/18/2022] Open
Abstract
Numerous genetic studies have established a role for rare genomic variants in Congenital Heart Disease (CHD) at the copy number variation (CNV) and de novo variant (DNV) level. To identify novel haploinsufficient CHD disease genes, we performed an integrative analysis of CNVs and DNVs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm. We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed variation rate testing for DNVs identified in 2,489 parent-offspring trios. Our analysis revealed 21 genes which were significantly affected by rare CNVs and/or DNVs in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1) have only been associated in small cases series or show new associations with CHD. In addition, a systems level analysis revealed affected protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes and pathways.
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Affiliation(s)
- Enrique Audain
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Anna Wilsdon
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Jeroen Breckpot
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Tomas W. Fitzgerald
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Anne-Karin Kahlert
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Alejandro Sifrim
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Hashim Abdul-Khaliq
- Clinic for Pediatric Cardiology—University Hospital of Saarland, Homburg (Saar), Germany
| | - Mads Bak
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne S. Bassett
- Toronto Congenital Cardiac Centre for Adults, and Division of Cardiology, Department of Medicine, University Health Network, Toronto, Canada
- Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Woodrow D. Benson
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Felix Berger
- Department of Congenital Heart Disease—Pediatric Cardiology, German Heart Center Berlin, Berlin, Germany
| | - Ingo Daehnert
- Department of Pediatric Cardiology and Congenital Heart Disease, Heart Center, University of Leipzig, Leipzig, Germany
| | - Koenraad Devriendt
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sven Dittrich
- Department of Pediatric Cardiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Piers EF Daubeney
- Division of Paediatric Cardiology, Royal Brompton Hospital, London, United Kingdom
| | - Vidu Garg
- The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Center for Cardiovascular Research, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Kirstin Hoff
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Philipp Hofmann
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Gregor Dombrowsky
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Thomas Pickardt
- Competence Network for Congenital Heart Defects, Berlin, Germany
| | - Ulrike Bauer
- Competence Network for Congenital Heart Defects, Berlin, Germany
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Sabine Klaassen
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Pediatric Cardiology, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Hans-Heiner Kramer
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Christian R. Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Dianna M. Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Scott Lemaire
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph S. Coselli
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Michael E. Mitchell
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Aoy Tomita-Mitchell
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Siddharth K. Prakash
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Karl Stamm
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Alexandre F. R. Stewart
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
| | - Candice K. Silversides
- Toronto Congenital Cardiac Centre for Adults, and Division of Cardiology, Department of Medicine, University Health Network, Toronto, Canada
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Brigitte Stiller
- Department of Congenital Heart Disease and Pediatric Cardiology, University Heart Center Freiburg—Bad Krozingen, Freiburg, Germany
| | - Jill A. Rosenfeld
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Inga Vater
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Alex V. Postma
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Almuth Caliebe
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - J. David Brook
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Saint-Justine Research Centre, Université de Montréal, Montreal, Canada
| | - Matthew E. Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Bernard Thienpont
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Lars Allan Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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3
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Fernandes AC, da Silva VH, Goes CP, Moreira GCM, Godoy TF, Ibelli AMG, Peixoto JDO, Cantão ME, Ledur MC, de Rezende FM, Coutinho LL. Genome-wide detection of CNVs and their association with performance traits in broilers. BMC Genomics 2021; 22:354. [PMID: 34001004 PMCID: PMC8130382 DOI: 10.1186/s12864-021-07676-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
Background Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age. Results We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels. Conclusions Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07676-1.
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Affiliation(s)
- Anna Carolina Fernandes
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - Vinicius Henrique da Silva
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - Carolina Purcell Goes
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | | | - Thaís Fernanda Godoy
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | | | - Jane de Oliveira Peixoto
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Maurício Egídio Cantão
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Mônica Corrêa Ledur
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | | | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil.
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Billingsley KJ, Bandres-Ciga S, Ding J, Hernandez D, Gibbs JR, Blauwendraat C. MIDN locus structural variants and Parkinson's Disease risk. Ann Clin Transl Neurol 2020; 7:602-603. [PMID: 32212230 PMCID: PMC7187709 DOI: 10.1002/acn3.51012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/21/2020] [Indexed: 01/24/2023] Open
Affiliation(s)
- Kimberley J Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
| | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
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5
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Piluso G, Monteleone P, Galderisi S, Giugliano T, Bertolino A, Rocca P, Rossi A, Mucci A, Aguglia E, Andriola I, Bellomo A, Comparelli A, Gambi F, Fagiolini A, Marchesi C, Roncone R, Sacchetti E, Santonastaso P, Siracusano A, Stratta P, Tortorella A, Steardo L, Bucci P, Nigro V, Maj M. Assessment of de novo copy-number variations in Italian patients with schizophrenia: Detection of putative mutations involving regulatory enhancer elements. World J Biol Psychiatry 2019; 20:126-136. [PMID: 29069978 DOI: 10.1080/15622975.2017.1395072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVES Variants appearing de novo in genes regulating key neurodevelopmental processes and/or in non-coding cis-regulatory elements (CREs), as enhancers, may increase the risk for schizophrenia. However, CREs involvement in schizophrenia needs to be explored more deeply. METHODS We investigated de novo copy-number variations (CNVs) in the whole-genomic DNA obtained from 46 family trios of schizophrenia probands by using the Enhancer Chip, a customised array CGH able to investigate the whole genome with a 300-kb resolution, specific disease loci at a ten-fold higher resolution, and which was highly enriched in probes in more than 1,250 enhancer elements selected from Vista Enhancer Browser. RESULTS In seven patients, we found de novo CNVs, two of which overlapped VISTA enhancer elements. De novo CNVs encompass genes (CNTNAP2, MAGI1, TSPAN7 and MET) involved in brain development, while that involving the enhancer element hs1043, also includes ZIC1, which plays a role in neural development and is responsible of behavioural abnormalities in Zic mutant mice. CONCLUSIONS These findings provide further evidence for the involvement of de novo CNVs in the pathogenesis of schizophrenia and suggest that CNVs affecting regulatory enhancer elements could contribute to the genetic vulnerability to the disorder.
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Affiliation(s)
- Giulio Piluso
- a Department of Biochemistry, Biophysics and General Pathology , University of Campania "Luigi Vanvitelli" , Naples , Italy
| | - Palmiero Monteleone
- b Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Section of Neuroscience , University of Salerno , Salerno , Italy
| | - Silvana Galderisi
- c Department of Psychiatry , University of Campania "Luigi Vanvitelli" , Naples , Italy
| | - Teresa Giugliano
- a Department of Biochemistry, Biophysics and General Pathology , University of Campania "Luigi Vanvitelli" , Naples , Italy
| | - Alessandro Bertolino
- d Department of Neurological and Psychiatric Sciences , University of Bari , Bari , Italy
| | - Paola Rocca
- e Department of Neuroscience, Section of Psychiatry , University of Turin , Turin , Italy
| | - Alessandro Rossi
- f Department of Biotechnological and Applied Clinical Sciences, Section of Psychiatry , University of L'Aquila , L'Aquila , Italy
| | - Armida Mucci
- c Department of Psychiatry , University of Campania "Luigi Vanvitelli" , Naples , Italy
| | - Eugenio Aguglia
- g Department of Clinical and Molecular Biomedicine, Psychiatry Unit , University of Catania , Catania , Italy
| | - Ileana Andriola
- d Department of Neurological and Psychiatric Sciences , University of Bari , Bari , Italy
| | - Antonello Bellomo
- h Department of Medical Sciences, Psychiatry Unit , University of Foggia , Foggia , Italy
| | - Anna Comparelli
- i Department of Neurosciences, Mental Health and Sensory Organs , S. Andrea Hospital, Sapienza University of Rome , Rome , Italy
| | - Francesco Gambi
- j Department of Neuroscience and Imaging, Chair of Psychiatry , G. D'Annunzio University , Chieti , Italy
| | - Andrea Fagiolini
- k Department of Molecular Medicine and Clinical Department of Mental Health , University of Siena , Siena , Italy
| | - Carlo Marchesi
- l Department of Neuroscience, Psychiatry Unit , University of Parma , Parma , Italy
| | - Rita Roncone
- m Department of Life, Health and Environmental Sciences, Unit of Psychiatry , University of L'Aquila , L'Aquila , Italy
| | - Emilio Sacchetti
- n Psychiatric Unit, School of Medicine, Department of Mental Health , University of Brescia and Spedali Civili Hospital , Brescia , Italy
| | - Paolo Santonastaso
- o Psychiatric Clinic, Department of Neurosciences , University of Padua , Padua , Italy
| | - Alberto Siracusano
- p Department of Systems Medicine, Chair of Psychiatry , Tor Vergata University of Rome , Rome , Italy
| | - Paolo Stratta
- f Department of Biotechnological and Applied Clinical Sciences, Section of Psychiatry , University of L'Aquila , L'Aquila , Italy
| | | | - Luca Steardo
- c Department of Psychiatry , University of Campania "Luigi Vanvitelli" , Naples , Italy
| | - Paola Bucci
- c Department of Psychiatry , University of Campania "Luigi Vanvitelli" , Naples , Italy
| | - Vincenzo Nigro
- a Department of Biochemistry, Biophysics and General Pathology , University of Campania "Luigi Vanvitelli" , Naples , Italy
| | - Mario Maj
- c Department of Psychiatry , University of Campania "Luigi Vanvitelli" , Naples , Italy
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Calling Chromosome Alterations, DNA Methylation Statuses, and Mutations in Tumors by Simple Targeted Next-Generation Sequencing. J Mol Diagn 2017; 19:776-787. [DOI: 10.1016/j.jmoldx.2017.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
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Uebe S, Ehrlicher M, Ekici AB, Behrens F, Böhm B, Homuth G, Schurmann C, Völker U, Jünger M, Nauck M, Völzke H, Traupe H, Krawczak M, Burkhardt H, Reis A, Hüffmeier U. Genome-wide association and targeted analysis of copy number variants with psoriatic arthritis in German patients. BMC MEDICAL GENETICS 2017; 18:92. [PMID: 28835222 PMCID: PMC5569473 DOI: 10.1186/s12881-017-0447-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 07/31/2017] [Indexed: 01/16/2023]
Abstract
Background Psoriatic Arthritis (PsA) is a chronic inflammatory disease of the joints. PsA is etiologically complex, and 11 susceptibility loci have been identified so far. Most of these overlap with loci associated with psoriasis vulgaris (PsV), the most common psoriatic skin manifestation which is also frequently seen in PsA patients. In addition, two copy number variants (CNVs) are associated with PsV, one of which, located within the LCE3 gene cluster, is also associated with PsA. Finally, an intergenic deletion has been reported as a PsA-specific CNV. Methods We performed a genome-wide association study (GWAS) of CNVs in PsA and assessed the contribution to disease risk by CNVs at known psoriasis susceptibility loci. Results After stringent quality assessment and validation of CNVs of the GWAS with an alternative quantitative method, two significantly associated CNVs remained, one near UXS1, the other one at the TRB locus. However, MLPA analysis did not confirm the CN state in ~1/3 of individuals, and an analysis of an independent case-control-study failed to confirm the initial associations. Furthermore, detailed PCR-based analysis of the sequence at TRB revealed the existence of a more complex genomic sequence most accurately represented by freeze hg18 which accordingly failed to confirm the hg19 sequence. Only rare CNVs were detected at psoriasis susceptibility loci. At three of 12 susceptibility loci with CNVs (CSMD1, IL12B, RYR2), CN variability was confirmed independently by MLPA. Overall, the rate of CNV confirmation by MLPA was strongly dependent upon CNV type, CNV size and the number of array markers involved in a CNV. Conclusion Although we identified PsA associations at several loci and confirmed that the common CNVs at these sites were real, ~1/3 of the common CNV states could not be reproduced. Furthermore, replication analysis failed to confirm the original association. Furthermore, SNP array-based analyses of CNVs were found to be more reliable for deletions than duplications, independent of the respective CNV allele frequency. CNVs are thus good candidate disease variants, while the methods to detect them should be applied cautiously and reproduced by an independent method. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0447-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Maria Ehrlicher
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Arif Bülent Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Frank Behrens
- Division of Rheumatology and IME Fraunhofer Project Group Translational Medicine & Pharmacology, Goethe University, Frankfurt/Main, Germany
| | - Beate Böhm
- Division of Rheumatology and IME Fraunhofer Project Group Translational Medicine & Pharmacology, Goethe University, Frankfurt/Main, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Michael Jünger
- Clinic of Dermatology, University of Greifswald, Greifswald, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University of Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
| | - Heiko Traupe
- Department of Dermatology, University of Münster, Münster, Germany
| | - Michael Krawczak
- Institute for Medical Informatics and Statistics, Christian-Albrechts University Kiel, Kiel, Germany
| | - Harald Burkhardt
- Division of Rheumatology and IME Fraunhofer Project Group Translational Medicine & Pharmacology, Goethe University, Frankfurt/Main, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany.
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8
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Chung RH, Chiu YF, Hung YJ, Lee WJ, Wu KD, Chen HL, Lin MW, Chen YDI, Quertermous T, Hsiung CA. Genome-wide copy number variation analysis identified deletions in SFMBT1 associated with fasting plasma glucose in a Han Chinese population. BMC Genomics 2017; 18:591. [PMID: 28789618 PMCID: PMC5549306 DOI: 10.1186/s12864-017-3975-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/31/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Fasting glucose and fasting insulin are glycemic traits closely related to diabetes, and understanding the role of genetic factors in these traits can help reveal the etiology of type 2 diabetes. Although single nucleotide polymorphisms (SNPs) in several candidate genes have been found to be associated with fasting glucose and fasting insulin, copy number variations (CNVs), which have been reported to be associated with several complex traits, have not been reported for association with these two traits. We aimed to identify CNVs associated with fasting glucose and fasting insulin. RESULTS We conducted a genome-wide CNV association analysis for fasting plasma glucose (FPG) and fasting plasma insulin (FPI) using a family-based genome-wide association study sample from a Han Chinese population in Taiwan. A family-based CNV association test was developed in this study to identify common CNVs (i.e., CNVs with frequencies ≥ 5%), and a generalized estimating equation approach was used to test the associations between the traits and counts of global rare CNVs (i.e., CNVs with frequencies <5%). We found a significant genome-wide association for common deletions with a frequency of 5.2% in the Scm-like with four mbt domains 1 (SFMBT1) gene with FPG (association p-value = 2×10-4 and an adjusted p-value = 0.0478 for multiple testing). No significant association was observed between global rare CNVs and FPG or FPI. The deletions in 20 individuals with DNA samples available were successfully validated using PCR-based amplification. The association of the deletions in SFMBT1 with FPG was further evaluated using an independent population-based replication sample obtained from the Taiwan Biobank. An association p-value of 0.065, which was close to the significance level of 0.05, for FPG was obtained by testing 9 individuals with CNVs in the SFMBT1 gene region and 11,692 individuals with normal copies in the replication cohort. CONCLUSIONS Previous studies have found that SNPs in SFMBT1 are associated with blood pressure and serum urate concentration, suggesting that SFMBT1 may have functional implications in some metabolic-related traits.
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Affiliation(s)
- Ren-Hua Chung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, No 35, Keyan Road, Zhunan, Miaoli, 350, Taiwan
| | - Yen-Feng Chiu
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, No 35, Keyan Road, Zhunan, Miaoli, 350, Taiwan
| | - Yi-Jen Hung
- Division of Endocrinology and Metabolism, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Social Work, Tunghai University, Taichung, Taiwan
| | - Kwan-Dun Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hui-Ling Chen
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, No 35, Keyan Road, Zhunan, Miaoli, 350, Taiwan
| | - Ming-Wei Lin
- Institute of Public Health, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Yii-Der I Chen
- Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Thomas Quertermous
- Division of Cardiovascular Medicine and Stanford Cardiovascular Institute, Falk Cardiovascular Research Center, Stanford University, Stanford, California, USA
| | - Chao A Hsiung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, No 35, Keyan Road, Zhunan, Miaoli, 350, Taiwan.
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9
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Sapkota Y, Narasimhan A, Kumaran M, Sehrawat BS, Damaraju S. A Genome-Wide Association Study to Identify Potential Germline Copy Number Variants for Sporadic Breast Cancer Susceptibility. Cytogenet Genome Res 2016; 149:156-164. [PMID: 27668787 DOI: 10.1159/000448558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/19/2022] Open
Abstract
Breast cancer (BC) predisposition in populations arises from both genetic and nongenetic risk factors. Structural variations such as copy number variations (CNVs) are heritable determinants for disease susceptibility. The primary objectives of this study are (1) to identify CNVs associated with sporadic BC using a genome-wide association study (GWAS) design; (2) to utilize 2 distinct CNV calling algorithms to identify concordant CNVs as a strategy to reduce false positive associations in the hypothesis-generating GWAS discovery phase, and (3) to identify potential candidate CNVs for follow-up replication studies. We used Affymetrix SNP Array 6.0 data profiled on Caucasian subjects (422 cases/348 controls) to call CNVs using algorithms implemented in Nexus Copy Number and Partek Genomics Suite software. Nexus algorithm identified CNVs associated with BC (731 autosomal CNVs with >5% frequency in the total sample and Q < 0.05). Thirteen CNVs were identified when Partek algorithm-called CNVs were overlapped with Nexus-identified CNVs; these CNVs showed concordances for frequency, effect size, and direction. Coding genes present within BC-associated CNVs were known to play a role in disease etiology and prognosis. Long noncoding RNAs identified within CNVs showed tissue-specific expression, indicating potential functional relevance of the findings. The identified candidate CNVs warrant independent replication.
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Affiliation(s)
- Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tenn., USA
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10
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Noll AC, Miller NA, Smith LD, Yoo B, Fiedler S, Cooley LD, Willig LK, Petrikin JE, Cakici J, Lesko J, Newton A, Detherage K, Thiffault I, Saunders CJ, Farrow EG, Kingsmore SF. Clinical detection of deletion structural variants in whole-genome sequences. NPJ Genom Med 2016; 1:16026. [PMID: 29263817 PMCID: PMC5685307 DOI: 10.1038/npjgenmed.2016.26] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 12/13/2022] Open
Abstract
Optimal management of acutely ill infants with monogenetic diseases requires rapid identification of causative haplotypes. Whole-genome sequencing (WGS) has been shown to identify pathogenic nucleotide variants in such infants. Deletion structural variants (DSVs, >50 nt) are implicated in many genetic diseases, and tools have been designed to identify DSVs using short-read WGS. Optimisation and integration of these tools into a WGS pipeline could improve diagnostic sensitivity and specificity of WGS. In addition, it may improve turnaround time when compared with current CNV assays, enhancing utility in acute settings. Here we describe DSV detection methods for use in WGS for rapid diagnosis in acutely ill infants: SKALD (Screening Konsensus and Annotation of Large Deletions) combines calls from two tools (Breakdancer and GenomeStrip) with calibrated filters and clinical interpretation rules. In four WGS runs, the average analytic precision (positive predictive value) of SKALD was 78%, and recall (sensitivity) was 27%, when compared with validated reference DSV calls. When retrospectively applied to a cohort of 36 families with acutely ill infants SKALD identified causative DSVs in two. The first was heterozygous deletion of exons 1–3 of MMP21 in trans with a heterozygous frame-shift deletion in two siblings with transposition of the great arteries and heterotaxy. In a newborn female with dysmorphic features, ventricular septal defect and persistent pulmonary hypertension, SKALD identified the breakpoints of a heterozygous, de novo 1p36.32p36.13 deletion. In summary, consensus DSV calling, implemented in an 8-h computational pipeline with parameterised filtering, has the potential to increase the diagnostic yield of WGS in acutely ill neonates and discover novel disease genes.
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Affiliation(s)
- Aaron C Noll
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Heartland Institute for Clinical and Translational Research, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Heartland Institute for Clinical and Translational Research, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Byunggil Yoo
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Stephanie Fiedler
- Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Linda D Cooley
- Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA.,Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Julie Cakici
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - John Lesko
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Angela Newton
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Kali Detherage
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA.,Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA.,Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Stephen F Kingsmore
- Heartland Institute for Clinical and Translational Research, University of Kansas Medical Center, Kansas City, KS, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
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11
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A significant risk locus on 19q13 for bipolar disorder identified using a combined genome-wide linkage and copy number variation analysis. BioData Min 2015; 8:42. [PMID: 26692414 PMCID: PMC4683747 DOI: 10.1186/s13040-015-0076-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/07/2015] [Indexed: 11/13/2022] Open
Abstract
Background The genetic background to bipolar disorder (BPD) has been attributed to different genetic and genomic risk factors. In the present study we hypothesized that inherited copy number variations (CNVs) contribute to susceptibility of BPD. We screened 637 BP-pedigrees from the NIMH Genetic Initiative and gave priority to 46 pedigrees. In this subsample we performed parametric and non-parametric genome-wide linkage analyses using ~21,000 SNP-markers. We developed an algorithm to test for linkage restricted to regions with CNVs that are shared within and across families. Results For the combined CNV and linkage analysis, one region on 19q13 survived correction for multiple comparisons and replicates a previous BPD risk locus. The shared CNV map to the pregnancy-specific glycoprotein (PSG) gene, a gene-family not previously implicated in BPD etiology. Two SNPs in the shared CNV are likely transcription factor binding sites and are linked to expression of an F-box binding gene, a key regulator of neuronal pathways suggested to be involved in BPD etiology. Conclusions Our CNV-weighted linkage approach identifies a risk locus for BPD on 19q13 and forms a useful tool to future studies to unravel part of the genetic vulnerability to BPD. Electronic supplementary material The online version of this article (doi:10.1186/s13040-015-0076-y) contains supplementary material, which is available to authorized users.
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12
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Cava C, Bertoli G, Castiglioni I. Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential. BMC SYSTEMS BIOLOGY 2015; 9:62. [PMID: 26391647 PMCID: PMC4578257 DOI: 10.1186/s12918-015-0211-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/15/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome. Combined analyses of molecular data at multiple levels, such as DNA copy-number alteration, mRNA and miRNA expression, can clarify biological functions and pathways deregulated in cancer. The integrative methods that are used to investigate these data involve different fields, including biology, bioinformatics, and statistics. RESULTS These methodologies are presented in this review, and their implementation in breast cancer is discussed with a focus on integration strategies. We report current applications, recent studies and interesting results leading to the identification of candidate biomarkers for diagnosis, prognosis, and therapy in breast cancer by using both individual and combined analyses. CONCLUSION This review presents a state of art of the role of different technologies in breast cancer based on the integration of genetics and epigenetics, and shares some issues related to the new opportunities and challenges offered by the application of such integrative approaches.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
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13
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Walker LC, Wiggins GAR, Pearson JF. The Role of Constitutional Copy Number Variants in Breast Cancer. ACTA ACUST UNITED AC 2015; 4:407-23. [PMID: 27600231 PMCID: PMC4996380 DOI: 10.3390/microarrays4030407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 08/26/2015] [Accepted: 09/01/2015] [Indexed: 01/16/2023]
Abstract
Constitutional copy number variants (CNVs) include inherited and de novo deviations from a diploid state at a defined genomic region. These variants contribute significantly to genetic variation and disease in humans, including breast cancer susceptibility. Identification of genetic risk factors for breast cancer in recent years has been dominated by the use of genome-wide technologies, such as single nucleotide polymorphism (SNP)-arrays, with a significant focus on single nucleotide variants. To date, these large datasets have been underutilised for generating genome-wide CNV profiles despite offering a massive resource for assessing the contribution of these structural variants to breast cancer risk. Technical challenges remain in determining the location and distribution of CNVs across the human genome due to the accuracy of computational prediction algorithms and resolution of the array data. Moreover, better methods are required for interpreting the functional effect of newly discovered CNVs. In this review, we explore current and future application of SNP array technology to assess rare and common CNVs in association with breast cancer risk in humans.
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Affiliation(s)
- Logan C Walker
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch 8140, New Zealand.
| | - George A R Wiggins
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch 8140, New Zealand.
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch 8140, New Zealand.
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14
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Nutsua ME, Fischer A, Nebel A, Hofmann S, Schreiber S, Krawczak M, Nothnagel M. Family-Based Benchmarking of Copy Number Variation Detection Software. PLoS One 2015. [PMID: 26197066 PMCID: PMC4510559 DOI: 10.1371/journal.pone.0133465] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The analysis of structural variants, in particular of copy-number variations (CNVs), has proven valuable in unraveling the genetic basis of human diseases. Hence, a large number of algorithms have been developed for the detection of CNVs in SNP array signal intensity data. Using the European and African HapMap trio data, we undertook a comparative evaluation of six commonly used CNV detection software tools, namely Affymetrix Power Tools (APT), QuantiSNP, PennCNV, GLAD, R-gada and VEGA, and assessed their level of pair-wise prediction concordance. The tool-specific CNV prediction accuracy was assessed in silico by way of intra-familial validation. Software tools differed greatly in terms of the number and length of the CNVs predicted as well as the number of markers included in a CNV. All software tools predicted substantially more deletions than duplications. Intra-familial validation revealed consistently low levels of prediction accuracy as measured by the proportion of validated CNVs (34-60%). Moreover, up to 20% of apparent family-based validations were found to be due to chance alone. Software using Hidden Markov models (HMM) showed a trend to predict fewer CNVs than segmentation-based algorithms albeit with greater validity. PennCNV yielded the highest prediction accuracy (60.9%). Finally, the pairwise concordance of CNV prediction was found to vary widely with the software tools involved. We recommend HMM-based software, in particular PennCNV, rather than segmentation-based algorithms when validity is the primary concern of CNV detection. QuantiSNP may be used as an additional tool to detect sets of CNVs not detectable by the other tools. Our study also reemphasizes the need for laboratory-based validation, such as qPCR, of CNVs predicted in silico.
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Affiliation(s)
- Marcel Elie Nutsua
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Annegret Fischer
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Sylvia Hofmann
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
| | - Michael Nothnagel
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany; Cologne Center for Genomics, University of Cologne, Cologne, Germany
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15
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Sakai M, Watanabe Y, Someya T, Araki K, Shibuya M, Niizato K, Oshima K, Kunii Y, Yabe H, Matsumoto J, Wada A, Hino M, Hashimoto T, Hishimoto A, Kitamura N, Iritani S, Shirakawa O, Maeda K, Miyashita A, Niwa SI, Takahashi H, Kakita A, Kuwano R, Nawa H. Assessment of copy number variations in the brain genome of schizophrenia patients. Mol Cytogenet 2015; 8:46. [PMID: 26136833 PMCID: PMC4487564 DOI: 10.1186/s13039-015-0144-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/12/2015] [Indexed: 11/28/2022] Open
Abstract
Background Cytogenomic mutations and chromosomal abnormality are implicated in the neuropathology of several brain diseases. Cell heterogeneity of brain tissues makes their detection and validation difficult, however. In the present study, we analyzed gene dosage alterations in brain DNA of schizophrenia patients and compared those with the copy number variations (CNVs) identified in schizophrenia patients as well as with those in Asian lymphocyte DNA and attempted to obtain hints at the pathological contribution of cytogenomic instability to schizophrenia. Results Brain DNA was extracted from postmortem striatum of schizophrenia patients and control subjects (n = 48 each) and subjected to the direct two color microarray analysis that limits technical data variations. Disease-associated biases of relative DNA doses were statistically analyzed with Bonferroni’s compensation on the premise of brain cell mosaicism. We found that the relative gene dosage of 85 regions significantly varied among a million of probe sites. In the candidate CNV regions, 26 regions had no overlaps with the common CNVs found in Asian populations and included the genes (i.e., ANTXRL, CHST9, DNM3, NDST3, SDK1, STRC, SKY) that are associated with schizophrenia and/or other psychiatric diseases. The majority of these candidate CNVs exhibited high statistical probabilities but their signal differences in gene dosage were less than 1.5-fold. For test evaluation, we rather selected the 10 candidate CNV regions that exhibited higher aberration scores or larger global effects and were thus confirmable by PCR. Quantitative PCR verified the loss of gene dosage at two loci (1p36.21 and 1p13.3) and confirmed the global variation of the copy number distributions at two loci (11p15.4 and 13q21.1), both indicating the utility of the present strategy. These test loci, however, exhibited the same somatic CNV patterns in the other brain region. Conclusions The present study lists the candidate regions potentially representing cytogenomic CNVs in the brain of schizophrenia patients, although the significant but modest alterations in their brain genome doses largely remain to be characterized further. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0144-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miwako Sakai
- Department of Molecular Neurobiology, Brain Research Institute, Niigata University, 1-757, Asahimachi-dori, 951-8585 Niigata, Japan ; Department of Psychiatry, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-dori, 951-8510 Niigata, Japan
| | - Yuichiro Watanabe
- Department of Psychiatry, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-dori, 951-8510 Niigata, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-dori, 951-8510 Niigata, Japan
| | - Kazuaki Araki
- Department of Molecular Neurobiology, Brain Research Institute, Niigata University, 1-757, Asahimachi-dori, 951-8585 Niigata, Japan
| | - Masako Shibuya
- Department of Psychiatry, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-dori, 951-8510 Niigata, Japan
| | | | | | - Yasuto Kunii
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Hirooki Yabe
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Junya Matsumoto
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Akira Wada
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Mizuki Hino
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Takeshi Hashimoto
- Division of Psychiatry and Neurology, Kobe University Graduate School of Medicine, 650-0017 Kobe, Hyogo Japan
| | - Akitoyo Hishimoto
- Division of Psychiatry and Neurology, Kobe University Graduate School of Medicine, 650-0017 Kobe, Hyogo Japan
| | - Noboru Kitamura
- Division of Psychiatry and Neurology, Kobe University Graduate School of Medicine, 650-0017 Kobe, Hyogo Japan
| | - Shuji Iritani
- Matsuzawa Hospital, Setagaya-ku, 156-0057 Tokyo, Japan ; Department of Mental Health, Nagoya University Graduate School of Medicine, 466-8550 Nagoya, Aichi Japan
| | - Osamu Shirakawa
- Division of Psychiatry and Neurology, Kobe University Graduate School of Medicine, 650-0017 Kobe, Hyogo Japan ; Department of Neuropsychiatry, Kinki University Faculty of Medicine, 589-8511 Osaka-Sayama, Osaka Japan
| | - Kiyoshi Maeda
- Division of Psychiatry and Neurology, Kobe University Graduate School of Medicine, 650-0017 Kobe, Hyogo Japan ; Department of Social Rehabilitation, Kobe University School of Medicine, 654-0142 Hyogo, Japan
| | - Akinori Miyashita
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 951-8585 Niigata, Japan
| | - Shin-Ichi Niwa
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Hitoshi Takahashi
- Pathology and Brain Disease Research Center, Brain Research Institute, Niigata University, 951-8585 Niigata, Japan
| | - Akiyoshi Kakita
- Pathology and Brain Disease Research Center, Brain Research Institute, Niigata University, 951-8585 Niigata, Japan
| | - Ryozo Kuwano
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 951-8585 Niigata, Japan
| | - Hiroyuki Nawa
- Department of Molecular Neurobiology, Brain Research Institute, Niigata University, 1-757, Asahimachi-dori, 951-8585 Niigata, Japan
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Brenndörfer J, Altmann A, Widner-Andrä R, Pütz B, Czamara D, Tilch E, Kam-Thong T, Weber P, Rex-Haffner M, Bettecken T, Bultmann A, Müller-Myhsok B, Binder EE, Landgraf R, Czibere L. Connecting Anxiety and Genomic Copy Number Variation: A Genome-Wide Analysis in CD-1 Mice. PLoS One 2015; 10:e0128465. [PMID: 26011321 PMCID: PMC4444327 DOI: 10.1371/journal.pone.0128465] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 04/27/2015] [Indexed: 12/05/2022] Open
Abstract
Genomic copy number variants (CNVs) have been implicated in multiple psychiatric disorders, but not much is known about their influence on anxiety disorders specifically. Using next-generation sequencing (NGS) and two additional array-based genotyping approaches, we detected CNVs in a mouse model consisting of two inbred mouse lines showing high (HAB) and low (LAB) anxiety-related behavior, respectively. An influence of CNVs on gene expression in the central (CeA) and basolateral (BLA) amygdala, paraventricular nucleus (PVN), and cingulate cortex (Cg) was shown by a two-proportion Z-test (p = 1.6 x 10-31), with a positive correlation in the CeA (p = 0.0062), PVN (p = 0.0046) and Cg (p = 0.0114), indicating a contribution of CNVs to the genetic predisposition to trait anxiety in the specific context of HAB/LAB mice. In order to confirm anxiety-relevant CNVs and corresponding genes in a second mouse model, we further examined CD-1 outbred mice. We revealed the distribution of CNVs by genotyping 64 CD 1 individuals using a high-density genotyping array (Jackson Laboratory). 78 genes within those CNVs were identified to show nominally significant association (48 genes), or a statistical trend in their association (30 genes) with the time animals spent on the open arms of the elevated plus-maze (EPM). Fifteen of them were considered promising candidate genes of anxiety-related behavior as we could show a significant overlap (permutation test, p = 0.0051) with genes within HAB/LAB CNVs. Thus, here we provide what is to our knowledge the first extensive catalogue of CNVs in CD-1 mice and potential corresponding candidate genes linked to anxiety-related behavior in mice.
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Affiliation(s)
- Julia Brenndörfer
- Department of Behavioral Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
- * E-mail:
| | - André Altmann
- Department of Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Regina Widner-Andrä
- Department of Behavioral Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Benno Pütz
- Department of Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- Department of Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Erik Tilch
- Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Tony Kam-Thong
- Department of Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Peter Weber
- Department of Molecular Genetics of Affective Disorders, Max Planck Institute of Psychiatry, Munich, Germany
| | - Monika Rex-Haffner
- Department of Molecular Genetics of Affective Disorders, Max Planck Institute of Psychiatry, Munich, Germany
| | - Thomas Bettecken
- Department of Behavioral Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Andrea Bultmann
- Department of Behavioral Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Bertram Müller-Myhsok
- Department of Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Elisabeth E. Binder
- Department of Molecular Genetics of Affective Disorders, Max Planck Institute of Psychiatry, Munich, Germany
| | - Rainer Landgraf
- Department of Behavioral Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Ludwig Czibere
- Department of Behavioral Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
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Lal D, Ruppert AK, Trucks H, Schulz H, de Kovel CG, Kasteleijn-Nolst Trenité D, Sonsma ACM, Koeleman BP, Lindhout D, Weber YG, Lerche H, Kapser C, Schankin CJ, Kunz WS, Surges R, Elger CE, Gaus V, Schmitz B, Helbig I, Muhle H, Stephani U, Klein KM, Rosenow F, Neubauer BA, Reinthaler EM, Zimprich F, Feucht M, Møller RS, Hjalgrim H, De Jonghe P, Suls A, Lieb W, Franke A, Strauch K, Gieger C, Schurmann C, Schminke U, Nürnberg P, Sander T. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies. PLoS Genet 2015; 11:e1005226. [PMID: 25950944 PMCID: PMC4423931 DOI: 10.1371/journal.pgen.1005226] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/16/2015] [Indexed: 01/06/2023] Open
Abstract
Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17) relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6) or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1) were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1). Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes.
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Affiliation(s)
- Dennis Lal
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
- EPICURE Consortium
| | - Ann-Kathrin Ruppert
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Holger Trucks
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Herbert Schulz
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Carolien G. de Kovel
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Anja C. M. Sonsma
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P. Koeleman
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dick Lindhout
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- SEIN Epilepsy Institute in the Netherlands, Hoofddorp, The Netherlands
| | - Yvonne G. Weber
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Holger Lerche
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Kapser
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Christoph J. Schankin
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Wolfram S. Kunz
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Rainer Surges
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Christian E. Elger
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Verena Gaus
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
| | - Bettina Schmitz
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
- Department of Neurology, Vivantes Humboldt-Klinikum, Berlin, Germany
| | - Ingo Helbig
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Hiltrud Muhle
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Ulrich Stephani
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Karl M. Klein
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Felix Rosenow
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Bernd A. Neubauer
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
| | - Eva M. Reinthaler
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Fritz Zimprich
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Martha Feucht
- EPICURE Consortium
- Department of Pediatrics and Neonatology, Medical University of Vienna, Vienna, Austria
| | - Rikke S. Møller
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Helle Hjalgrim
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Peter De Jonghe
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Christian Albrechts University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, and Chair of Genetic Epidemiology, Ludwig-Maximilians-University, Munich, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University, Greifswald, Germany
| | - Ulf Schminke
- Department of Neurology, University Medicine Greifswald, Ernst Moritz Arndt University, Greifswald, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- EPICURE Consortium
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | - Thomas Sander
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
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Abstract
Monozygotic (MZ) twins are genetically identical at conception, making them informative subjects for studies on somatic mutations. Copy number variants (CNVs) are responsible for a substantial part of genetic variation, have relatively high mutation rates, and are likely to be involved in phenotypic variation. We conducted a genome-wide survey for post-twinning de novo CNVs in 1,097 MZ twin pairs. Comparisons between MZ twins were made by CNVs measured in DNA from blood or buccal epithelium with the Affymetrix 6.0 microarray and two calling algorithms. In addition, CNV concordance rates were compared between the different sources of DNA, and gene-enrichment association analyses were conducted for thought problems (TP) and attention problems (AP) using CNVs concordant within MZ pairs. We found a total of 153 putative post-twinning de novo CNVs >100 kb, of which the majority resided in 15q11.2. Based on the discordance of raw intensity signals a selection was made of 20 de novo CNVs for a qPCR validation experiments. Two out of 20 post-twinning de novo CNVs were validated with qPCR in the same twin pair. The 13-year-old MZ twin pair that showed two discordances in CN in 15q11.2 in their buccal DNA did not show large phenotypic differences. From the remaining 18 putative de novo CNVs, 17 were deletions or duplications that were concordant within MZ twin pairs. Concordance rates within twin pairs of CNV calls with CN ≠ 2 were ~80%. Buccal epithelium-derived DNA showed a slightly but significantly higher concordance rate, and blood-derived DNA showed significantly more concordant CNVs per twin pair. The gene-enrichment analyses on concordant CNVs showed no significant associations between CNVs overlapping with genes involved in neuronal processes and TP or AP after accounting for the source of DNA.
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O’Dushlaine C, Ripke S, Ruderfer DM, Hamilton SP, Fava M, Iosifescu DV, Kohane IS, Churchill SE, Castro VM, Clements CC, Blumenthal SR, Murphy SN, Smoller JW, Perlis RH. Rare copy number variation in treatment-resistant major depressive disorder. Biol Psychiatry 2014; 76:536-41. [PMID: 24529801 PMCID: PMC4104153 DOI: 10.1016/j.biopsych.2013.10.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/03/2013] [Accepted: 10/26/2013] [Indexed: 12/28/2022]
Abstract
BACKGROUND While antidepressant treatment response appears to be partially heritable, no consistent genetic associations have been identified. Large, rare copy number variants (CNVs) play a role in other neuropsychiatric diseases, so we assessed their association with treatment-resistant depression (TRD). METHODS We analyzed data from two genome-wide association studies comprising 1263 Caucasian patients with major depressive disorder. One was drawn from a large health system by applying natural language processing to electronic health records (i2b2 cohort). The second consisted of a multicenter study of sequential antidepressant treatments, Sequenced Treatment Alternatives to Relieve Depression. The Birdsuite package was used to identify rare deletions and duplications. Individuals without symptomatic remission, despite two antidepressant treatment trials, were contrasted with those who remitted with a first treatment trial. RESULTS CNV data were derived for 778 subjects in the i2b2 cohort, including 300 subjects (37%) with TRD, and 485 subjects in Sequenced Treatment Alternatives to Relieve Depression cohort, including 152 (31%) with TRD. CNV burden analyses identified modest enrichment of duplications in cases (empirical p = .04 for duplications of 100-200 kilobase) and a particular deletion region spanning gene PABPC4L (empirical p = .02, 6 cases: 0 controls). Pathway analysis suggested enrichment of CNVs intersecting genes regulating actin cytoskeleton. However, none of these associations survived genome-wide correction. CONCLUSIONS Contribution of rare CNVs to TRD appears to be modest, individually or in aggregate. The electronic health record-based methodology demonstrated here should facilitate collection of larger TRD cohorts necessary to further characterize these effects.
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Akutagava-Martins GC, Salatino-Oliveira A, Genro JP, Contini V, Polanczyk G, Zeni C, Chazan R, Kieling C, Anselmi L, Menezes AMB, Grevet EH, Bau CHD, Rohde LA, Hutz MH. Glutamatergic copy number variants and their role in attention-deficit/hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:502-9. [PMID: 24985920 DOI: 10.1002/ajmg.b.32253] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/27/2014] [Indexed: 01/22/2023]
Abstract
Attention-Deficit/Hyperactivity Disorder (ADHD) is a common neurodevelopmental disorder with a strong genetic component. The glutamate metabotropic receptor genes (GRMs) have been considered potential candidates for ADHD susceptibility. The aim of the present study was to investigate if copy number variants (CNVs) in GRM1, GRM5, and GRM8 genes are overrepresented in ADHD subjects. A total of 1038 individuals with ADHD and 1057 subjects without this disorder were investigated. No significant difference in the total number of CNVs was found comparing the entire ADHD sample and the population sample without ADHD (P = 0.326, OR = 1.112, 95% CI = 0.762-1.624). The presence of CNVs was associated with lower intelligence quotient (IQ) scores in ADHD samples (P = 0.026, OR = 1.824, 95% CI = 1.066-3.121) but not in the sample of individuals without ADHD. CNVs in GRM5 were associated with presence of anxiety disorders in ADHD cases (P = 0.002, OR = 3.915, 95% CI = 1.631-9.402), but not in individuals without ADHD. Taken together, our results suggest a role for glutamate in ADHD as CNVs in the glutamatergic genes investigated herein were associated with cognitive and clinical characteristics of ADHD individuals.
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Masson AL, Talseth-Palmer BA, Evans TJ, Grice DM, Hannan GN, Scott RJ. Expanding the genetic basis of copy number variation in familial breast cancer. Hered Cancer Clin Pract 2014; 12:15. [PMID: 24955146 PMCID: PMC4064283 DOI: 10.1186/1897-4287-12-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/14/2014] [Indexed: 12/13/2022] Open
Abstract
Introduction Familial breast cancer (fBC) is generally associated with an early age of diagnosis and a higher frequency of disease among family members. Over the past two decades a number of genes have been identified that are unequivocally associated with breast cancer (BC) risk but there remain a significant proportion of families that cannot be accounted for by these genes. Copy number variants (CNVs) are a form of genetic variation yet to be fully explored for their contribution to fBC. CNVs exert their effects by either being associated with whole or partial gene deletions or duplications and by interrupting epigenetic patterning thereby contributing to disease development. CNV analysis can also be used to identify new genes and loci which may be associated with disease risk. Methods The Affymetrix Cytogenetic Whole Genome 2.7 M (Cyto2.7 M) arrays were used to detect regions of genomic re-arrangement in a cohort of 129 fBC BRCA1/BRCA2 mutation negative patients with a young age of diagnosis (<50 years) compared to 40 unaffected healthy controls (>55 years of age). Results CNV analysis revealed the presence of 275 unique rearrangements that were not present in the control population suggestive of their involvement in BC risk. Several CNVs were found that have been previously reported as BC susceptibility genes. This included CNVs in RPA3, NBN (NBS1), MRE11A and CYP19A1 in five unrelated fBC patients suggesting that these genes are involved in BC initiation and/or progression. Of special interest was the identification of WWOX and FHIT rearrangements in three unrelated fBC patients. Conclusions This study has identified a number of CNVs that potentially contribute to BC initiation and/or progression. The identification of CNVs that are associated with known tumour suppressor genes is of special interest that warrants further larger studies to understand their precise role in fBC.
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Affiliation(s)
- Amy L Masson
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia ; School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Bente A Talseth-Palmer
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia ; School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Tiffany-Jane Evans
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia ; School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Desma M Grice
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia ; CSIRO Preventative Health Flagship and Animal, CSIRO Food and Health Sciences Division, North Ryde, NSW 2113, Australia
| | - Garry N Hannan
- CSIRO Preventative Health Flagship and Animal, CSIRO Food and Health Sciences Division, North Ryde, NSW 2113, Australia
| | - Rodney J Scott
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia ; Division of Molecular Medicine, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, NSW 2305, Australia ; School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
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22
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Ulloa AE, Chen J, Vergara VM, Calhoun V, Liu J. Association between copy number variation losses and alcohol dependence across African American and European American ethnic groups. Alcohol Clin Exp Res 2014; 38:1266-74. [PMID: 24512105 PMCID: PMC3999255 DOI: 10.1111/acer.12364] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/21/2013] [Indexed: 11/30/2022]
Abstract
BACKGROUND Copy number variations (CNVs) are structural genetic mutations consisting of segmental gains or losses in DNA sequence. Although CNVs contribute substantially to genomic variation, few genetic and imaging studies report association of CNVs with alcohol dependence (AD). Our purpose is to find evidence of this association across ethnic populations and genders. This work is the first AD-CNV study across ethnic groups and the first to include the African American (AA) population. METHODS This study considers 2 CNV data sets, one for discovery (2,345 samples) and the other for validation (239 samples), both including subjects with AD and healthy controls of European and African ancestry. Our analysis assesses the association between AD and CNV losses across ethnic groups and gender by examining the effect of overall losses across the whole genome, collective losses within individual cytogenetic bands, and specific losses in CNV regions. RESULTS Results from the discovery data set showed an association between CNV losses within 16q12.2 and AD diagnosis (p = 4.53 × 10(-3) ). An overlapping CNV region from the validation data set exhibited the same direction of effect with respect to AD (p = 0.051). This CNV region affects the genes CES1p1 and CES1, which are members of the carboxylesterase (CES) family. The enzyme encoded by CES1 is a major liver enzyme that typically catalyzes the decomposition of ester into alcohol and carboxylic acid and is involved in drug or xenobiotics, fatty acid, and cholesterol metabolisms. In addition, the most significantly associated CNV region was located at 9p21.2 (p = 1.9 × 10(-3) ) in our discovery data set. Although not observed in the validation data set, probably due to small sample size, this result might hold potential connection to AD given its connection with neuronal death. In contrast, we did not find any association between AD and the overall total losses or the collective losses within individual cytogenetic bands. CONCLUSIONS Overall, our study provides evidence that the specific CNVs at 16q12.2 contribute to the development of alcoholism in AA and European American populations.
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Affiliation(s)
| | - Jiayu Chen
- Electrical and Computer Engineering Department, University of New Mexico
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute
| | - Victor Manuel Vergara
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute
| | - Vince Calhoun
- Electrical and Computer Engineering Department, University of New Mexico
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute
| | - Jingyu Liu
- Electrical and Computer Engineering Department, University of New Mexico
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute
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Castellani CA, Melka MG, Wishart AE, Locke MEO, Awamleh Z, O'Reilly RL, Singh SM. Biological relevance of CNV calling methods using familial relatedness including monozygotic twins. BMC Bioinformatics 2014; 15:114. [PMID: 24750645 PMCID: PMC4021055 DOI: 10.1186/1471-2105-15-114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Studies involving the analysis of structural variation including Copy Number Variation (CNV) have recently exploded in the literature. Furthermore, CNVs have been associated with a number of complex diseases and neurodevelopmental disorders. Common methods for CNV detection use SNP, CNV, or CGH arrays, where the signal intensities of consecutive probes are used to define the number of copies associated with a given genomic region. These practices pose a number of challenges that interfere with the ability of available methods to accurately call CNVs. It has, therefore, become necessary to develop experimental protocols to test the reliability of CNV calling methods from microarray data so that researchers can properly discriminate biologically relevant data from noise. RESULTS We have developed a workflow for the integration of data from multiple CNV calling algorithms using the same array results. It uses four CNV calling programs: PennCNV (PC), Affymetrix® Genotyping Console™ (AGC), Partek® Genomics Suite™ (PGS) and Golden Helix SVS™ (GH) to analyze CEL files from the Affymetrix® Human SNP 6.0 Array™. To assess the relative suitability of each program, we used individuals of known genetic relationships. We found significant differences in CNV calls obtained by different CNV calling programs. CONCLUSIONS Although the programs showed variable patterns of CNVs in the same individuals, their distribution in individuals of different degrees of genetic relatedness has allowed us to offer two suggestions. The first involves the use of multiple algorithms for the detection of the largest possible number of CNVs, and the second suggests the use of PennCNV over all other methods when the use of only one software program is desirable.
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Affiliation(s)
| | | | | | | | | | | | - Shiva M Singh
- Department of Biology, The University of Western Ontario, London N6A 5B7, ON, Canada.
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Zhang X, Du R, Li S, Zhang F, Jin L, Wang H. Evaluation of copy number variation detection for a SNP array platform. BMC Bioinformatics 2014; 15:50. [PMID: 24555668 PMCID: PMC4015297 DOI: 10.1186/1471-2105-15-50] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Accepted: 02/06/2014] [Indexed: 11/26/2022] Open
Abstract
Background Copy Number Variations (CNVs) are usually inferred from Single Nucleotide Polymorphism (SNP) arrays by use of some software packages based on given algorithms. However, there is no clear understanding of the performance of these software packages; it is therefore difficult to select one or several software packages for CNV detection based on the SNP array platform. We selected four publicly available software packages designed for CNV calling from an Affymetrix SNP array, including Birdsuite, dChip, Genotyping Console (GTC) and PennCNV. The publicly available dataset generated by Array-based Comparative Genomic Hybridization (CGH), with a resolution of 24 million probes per sample, was considered to be the “gold standard”. Compared with the CGH-based dataset, the success rate, average stability rate, sensitivity, consistence and reproducibility of these four software packages were assessed compared with the “gold standard”. Specially, we also compared the efficiency of detecting CNVs simultaneously by two, three and all of the software packages with that by a single software package. Results Simply from the quantity of the detected CNVs, Birdsuite detected the most while GTC detected the least. We found that Birdsuite and dChip had obvious detecting bias. And GTC seemed to be inferior because of the least amount of CNVs it detected. Thereafter we investigated the detection consistency produced by one certain software package and the rest three software suits. We found that the consistency of dChip was the lowest while GTC was the highest. Compared with the CNVs detecting result of CGH, in the matching group, GTC called the most matching CNVs, PennCNV-Affy ranked second. In the non-overlapping group, GTC called the least CNVs. With regards to the reproducibility of CNV calling, larger CNVs were usually replicated better. PennCNV-Affy shows the best consistency while Birdsuite shows the poorest. Conclusion We found that PennCNV outperformed the other three packages in the sensitivity and specificity of CNV calling. Obviously, each calling method had its own limitations and advantages for different data analysis. Therefore, the optimized calling methods might be identified using multiple algorithms to evaluate the concordance and discordance of SNP array-based CNV calling.
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Affiliation(s)
| | | | | | | | | | - Hongyan Wang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.
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Hu XY, Bai XM, Qiao X, Zhu YQ. Copy number variation at 6q13 is associated with lung cancer risk in a Han Chinese population. Exp Lung Res 2013; 39:427-33. [PMID: 24245924 DOI: 10.3109/01902148.2013.822946] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Copy number variations (CNVs), a major source of human genetic polymorphism, have been suggested to have an important role in genetic susceptibility to common diseases such as cancer, immune diseases, and neurological disorders. Lung cancer is a multifactorial tumor closely associated with genetic background. Previous genome-wide association studies have identified single nucleotide polymorphisms (SNPs) that are associated with lung cancer susceptibility. This study examined the CNVR2966.1 at 6q13 and its association with lung cancer susceptibility. The CNVR2966.1 was found to be a 10,379 bp nucleotides deletion/insertion within the uniform boundaries chromosome 6: 74,648,791-74,659,169. The risk of lung cancer observed in 503 cases and 623 controls was significantly associated with copy number of CNVR2966.1, with the odds ratio (OR) being 1.38 [95% confidence interval (CI) = 1.05-1.79; P = .007] for one copy genotype compared with two copies genotype. These results suggest that CNVR2966.1 is associated with lung cancer risk.
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Affiliation(s)
- Xiao-Yun Hu
- 1Department of Respiratory Medicine, The First People's Hospital, Wujiang, Jiangsu, China
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Copy Number Studies in Noisy Samples. MICROARRAYS 2013; 2:284-303. [PMID: 27605193 PMCID: PMC5003442 DOI: 10.3390/microarrays2040284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 10/24/2013] [Accepted: 10/25/2013] [Indexed: 11/17/2022]
Abstract
System noise was analyzed in 77 Affymetrix 6.0 samples from a previous clinical study of copy number variation (CNV). Twenty-three samples were classified as eligible for CNV detection, 29 samples as ineligible and 25 were classified as being of intermediate quality. New software (“noise-free-cnv”) was developed to visualize the data and reduce system noise. Fresh DNA preparations were more likely to yield eligible samples (p < 0.001). Eligible samples had higher rates of successfully genotyped SNPs (p < 0.001) and lower variance of signal intensities (p < 0.001), yielded fewer CNV findings after Birdview analysis (p < 0.001), and showed a tendency to yield fewer PennCNV calls (p = 0.053). The noise-free-cnv software visualized trend patterns of noise in the signal intensities across the ordered SNPs, including a wave pattern of noise, being co-linear with the banding pattern of metaphase chromosomes, as well as system deviations of individual probe sets (per-SNP noise). Wave noise and per-SNP noise occurred independently and could be separately removed from the samples. We recommend a two-step procedure of CNV validation, including noise reduction and visual inspection of all CNV calls, prior to molecular validation of a selected number of putative CNVs.
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Bendjilali N, Kim H, Weinsheimer S, Guo DE, Kwok PY, Zaroff JG, Sidney S, Lawton MT, McCulloch CE, Koeleman BPC, Klijn CJM, Young WL, Pawlikowska L. A genome-wide investigation of copy number variation in patients with sporadic brain arteriovenous malformation. PLoS One 2013; 8:e71434. [PMID: 24098321 PMCID: PMC3789669 DOI: 10.1371/journal.pone.0071434] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 06/30/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Brain arteriovenous malformations (BAVM) are clusters of abnormal blood vessels, with shunting of blood from the arterial to venous circulation and a high risk of rupture and intracranial hemorrhage. Most BAVMs are sporadic, but also occur in patients with Hereditary Hemorrhagic Telangiectasia, a Mendelian disorder caused by mutations in genes in the transforming growth factor beta (TGFβ) signaling pathway. METHODS To investigate whether copy number variations (CNVs) contribute to risk of sporadic BAVM, we performed a genome-wide association study in 371 sporadic BAVM cases and 563 healthy controls, all Caucasian. Cases and controls were genotyped using the Affymetrix 6.0 array. CNVs were called using the PennCNV and Birdsuite algorithms and analyzed via segment-based and gene-based approaches. Common and rare CNVs were evaluated for association with BAVM. RESULTS A CNV region on 1p36.13, containing the neuroblastoma breakpoint family, member 1 gene (NBPF1), was significantly enriched with duplications in BAVM cases compared to controls (P = 2.2×10(-9)); NBPF1 was also significantly associated with BAVM in gene-based analysis using both PennCNV and Birdsuite. We experimentally validated the 1p36.13 duplication; however, the association did not replicate in an independent cohort of 184 sporadic BAVM cases and 182 controls (OR = 0.81, P = 0.8). Rare CNV analysis did not identify genes significantly associated with BAVM. CONCLUSION We did not identify common CNVs associated with sporadic BAVM that replicated in an independent cohort. Replication in larger cohorts is required to elucidate the possible role of common or rare CNVs in BAVM pathogenesis.
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Affiliation(s)
- Nasrine Bendjilali
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
| | - Helen Kim
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Shantel Weinsheimer
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
| | - Diana E. Guo
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Jonathan G. Zaroff
- Kaiser Northern California Division of Research, San Francisco, California, United States of America
| | - Stephen Sidney
- Kaiser Northern California Division of Research, San Francisco, California, United States of America
| | - Michael T. Lawton
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Charles E. McCulloch
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Bobby P. C. Koeleman
- Department of Medical Genetics, University Medical Center, Utrecht, The Netherlands
| | - Catharina J. M. Klijn
- Department of Neurology and Neurosurgery, Rudolf Magnus Institute of Neuroscience, University Medical Center, Utrecht, The Netherlands
| | - William L. Young
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, United States of America
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Ludmila Pawlikowska
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Tiwari VN, Sundaram SK, Chugani HT, Huq AHMM. Infantile spasms are associated with abnormal copy number variations. J Child Neurol 2013; 28:1191-6. [PMID: 22914377 DOI: 10.1177/0883073812453496] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The authors tested the hypothesis that de novo copy number variations (CNVs) implicated in known genomic disorders ("pathogenic CNVs") are significant predisposing factors of infantile spasms. The authors performed a genome-wide analysis of single-nucleotide polymorphism genotyping microarray data to identify the role of de novo/known pathogenic large CNVs in 13 trios of children affected by infantile spasms. A rare, large (4.8 Mb) de novo duplication was detected in the 15q11-13 region of 1 patient. In addition, 3 known pathogenic CNVs (present in the patient as well as 1 of the parents) were detected in total. In 1 patient, a known pathogenic deletion was detected in the region of 2q32.3. Similarly, in 1 other patient, 2 known pathogenic deletions in the regions of 16p11.2 and Xp22.13 (containing CDKL5) were detected. These findings suggest that some specific pathogenic CNVs predispose to infantile spasms and may be associated with different phenotypes.
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Affiliation(s)
- Vijay N Tiwari
- 1Department of Pediatrics, Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
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Ho Jang G, Christie JD, Feng R. A method for calling copy number polymorphism using haplotypes. Front Genet 2013; 4:165. [PMID: 24069028 PMCID: PMC3780619 DOI: 10.3389/fgene.2013.00165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/07/2013] [Indexed: 12/15/2022] Open
Abstract
Single nucleotide polymorphism (SNP) and copy number variation (CNV) are both widespread characteristic of the human genome, but are often called separately on common genotyping platforms. To capture integrated SNP and CNV information, methods have been developed for calling allelic specific copy numbers or so called copy number polymorphism (CNP), using limited inter-marker correlation. In this paper, we proposed a haplotype-based maximum likelihood method to call CNP, which takes advantage of the valuable multi-locus linkage disequilibrium (LD) information in the population. We also developed a computationally efficient algorithm to estimate haplotype frequencies and optimize individual CNP calls iteratively, even at presence of missing data. Through simulations, we demonstrated our model is more sensitive and accurate in detecting various CNV regions, compared with commonly-used CNV calling methods including PennCNV, another hidden Markov model (HMM) using CNP, a scan statistic, segCNV, and cnvHap. Our method often performs better in the regions with higher LD, in longer CNV regions, and in common CNV than the opposite. We implemented our method on the genotypes of 90 HapMap CEU samples and 23 patients with acute lung injury (ALI). For each ALI patient the genotyping was performed twice. The CNPs from our method show good consistency and accuracy comparable to others.
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Affiliation(s)
- Gun Ho Jang
- Department of Biostatistics and Epidemiology, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Philadelphia, PA, USA
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Masson AL, Talseth-Palmer BA, Evans TJ, Grice DM, Duesing K, Hannan GN, Scott RJ. Copy number variation in hereditary non-polyposis colorectal cancer. Genes (Basel) 2013; 4:536-55. [PMID: 24705261 PMCID: PMC3927572 DOI: 10.3390/genes4040536] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/02/2013] [Accepted: 09/11/2013] [Indexed: 12/12/2022] Open
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) is the commonest form of inherited colorectal cancer (CRC) predisposition and by definition describes families which conform to the Amsterdam Criteria or reiterations thereof. In ~50% of patients adhering to the Amsterdam criteria germline variants are identified in one of four DNA Mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2. Loss of function of any one of these genes results in a failure to repair DNA errors occurring during replication which can be most easily observed as DNA microsatellite instability (MSI)—a hallmark feature of this disease. The remaining 50% of patients without a genetic diagnosis of disease may harbour more cryptic changes within or adjacent to MLH1, MSH2, MSH6 or PMS2 or elsewhere in the genome. We used a high density cytogenetic array to screen for deletions or duplications in a series of patients, all of whom adhered to the Amsterdam/Bethesda criteria, to determine if genomic re-arrangements could account for a proportion of patients that had been shown not to harbour causative mutations as assessed by standard diagnostic techniques. The study has revealed some associations between copy number variants (CNVs) and HNPCC mutation negative cases and further highlights difficulties associated with CNV analysis.
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Affiliation(s)
- Amy L. Masson
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
| | - Bente A. Talseth-Palmer
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
| | - Tiffany-Jane Evans
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
| | - Desma M. Grice
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- CSIRO Preventative Health Flagship and Division of Animal, Food and Health Sciences, North Ryde, New South Wales, 2113, Australia; E-Mails: (K.D.); (G.N.H.)
| | - Konsta Duesing
- CSIRO Preventative Health Flagship and Division of Animal, Food and Health Sciences, North Ryde, New South Wales, 2113, Australia; E-Mails: (K.D.); (G.N.H.)
| | - Garry N. Hannan
- CSIRO Preventative Health Flagship and Division of Animal, Food and Health Sciences, North Ryde, New South Wales, 2113, Australia; E-Mails: (K.D.); (G.N.H.)
| | - Rodney J. Scott
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
- Division of Molecular Medicine, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, New South Wales, 2305, Australia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +61-2-4921-4974; Fax: +61-2-4921-4253
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Abstract
MOTIVATION Data quality is a critical issue in the analyses of DNA copy number alterations obtained from microarrays. It is commonly assumed that copy number alteration data can be modeled as piecewise constant and the measurement errors of different probes are independent. However, these assumptions do not always hold in practice. In some published datasets, we find that measurement errors are highly correlated between probes that interrogate nearby genomic loci, and the piecewise-constant model does not fit the data well. The correlated errors cause problems in downstream analysis, leading to a large number of DNA segments falsely identified as having copy number gains and losses. METHOD We developed a simple tool, called autocorrelation scanning profile, to assess the dependence of measurement error between neighboring probes. RESULTS Autocorrelation scanning profile can be used to check data quality and refine the analysis of DNA copy number data, which we demonstrate in some typical datasets. CONTACT lzhangli@mdanderson.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Liangcai Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA and Department of Biophysics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
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Metzger J, Philipp U, Lopes MS, da Camara Machado A, Felicetti M, Silvestrelli M, Distl O. Analysis of copy number variants by three detection algorithms and their association with body size in horses. BMC Genomics 2013; 14:487. [PMID: 23865711 PMCID: PMC3720552 DOI: 10.1186/1471-2164-14-487] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 07/15/2013] [Indexed: 12/14/2022] Open
Abstract
Background Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard comparative evaluation of CNVs in horses using three different CNV detection programs and to identify genomic regions associated with body size in horses. Results Analysis was performed using the Illumina Equine SNP50 genotyping beadchip for 854 horses. CNVs were detected by three different algorithms, CNVPartition, PennCNV and QuantiSNP. Comparative analysis revealed 50 CNVs that affected 153 different genes mainly involved in sensory perception, signal transduction and cellular components. Genome-wide association analysis for body size showed highly significant deleted regions on ECA1, ECA8 and ECA9. Homologous regions to the detected CNVs on ECA1 and ECA9 have also been shown to be correlated with human height. Conclusions Comparative analysis of CNV detection algorithms was useful to increase the specificity of CNV detection but had certain limitations dependent on the detection tool. GWAS revealed genome-wide associated CNVs for body size in horses.
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Affiliation(s)
- Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany
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Veerappa AM, Vishweswaraiah S, Lingaiah K, Murthy M, Manjegowda DS, Nayaka R, Ramachandra NB. Unravelling the complexity of human olfactory receptor repertoire by copy number analysis across population using high resolution arrays. PLoS One 2013; 8:e66843. [PMID: 23843967 PMCID: PMC3700933 DOI: 10.1371/journal.pone.0066843] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 05/05/2013] [Indexed: 11/19/2022] Open
Abstract
Olfactory receptors (OR), responsible for detection of odor molecules, belong to the largest family of genes and are highly polymorphic in nature having distinct polymorphisms associated with specific regions around the globe. Since there are no reports on the presence of copy number variations in OR repertoire of Indian population, the present investigation in 43 Indians along with 270 HapMap and 31 Tibetan samples was undertaken to study genome variability and evolution. Analysis was performed using Affymetrix Genome-Wide Human SNP Array 6.0 chip, Affymterix CytoScan® High-Density array, HD-CNV, and MAFFT program. We observed a total of 1527 OR genes in 503 CNV events from 81.3% of the study group, which includes 67.6% duplications and 32.4% deletions encompassing more of genes than pseudogenes. We report human genotypic variation in functional OR repertoire size across populations and it was found that the combinatorial effect of both “orthologous obtained from closely related species” and “paralogous derived sequences” provide the complexity to the continuously occurring OR CNVs.
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Affiliation(s)
- Avinash M. Veerappa
- Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, India
| | - Sangeetha Vishweswaraiah
- Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, India
| | - Kusuma Lingaiah
- Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, India
| | - Megha Murthy
- Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, India
| | - Dinesh S. Manjegowda
- Department of Anatomy, Yenepoya Medical College, Yenepoya University, Mangalore, India
| | - Radhika Nayaka
- Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, India
| | - Nallur B. Ramachandra
- Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, India
- * E-mail:
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Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data. MICROARRAYS 2013; 2:171-85. [PMID: 27605188 PMCID: PMC5003459 DOI: 10.3390/microarrays2030171] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/04/2013] [Accepted: 06/05/2013] [Indexed: 11/23/2022]
Abstract
Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome. The data from single nucleotide polymorphism (SNP) microarrays are now routinely used for genotyping, but they also can be utilized for copy number detection. Substantial progress has been made in array design and CNV calling algorithms and at least 10 comparison studies in humans have been published to assess them. In this review, we first survey the literature on existing microarray platforms and CNV calling algorithms. We then examine a number of CNV calling tools to evaluate their impacts using bovine high-density SNP data. Large incongruities in the results from different CNV calling tools highlight the need for standardizing array data collection, quality assessment and experimental validation. Only after careful experimental design and rigorous data filtering can the impacts of CNVs on both normal phenotypic variability and disease susceptibility be fully revealed.
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Oros KK, Arcand SL, Bayani J, Squire JA, Mes-Masson AM, Tonin PN, Greenwood CM. Analysis of genomic abnormalities in tumors: a review of available methods for Illumina two-color SNP genotyping and evaluation of performance. Cancer Genet 2013; 206:103-15. [DOI: 10.1016/j.cancergen.2013.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 10/26/2022]
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Talseth-Palmer BA, Holliday EG, Evans TJ, McEvoy M, Attia J, Grice DM, Masson AL, Meldrum C, Spigelman A, Scott RJ. Continuing difficulties in interpreting CNV data: lessons from a genome-wide CNV association study of Australian HNPCC/lynch syndrome patients. BMC Med Genomics 2013; 6:10. [PMID: 23531357 PMCID: PMC3626775 DOI: 10.1186/1755-8794-6-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 03/18/2013] [Indexed: 01/13/2023] Open
Abstract
Background Hereditary non-polyposis colorectal cancer (HNPCC)/Lynch syndrome (LS) is a cancer syndrome characterised by early-onset epithelial cancers, especially colorectal cancer (CRC) and endometrial cancer. The aim of the current study was to use SNP-array technology to identify genomic aberrations which could contribute to the increased risk of cancer in HNPCC/LS patients. Methods Individuals diagnosed with HNPCC/LS (100) and healthy controls (384) were genotyped using the Illumina Human610-Quad SNP-arrays. Copy number variation (CNV) calling and association analyses were performed using Nexus software, with significant results validated using QuantiSNP. TaqMan Copy-Number assays were used for verification of CNVs showing significant association with HNPCC/LS identified by both software programs. Results We detected copy number (CN) gains associated with HNPCC/LS status on chromosome 7q11.21 (28% cases and 0% controls, Nexus; p = 3.60E-20 and QuantiSNP; p < 1.00E-16) and 16p11.2 (46% in cases, while a CN loss was observed in 23% of controls, Nexus; p = 4.93E-21 and QuantiSNP; p = 5.00E-06) via in silico analyses. TaqMan Copy-Number assay was used for validation of CNVs showing significant association with HNPCC/LS. In addition, CNV burden (total CNV length, average CNV length and number of observed CNV events) was significantly greater in cases compared to controls. Conclusion A greater CNV burden was identified in HNPCC/LS cases compared to controls supporting the notion of higher genomic instability in these patients. One intergenic locus on chromosome 7q11.21 is possibly associated with HNPCC/LS and deserves further investigation. The results from this study highlight the complexities of fluorescent based CNV analyses. The inefficiency of both CNV detection methods to reproducibly detect observed CNVs demonstrates the need for sequence data to be considered alongside intensity data to avoid false positive results.
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Affiliation(s)
- Bente A Talseth-Palmer
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia.
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Walters RG, Coin LJM, Ruokonen A, de Smith AJ, El-Sayed Moustafa JS, Jacquemont S, Elliott P, Esko T, Hartikainen AL, Laitinen J, Männik K, Martinet D, Meyre D, Nauck M, Schurmann C, Sladek R, Thorleifsson G, Thorsteinsdóttir U, Valsesia A, Waeber G, Zufferey F, Balkau B, Pattou F, Metspalu A, Völzke H, Vollenweider P, Stefansson K, Järvelin MR, Beckmann JS, Froguel P, Blakemore AIF. Rare genomic structural variants in complex disease: lessons from the replication of associations with obesity. PLoS One 2013; 8:e58048. [PMID: 23554873 PMCID: PMC3595275 DOI: 10.1371/journal.pone.0058048] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 01/30/2013] [Indexed: 01/19/2023] Open
Abstract
The limited ability of common variants to account for the genetic contribution to complex disease has prompted searches for rare variants of large effect, to partly explain the 'missing heritability'. Analyses of genome-wide genotyping data have identified genomic structural variants (GSVs) as a source of such rare causal variants. Recent studies have reported multiple GSV loci associated with risk of obesity. We attempted to replicate these associations by similar analysis of two familial-obesity case-control cohorts and a population cohort, and detected GSVs at 11 out of 18 loci, at frequencies similar to those previously reported. Based on their reported frequencies and effect sizes (OR≥25), we had sufficient statistical power to detect the large majority (80%) of genuine associations at these loci. However, only one obesity association was replicated. Deletion of a 220 kb region on chromosome 16p11.2 has a carrier population frequency of 2×10(-4) (95% confidence interval [9.6×10(-5)-3.1×10(-4)]); accounts overall for 0.5% [0.19%-0.82%] of severe childhood obesity cases (P = 3.8×10(-10); odds ratio = 25.0 [9.9-60.6]); and results in a mean body mass index (BMI) increase of 5.8 kg.m(-2) [1.8-10.3] in adults from the general population. We also attempted replication using BMI as a quantitative trait in our population cohort; associations with BMI at or near nominal significance were detected at two further loci near KIF2B and within FOXP2, but these did not survive correction for multiple testing. These findings emphasise several issues of importance when conducting rare GSV association, including the need for careful cohort selection and replication strategy, accurate GSV identification, and appropriate correction for multiple testing and/or control of false discovery rate. Moreover, they highlight the potential difficulty in replicating rare CNV associations across different populations. Nevertheless, we show that such studies are potentially valuable for the identification of variants making an appreciable contribution to complex disease.
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Affiliation(s)
- Robin G. Walters
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Clinical Trial Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford, United Kingdom
| | - Lachlan J. M. Coin
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Aimo Ruokonen
- Institute of Diagnostics, Clinical Chemistry, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Adam J. de Smith
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | | | - Sebastien Jacquemont
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- MRC Health Protection Agency (HPA) Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Tõnu Esko
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Anna-Liisa Hartikainen
- Institute of Clinical Sciences/Obstetrics and Gynecology, University of Oulu, Oulu, Finland
| | | | - Katrin Männik
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- The Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Danielle Martinet
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - David Meyre
- CNRS 8199-Institute of Biology, Pasteur Institute, Lille, France
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Rob Sladek
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
- Department of Medicine and Human Genetics, McGill University, Montreal, Canada
| | | | - Unnur Thorsteinsdóttir
- deCODE Genetics, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Armand Valsesia
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Gerard Waeber
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Flore Zufferey
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Beverley Balkau
- INSERM, CESP Centre for Research in Epidemiology and Population Health, U1018, Villejuif, France
- University Paris Sud 11, UMRS 1018, Villejuif, France
| | - François Pattou
- INSERM U859, Lille, France
- Université Lille Nord de France, Centre Hospitalier Universitaire Lille, Lille, France
| | - Andres Metspalu
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Henry Völzke
- Institute for Community Medicine, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Peter Vollenweider
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Kári Stefansson
- deCODE Genetics, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- MRC Health Protection Agency (HPA) Centre for Environment and Health, Imperial College London, London, United Kingdom
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Lifecourse and Services, National Institute for Health and Welfare, Oulu, Finland
| | - Jacques S. Beckmann
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Philippe Froguel
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- CNRS 8199-Institute of Biology, Pasteur Institute, Lille, France
| | - Alexandra I. F. Blakemore
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Section of Investigative Medicine, Imperial College London, London, United Kingdom
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MacLeod AK, Davies G, Payton A, Tenesa A, Harris SE, Liewald D, Ke X, Luciano M, Lopez LM, Gow AJ, Corley J, Redmond P, McNeill G, Pickles A, Ollier W, Horan M, Starr JM, Pendleton N, Thomson PA, Porteous DJ, Deary IJ. Genetic copy number variation and general cognitive ability. PLoS One 2012; 7:e37385. [PMID: 23300510 PMCID: PMC3530597 DOI: 10.1371/journal.pone.0037385] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 04/18/2012] [Indexed: 01/06/2023] Open
Abstract
Differences in genomic structure between individuals are ubiquitous features of human genetic variation. Specific copy number variants (CNVs) have been associated with susceptibility to numerous complex psychiatric disorders, including attention-deficit-hyperactivity disorder, autism-spectrum disorders and schizophrenia. These disorders often display co-morbidity with low intelligence. Rare chromosomal deletions and duplications are associated with these disorders, so it has been suggested that these deletions or duplications may be associated with differences in intelligence. Here we investigate associations between large (≥500kb), rare (<1% population frequency) CNVs and both fluid and crystallized intelligence in community-dwelling older people. We observe no significant associations between intelligence and total CNV load. Examining individual CNV regions previously implicated in neuropsychological disorders, we find suggestive evidence that CNV regions around SHANK3 are associated with fluid intelligence as derived from a battery of cognitive tests. This is the first study to examine the effects of rare CNVs as called by multiple algorithms on cognition in a large non-clinical sample, and finds no effects of such variants on general cognitive ability.
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Affiliation(s)
- Andrew K. MacLeod
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Gail Davies
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Antony Payton
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, United Kingdom
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Xiayi Ke
- Medical Research Council Centre of Epidemiology for Child Health, University College London Institute of Child Health, London, United Kingdom
| | - Michelle Luciano
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Lorna M. Lopez
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alan J. Gow
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Janie Corley
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Redmond
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Geraldine McNeill
- Institute of Applied Health Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Andrew Pickles
- School of Epidemiology and Health Science, Department of Medicine, University of Manchester, Manchester, United Kingdom
| | - William Ollier
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, United Kingdom
| | - Michael Horan
- School of Community-Based Medicine, Neurodegeneration Research Group, University of Manchester, Manchester, United Kingdom
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Geriatric Medicine Unit, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil Pendleton
- School of Community-Based Medicine, Neurodegeneration Research Group, University of Manchester, Manchester, United Kingdom
| | - Pippa A. Thomson
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David J. Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
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Li W, Olivier M. Current analysis platforms and methods for detecting copy number variation. Physiol Genomics 2012; 45:1-16. [PMID: 23132758 DOI: 10.1152/physiolgenomics.00082.2012] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Copy number variation (CNV), generated through duplication or deletion events that affect one or more loci, is widespread in the human genomes and is often associated with functional consequences that may include changes in gene expression levels or fusion of genes. Genome-wide association studies indicate that some disease phenotypes and physiological pathways might be impacted by CNV in a small number of characterized genomic regions. However, the pervasiveness and full impact of such variation remains unclear. Suitable analytic methods are needed to thoroughly mine human genomes for genomic structural variation, and to explore the interplay between observed CNV and disease phenotypes, but many medical researchers are unfamiliar with the features and nuances of recently developed technologies for detecting CNV. In this article, we evaluate a suite of commonly used and recently developed approaches to uncovering genome-wide CNVs and discuss the relative merits of each.
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Affiliation(s)
- Wenli Li
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Grayton HM, Fernandes C, Rujescu D, Collier DA. Copy number variations in neurodevelopmental disorders. Prog Neurobiol 2012; 99:81-91. [DOI: 10.1016/j.pneurobio.2012.07.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 07/20/2011] [Accepted: 07/09/2012] [Indexed: 10/28/2022]
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Luciano M, MacLeod AK, Payton A, Davies G, Ke X, Tenesa A, Ollier W, Starr JM, Horan MA, Pendleton N, Thomson PA, Porteous DJ, Deary IJ. Effects of gene copy number variants on personality and mood in ageing cohorts. PERSONALITY AND INDIVIDUAL DIFFERENCES 2012. [DOI: 10.1016/j.paid.2011.12.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Chua EW, Kennedy MA. Current State and Future Prospects of Direct-to-Consumer Pharmacogenetics. Front Pharmacol 2012; 3:152. [PMID: 22934000 PMCID: PMC3422723 DOI: 10.3389/fphar.2012.00152] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 07/24/2012] [Indexed: 11/29/2022] Open
Abstract
Direct-to-consumer (DTC) DNA testing has grown from contentious beginnings into a global industry, by providing a wide range of personal genomic information directly to its clients. These companies, typified by the well-established 23andMe, generally carry out a gene-chip analysis of single-nucleotide polymorphisms (SNPs) using DNA extracted from a saliva sample. These genetic data are then assimilated and provided direct to the client, with varying degrees of interpretation. Although much debate has focused on the limitations and ethical aspects of providing genotypes for disease risk alleles, the provision of pharmacogenetic results by DTC companies is less studied. We set out to evaluate current DTC pharmacogenetics offerings, and then to consider how these services might best evolve and adapt in order to play a potentially useful future role in delivery of personalized medicine.
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Affiliation(s)
- E W Chua
- Carney Centre for Pharmacogenomics, University of Otago Christchurch Christchurch, New Zealand
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Mosén-Ansorena D, Aransay AM, Rodríguez-Ezpeleta N. Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data. BMC Bioinformatics 2012; 13:192. [PMID: 22870940 PMCID: PMC3472297 DOI: 10.1186/1471-2105-13-192] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 06/30/2012] [Indexed: 01/29/2023] Open
Abstract
Background The detection of genomic copy number alterations (CNA) in cancer based on SNP arrays requires methods that take into account tumour specific factors such as normal cell contamination and tumour heterogeneity. A number of tools have been recently developed but their performance needs yet to be thoroughly assessed. To this aim, a comprehensive model that integrates the factors of normal cell contamination and intra-tumour heterogeneity and that can be translated to synthetic data on which to perform benchmarks is indispensable. Results We propose such model and implement it in an R package called CnaGen to synthetically generate a wide range of alterations under different normal cell contamination levels. Six recently published methods for CNA and loss of heterozygosity (LOH) detection on tumour samples were assessed on this synthetic data and on a dilution series of a breast cancer cell-line: ASCAT, GAP, GenoCNA, GPHMM, MixHMM and OncoSNP. We report the recall rates in terms of normal cell contamination levels and alteration characteristics: length, copy number and LOH state, as well as the false discovery rate distribution for each copy number under different normal cell contamination levels. Assessed methods are in general better at detecting alterations with low copy number and under a little normal cell contamination levels. All methods except GPHMM, which failed to recognize the alteration pattern in the cell-line samples, provided similar results for the synthetic and cell-line sample sets. MixHMM and GenoCNA are the poorliest performing methods, while GAP generally performed better. This supports the viability of approaches other than the common hidden Markov model (HMM)-based. Conclusions We devised and implemented a comprehensive model to generate data that simulate tumoural samples genotyped using SNP arrays. The validity of the model is supported by the similarity of the results obtained with synthetic and real data. Based on these results and on the software implementation of the methods, we recommend GAP for advanced users and GPHMM for a fully driven analysis.
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Affiliation(s)
- David Mosén-Ansorena
- Genome Analysis Platform, CIC bioGUNE-CIBERehd, Technologic Park of Bizkaia, Building 502, 48160 Derio, Spain.
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Kim KI, Kim TK, Kim IW, Ahn KS, Yoon SS, Shin WG, Oh JM. Copy number variations in normal karyotype acute myeloid leukaemia and their association with treatment response. Basic Clin Pharmacol Toxicol 2012; 111:317-24. [PMID: 22672209 DOI: 10.1111/j.1742-7843.2012.00904.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 05/15/2012] [Indexed: 12/01/2022]
Abstract
Copy number variation (CNV) has been reported to be associated with chemotherapy response, which affects disease prognosis. Here, we determined the frequency of genome-wide cytogenetic CNV aberrations in Korean patients with normal karyotype (NK) acute myeloid leukaemia (AML) and tested whether these genomic variations contribute to differences in Ara-C and anthracycline-based chemotherapy responses. Bone marrow aspirates and blood from 30 previously untreated de novo NK-AML patients were provided at the time of diagnosis for copy number analysis. Possible associations between cytogenetic aberrations and clinical parameters were analysed. CNVs were identified in 23 (76.7%) of the 30 cases tested. Multivariate analyses controlled for other clinical co-variates showed that patients having copy number loss had a decreased probability of complete remission (OR, 0.015 [95% CI, 0-0.737], p = 0.035). Patients who had a copy number gain of more than four regions tended to have shorter event-free survival (EFS) (p = 0.083) with multivariate analysis showing that CNV increase is an independent predictive factor for shorter EFS (HR, 22.104 [95% CI, 1.644-297.157], p = 0.020). In addition, we identified candidate genes that may be involved in Ara-C and anthracycline drug response in Korean patients with NK-AML. These results suggest that CNVs may affect the success of Ara-C and anthracycline-based chemotherapy in Korean patients with NK-AML.
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Affiliation(s)
- Kyung Im Kim
- College of Pharmacy, Seoul National University, Seoul, Korea
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Erickson SW, MacLeod SL, Hobbs CA. Cheek swabs, SNP chips, and CNVs: assessing the quality of copy number variant calls generated with subject-collected mail-in buccal brush DNA samples on a high-density genotyping microarray. BMC MEDICAL GENETICS 2012; 13:51. [PMID: 22734463 PMCID: PMC3506514 DOI: 10.1186/1471-2350-13-51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 06/21/2012] [Indexed: 01/15/2023]
Abstract
Background Multiple investigators have established the feasibility of using buccal brush samples to genotype single nucleotide polymorphisms (SNPs) with high-density genome-wide microarrays, but there is currently no consensus on the accuracy of copy number variants (CNVs) inferred from these data. Regardless of the source of DNA, it is more difficult to detect CNVs than to genotype SNPs using these microarrays, and it therefore remains an open question whether buccal brush samples provide enough high-quality DNA for this purpose. Methods To demonstrate the quality of CNV calls generated from DNA extracted from buccal samples, compared to calls generated from blood samples, we evaluated the concordance of calls from individuals who provided both sample types. The Illumina Human660W-Quad BeadChip was used to determine SNPs and CNVs of 39 Arkansas participants in the National Birth Defects Prevention Study (NBDPS), including 16 mother-infant dyads, who provided both whole blood and buccal brush DNA samples. Results We observed a 99.9% concordance rate of SNP calls in the 39 blood–buccal pairs. From the same dataset, we performed a similar analysis of CNVs. Each of the 78 samples was independently segmented into regions of like copy number using the Optimal Segmentation algorithm of Golden Helix SNP & Variation Suite 7. Across 640,663 loci on 22 autosomal chromosomes, segment-mean log R ratios had an average correlation of 0.899 between blood-buccal pairs of samples from the same individual, while the average correlation between all possible blood-buccal pairs of samples from unrelated individuals was 0.318. An independent analysis using the QuantiSNP algorithm produced average correlations of 0.943 between blood-buccal pairs from the same individual versus 0.332 between samples from unrelated individuals. Segment-mean log R ratios had an average correlation of 0.539 between mother-offspring dyads of buccal samples, which was not statistically significantly different than the average correlation of 0.526 between mother-offspring dyads of blood samples (p=0.302). Conclusions We observed performance from the subject-collected mail-in buccal brush samples comparable to that of blood. These results show that such DNA samples can be used for genome-wide scans of both SNPs and CNVs, and that high rates of CNV concordance were achieved whether using a change-point-based algorithm or one based on a hidden Markov model (HMM).
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Affiliation(s)
- Stephen W Erickson
- Department of Biostatistics, College of Medicine, University of Arkansas for Medical Science, 4301 W, Markham Street, Mail Slot 781, Little Rock, AR 72205-7199, USA.
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Valsesia A, Stevenson BJ, Waterworth D, Mooser V, Vollenweider P, Waeber G, Jongeneel CV, Beckmann JS, Kutalik Z, Bergmann S. Identification and validation of copy number variants using SNP genotyping arrays from a large clinical cohort. BMC Genomics 2012; 13:241. [PMID: 22702538 PMCID: PMC3464625 DOI: 10.1186/1471-2164-13-241] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 06/15/2012] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Genotypes obtained with commercial SNP arrays have been extensively used in many large case-control or population-based cohorts for SNP-based genome-wide association studies for a multitude of traits. Yet, these genotypes capture only a small fraction of the variance of the studied traits. Genomic structural variants (GSV) such as Copy Number Variation (CNV) may account for part of the missing heritability, but their comprehensive detection requires either next-generation arrays or sequencing. Sophisticated algorithms that infer CNVs by combining the intensities from SNP-probes for the two alleles can already be used to extract a partial view of such GSV from existing data sets. RESULTS Here we present several advances to facilitate the latter approach. First, we introduce a novel CNV detection method based on a Gaussian Mixture Model. Second, we propose a new algorithm, PCA merge, for combining copy-number profiles from many individuals into consensus regions. We applied both our new methods as well as existing ones to data from 5612 individuals from the CoLaus study who were genotyped on Affymetrix 500K arrays. We developed a number of procedures in order to evaluate the performance of the different methods. This includes comparison with previously published CNVs as well as using a replication sample of 239 individuals, genotyped with Illumina 550K arrays. We also established a new evaluation procedure that employs the fact that related individuals are expected to share their CNVs more frequently than randomly selected individuals. The ability to detect both rare and common CNVs provides a valuable resource that will facilitate association studies exploring potential phenotypic associations with CNVs. CONCLUSION Our new methodologies for CNV detection and their evaluation will help in extracting additional information from the large amount of SNP-genotyping data on various cohorts and use this to explore structural variants and their impact on complex traits.
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Affiliation(s)
- Armand Valsesia
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
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Wang Q, Peng P, Qian M, Wan L, Deng M. Hybridization and amplification rate correction for affymetrix SNP arrays. BMC Med Genomics 2012; 5:24. [PMID: 22691279 PMCID: PMC3428662 DOI: 10.1186/1755-8794-5-24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 06/12/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Copy number variation (CNV) is essential to understand the pathology of many complex diseases at the DNA level. Affymetrix SNP arrays, which are widely used for CNV studies, significantly depend on accurate copy number (CN) estimation. Nevertheless, CN estimation may be biased by several factors, including cross-hybridization and training sample batch, as well as genomic waves of intensities induced by sequence-dependent hybridization rate and amplification efficiency. Since many available algorithms only address one or two of the three factors, a high false discovery rate (FDR) often results when identifying CNV. Therefore, we have developed a new CNV detection pipeline which is based on hybridization and amplification rate correction (CNVhac). METHODS CNVhac first estimates the allelic concentrations (ACs) of target sequences by using the sample independent parameters trained through physicochemical hybridization law. Then the raw CN is estimated by taking the ratio of AC to the corresponding average AC from a reference sample set for one specific site. Finally, a hidden Markov model (HMM) segmentation process is implemented to detect CNV regions. RESULTS Based on public HapMap data, the results show that CNVhac effectively smoothes the genomic waves and facilitates more accurate raw CN estimates compared to other methods. Moreover, CNVhac alleviates, to a certain extent, the sample dependence of inference and makes CNV calling with appreciable low FDRs. CONCLUSION CNVhac is an effective approach to address the common difficulties in SNP array analysis, and the working principles of CNVhac can be easily extended to other platforms.
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Affiliation(s)
- Quan Wang
- Center for Theoretical Biology, Peking University, Beijing 100871, People's Republic of China
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48
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Taormina PL, Trask JAS, Smith DG, Kanthaswamy S. Variation in CCL3L1 copy number in rhesus macaques (Macaca mulatta). Comp Med 2012; 62:218-24. [PMID: 22776055 PMCID: PMC3364972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/22/2011] [Accepted: 12/05/2011] [Indexed: 06/01/2023]
Abstract
We used real-time quantitative PCR (qPCR) methodology to examine copy number variation (CNV) of the CCL3L1 gene among pure Indian-origin, pure Chinese-origin, and hybrid Indian-Chinese rhesus macaques (Macaca mulatta). CNV among purebred macaques fell within expected ranges, with Indian macaques having lower copy numbers than those of Chinese macaques. Compared with the purebred macaques, Indian-Chinese hybrid rhesus macaques showed much greater variance in copy number and an intermediate average copy number. Copy numbers of CCL3L1 in rhesus macaque trios (sire, dam, and offspring) were consistent with Mendelian inheritance.
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Affiliation(s)
| | | | - David G Smith
- Forensic Science Graduate Program
- Molecular Anthropology Laboratory
- California National Primate Research Center
| | - Sreetharan Kanthaswamy
- Forensic Science Graduate Program
- Molecular Anthropology Laboratory
- California National Primate Research Center
- Department of Environmental Toxicology, University of California, Davis, California
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49
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Karlsson R, Graae L, Lekman M, Wang D, Favis R, Axelsson T, Galter D, Belin AC, Paddock S. MAGI1 copy number variation in bipolar affective disorder and schizophrenia. Biol Psychiatry 2012; 71:922-30. [PMID: 22381734 DOI: 10.1016/j.biopsych.2012.01.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 01/11/2012] [Accepted: 01/12/2012] [Indexed: 12/12/2022]
Abstract
BACKGROUND Bipolar affective disorder (BPAD) and schizophrenia (SZ) are devastating psychiatric disorders that each affect about 1% of the population worldwide. Identification of new drug targets is an important step toward better treatment of these poorly understood diseases. METHODS Genome-wide copy number variation (CNV) was assessed and variants were ranked by co-occurrence with disease in 48 BPAD families. Additional support for involvement of the highest-ranking CNV from the family-based analysis in psychiatric disease was obtained through analysis of 4084 samples with BPAD, SZ, or schizoaffective disorder. Finally, a pooled analysis of in-house and published datasets was carried out including 10,925 cases with BPAD, SZ, or schizoaffective disorder and 16,747 controls. RESULTS In the family-based analysis, an approximately 200 kilobase (kb) deletion in the first intron of the MAGI1 gene was identified that segregated with BPAD in a pedigree (six out of six affected individuals; parametric logarithm of the odds score = 1.14). In the pooled analysis, seven additional insertions or deletions over 100 kb were identified in MAGI1 in cases, while only two such CNV events were identified in the same gene in controls (p = .023; Fisher's exact test). Because earlier work had identified a CNV in the close relative MAGI2 in SZ, the study was extended to include MAGI2. In the pooled analysis of MAGI2, two large deletions were found in cases, and two duplications were detected in controls. CONCLUSIONS Results presented herein provide further evidence for a role of MAGI1 and MAGI2 in BPAD and SZ etiology.
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Affiliation(s)
- Robert Karlsson
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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Wineinger NE, Tiwari HK. The impact of errors in copy number variation detection algorithms on association results. PLoS One 2012; 7:e32396. [PMID: 22523537 PMCID: PMC3327691 DOI: 10.1371/journal.pone.0032396] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 01/30/2012] [Indexed: 11/27/2022] Open
Abstract
The inaccuracy of copy number variation (CNV) detection on single nucleotide polymorphism (SNP) arrays has recently been brought to attention. Such high error rates will undoubtedly have ramifications on downstream association testing. We examined this effect for a wide range of scenarios and found a noticeable decrease in power for error rates typical of CNV calling algorithms. We compared power using CNV calls to the log relative ratio and found the latter to be superior when error rates are moderate to large or when the CNV size is small. It is our recommendation that CNV researchers use intensity measurements as an alternative to CNV calls in these scenarios.
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Affiliation(s)
- Nathan E Wineinger
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama, Birmingham, Alabama, United States of America.
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