Copy number variation in familial Parkinson disease

Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2. PARK2 has a recessive mode of inheritance; however, recent evidence demonstrates that a single CNV in PARK2 (but not a single missense mutation) may increase risk for PD. We rece...

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Published inPloS one Vol. 6; no. 8; p. e20988
Main Authors Pankratz, Nathan, Dumitriu, Alexandra, Hetrick, Kurt N, Sun, Mei, Latourelle, Jeanne C, Wilk, Jemma B, Halter, Cheryl, Doheny, Kimberly F, Gusella, James F, Nichols, William C, Myers, Richard H, Foroud, Tatiana, DeStefano, Anita L
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 02.08.2011
Public Library of Science (PLoS)
Subjects
Algorithms
Biology
Cell lines
Clonal deletion
Copy number
Deoxyribonucleic acid
DNA
DNA Copy Number Variations
Drug dosages
Gel electrophoresis
Gender
Gene deletion
Gene frequency
Genes
Genetic aspects
Genetic research
Genome-wide association studies
Genome-Wide Association Study
Genomes
Genomics
Heredity
Heterozygosity
Hospitals
Humans
Loci
Loss of heterozygosity
LRRK2 protein
Medicine
Minisatellite Repeats
Missense mutation
Movement disorders
Mutation
Neurodegenerative diseases
Neurology
Parkinson disease
Parkinson Disease - genetics
Parkinson's disease
Parkinsons disease
Pathogenesis
Polymerase Chain Reaction
Quality assessment
Quality control
Risk factors
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Studies
Indiana
United States > US
Massachusetts
Indianapolis Indiana
Ohio
Maryland
Baltimore Maryland
Online AccessGet full text

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Abstract Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2. PARK2 has a recessive mode of inheritance; however, recent evidence demonstrates that a single CNV in PARK2 (but not a single missense mutation) may increase risk for PD. We recently performed a genome-wide association study for PD that excluded individuals known to have either a LRRK2 mutation or two PARK2 mutations. Data from the Illumina370Duo arrays were re-clustered using only white individuals with high quality intensity data, and CNV calls were made using two algorithms, PennCNV and QuantiSNP. After quality assessment, the final sample included 816 cases and 856 controls. Results varied between the two CNV calling algorithms for many regions, including the PARK2 locus (genome-wide p = 0.04 for PennCNV and p = 0.13 for QuantiSNP). However, there was consistent evidence with both algorithms for two novel genes, USP32 and DOCK5 (empirical, genome-wide p-values<0.001). PARK2 CNVs tended to be larger, and all instances that were molecularly tested were validated. In contrast, the CNVs in both novel loci were smaller and failed to replicate using real-time PCR, MLPA, and gel electrophoresis. The DOCK5 variation is more akin to a VNTR than a typical CNV and the association is likely caused by artifact due to DNA source. DNA for all the cases was derived from whole blood, while the DNA for all controls was derived from lymphoblast cell lines. The USP32 locus contains many SNPs with low minor allele frequency leading to a loss of heterozygosity that may have been spuriously interpreted by the CNV calling algorithms as support for a deletion. Thus, only the CNVs within the PARK2 locus could be molecularly validated and associated with PD susceptibility.
AbstractList Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2 . PARK2 has a recessive mode of inheritance; however, recent evidence demonstrates that a single CNV in PARK2 (but not a single missense mutation) may increase risk for PD. We recently performed a genome-wide association study for PD that excluded individuals known to have either a LRRK2 mutation or two PARK2 mutations. Data from the Illumina370Duo arrays were re-clustered using only white individuals with high quality intensity data, and CNV calls were made using two algorithms, PennCNV and QuantiSNP. After quality assessment, the final sample included 816 cases and 856 controls. Results varied between the two CNV calling algorithms for many regions, including the PARK2 locus (genome-wide p = 0.04 for PennCNV and p = 0.13 for QuantiSNP). However, there was consistent evidence with both algorithms for two novel genes, USP32 and DOCK5 (empirical, genome-wide p-values<0.001). PARK2 CNVs tended to be larger, and all instances that were molecularly tested were validated. In contrast, the CNVs in both novel loci were smaller and failed to replicate using real-time PCR, MLPA, and gel electrophoresis. The DOCK5 variation is more akin to a VNTR than a typical CNV and the association is likely caused by artifact due to DNA source. DNA for all the cases was derived from whole blood, while the DNA for all controls was derived from lymphoblast cell lines. The USP32 locus contains many SNPs with low minor allele frequency leading to a loss of heterozygosity that may have been spuriously interpreted by the CNV calling algorithms as support for a deletion. Thus, only the CNVs within the PARK2 locus could be molecularly validated and associated with PD susceptibility.
Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2. PARK2 has a recessive mode of inheritance; however, recent evidence demonstrates that a single CNV in PARK2 (but not a single missense mutation) may increase risk for PD. We recently performed a genome-wide association study for PD that excluded individuals known to have either a LRRK2 mutation or two PARK2 mutations. Data from the Illumina370Duo arrays were re-clustered using only white individuals with high quality intensity data, and CNV calls were made using two algorithms, PennCNV and QuantiSNP. After quality assessment, the final sample included 816 cases and 856 controls. Results varied between the two CNV calling algorithms for many regions, including the PARK2 locus (genome-wide p = 0.04 for PennCNV and p = 0.13 for QuantiSNP). However, there was consistent evidence with both algorithms for two novel genes, USP32 and DOCK5 (empirical, genome-wide p-values<0.001). PARK2 CNVs tended to be larger, and all instances that were molecularly tested were validated. In contrast, the CNVs in both novel loci were smaller and failed to replicate using real-time PCR, MLPA, and gel electrophoresis. The DOCK5 variation is more akin to a VNTR than a typical CNV and the association is likely caused by artifact due to DNA source. DNA for all the cases was derived from whole blood, while the DNA for all controls was derived from lymphoblast cell lines. The USP32 locus contains many SNPs with low minor allele frequency leading to a loss of heterozygosity that may have been spuriously interpreted by the CNV calling algorithms as support for a deletion. Thus, only the CNVs within the PARK2 locus could be molecularly validated and associated with PD susceptibility.
Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2. PARK2 has a recessive mode of inheritance; however, recent evidence demonstrates that a single CNV in PARK2 (but not a single missense mutation) may increase risk for PD. We recently performed a genome-wide association study for PD that excluded individuals known to have either a LRRK2 mutation or two PARK2 mutations. Data from the Illumina370Duo arrays were re-clustered using only white individuals with high quality intensity data, and CNV calls were made using two algorithms, PennCNV and QuantiSNP. After quality assessment, the final sample included 816 cases and 856 controls. Results varied between the two CNV calling algorithms for many regions, including the PARK2 locus (genome-wide p = 0.04 for PennCNV and p = 0.13 for QuantiSNP). However, there was consistent evidence with both algorithms for two novel genes, USP32 and DOCK5 (empirical, genome-wide p-values<0.001). PARK2 CNVs tended to be larger, and all instances that were molecularly tested were validated. In contrast, the CNVs in both novel loci were smaller and failed to replicate using real-time PCR, MLPA, and gel electrophoresis. The DOCK5 variation is more akin to a VNTR than a typical CNV and the association is likely caused by artifact due to DNA source. DNA for all the cases was derived from whole blood, while the DNA for all controls was derived from lymphoblast cell lines. The USP32 locus contains many SNPs with low minor allele frequency leading to a loss of heterozygosity that may have been spuriously interpreted by the CNV calling algorithms as support for a deletion. Thus, only the CNVs within the PARK2 locus could be molecularly validated and associated with PD susceptibility.Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2. PARK2 has a recessive mode of inheritance; however, recent evidence demonstrates that a single CNV in PARK2 (but not a single missense mutation) may increase risk for PD. We recently performed a genome-wide association study for PD that excluded individuals known to have either a LRRK2 mutation or two PARK2 mutations. Data from the Illumina370Duo arrays were re-clustered using only white individuals with high quality intensity data, and CNV calls were made using two algorithms, PennCNV and QuantiSNP. After quality assessment, the final sample included 816 cases and 856 controls. Results varied between the two CNV calling algorithms for many regions, including the PARK2 locus (genome-wide p = 0.04 for PennCNV and p = 0.13 for QuantiSNP). However, there was consistent evidence with both algorithms for two novel genes, USP32 and DOCK5 (empirical, genome-wide p-values<0.001). PARK2 CNVs tended to be larger, and all instances that were molecularly tested were validated. In contrast, the CNVs in both novel loci were smaller and failed to replicate using real-time PCR, MLPA, and gel electrophoresis. The DOCK5 variation is more akin to a VNTR than a typical CNV and the association is likely caused by artifact due to DNA source. DNA for all the cases was derived from whole blood, while the DNA for all controls was derived from lymphoblast cell lines. The USP32 locus contains many SNPs with low minor allele frequency leading to a loss of heterozygosity that may have been spuriously interpreted by the CNV calling algorithms as support for a deletion. Thus, only the CNVs within the PARK2 locus could be molecularly validated and associated with PD susceptibility.
Audience Academic
Author Halter, Cheryl
Foroud, Tatiana
Doheny, Kimberly F
Dumitriu, Alexandra
DeStefano, Anita L
Gusella, James F
Latourelle, Jeanne C
Wilk, Jemma B
Hetrick, Kurt N
Pankratz, Nathan
Nichols, William C
Sun, Mei
Myers, Richard H
AuthorAffiliation Public Library of Science, United Kingdom
4 Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
6 Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
9 Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
2 Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
5 Department of Neurology, Harvard Medical School, Boston, Massachusetts, United States of America
1 Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
7 Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
3 Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of
AuthorAffiliation_xml – name: 1 Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
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– name: Public Library of Science, United Kingdom
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– name: 5 Department of Neurology, Harvard Medical School, Boston, Massachusetts, United States of America
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– name: 8 Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/21829596$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
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Calabrese, V
Harris, J
Thompson, K
Fernandez, H
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O'Brien, C
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2011 Pankratz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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Conceived and designed the experiments: NP AD KNH MS JFG JL JBW RHM TF ALD. Performed the experiments: NP AD KNH MS KFD JFG WCN ALD. Analyzed the data: NP AD JL JBW KNH ALD. Contributed reagents/materials/analysis tools: KNH KFD CH WCN JFG. Wrote the paper: NP AD KNH MS JL JBW CH KFD JFG WCN RHM TF ALD. Take responsibility for the PSG-PROGENI Investigators, Coordinators and Molecular Genetic Laboratories: NP WCN TF. Take responsibility for the GenePD Investigators, Coordinators and Molecular Genetic Laboratories: JFG RHM ALD.
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Snippet Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2. PARK2 has a recessive mode of...
Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2 . PARK2 has a recessive mode of...
Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2 . PARK2 has a recessive mode of...
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StartPage e20988
SubjectTerms Algorithms
Biology
Cell lines
Clonal deletion
Copy number
Deoxyribonucleic acid
DNA
DNA Copy Number Variations
Drug dosages
Gel electrophoresis
Gender
Gene deletion
Gene frequency
Genes
Genetic aspects
Genetic research
Genome-wide association studies
Genome-Wide Association Study
Genomes
Genomics
Heredity
Heterozygosity
Hospitals
Humans
Loci
Loss of heterozygosity
LRRK2 protein
Medicine
Minisatellite Repeats
Missense mutation
Movement disorders
Mutation
Neurodegenerative diseases
Neurology
Parkinson disease
Parkinson Disease - genetics
Parkinson's disease
Parkinsons disease
Pathogenesis
Polymerase Chain Reaction
Quality assessment
Quality control
Risk factors
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Studies
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Title Copy number variation in familial Parkinson disease
URI https://www.ncbi.nlm.nih.gov/pubmed/21829596
https://www.proquest.com/docview/1306890292
https://www.proquest.com/docview/893721032
https://pubmed.ncbi.nlm.nih.gov/PMC3149037
https://doaj.org/article/35b500ab30934e039c31e84cc71c44a4
http://dx.doi.org/10.1371/journal.pone.0020988
Volume 6
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