Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project
Alzheimer’s Disease (AD) is a progressive neurologic disease and the most common form of dementia. While the causes of AD are not completely understood, genetics plays a key role in the etiology of AD, and thus finding genetic factors holds the potential to uncover novel AD mechanisms. For this stud...
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| Published in | Frontiers in genetics Vol. 12; p. 752390 |
|---|---|
| Main Authors | , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Switzerland
Frontiers Media S.A
04.11.2021
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1664-8021 1664-8021 |
| DOI | 10.3389/fgene.2021.752390 |
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| Abstract | Alzheimer’s Disease (AD) is a progressive neurologic disease and the most common form of dementia. While the causes of AD are not completely understood, genetics plays a key role in the etiology of AD, and thus finding genetic factors holds the potential to uncover novel AD mechanisms. For this study, we focus on copy number variation (CNV) detection and burden analysis. Leveraging whole-genome sequence (WGS) data released by Alzheimer’s Disease Sequencing Project (ADSP), we developed a scalable bioinformatics pipeline to identify CNVs. This pipeline was applied to 1,737 AD cases and 2,063 cognitively normal controls. As a result, we observed 237,306 and 42,767 deletions and duplications, respectively, with an average of 2,255 deletions and 1,820 duplications per subject. The burden tests show that Non-Hispanic-White cases on average have 16 more duplications than controls do (
p
-value 2e-6), and Hispanic cases have larger deletions than controls do (
p
-value 6.8e-5). |
|---|---|
| AbstractList | Alzheimer's Disease (AD) is a progressive neurologic disease and the most common form of dementia. While the causes of AD are not completely understood, genetics plays a key role in the etiology of AD, and thus finding genetic factors holds the potential to uncover novel AD mechanisms. For this study, we focus on copy number variation (CNV) detection and burden analysis. Leveraging whole-genome sequence (WGS) data released by Alzheimer's Disease Sequencing Project (ADSP), we developed a scalable bioinformatics pipeline to identify CNVs. This pipeline was applied to 1,737 AD cases and 2,063 cognitively normal controls. As a result, we observed 237,306 and 42,767 deletions and duplications, respectively, with an average of 2,255 deletions and 1,820 duplications per subject. The burden tests show that Non-Hispanic-White cases on average have 16 more duplications than controls do (
-value 2e-6), and Hispanic cases have larger deletions than controls do (
-value 6.8e-5). Alzheimer's Disease (AD) is a progressive neurologic disease and the most common form of dementia. While the causes of AD are not completely understood, genetics plays a key role in the etiology of AD, and thus finding genetic factors holds the potential to uncover novel AD mechanisms. For this study, we focus on copy number variation (CNV) detection and burden analysis. Leveraging whole-genome sequence (WGS) data released by Alzheimer's Disease Sequencing Project (ADSP), we developed a scalable bioinformatics pipeline to identify CNVs. This pipeline was applied to 1,737 AD cases and 2,063 cognitively normal controls. As a result, we observed 237,306 and 42,767 deletions and duplications, respectively, with an average of 2,255 deletions and 1,820 duplications per subject. The burden tests show that Non-Hispanic-White cases on average have 16 more duplications than controls do (p-value 2e-6), and Hispanic cases have larger deletions than controls do (p-value 6.8e-5).Alzheimer's Disease (AD) is a progressive neurologic disease and the most common form of dementia. While the causes of AD are not completely understood, genetics plays a key role in the etiology of AD, and thus finding genetic factors holds the potential to uncover novel AD mechanisms. For this study, we focus on copy number variation (CNV) detection and burden analysis. Leveraging whole-genome sequence (WGS) data released by Alzheimer's Disease Sequencing Project (ADSP), we developed a scalable bioinformatics pipeline to identify CNVs. This pipeline was applied to 1,737 AD cases and 2,063 cognitively normal controls. As a result, we observed 237,306 and 42,767 deletions and duplications, respectively, with an average of 2,255 deletions and 1,820 duplications per subject. The burden tests show that Non-Hispanic-White cases on average have 16 more duplications than controls do (p-value 2e-6), and Hispanic cases have larger deletions than controls do (p-value 6.8e-5). Alzheimer’s Disease (AD) is a progressive neurologic disease and the most common form of dementia. While the causes of AD are not completely understood, genetics plays a key role in the etiology of AD, and thus finding genetic factors holds the potential to uncover novel AD mechanisms. For this study, we focus on copy number variation (CNV) detection and burden analysis. Leveraging whole-genome sequence (WGS) data released by Alzheimer’s Disease Sequencing Project (ADSP), we developed a scalable bioinformatics pipeline to identify CNVs. This pipeline was applied to 1,737 AD cases and 2,063 cognitively normal controls. As a result, we observed 237,306 and 42,767 deletions and duplications, respectively, with an average of 2,255 deletions and 1,820 duplications per subject. The burden tests show that Non-Hispanic-White cases on average have 16 more duplications than controls do ( p -value 2e-6), and Hispanic cases have larger deletions than controls do ( p -value 6.8e-5). Alzheimer’s Disease (AD) is a progressive neurologic disease and the most common form of dementia. While the causes of AD are not completely understood, genetics plays a key role in the etiology of AD, and thus finding genetic factors holds the potential to uncover novel AD mechanisms. For this study, we focus on copy number variation (CNV) detection and burden analysis. Leveraging whole-genome sequence (WGS) data released by Alzheimer’s Disease Sequencing Project (ADSP), we developed a scalable bioinformatics pipeline to identify CNVs. This pipeline was applied to 1,737 AD cases and 2,063 cognitively normal controls. As a result, we observed 237,306 and 42,767 deletions and duplications, respectively, with an average of 2,255 deletions and 1,820 duplications per subject. The burden tests show that Non-Hispanic-White cases on average have 16 more duplications than controls do (p-value 2e-6), and Hispanic cases have larger deletions than controls do (p-value 6.8e-5). |
| Author | Lee, Wan-Ping Wang, Li-San Schellenberg, Gerard D. Tzeng, Jung-Ying Lu, Wenbin Tucci, Albert A. Kuzma, Amanda B. Leung, Yuk Yee Conery, Mitchell Chou, Yi-Fan Valladares, Otto |
| AuthorAffiliation | 4 Bioinformatics Research Center, North Carolina State University, Raleigh , NC , United States 2 Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia , PA , United States 6 Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia , PA , United States 5 Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia , PA , United States 7 Department of Statistics, North Carolina State University, Raleigh , NC , United States 1 Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia , PA , United States 3 Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia , PA , United States |
| AuthorAffiliation_xml | – name: 2 Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia , PA , United States – name: 6 Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia , PA , United States – name: 4 Bioinformatics Research Center, North Carolina State University, Raleigh , NC , United States – name: 5 Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia , PA , United States – name: 3 Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia , PA , United States – name: 1 Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia , PA , United States – name: 7 Department of Statistics, North Carolina State University, Raleigh , NC , United States |
| Author_xml | – sequence: 1 givenname: Wan-Ping surname: Lee fullname: Lee, Wan-Ping – sequence: 2 givenname: Albert A. surname: Tucci fullname: Tucci, Albert A. – sequence: 3 givenname: Mitchell surname: Conery fullname: Conery, Mitchell – sequence: 4 givenname: Yuk Yee surname: Leung fullname: Leung, Yuk Yee – sequence: 5 givenname: Amanda B. surname: Kuzma fullname: Kuzma, Amanda B. – sequence: 6 givenname: Otto surname: Valladares fullname: Valladares, Otto – sequence: 7 givenname: Yi-Fan surname: Chou fullname: Chou, Yi-Fan – sequence: 8 givenname: Wenbin surname: Lu fullname: Lu, Wenbin – sequence: 9 givenname: Li-San surname: Wang fullname: Wang, Li-San – sequence: 10 givenname: Gerard D. surname: Schellenberg fullname: Schellenberg, Gerard D. – sequence: 11 givenname: Jung-Ying surname: Tzeng fullname: Tzeng, Jung-Ying |
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| Cites_doi | 10.1101/gr.114876.110 10.1212/NXG.0000000000000194 10.1038/tp.2015.64 10.1002/alz.043341 10.3233/jad-2010-1212 10.2174/1389202919666180330153842 10.1016/j.jfma.2013.01.005 10.4061/2011/729478 10.1371/journal.pmed.1002270 10.1038/mp.2011.24 10.1038/ng.909 10.1016/j.cell.2012.02.039 10.2217/14622416.9.8.1143 10.1038/s41467-019-13341-9 10.1038/nature15394 10.1038/ng2080 10.1186/s13059-020-1941-7 10.1093/bioinformatics/btq033 10.1371/journal.pone.0079771 10.1186/gb-2014-15-6-r84 10.1093/gigascience/giab008 10.1038/s41586-020-2287-8 10.1038/s41593-020-0599-5 10.1097/wad.0b013e318142774e 10.1038/nrg3240 10.1186/s13742-015-0047-8 10.3233/jad-132693 10.1038/nature09534 10.1016/j.ajhg.2009.03.010 10.1101/2021.03.16.21252173 10.1186/s13059-019-1909-7 10.1016/j.jalz.2016.08.018 10.3233/JAD-2012-121285 10.3233/jad-2006-9s338 |
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| Copyright | Copyright © 2021 Lee, Tucci, Conery, Leung, Kuzma, Valladares, Chou, Lu, Wang, Schellenberg and Tzeng. Copyright © 2021 Lee, Tucci, Conery, Leung, Kuzma, Valladares, Chou, Lu, Wang, Schellenberg and Tzeng. 2021 Lee, Tucci, Conery, Leung, Kuzma, Valladares, Chou, Lu, Wang, Schellenberg and Tzeng |
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| Keywords | whole-genome sequence (WGS) CNV association test NGS—next generation sequencing copy number variation—CNV Alzheiemer’s disease |
| Language | English |
| License | Copyright © 2021 Lee, Tucci, Conery, Leung, Kuzma, Valladares, Chou, Lu, Wang, Schellenberg and Tzeng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Edited by: Claudia Gonzaga-Jauregui, Universidad Nacional Autónoma de México, Mexico This article was submitted to Human and Medical Genomics, a section of the journal Frontiers in Genetics These authors have contributed equally to this work and share first authorship Reviewed by: Audrey Qiuyan Fu, University of Idaho, United States Nancy Monroy-Jaramillo, National Institute of Neurology and Neurosurgery, Mexico |
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| Snippet | Alzheimer’s Disease (AD) is a progressive neurologic disease and the most common form of dementia. While the causes of AD are not completely understood,... Alzheimer's Disease (AD) is a progressive neurologic disease and the most common form of dementia. While the causes of AD are not completely understood,... |
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| SubjectTerms | Alzheiemer’s disease CNV association test copy number variation—CNV Genetics NGS—next generation sequencing whole-genome sequence (WGS) |
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| Title | Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/34804120 https://www.proquest.com/docview/2600823315 https://pubmed.ncbi.nlm.nih.gov/PMC8599981 https://doaj.org/article/631c6e2012e64644aa1bb9fe8e8e33d6 |
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