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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Autores principales:	Wan-Ping Lee, Albert A. Tucci, Mitchell Conery, Yuk Yee Leung, Amanda B. Kuzma, Otto Valladares, Yi-Fan Chou, Wenbin Lu, Li-San Wang, Gerard D. Schellenberg, Jung-Ying Tzeng
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	copy number variation—CNV Alzheiemer’s disease whole-genome sequence (WGS) CNV association test NGS—next generation sequencing Genetics QH426-470
Acceso en línea:	https://doaj.org/article/631c6e2012e64644aa1bb9fe8e8e33d6
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spelling	oai:doaj.org-article:631c6e2012e64644aa1bb9fe8e8e33d62021-11-04T06:46:57ZCopy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project1664-802110.3389/fgene.2021.752390https://doaj.org/article/631c6e2012e64644aa1bb9fe8e8e33d62021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.752390/fullhttps://doaj.org/toc/1664-8021Alzheimer’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).Wan-Ping LeeWan-Ping LeeWan-Ping LeeAlbert A. TucciMitchell ConeryMitchell ConeryYuk Yee LeungYuk Yee LeungYuk Yee LeungAmanda B. KuzmaOtto ValladaresYi-Fan ChouWenbin LuLi-San WangLi-San WangLi-San WangGerard D. SchellenbergGerard D. SchellenbergJung-Ying TzengJung-Ying TzengFrontiers Media S.A.articlecopy number variation—CNVAlzheiemer’s diseasewhole-genome sequence (WGS)CNV association testNGS—next generation sequencingGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	copy number variation—CNV Alzheiemer’s disease whole-genome sequence (WGS) CNV association test NGS—next generation sequencing Genetics QH426-470
spellingShingle	copy number variation—CNV Alzheiemer’s disease whole-genome sequence (WGS) CNV association test NGS—next generation sequencing Genetics QH426-470 Wan-Ping Lee Wan-Ping Lee Wan-Ping Lee Albert A. Tucci Mitchell Conery Mitchell Conery Yuk Yee Leung Yuk Yee Leung Yuk Yee Leung Amanda B. Kuzma Otto Valladares Yi-Fan Chou Wenbin Lu Li-San Wang Li-San Wang Li-San Wang Gerard D. Schellenberg Gerard D. Schellenberg Jung-Ying Tzeng Jung-Ying Tzeng Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project
description	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).
format	article
author	Wan-Ping Lee Wan-Ping Lee Wan-Ping Lee Albert A. Tucci Mitchell Conery Mitchell Conery Yuk Yee Leung Yuk Yee Leung Yuk Yee Leung Amanda B. Kuzma Otto Valladares Yi-Fan Chou Wenbin Lu Li-San Wang Li-San Wang Li-San Wang Gerard D. Schellenberg Gerard D. Schellenberg Jung-Ying Tzeng Jung-Ying Tzeng
author_facet	Wan-Ping Lee Wan-Ping Lee Wan-Ping Lee Albert A. Tucci Mitchell Conery Mitchell Conery Yuk Yee Leung Yuk Yee Leung Yuk Yee Leung Amanda B. Kuzma Otto Valladares Yi-Fan Chou Wenbin Lu Li-San Wang Li-San Wang Li-San Wang Gerard D. Schellenberg Gerard D. Schellenberg Jung-Ying Tzeng Jung-Ying Tzeng
author_sort	Wan-Ping Lee
title	Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project
title_short	Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project
title_full	Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project
title_fullStr	Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project
title_full_unstemmed	Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project
title_sort	copy number variation identification on 3,800 alzheimer’s disease whole genome sequencing data from the alzheimer’s disease sequencing project
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/631c6e2012e64644aa1bb9fe8e8e33d6
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Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project

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