Alzheimer's Disease Sequencing Project Release 4 Whole Genome Sequencing Dataset

Yuk Yee Leung; Wan-Ping Lee; Amanda B Kuzma; Heather Nicaretta; Otto Valladares; Prabhakaran Gangadharan; Liming Qu; Yi Zhao; Youli Ren; Po-Liang Cheng; Pavel P Kuksa; Hui Wang; Heather White; Zivadin Katanic; Lauren Bass; Naveen Saravanan; Emily Greenfest-Allen; Maureen Kirsch; Laura Cantwell; Taha Iqbal; Nicholas R Wheeler; John J Farrell; Congcong Zhu; Shannon L Turner; Tamil I Gunasekaran; Pedro R Mena; Jimmy Jin; Luke Carter; Alzheimer’s Disease Sequencing Project; Xiaoling Zhang; Badri N Vardarajan; Arthur Toga; Michael Cuccaro; Timothy J Hohman; William S Bush; Adam C Naj; Eden Martin; Clifton Dalgard; Brian W Kunkle; Lindsay A Farrer; Richard P Mayeux; Jonathan L Haines; Margaret A Pericak-Vance; Gerard D Schellenberg; Li-San Wang

doi:10.1101/2024.12.03.24317000

Alzheimer's Disease Sequencing Project Release 4 Whole Genome Sequencing Dataset

medRxiv [Preprint]. 2024 Dec 6:2024.12.03.24317000. doi: 10.1101/2024.12.03.24317000.

Authors

Yuk Yee Leung^{1

2}, Wan-Ping Lee^{1

2}, Amanda B Kuzma^{1

2}, Heather Nicaretta^{1

2}, Otto Valladares^{1

2}, Prabhakaran Gangadharan^{1

2}, Liming Qu^{1

2}, Yi Zhao^{1

2}, Youli Ren^{1

2}, Po-Liang Cheng^{1

2}, Pavel P Kuksa^{1

2}, Hui Wang^{1

2}, Heather White^{1

2}, Zivadin Katanic^{1

2}, Lauren Bass^{1

2}, Naveen Saravanan^{1

2}, Emily Greenfest-Allen^{1

2}, Maureen Kirsch^{1

2}, Laura Cantwell^{1

2}, Taha Iqbal^{1

3}, Nicholas R Wheeler^{4

5}, John J Farrell^{6

7}, Congcong Zhu^{6

7}, Shannon L Turner^{8

9}, Tamil I Gunasekaran^{10

11}, Pedro R Mena¹², Jimmy Jin^{1

2}, Luke Carter^{1

2}; Alzheimer’s Disease Sequencing Project; Xiaoling Zhang^{6

7}, Badri N Vardarajan^{10

11}, Arthur Toga¹³, Michael Cuccaro¹², Timothy J Hohman^{8

9}, William S Bush^{4

5}, Adam C Naj^{1

3}, Eden Martin¹², Clifton Dalgard¹⁴, Brian W Kunkle¹², Lindsay A Farrer^{6

7}, Richard P Mayeux^{10

11}, Jonathan L Haines^{4

5}, Margaret A Pericak-Vance¹², Gerard D Schellenberg¹, Li-San Wang^{1

2}

Affiliations

¹ Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
² Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
³ Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
⁴ Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
⁵ Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
⁶ Department of Medicine, Biostatistics & Bioinformatics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
⁷ Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
⁸ Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA.
⁹ Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
¹⁰ Columbia University Irving Medical Center, New York, NY, USA.
¹¹ Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
¹² Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
¹³ Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California.
¹⁴ Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.

Abstract

The Alzheimer's Disease Sequencing Project (ADSP) is a national initiative to understand the genetic architecture of Alzheimer's Disease and Related Dementias (AD/ADRD) by sequencing whole genomes of affected participants and age-matched cognitive controls from diverse populations. The Genome Center for Alzheimer's Disease (GCAD) processed whole-genome sequencing data from 36,361 ADSP participants, including 35,014 genetically unique participants of which 45% are from non-European ancestry, across 17 cohorts in 14 countries in this fourth release (R4). This sequencing effort identified 387 million bi-allelic variants, 42 million short insertions/deletions, and 2.2 million structural variants. Annotations and quality control data are available for all variants and samples. Additionally, detailed phenotypes from 15,927 participants across 10 domains are also provided. A linkage disequilibrium panel was created using unrelated AD cases and controls. Researchers can access and analyze the genetic data via NIAGADS Data Sharing Service, the VariXam tool, or NIAGADS GenomicsDB.

Publication types

Preprint

Abstract

Publication types

Grants and funding