NG00174-Whole Genome Sequencing (WGS) and SNP Array data for the SEA-AD Consortium Cohort

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Description

This dataset contains whole genome sequencing (WGS) and genotyping SNP array data for the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) consortium’s 84 donor cohort.

Whole genome sequencing data includes 84 samples that were sent to The American Genome Center for sequencing on the Illumina NovaSeq and then to the Genome Center for Alzheimer’s Disease (GCAD) for processing. Files provided in this dataset include CRAMs, gVCFs, and a “preview” joint genotype-called project level VCF.

80 samples from the SEA-AD cohort were genotyped by the Center for Applied Genomics at the Children’s Hospital of Philadelphia using the Illumina Infinium Global Screening Array (GSA-24v3-0_A1). Raw genotypes are provided in the PLINK binary format on GRCh38.

There are no phenotypes provided within this dataset, but instead are available via SEA-AD.org as open access here: SEA-AD Data Access

Sample Summary per Data Type

Sample Set	Accession	Data Type	Number of Samples
SEA-AD WGS	snd10108	Whole Genome Sequencing	84
SEA-AD Array data	snd10109	Genotyping SNP Array	80

Available Filesets

Name	Accession	Latest Release	Description
SEA-AD WGS and Array data	fsa000117	NG00174.v1	PLINK files, CRAMs, gVCFs, and pVCFs

View the File Manifest for a full list of files released in this dataset.

For more demographic information about the subjects, navigate to the sample set below.

Sample Set	Accession Number	Number of Subjects	Number of Samples
SEA-AD WGS	snd10108	84	84
SEA-AD Array data	snd10109	80	80

Consent Level	Number of Subjects
DS-ADRDAGE-IRB-PUB	84

Acknowledgment statement for any data distributed by NIAGADS:

Data for this study were prepared, archived, and distributed by the National Institute on Aging Alzheimer’s Disease Data Storage Site (NIAGADS) at the University of Pennsylvania (U24-AG041689), funded by the National Institute on Aging.

Use the study-specific acknowledgement statements below (as applicable):

For investigators using any data from this dataset:

Please cite/reference the use of NIAGADS data by including the accession NG00174.

For investigators using The Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) (sa000065) data:

The SEA-AD consortium is supported by a National Institute on Aging (NIA). We thank the participants of the ADRC and the ACT study for the data they have provided and the many ADRC and ACT investigators and staff who steward that data. You can learn more about the UW ADRC at https://depts.washington.edu/mbwc/adrc and ACT at https://actagingstudy.org/. We thank members of the Allen Institute team who contributed to the development of the Seattle Alzheimer’s Disease Brain Cell Atlas Consortium’s web portal at SEA-AD.org.

The Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) consortium is supported by the National Institute on Aging (NIA) grant U19AG060909. The study data were generated from postmortem brain tissue donated to the University of Washington BRaIN laboratory and Precision Neuropathology Core, which is supported by the UW ADRC (NIA grant no. P30AG066509, previously no. P50AG005136), the ACT study (NIA grant no. U19AG066567) and U24AG072458, U24NS135561, U24NS133945, U24NS133949, RF1AG065406, R01NS105984, R01AG60942 and UM1MH130981. Additionally, ACT data collection for this work was supported, in part, by prior funding from the NIA (no. U01AG006781) and the Nancy and Buster Alvord Endowment (to C. Dirk Keene). The Alzheimer’s Disease Genetics Consortium (ADGC grant U01AG032984) funded whole genome sequencing and genotyping of the samples. The Center for Applied Genomics at the Children’s Hospital of Philadelphia Research Institute performed genotyping of samples. The American Genome Center at the Uniformed Services University of the Health Sciences (U01AG057659) performed the sequencing. The Genome Center for Alzheimer’s Disease (GCAD grant U54AG052427) processed the data.

Total number of samples: 84

Sex

Race

Ethnicity

Diagnosis

APOE

Female 51 60.7 %

Male 33 39.3 %

221 (1.2%)
2311 (13.1%)
242 (2.4%)
3347 (56.0%)
3417 (20.2%)
446 (7.1%)

AD
Control	17	20.2%
Case	147	175.0%

Not Hispanic or Latino

97.6%

Hispanic or Latino

1.2%

Not Applicable/Not Available

1.2%

NG00174-Whole Genome Sequencing (WGS) and SNP Array data for the SEA-AD Consortium Cohort

Overview

Description

Sample Summary per Data Type

Available Filesets

Sample information

Related Studies

Consent Levels

Acknowledgement

Acknowledgment statement for any data distributed by NIAGADS:

For investigators using any data from this dataset:

For investigators using The Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) (sa000065) data:

Related Publications

Total number of samples: 84