---
title: "AMP-AD WGS"
id: "2393"
type: "sample_set"
slug: "snd10011"
published_at: "2021-02-24T00:57:13+00:00"
modified_at: "2023-12-14T22:27:14+00:00"
url: "https://dss.niagads.org/sample-sets/snd10011/"
markdown_url: "https://dss.niagads.org/sample-sets/snd10011.md"
excerpt: "AMP-AD samples from the ROSMAP, MayoRNAseq, and Mount Sinai Brain Bank cohorts were whole-genome sequenced at New York Genome Center on the HiSeqX machine. FASTQ files were sent to GCAD for processing on the VCPA1.1 pipeline. 1326 samples passed sequencing..."
---

## Description

AMP-AD samples from the ROSMAP, MayoRNAseq, and Mount Sinai Brain Bank cohorts were whole-genome sequenced at New York Genome Center on the HiSeqX machine. FASTQ files were sent to GCAD for processing on the VCPA1.1 pipeline. 1326 samples passed sequencing metrics and quality control. Additional information about each of the three studies can be obtained from the [AMP-AD Knowledge Portal](https://adknowledgeportal.synapse.org/Explore/Data?QueryWrapper0=%7B%22sql%22%3A%22SELECT%20*%20FROM%20syn11346063%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22assay%22%2C%22facetValues%22%3A%5B%22wholeGenomeSeq%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22study%22%2C%22facetValues%22%3A%5B%22ROSMAP%22%2C%22MayoRNAseq%22%2C%22MSBB%22%5D%7D%5D%7D)
.

## Cohorts

- [Mayo Clinic (MAYO)](https://dss.niagads.org/cohorts/mayo/)
- [Mount Sinai Brain Bank (MSBB)](https://dss.niagads.org/cohorts/mount-sinai-brain-bank-msbb/)
- [Progressive Supranuclear Palsy (PSP)](https://dss.niagads.org/cohorts/progressive-supranuclear-palsy-psp/)
- [Religious Orders Study/Memory and Aging Project (ROSMAP)](https://dss.niagads.org/cohorts/religious-orders-study-memory-and-aging-project-rosmap/)

## Sex

### Total number of samples: 1,326

Female85964.8 %

Male46735.2 %

## Race

### Total number of samples: 1,326

| Asian | 1 |
| --- | --- |
| Black or African American | 33 |
| White | 1,261 |
| Other | 23 |
| NA | 8 |

## Ethnicity

### Total number of samples: 1,326

Not Hispanic or Latino

1,218

91.9%

Hispanic or Latino

24

1.8%

Not Applicable/Not Available

84

6.3%

## Diagnosis

### Total number of samples: 1,326

| AD |  |  |
| --- | --- | --- |
| Control | 468 | 35.3% |
| Case | 736 | 55.5% |
| Unknown | 39 | 2.9% |

| PSP |  |  |
| --- | --- | --- |
| Case | 83 | 6.3% |

## APOE

### Total number of samples: 1,326

- 225 (0.4%)
- 2393 (7.0%)
- 2414 (1.1%)
- 33509 (38.4%)
- 34218 (16.4%)
- 4424 (1.8%)
- NA463 (34.9%)