---
title: "AMP-AD WGS – SV Calls"
id: "4726"
type: "sample_set"
slug: "snd10041"
published_at: "2023-04-24T14:29:02+00:00"
modified_at: "2023-04-26T19:33:46+00:00"
url: "https://dss.niagads.org/sample-sets/snd10041/"
markdown_url: "https://dss.niagads.org/sample-sets/snd10041.md"
excerpt: "The AMP-AD WGS sampleset was sequenced on the Illumina HiSeqX sequencer (v2.5 chemistry) and made available from four aging and Alzheimer’s disease cohorts: Religious Orders Study (ROS) and Memory and Aging Project (MAP), Mayo Clinic, and Mount Sinai Brain Bank..."
---

## Description

The AMP-AD WGS sampleset was sequenced on the Illumina HiSeqX sequencer (v2.5 chemistry) and made available from four aging and Alzheimer’s disease cohorts: Religious Orders Study (ROS) and Memory and Aging Project (MAP), Mayo Clinic, and Mount Sinai Brain Bank (MSBB). Structural variation discovery quality control identified 46,197 SVs in Mayo Clinic (349 samples), 52,451 SVs in MSBB (305 samples), and 72,348 SVs in ROS/MAP (715 samples), totaling 170,966 across 1,369 samples. Subjects in ROS/MAP not consented for individual SV calls were removed from the individual level data submission but are still part of the aggregate association summary statistics.

## 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/)
- [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: 1,369

Female86663.3 %

Male50336.7 %

## Diagnosis

### Total number of samples: 1,369

| AD |  |  |
| --- | --- | --- |
| Control | 294 | 21.5% |
| Case | 540 | 39.4% |

| PSP |  |  |
| --- | --- | --- |
| Case | 83 | 6.1% |

| Other |  |  |
| --- | --- | --- |
| Other | 452 | 33.0% |

## APOE

### Total number of samples: 1,369

- 227 (0.5%)
- 23133 (9.7%)
- 2414 (1.0%)
- 33695 (50.8%)
- 34285 (20.8%)
- 4427 (2.0%)
- NA208 (15.2%)