CONP Portal | Dataset

Keywords: Alzheimer Disease Exome Sequencing WES
Alzheimer Disease Whole Exome Sequencing
Creators: The Montreal Neurological Institute and Hospital Bioinformatics Core
Principal Investigator: The Montreal Neurological Institute and Hospital Bioinformatics Core
Contact: The Montreal Neurological Institute and Hospital Bioinformatics Core, neurobioinfo@mcgill.ca
Licenses: CC BY-SA
Version: 1.0
Modalities: Exome sequencing FASTQ files BAM alignments gVCF/VCF files
Formats: FASTQ FILES BAM ALIGNMENTS GVCF/VCF FILES
Size: 10.4 GB
No of Files: 15
No of Subjects: 4
Browse on GitHub: https://github.com/conpdatasets/cbig_alzheimers_disease_wes
Project Landing Page: https://cbigr.loris.ca/
Registration Page: https://cbigr-open.loris.ca/login/request-account/
Metadata file: DATS.json
Is About: Homo sapiens
Description:
Whole exome sequencing data from 4 individuals with Alzheimer Disease were recruited at the Montreal Neurological Institute and Hospital. Recruiting clinician was Dr. Guy Rouleau. Sequencing reads were processed using a Burrows-Wheeler Aligner (BWA) alignment, Genome Analysis Toolkit (GATK)/Picard post-alignment, and GATK HaplotypeCaller calling pipeline.

Dataset README information

README.md

OVERVIEW

The Montreal Neurological Institute and Hospital (The Neuro) Bioinformatics Core is responsible for processing, consolidating, and storing the genomics data generated for the range of studies being performed by the institute’s researchers and clinicians. As such, the data are sorted into sets based on the sequencing methodology used and the phenotype of study. The Neuro's commitment to open science practices have resulted in all of the data being made publicly available through the C-BIG initiative, following appropriate ethical approvals and the principal investigator(s) consent.

Largely, these genomics datasets were generated for the purposes of novel gene-disease relationship discovery, although other analyses may have also been performed. We recommend contacting the recruiting principal investigator(s), outlined below, for full details regarding the previous use of these datasets.

Dataset contents

  • 10.3577 GB
  • FASTQ files, BAM alignments, and gVCF/VCF files
  • 4 Subjects

METHODS

-- Recruitment --

Patients diagnosed with Alzheimer Disease were recruited at The Montreal Neurological Institute and Hospital (The Neuro) in the clinic of Dr. Guy Rouleau. All indivduals provided informed consent.

-- Data Acquisition --

Whole blood was obtained from all individuals and DNA was isolated. Whole exome sequencing was performed using either the Illumina NovaSeq 6000 or the Illumina HiSeq. Sequencing reads were processed using a Burrows-Wheeler Aligner (BWA) alignment, Genome Analysis Toolkit (GATK)/Picard post-alignment, and GATK HaplotypeCaller calling pipeline.

Sequencing details:

                Machine-pairing Sequencing_center Capture_type_kit          Date
          Illumina_GAIIx_Paired                HK   Exome_SS_38Mbp    2017_10_06
              ABI_SOLID4_Single              SteJ   Exome_SS_50Mbp    2010_11_30
          Illumina_HiSeq_paired                IC      Exome_NG_V3          2016
     Illumina_HiSeq_4000_Paired          Macrogen      Exome_SS_V5    2016_03_08