ID

45842

Description

Principal Investigator: Steven McCarroll, PhD, The Broad Institute of MIT and Harvard, Cambridge, MA, USA MeSH: Schizophrenia,Bipolar Disorder https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001020 The Center for Genomic Psychiatry at the University of Southern California (USC), SUNY Downstate and an extensive network of academic medical centers have created the Genomic Psychiatry Cohort (GPC). The GPC consists of a large clinical cohort of patients with schizophrenia, bipolar disorder, and healthy controls. The data generation of genotyping and whole genome sequencing of the GPC has been done in collaboration with the USC and the Broad Institute of MIT and Harvard. Genome-wide association studies are being performed with the samples to identify genetic risks for psychiatric disease. Genotyping is also being used to determine ancestry informative markers and replication of candidate genes. Whole genome sequencing identifies functional variants associated with disease risk.

Link

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001020

Keywords

  1. 8/24/23 8/24/23 - Arman Ghanaat
Copyright Holder

Steven McCarroll, PhD, The Broad Institute of MIT and Harvard, Cambridge, MA, USA

Uploaded on

August 24, 2023

DOI

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License

Creative Commons BY 4.0

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dbGaP phs001020 Genomic Psychiatry Cohort (GPC) Whole Genome Sequencing and Genotyping Study

This sample attributes table informs of body site where sample was collected, sample analyte type, sample tumor status, sample histology, whether 30X mean coverage was achieved in the sample during sequencing, and site where sequencing took place.

pht005784
Description

pht005784

Alias
UMLS CUI [1,1]
C3846158
De-identified Sample ID
Description

SAMPID

Data type

string

Alias
UMLS CUI [1,1]
C4684638
UMLS CUI [1,2]
C1299222
Body site where sample was collected
Description

BODY_SITE

Data type

string

Alias
UMLS CUI [1,1]
C0449705
Analyte Type
Description

ANALYTE_TYPE

Data type

string

Alias
UMLS CUI [1,1]
C4744818
Tumor status
Description

IS_TUMOR

Data type

text

Alias
UMLS CUI [1,1]
C0475752
Cell or tissue type or subtype of sample
Description

HISTOLOGICAL_TYPE

Data type

string

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0007634
UMLS CUI [1,3]
C0332307
UMLS CUI [1,4]
C0449560
UMLS CUI [1,5]
C1292533
Samples meeting 30X mean coverage encoded value
Description

Coverage_Pass

Data type

text

Alias
UMLS CUI [1,1]
C1294197
UMLS CUI [1,2]
C4743987
UMLS CUI [1,3]
C3816446
Site where sequencing occurred
Description

SITE

Data type

string

Alias
UMLS CUI [1,1]
C5667250

Similar models

This sample attributes table informs of body site where sample was collected, sample analyte type, sample tumor status, sample histology, whether 30X mean coverage was achieved in the sample during sequencing, and site where sequencing took place.

Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
pht005784
C3846158 (UMLS CUI [1,1])
SAMPID
Item
De-identified Sample ID
string
C4684638 (UMLS CUI [1,1])
C1299222 (UMLS CUI [1,2])
Item
Body site where sample was collected
string
C0449705 (UMLS CUI [1,1])
Code List
Body site where sample was collected
CL Item
BLOOD (BLOOD)
Item
Analyte Type
string
C4744818 (UMLS CUI [1,1])
Code List
Analyte Type
CL Item
DNA (DNA)
Item
Tumor status
text
C0475752 (UMLS CUI [1,1])
Code List
Tumor status
CL Item
Is not a tumor (N)
C0027651 (UMLS CUI [1,1])
C1518422 (UMLS CUI [1,2])
Item
Cell or tissue type or subtype of sample
string
C2347026 (UMLS CUI [1,1])
C0007634 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C0449560 (UMLS CUI [1,4])
C1292533 (UMLS CUI [1,5])
Code List
Cell or tissue type or subtype of sample
CL Item
BLOOD (BLOOD)
Item
Samples meeting 30X mean coverage encoded value
text
C1294197 (UMLS CUI [1,1])
C4743987 (UMLS CUI [1,2])
C3816446 (UMLS CUI [1,3])
Code List
Samples meeting 30X mean coverage encoded value
CL Item
not provided (Missing)
CL Item
No (N)
CL Item
Yes (Y)
SITE
Item
Site where sequencing occurred
string
C5667250 (UMLS CUI [1,1])

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