ID

45620

Description

Principal Investigator: Jeffrey P. MacKeigan, PhD, Van Andel Institute, Grand Rapids, MI, USA MeSH: Tuberous Sclerosis https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001357 In this study, we characterized the genomic landscape of tuberous sclerosis complex (TSC), a rare genetic disease causing multisystem growth of benign tumors and other hamartomatous lesions. We analyzed 127 human tissues, including 111 TSC-associated samples and 16 non-TSC negative controls, using multiple genomic platforms including whole exome sequencing, targeted sequencing of known disease-causative loci (*TSC1* and *TSC2*), mRNA sequencing, high-density SNP arrays, and DNA methylation arrays.

Link

dbGaP study = phs001357

Keywords

Versions (1)
  1. 2/27/23 2/27/23 - Simon Heim
Copyright Holder

Jeffrey P. MacKeigan, PhD, Van Andel Institute, Grand Rapids, MI, USA

Uploaded on

February 27, 2023

DOI

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License

Creative Commons BY 4.0
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dbGaP phs001357 The Genomic Landscape of Tuberous Sclerosis Complex (TSC)

English

Eligibility Criteria

5 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0680251
Samples from TSC patients or non-TSC organ donors were acquired from the NIH NeuroBioBank's Brain and Tissue Repository at the University of Maryland, Houston McGovern Medical School at the University of Texas, Cincinnati Children's Hospital Medical Center, New York University School of Medicine, and Helen DeVos Children's Hospital. Samples were reviewed by a certified clinical pathologist to confirm tissue type and assess integrity, whenever possible (samples with inconsistent, unlikely to be consistent, or unclear diagnoses were excluded from the study). Tissues that failed to produce a sufficient amount of high-uality DNA and/or RNA for sequencing or other array-based analyses were excluded. Samples were also excluded if they failed to produce usable data on two of three DNA platforms (WES, SNP array, targeted TSC sequencing), with the exception of one non-tumor tissue sample in which the germline mutation was identified in the completed platform (eliminating the need for the additional platforms to be completed).
Description

Samples from TSC patients or non-TSC organ donors were acquired from the NIH NeuroBioBank's Brain and Tissue Repository at the University of Maryland, Houston McGovern Medical School at the University of Texas, Cincinnati Children's Hospital Medical Center, New York University School of Medicine, and Helen DeVos Children's Hospital. Samples were reviewed by a certified clinical pathologist to confirm tissue type and assess integrity, whenever possible (samples with inconsistent, unlikely to be consistent, or unclear diagnoses were excluded from the study). Tissues that failed to produce a sufficient amount of high-uality DNA and/or RNA for sequencing or other array-based analyses were excluded. Samples were also excluded if they failed to produce usable data on two of three DNA platforms (WES, SNP array, targeted TSC sequencing), with the exception of one non-tumor tissue sample in which the germline mutation was identified in the completed platform (eliminating the need for the additional platforms to be completed).

Data type

boolean

Alias
UMLS CUI [1,1]
C0370003
UMLS CUI [1,2]
C0041341
UMLS CUI [1,3]
C0029206
UMLS CUI [1,4]
C0027468
UMLS CUI [1,5]
C0040278
UMLS CUI [1,6]
C3847505
UMLS CUI [1,7]
C3846158
UMLS CUI [1,8]
C0334901
UMLS CUI [1,9]
C1709940
UMLS CUI [1,10]
C0521091
UMLS CUI [1,11]
C2713035
UMLS CUI [1,12]
C0518718
UMLS CUI [1,13]
C0680251
UMLS CUI [1,14]
C1299582
UMLS CUI [1,15]
C4708858
UMLS CUI [1,16]
C0012854
UMLS CUI [1,17]
C0035668
UMLS CUI [1,18]
C1547867
UMLS CUI [1,19]
C1561491
UMLS CUI [1,20]
C3640077
UMLS CUI [1,21]
C3897601
UMLS CUI [1,22]
C1705847
UMLS CUI [1,23]
C5237809
UMLS CUI [1,24]
C0206530
UMLS CUI [1,25]
C2964215
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Similar models

Eligibility Criteria

5 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
C1512693 (UMLS CUI [1,1])
C0680251 (UMLS CUI [1,2])
Samples from TSC patients or non-TSC organ donors were acquired from the NIH NeuroBioBank's Brain and Tissue Repository at the University of Maryland, Houston McGovern Medical School at the University of Texas, Cincinnati Children's Hospital Medical Center, New York University School of Medicine, and Helen DeVos Children's Hospital. Samples were reviewed by a certified clinical pathologist to confirm tissue type and assess integrity, whenever possible (samples with inconsistent, unlikely to be consistent, or unclear diagnoses were excluded from the study). Tissues that failed to produce a sufficient amount of high-uality DNA and/or RNA for sequencing or other array-based analyses were excluded. Samples were also excluded if they failed to produce usable data on two of three DNA platforms (WES, SNP array, targeted TSC sequencing), with the exception of one non-tumor tissue sample in which the germline mutation was identified in the completed platform (eliminating the need for the additional platforms to be completed).
Item
Samples from TSC patients or non-TSC organ donors were acquired from the NIH NeuroBioBank's Brain and Tissue Repository at the University of Maryland, Houston McGovern Medical School at the University of Texas, Cincinnati Children's Hospital Medical Center, New York University School of Medicine, and Helen DeVos Children's Hospital. Samples were reviewed by a certified clinical pathologist to confirm tissue type and assess integrity, whenever possible (samples with inconsistent, unlikely to be consistent, or unclear diagnoses were excluded from the study). Tissues that failed to produce a sufficient amount of high-uality DNA and/or RNA for sequencing or other array-based analyses were excluded. Samples were also excluded if they failed to produce usable data on two of three DNA platforms (WES, SNP array, targeted TSC sequencing), with the exception of one non-tumor tissue sample in which the germline mutation was identified in the completed platform (eliminating the need for the additional platforms to be completed).
boolean
C0370003 (UMLS CUI [1,1])
C0041341 (UMLS CUI [1,2])
C0029206 (UMLS CUI [1,3])
C0027468 (UMLS CUI [1,4])
C0040278 (UMLS CUI [1,5])
C3847505 (UMLS CUI [1,6])
C3846158 (UMLS CUI [1,7])
C0334901 (UMLS CUI [1,8])
C1709940 (UMLS CUI [1,9])
C0521091 (UMLS CUI [1,10])
C2713035 (UMLS CUI [1,11])
C0518718 (UMLS CUI [1,12])
C0680251 (UMLS CUI [1,13])
C1299582 (UMLS CUI [1,14])
C4708858 (UMLS CUI [1,15])
C0012854 (UMLS CUI [1,16])
C0035668 (UMLS CUI [1,17])
C1547867 (UMLS CUI [1,18])
C1561491 (UMLS CUI [1,19])
C3640077 (UMLS CUI [1,20])
C3897601 (UMLS CUI [1,21])
C1705847 (UMLS CUI [1,22])
C5237809 (UMLS CUI [1,23])
C0206530 (UMLS CUI [1,24])
C2964215 (UMLS CUI [1,25])
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