ID

45184

Beschreibung

Principal Investigator: Michael A. Dyer, PhD, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA MeSH: Retinoblastoma https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000352 Retinoblastoma is a pediatric cancer of the developing retina. All retinoblastomas are believed to initiate with biallelic inactivation of the RB1 gene. To identify subsequent genetic lesions in retinoblastoma, we performed whole genome sequencing of tumor and normal DNA of 4 children with retinoblastoma and one matched orthotopic xenograft. Both alleles of RB1 were inactivated in the tumor samples. 3 of the patients had sporadic retinoblastoma and one patient had inherited retinoblastoma. Overall, there were few single nucleotide changes in coding regions of the genome and some of the tumors had few chromosomal lesions. There were very few new genetic lesions in the xenograft compared to the primary tumor. These data suggest that the genome in retinoblastoma is more stable than previously believed and there are relatively few recurrent genetic lesions in known cancer pathways other than the RB1 pathway.

Link

dbGaP study = phs000352

Stichworte

Versionen (2)
  1. 20.08.22 20.08.22 - Simon Heim
  2. 12.10.22 12.10.22 - Adrian Schulz
Rechteinhaber

Michael A. Dyer, PhD, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA

Hochgeladen am

12. Oktober 2022

DOI

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Lizenz

Creative Commons BY 4.0
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dbGaP phs000352 Sequencing of Retinoblastoma

Englisch

Eligibility Criteria

6 Formulare  
  1. StudyEvent: SEV1
    1. Eligibility Criteria
    2. This data table contains subject IDs and consent group information. The data table also includes a mapping of subject IDs to other subject ID aliases.
    3. The data table contains a mapping of subject ID to sample ID. Samples are the final preps submitted for sequencing. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes a mapping of sample IDs to other sample ID aliases.
    4. This subject phenotype table includes subjects diagnosed with retinoblastoma. The variables are was the disease sporadic or inherited, age at diagnosis, additional information regarding molecular testing, primary treatment protocol, relapse information, bone marrow transplant status, presence of genetic lesions, tumor purity, type of specimen and site where tissue was extracted. Additionally, there are 2 sociodemography variables: gender and ethnicity.
    5. This sample attributes table includes variables indicating the tumor/normal status, the body site where the sample was extracted, sample analyte type, histological type, primary tumor location, and whether sample was a xenograft. Note: the primary tumor location refers to the subject's primary tumor location and is independent from where the sample was extracted.
    6. This data table contains a mapping of sample ID to NCBI GEO accessions.
Inclusion and exclusion criteria
Beschreibung

Inclusion and exclusion criteria

Cases of untreated retinoblastoma that had progressed and required surgical enucleation. The cases in this cohort have had whole genome sequencing of tumor and normal DNA performed. One of the cases had an orthotopic xenograft established from the primary tumor. Cases were selected that had appropriate consent for genetic studies, and suitable material for sequencing (high purity tumor populations and available normal DNA obtained).
Beschreibung

Cases of untreated retinoblastoma that had progressed and required surgical enucleation. The cases in this cohort have had whole genome sequencing of tumor and normal DNA performed. One of the cases had an orthotopic xenograft established from the primary tumor. Cases were selected that had appropriate consent for genetic studies, and suitable material for sequencing (high purity tumor populations and available normal DNA obtained).

Datentyp

boolean

Alias
UMLS CUI [1,1]
C0035335
UMLS CUI [1,2]
C1514873
UMLS CUI [1,3]
C0014392
UMLS CUI [1,4]
C1328887
UMLS CUI [1,5]
C0021430
UMLS CUI [1,6]
C2347026
UMLS CUI [1,7]
C1328887
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Ähnliche Modelle

Eligibility Criteria

6 Formulare
  1. StudyEvent: SEV1
    1. Eligibility Criteria
    2. This data table contains subject IDs and consent group information. The data table also includes a mapping of subject IDs to other subject ID aliases.
    3. The data table contains a mapping of subject ID to sample ID. Samples are the final preps submitted for sequencing. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes a mapping of sample IDs to other sample ID aliases.
    4. This subject phenotype table includes subjects diagnosed with retinoblastoma. The variables are was the disease sporadic or inherited, age at diagnosis, additional information regarding molecular testing, primary treatment protocol, relapse information, bone marrow transplant status, presence of genetic lesions, tumor purity, type of specimen and site where tissue was extracted. Additionally, there are 2 sociodemography variables: gender and ethnicity.
    5. This sample attributes table includes variables indicating the tumor/normal status, the body site where the sample was extracted, sample analyte type, histological type, primary tumor location, and whether sample was a xenograft. Note: the primary tumor location refers to the subject's primary tumor location and is independent from where the sample was extracted.
    6. This data table contains a mapping of sample ID to NCBI GEO accessions.
Name
Typ
Description | Question | Decode (Coded Value)
Datentyp
Alias
Item Group
Inclusion and exclusion criteria
Cases of untreated retinoblastoma that had progressed and required surgical enucleation. The cases in this cohort have had whole genome sequencing of tumor and normal DNA performed. One of the cases had an orthotopic xenograft established from the primary tumor. Cases were selected that had appropriate consent for genetic studies, and suitable material for sequencing (high purity tumor populations and available normal DNA obtained).
Item
Cases of untreated retinoblastoma that had progressed and required surgical enucleation. The cases in this cohort have had whole genome sequencing of tumor and normal DNA performed. One of the cases had an orthotopic xenograft established from the primary tumor. Cases were selected that had appropriate consent for genetic studies, and suitable material for sequencing (high purity tumor populations and available normal DNA obtained).
boolean
C0035335 (UMLS CUI [1,1])
C1514873 (UMLS CUI [1,2])
C0014392 (UMLS CUI [1,3])
C1328887 (UMLS CUI [1,4])
C0021430 (UMLS CUI [1,5])
C2347026 (UMLS CUI [1,6])
C1328887 (UMLS CUI [1,7])
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