ID

45702

Description

Principal Investigator: Todd Fehniger, MD, PhD, Washington University School of Medicine, St Louis, MO, USA MeSH: Lymphoma, Follicular https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001229 We performed exome sequencing of tumor (lymph node) and normal (skin) frozen tissue pairs from 24 patients in a discovery cohort with untreated follicular lymphoma (FL), relapsed FL, or transformed FL/iNHL (indolent non-Hodgkin lymphoma). From 24 patients, 28 tumor samples were exome sequenced including 1 patient with both untreated and relapse samples and 3 patients with samples derived from both bulk lymph node and following flow-sorting to purify light chain-restricted CD19+ lymphoma cells. We developed a custom capture assay (NimbleGen) that targets 7.05 MB corresponding to the exons and splice sites of 1716 genes (WUSM-LP). The custom capture genes included somatic nucleotide variants (SNVs) identified in our exome discovery cohort (898 genes) or SNVs previously published to be recurrently mutated in B cell NHL (818 genes). This custom capture reagent was used to sequence additional FFPE samples (and corresponding normal tissue, when available) from patients with follicular lymphoma. This approach was used to identify recurrently mutated genes in pathways in FL.

Link

dbGaP-study=phs001229

Keywords

Versions (1)
  1. 5/14/23 5/14/23 - Chiara Middel
Copyright Holder

Todd Fehniger, MD, PhD, Washington University School of Medicine, St Louis, MO, USA

Uploaded on

May 14, 2023

DOI

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License

Creative Commons BY 4.0
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dbGaP phs001229 Sequencing Follicular Lymphoma

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
For exome sequenced samples, all patients provided written informed consent for the use of their samples in sequencing as part of the Washington University School of Medicine (WUSM) Lymphoma Banking Program. All patients with adequate excisional biopsy tissue available from 2008-2013 were included. Non-malignant samples were also collected (skin punch biopsies). Pathology review was performed on frozen lymph node samples to confirm the diagnosis and estimate tumor cell content. Frozen sections (tumor and skin) were cut and used for genomic DNA isolation. For cases there were flow sorted, CD19+ and light chain restricted B cells were purified (>98% pure) using a Reflection instrument. For additional capture sequencing, a cohort of FL patients was identified from those evaluated at WUSM/Siteman Cancer Center from 2001-2013. Patients were included if FFPE blocks from an excisional biopsy and clinical information regarding initial treatment and follow-up were available. All FFPE tissue was reviewed to confirm the pathology diagnosis and marked for block punches in confirmed tumor-containing areas.
Description

Elig.phs001229.v1.p1.1

Data type

boolean

Alias
UMLS CUI [1,1]
C3854133
UMLS CUI [1,2]
C0021430
UMLS CUI [1,3]
C1524063
UMLS CUI [1,4]
C0370003
UMLS CUI [2,1]
C1512693
UMLS CUI [2,2]
C0470187
UMLS CUI [2,3]
C0184921
UMLS CUI [3,1]
C0200345
UMLS CUI [3,2]
C1518371
UMLS CUI [3,3]
C0870078
UMLS CUI [4,1]
C1521733
UMLS CUI [4,2]
C1704362
UMLS CUI [4,3]
C4039816
UMLS CUI [4,4]
C0024204
UMLS CUI [4,5]
C0750484
UMLS CUI [4,6]
C0011900
UMLS CUI [4,7]
C0006826
UMLS CUI [4,8]
C0007634
UMLS CUI [4,9]
C0456205
UMLS CUI [5,1]
C1524063
UMLS CUI [5,2]
C4039816
UMLS CUI [5,3]
C0205409
UMLS CUI [5,4]
C0887950
UMLS CUI [5,5]
C0012854
UMLS CUI [6,1]
C1698493
UMLS CUI [6,2]
C4288191
UMLS CUI [6,3]
C0803951
UMLS CUI [6,4]
C3846158
UMLS CUI [7,1]
C1524062
UMLS CUI [7,2]
C1328887
UMLS CUI [7,3]
C1269815
UMLS CUI [7,4]
C0024301
UMLS CUI [8,1]
C1512693
UMLS CUI [8,2]
C0470187
UMLS CUI [8,3]
C4039816
UMLS CUI [8,4]
C0184921
UMLS CUI [8,5]
C0205210
UMLS CUI [8,6]
C1533716
UMLS CUI [8,7]
C0205265
UMLS CUI [8,8]
C0087111
UMLS CUI [8,9]
C1522577
UMLS CUI [9,1]
C1704362
UMLS CUI [9,2]
C4039816
UMLS CUI [9,3]
C0750484
UMLS CUI [9,4]
C0011900
UMLS CUI [9,5]
C1708936
UMLS CUI [9,6]
C0205145
UMLS CUI [9,7]
C0006826
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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])
Elig.phs001229.v1.p1.1
Item
For exome sequenced samples, all patients provided written informed consent for the use of their samples in sequencing as part of the Washington University School of Medicine (WUSM) Lymphoma Banking Program. All patients with adequate excisional biopsy tissue available from 2008-2013 were included. Non-malignant samples were also collected (skin punch biopsies). Pathology review was performed on frozen lymph node samples to confirm the diagnosis and estimate tumor cell content. Frozen sections (tumor and skin) were cut and used for genomic DNA isolation. For cases there were flow sorted, CD19+ and light chain restricted B cells were purified (>98% pure) using a Reflection instrument. For additional capture sequencing, a cohort of FL patients was identified from those evaluated at WUSM/Siteman Cancer Center from 2001-2013. Patients were included if FFPE blocks from an excisional biopsy and clinical information regarding initial treatment and follow-up were available. All FFPE tissue was reviewed to confirm the pathology diagnosis and marked for block punches in confirmed tumor-containing areas.
boolean
C3854133 (UMLS CUI [1,1])
C0021430 (UMLS CUI [1,2])
C1524063 (UMLS CUI [1,3])
C0370003 (UMLS CUI [1,4])
C1512693 (UMLS CUI [2,1])
C0470187 (UMLS CUI [2,2])
C0184921 (UMLS CUI [2,3])
C0200345 (UMLS CUI [3,1])
C1518371 (UMLS CUI [3,2])
C0870078 (UMLS CUI [3,3])
C1521733 (UMLS CUI [4,1])
C1704362 (UMLS CUI [4,2])
C4039816 (UMLS CUI [4,3])
C0024204 (UMLS CUI [4,4])
C0750484 (UMLS CUI [4,5])
C0011900 (UMLS CUI [4,6])
C0006826 (UMLS CUI [4,7])
C0007634 (UMLS CUI [4,8])
C0456205 (UMLS CUI [4,9])
C1524063 (UMLS CUI [5,1])
C4039816 (UMLS CUI [5,2])
C0205409 (UMLS CUI [5,3])
C0887950 (UMLS CUI [5,4])
C0012854 (UMLS CUI [5,5])
C1698493 (UMLS CUI [6,1])
C4288191 (UMLS CUI [6,2])
C0803951 (UMLS CUI [6,3])
C3846158 (UMLS CUI [6,4])
C1524062 (UMLS CUI [7,1])
C1328887 (UMLS CUI [7,2])
C1269815 (UMLS CUI [7,3])
C0024301 (UMLS CUI [7,4])
C1512693 (UMLS CUI [8,1])
C0470187 (UMLS CUI [8,2])
C4039816 (UMLS CUI [8,3])
C0184921 (UMLS CUI [8,4])
C0205210 (UMLS CUI [8,5])
C1533716 (UMLS CUI [8,6])
C0205265 (UMLS CUI [8,7])
C0087111 (UMLS CUI [8,8])
C1522577 (UMLS CUI [8,9])
C1704362 (UMLS CUI [9,1])
C4039816 (UMLS CUI [9,2])
C0750484 (UMLS CUI [9,3])
C0011900 (UMLS CUI [9,4])
C1708936 (UMLS CUI [9,5])
C0205145 (UMLS CUI [9,6])
C0006826 (UMLS CUI [9,7])
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