ID

45386

Description

Principal Investigator: Arul M. Chinnaiyan, MD, PhD, University of Michigan, MI, USA MeSH: Neoplasms,Cholangiocarcinoma,Breast Neoplasms,Prostatic Neoplasms,Urinary Bladder Neoplasms,Mouth Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000602 In this study, patients with advanced cancer across all histologies were enrolled in our IRB approved clinical sequencing program, called MI-ONCOSEQ, to go through an integrative sequencing which includes whole exome sequencing of the tumor and matched normal, and transcriptome sequencing. Four index cases were identified which harbor gene rearrangements of FGFR2 including two cholangiocarcinoma cases, a metastatic breast cancer case, and a metastatic prostate cancer case. After extending our assessment of FGFR rearrangements across multiple tumor cohorts, including TCGA, we identified FGFR gene fusions with intact kinase domains of FGFR1, FGFR2, or FGFR3 in cholangiocarcinoma, breast cancer, prostate cancer, lung squamous cell cancer, bladder cancer, thyroid cancer, oral cancer, glioblastoma, and head and neck squamous cell cancer. All FGFR fusion partners tested exhibit oligomerization capability, suggesting a shared mode of kinase activation. Overexpression of FGFR fusion proteins in vitro induced cell proliferation, and bladder cancer cell lines that harbors FGFR3 fusion proteins exhibited enhanced susceptibility to pharmacologic inhibition in vitro and in vivo. Due to the combinatorial possibilities of FGFR family fusion to a variety of oligomerization partners, clinical sequencing efforts which incorporate transcriptome analysis for gene fusions are poised to identify rare, targetable FGFR fusions across diverse cancer types.

Link

dbGaP study = phs000602

Keywords

Versions (1)
  1. 11/11/22 11/11/22 - Simon Heim
Copyright Holder

Arul M. Chinnaiyan, MD, PhD, University of Michigan, MI, USA

Uploaded on

November 11, 2022

DOI

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License

Creative Commons BY 4.0
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dbGaP phs000602 Identification of Targetable FGFR Gene Fusions in Diverse Cancers

English

Eligibility Criteria

4 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0680251
*5.0 ELIGIBILITY*
Description

5.0 ELIGIBILITY

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
*5.1 Patient population*
Description

5.1 Patient population

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C2361270
This protocol is designed to collect biospecimens with annotated clinical data from patients with advanced or refractory cancer.
Description

This protocol is designed to collect biospecimens with annotated clinical data from patients with advanced or refractory cancer.

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C0200345
UMLS CUI [1,3]
C1516606
UMLS CUI [1,4]
C1552657
UMLS CUI [1,5]
C0877373
UMLS CUI [1,6]
C0677936
*5.2 Inclusion Criteria: (Must satisfy all criteria and either #3 or #4)*
Description

Elig.phs000602.v2.p1.4

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C1512693
A histologically or cytologically confirmed diagnosis of cancer.
Description

A histologically or cytologically confirmed diagnosis of cancer.

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C1512693
UMLS CUI [1,3]
C0920688
UMLS CUI [1,4]
C0679557
UMLS CUI [1,5]
C1298647
Patients with any advanced or refractory malignancy.
Description

Patients with any advanced or refractory malignancy.

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C1512693
UMLS CUI [1,3]
C0877373
UMLS CUI [1,4]
C0677936
Patients are undergoing standard of care surgeries or procedures where specimens will be first used for routine pathologic assessment and only then will leftover tissue be used for research purposes. **OR**
Description

Patients are undergoing standard of care surgeries or procedures where specimens will be first used for routine pathologic assessment and only then will leftover tissue be used for research purposes.

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C1512693
UMLS CUI [1,3]
C2936643
UMLS CUI [1,4]
C0543467
UMLS CUI [2,1]
C1516637
UMLS CUI [2,2]
C0205225
UMLS CUI [2,3]
C1524063
UMLS CUI [2,4]
C0370003
UMLS CUI [2,5]
C4086729
UMLS CUI [2,6]
C1524062
UMLS CUI [2,7]
C0040300
UMLS CUI [2,8]
C0242481
Patients must have tumor suitable for biopsy (as assessed by trained specialists in interventional radiology) and patients are medically fit to undergo a tissue biopsy or surgical procedure to get tumor tissue *OR* if patients do not have a tumor suitable for biopsy but have another tissue available for molecular evaluation.
Description

Patients must have tumor suitable for biopsy (as assessed by trained specialists in interventional radiology) and patients are medically fit to undergo a tissue biopsy or surgical procedure to get tumor tissue *OR* if patients do not have a tumor suitable for biopsy but have another tissue available for molecular evaluation.

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C1512693
UMLS CUI [1,3]
C0006826
UMLS CUI [1,4]
C0005558
UMLS CUI [1,5]
C0332149
UMLS CUI [1,6]
C1516048
UMLS CUI [1,7]
C0034602
UMLS CUI [1,8]
C2348234
UMLS CUI [1,9]
C4708589
UMLS CUI [1,10]
C0185275
UMLS CUI [2,1]
C1516637
UMLS CUI [2,2]
C1512693
UMLS CUI [2,3]
C1298908
UMLS CUI [2,4]
C4708589
UMLS CUI [2,5]
C0185275
UMLS CUI [2,6]
C0040300
UMLS CUI [2,7]
C2985722
UMLS CUI [2,8]
C2121080
Older than or equal to 18 years of age.
Description

Older than or equal to 18 years of age.

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C1512693
UMLS CUI [1,3]
C0001779
Procedure-specific signed informed consent prior to initiation of any study-related procedures.
Description

Procedure-specific signed informed consent prior to initiation of any study-related procedures.

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C0021430
UMLS CUI [1,3]
C1512693
UMLS CUI [1,4]
C1561610
UMLS CUI [1,5]
C5421123
Women and minorities are included in this protocol.
Description

Women and minorities are included in this protocol.

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C1512693
UMLS CUI [1,3]
C0026192
UMLS CUI [1,4]
C0043210
Patients with multiple malignancies remain eligible.
Description

Patients with multiple malignancies remain eligible.

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C0006826
UMLS CUI [1,3]
C1302261
UMLS CUI [1,4]
C1512693
Patients with an inherited cancer syndrome or a medical history suggestive of an inherited cancer syndrome remain eligible.
Description

Patients with an inherited cancer syndrome or a medical history suggestive of an inherited cancer syndrome remain eligible.

Data type

boolean

Alias
UMLS CUI [1,1]
C1516637
UMLS CUI [1,2]
C1302261
UMLS CUI [1,3]
C0027672
*5.3 Exclusion Criteria:*
Description

5.3 Exclusion Criteria:

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
It is the enrolling study physician's discretion to decide if a patient is not fit enough to undergo tissue biopsy.
Description

It is the enrolling study physician's discretion to decide if a patient is not fit enough to undergo tissue biopsy.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0008961
UMLS CUI [1,3]
C0022423
UMLS CUI [1,4]
C0750557
UMLS CUI [1,5]
C2586066
Patients who are incarcerated are not eligible to participate.
Description

Patients who are incarcerated are not eligible to participate.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0030705
UMLS CUI [1,3]
C0392751
UMLS CUI [1,4]
C1555471
Women who are pregnant.
Description

Women who are pregnant.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0033011
*5.4 Women of childbearing age.*
Description

5.4 Women of childbearing age.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C3831118
UMLS CUI [1,3]
C0043210
For women of childbearing age, there are no screening requirements. We note that most patients entering this study are seeking eligibility for therapy or other clinical trial, in which case they are generally asked to avoiding becoming pregnant and even exercise some form of contraception by their medical oncologist. For women of childbearing age, their referring medical oncologist will discuss necessity or role for appropriate contraception. This is not part of the study activity, nor is it required for participation.
Description

For women of childbearing age, there are no screening requirements. We note that most patients entering this study are seeking eligibility for therapy or other clinical trial, in which case they are generally asked to avoiding becoming pregnant and even exercise some form of contraception by their medical oncologist. For women of childbearing age, their referring medical oncologist will discuss necessity or role for appropriate contraception. This is not part of the study activity, nor is it required for participation.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0043210
UMLS CUI [1,3]
C3831118
UMLS CUI [1,4]
C0220908
UMLS CUI [1,5]
C1514873
UMLS CUI [1,6]
C1298908
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Similar models

Eligibility Criteria

4 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])
5.0 ELIGIBILITY
Item
*5.0 ELIGIBILITY*
boolean
C1516637 (UMLS CUI [1,1])
5.1 Patient population
Item
*5.1 Patient population*
boolean
C1516637 (UMLS CUI [1,1])
C2361270 (UMLS CUI [1,2])
This protocol is designed to collect biospecimens with annotated clinical data from patients with advanced or refractory cancer.
Item
This protocol is designed to collect biospecimens with annotated clinical data from patients with advanced or refractory cancer.
boolean
C1516637 (UMLS CUI [1,1])
C0200345 (UMLS CUI [1,2])
C1516606 (UMLS CUI [1,3])
C1552657 (UMLS CUI [1,4])
C0877373 (UMLS CUI [1,5])
C0677936 (UMLS CUI [1,6])
Elig.phs000602.v2.p1.4
Item
*5.2 Inclusion Criteria: (Must satisfy all criteria and either #3 or #4)*
boolean
C1516637 (UMLS CUI [1,1])
C1512693 (UMLS CUI [1,2])
A histologically or cytologically confirmed diagnosis of cancer.
Item
A histologically or cytologically confirmed diagnosis of cancer.
boolean
C1516637 (UMLS CUI [1,1])
C1512693 (UMLS CUI [1,2])
C0920688 (UMLS CUI [1,3])
C0679557 (UMLS CUI [1,4])
C1298647 (UMLS CUI [1,5])
Patients with any advanced or refractory malignancy.
Item
Patients with any advanced or refractory malignancy.
boolean
C1516637 (UMLS CUI [1,1])
C1512693 (UMLS CUI [1,2])
C0877373 (UMLS CUI [1,3])
C0677936 (UMLS CUI [1,4])
Patients are undergoing standard of care surgeries or procedures where specimens will be first used for routine pathologic assessment and only then will leftover tissue be used for research purposes.
Item
Patients are undergoing standard of care surgeries or procedures where specimens will be first used for routine pathologic assessment and only then will leftover tissue be used for research purposes. **OR**
boolean
C1516637 (UMLS CUI [1,1])
C1512693 (UMLS CUI [1,2])
C2936643 (UMLS CUI [1,3])
C0543467 (UMLS CUI [1,4])
C1516637 (UMLS CUI [2,1])
C0205225 (UMLS CUI [2,2])
C1524063 (UMLS CUI [2,3])
C0370003 (UMLS CUI [2,4])
C4086729 (UMLS CUI [2,5])
C1524062 (UMLS CUI [2,6])
C0040300 (UMLS CUI [2,7])
C0242481 (UMLS CUI [2,8])
Patients must have tumor suitable for biopsy (as assessed by trained specialists in interventional radiology) and patients are medically fit to undergo a tissue biopsy or surgical procedure to get tumor tissue *OR* if patients do not have a tumor suitable for biopsy but have another tissue available for molecular evaluation.
Item
Patients must have tumor suitable for biopsy (as assessed by trained specialists in interventional radiology) and patients are medically fit to undergo a tissue biopsy or surgical procedure to get tumor tissue *OR* if patients do not have a tumor suitable for biopsy but have another tissue available for molecular evaluation.
boolean
C1516637 (UMLS CUI [1,1])
C1512693 (UMLS CUI [1,2])
C0006826 (UMLS CUI [1,3])
C0005558 (UMLS CUI [1,4])
C0332149 (UMLS CUI [1,5])
C1516048 (UMLS CUI [1,6])
C0034602 (UMLS CUI [1,7])
C2348234 (UMLS CUI [1,8])
C4708589 (UMLS CUI [1,9])
C0185275 (UMLS CUI [1,10])
C1516637 (UMLS CUI [2,1])
C1512693 (UMLS CUI [2,2])
C1298908 (UMLS CUI [2,3])
C4708589 (UMLS CUI [2,4])
C0185275 (UMLS CUI [2,5])
C0040300 (UMLS CUI [2,6])
C2985722 (UMLS CUI [2,7])
C2121080 (UMLS CUI [2,8])
Older than or equal to 18 years of age.
Item
Older than or equal to 18 years of age.
boolean
C1516637 (UMLS CUI [1,1])
C1512693 (UMLS CUI [1,2])
C0001779 (UMLS CUI [1,3])
Procedure-specific signed informed consent prior to initiation of any study-related procedures.
Item
Procedure-specific signed informed consent prior to initiation of any study-related procedures.
boolean
C1516637 (UMLS CUI [1,1])
C0021430 (UMLS CUI [1,2])
C1512693 (UMLS CUI [1,3])
C1561610 (UMLS CUI [1,4])
C5421123 (UMLS CUI [1,5])
Women and minorities are included in this protocol.
Item
Women and minorities are included in this protocol.
boolean
C1516637 (UMLS CUI [1,1])
C1512693 (UMLS CUI [1,2])
C0026192 (UMLS CUI [1,3])
C0043210 (UMLS CUI [1,4])
Patients with multiple malignancies remain eligible.
Item
Patients with multiple malignancies remain eligible.
boolean
C1516637 (UMLS CUI [1,1])
C0006826 (UMLS CUI [1,2])
C1302261 (UMLS CUI [1,3])
C1512693 (UMLS CUI [1,4])
Patients with an inherited cancer syndrome or a medical history suggestive of an inherited cancer syndrome remain eligible.
Item
Patients with an inherited cancer syndrome or a medical history suggestive of an inherited cancer syndrome remain eligible.
boolean
C1516637 (UMLS CUI [1,1])
C1302261 (UMLS CUI [1,2])
C0027672 (UMLS CUI [1,3])
5.3 Exclusion Criteria:
Item
*5.3 Exclusion Criteria:*
boolean
C0680251 (UMLS CUI [1,1])
It is the enrolling study physician's discretion to decide if a patient is not fit enough to undergo tissue biopsy.
Item
It is the enrolling study physician's discretion to decide if a patient is not fit enough to undergo tissue biopsy.
boolean
C0680251 (UMLS CUI [1,1])
C0008961 (UMLS CUI [1,2])
C0022423 (UMLS CUI [1,3])
C0750557 (UMLS CUI [1,4])
C2586066 (UMLS CUI [1,5])
Patients who are incarcerated are not eligible to participate.
Item
Patients who are incarcerated are not eligible to participate.
boolean
C0680251 (UMLS CUI [1,1])
C0030705 (UMLS CUI [1,2])
C0392751 (UMLS CUI [1,3])
C1555471 (UMLS CUI [1,4])
Women who are pregnant.
Item
Women who are pregnant.
boolean
C0680251 (UMLS CUI [1,1])
C0033011 (UMLS CUI [1,2])
5.4 Women of childbearing age.
Item
*5.4 Women of childbearing age.*
boolean
C0680251 (UMLS CUI [1,1])
C3831118 (UMLS CUI [1,2])
C0043210 (UMLS CUI [1,3])
For women of childbearing age, there are no screening requirements. We note that most patients entering this study are seeking eligibility for therapy or other clinical trial, in which case they are generally asked to avoiding becoming pregnant and even exercise some form of contraception by their medical oncologist. For women of childbearing age, their referring medical oncologist will discuss necessity or role for appropriate contraception. This is not part of the study activity, nor is it required for participation.
Item
For women of childbearing age, there are no screening requirements. We note that most patients entering this study are seeking eligibility for therapy or other clinical trial, in which case they are generally asked to avoiding becoming pregnant and even exercise some form of contraception by their medical oncologist. For women of childbearing age, their referring medical oncologist will discuss necessity or role for appropriate contraception. This is not part of the study activity, nor is it required for participation.
boolean
C0680251 (UMLS CUI [1,1])
C0043210 (UMLS CUI [1,2])
C3831118 (UMLS CUI [1,3])
C0220908 (UMLS CUI [1,4])
C1514873 (UMLS CUI [1,5])
C1298908 (UMLS CUI [1,6])
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