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Genomic Medicine

Research

Home About Research Education Labs News Careers Contact

Our Laboratories

Genomic Medicine Institute laboratories are making discoveries in the areas of brain, cancer, heart, inflammation, systems biology, virology, and more.

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  • Research
  • Clinical Research
  • Biorepository

Clinical Research

Clinical Research

Researchers depend on patient data to advance their knowledge of human health and disease. Your participation in a research study can make the difference in finding answers. If you are interested in enrolling in a research study or clinical trial but don’t know where to start, learn more about the process here. Find some of the many clinical trials held in the Genomic Medicine Institute below.

The goal of this study is to learn more about tumors that form in and around the adrenal gland (pheochromocytoma and paraganglioma). Preliminary evidence suggests that inherited forms of these diseases are associated with mutations in genes involved in the succinate dehydrogenase pathways. We aim to characterize the relationship between these mutations and the disease, with the goal of improving diagnostic, prevention, and treatment techniques.

Qualifications
  1. EITHER, the patient has both of the following:
    • At least one pheochromocytoma or paraganglioma 
    • Clinical or molecular exclusion of Multiple Endocrine Neoplasia type 2 and von Hippel-Lindau syndrome 
  2. OR , the patient has a known mutation or variant of uncertain significance in any of the following genes:
    • SDHB
    • SDHC
    • SDHD

If you have questions about eligibility, please email  [email protected]  or fax (216.636.0009 or 216.445.6798) the patient's pedigree and a clinical summary to the GC coordinator.

Study Description

We are enrolling patients with pheochromocytoma and paraganglioma to study succinate dehydrogenase genes SDHB, SDHC, and SDHD. MEN 2A and VHL must be ruled-out through molecular testing or clinical assessment. We are also interested in enrolling patients who have a known SDHB, SDHC, or SDHD variants even if they have not developed pheochromocytoma or paraganglioma. Mutation and deletion analyses are performed on the SDHB, SDHC, and SDHD genes.

Methodology

We will extract DNA from patient blood samples to look for mutations, deletions, and/or duplications in the succinate dehydrogenase genes SDHB, SDHC, and SDHD.

Results of the Study

Clinically relevant results are provided via confidential email to the referring healthcare provider. Per our institutional IRB requirements, the exact nomenclature cannot be disclosed. However, if a deleterious mutation is identified, we can share the exact mutation nomenclature with the clinical lab of your choice for site-specific analysis. At present site-specific MLPA analysis is not clinically available, but we are happy to share abnormal MLPA results with the clinical lab of your choice as well.

The aim of this study is to learn more about susceptibility to cancer in patients with PTEN variants. The goal is to characterize the genetic changes that may increase an individual’s chances of developing cancer. The researchers are also looking to understand the relationship between microbes, cancer and autism spectrum disorder. For more information about this research study, view a summary (PDF).

If you are a patient who is interested in asking your healthcare provider for a referral, please  review the "The PTEN Study: Information for Prospective Participants" flyer (PDF) we wrote especially for you.

Qualifications

Inclusion criteria
Patients with the following will automatically qualify for study participation: 

  • Meets one of following combinations of criteria from our Clinical Features Checklist  (PDF)
    • 2 major criteria
    • 1 major criteria + 2 minor criteria
    • 3 minor criteria
  • Adult patients with a score of 10 or greater per the Cleveland Clinic PTEN Risk Calculator( Calculate Risk)
  • Pediatric patients with macrocephaly plus at least one of the following :
    • Autism/mental retardation/developmental delay 
    • Lipoma, biopsy-proven trichilemmomas, oral papilloma, or hemangioma 
    • Arteriovenous malformation 
    • One or more gastrointestinal polyps 
  • Known PTEN pathogenic or likely pathogenic variant, or variant of uncertain significance 
  • Lhermitte-Duclos disease 
  • Pigmented macules of the glans penis 
  • Clinical diagnosis of Proteus or Proteus-like syndrome 

Exclusion Criteria
Patients with the following will automatically be disqualified from study participation:

  • Patients without a documented OFC (head circumference) measurement 
  • Patients with non-PTEN genetic testing (i.e. BRCA1/2 testing) pending. 
  • Patients with qualifying features that can be explained by existing non- PTEN -related test results

Note: While we do not strictly require that other diagnoses be ruled out prior to enrolling patients in this study, we do ask that you help us use our research funding as wisely as possible. Our genetic counselor coordinator is glad to discuss the differential diagnosis or testing strategy for any patient. 

If you have questions about eligibility, please email [email protected] or fax (216.636.0009) the patient's pedigree and a clinical summary to our study staff.

Study Description

This is an integrated study with DNA, RNA, and protein studies of the PTEN gene and related pathways. We are studying the frequency of characteristics such as cancer diagnoses among those with PTEN alterations; working to clarify variants of uncertain significance; and exploring alternative mechanisms of disease in patients without identified variants. This is a multi-faceted research study that combines clinical patient information. We ultimately hope that this research will lead to the development of targeted molecular therapies for persons with PTEN alterations.

Methodology

Gene sequence abnormalities for the PTEN gene (coding region, exon/intron boundaries, flanking intronic sequences) are analyzed: 

  • Legacy samples (2005-2020) have all undergone mutation scanning and MLPA (large rearrangement) analysis of all nine PTEN exons.
  • The majority of research participants accrued beyond 2020 have already had clinical genetic testing in CLIA certified labs.
  • Research participants without genetic testing results who are interested in participating will be referred for clinical PTEN mutation and deletion/duplication testing, if warranted, after discussion of such cases during weekly family review meetings.
Results of the Study

Results will be shared with the patient in the form of publication summaries upon completion of the study. If, in the course of lab analysis, clinically relevant results become available, they will be reported to the medical provider of record.

How to Enroll

Healthcare provider referrals only (Patients may not self-enroll)

Please complete and forward the five documents in our enrollment packet, as well as all requested medical records ( see clinical features checklist).

If you have questions about eligibility, please email  [email protected]  or fax (216.636.0009) the patient's pedigree and a clinical summary to our study staff.

Scheduling with the Cleveland Clinic PTEN Multidisciplinary Clinic

New or returning patients interested in scheduling with the Cleveland Clinic PTEN Multidisciplinary Clinic should contact the PTEN Navigaor by phone at: 216-444-4044 or via email at: [email protected]. In the event the PTEN Navigator is assisting another caller, please leave a message with your name, return phone number and reason for your call. The PTEN Navigator will get back to you within 48 hours.

New PTEN Patient Scheduling
IIf you are a new patient scheduling with PTEN Multidisciplinary Clinic, please contact the PEN Navigator at: 216-444-4044 or by email: [email protected].You will be asked to forward insurance information as well as pertinent medical records and then you will be scheduled for a phone intake appointment with the PTEN Research Nurse.

During the intake, the nurse will ask you about your medical history, clinical genetic testing and any specialists that you may need to see.

After the intake call is completed, the PTEN Navigator will begin scheduling your appointments during your identified date(s) of availability.

Established PTEN Patient Scheduling
If you are a reurning patient to the PTEN Multidisciplinary Clinic, the PTEN Navigator will schedule a brief check-in call with the PTEN Research Nurse, and will schedule you with the PTEN Clinic according to available dates.

During the busiest seasons for the PTEN Clinic (spring, summer and fall) we may ask that you schedule your own specialist appointments so the PTEN Navigator can fully assist brand new PTEN Clinic patients.

Please call 866-320-4573 to schedule non-GMI appointments.

The purpose of this study is to learn more about the symptoms and characteristics of individuals with autism and PTEN alterations, with the goal of informing risk management guidelines. The researchers may also learn new things about the genetic, biochemical, cognitive and/or behavioral problems associated with autism and/or PTEN alterations that may help diagnosis and treatment of individuals in the future.

Qualifications

Patients qualify for this study if they

  • Individuals ages 18 months old and older at the time of consent who have a confirmed PTEN mutation [required]
  • Have been diagnosed with Autism Spectrum Disorder [optional]
  • Primary communicative language must be English or Spanish
Study Description

The goals of the study are to better understand molecular, brain, and behavioral differences and their development, identify markers of PTEN mutations with autism that can be used in future clinical trials, and to build a biorepository to continue to study patients and move toward better treatments.

For more information about this research study, please  view a summary  (PDF).

Methodology

This study has a two-year duration and involves three onsite visits for children and two onsite visits for adults. Study assessments may include medical history/family history, physical exam, neurobehavioral/cognitive evaluations, questionnaires/interviews, blood sample(s), optional seizure tracking, and, if applicable, electroencephalogram (EEG).

Results of the Study

Results will be shared with the patient in the form of publication summaries upon completion of the study. If, in the course of lab analysis, clinically relevant results become available, they will be reported to the medical provider of record.

How to Enroll

Patient opt-in and healthcare provider referrals accepted (Patients may self-enroll)

Please contact the PTEN clinical research team at 216.445.5850 or  [email protected] . You will be contacted by a member of the research staff who can explain what is involved with study participation as well as the informed consent and appointment scheduling process.

Biorepository

Biorepository

The GMB serves as the foundation for evidence-based research for the GMI, the Cleveland Clinic, and our collaborators. Our biorepository has received, catalogued, processed, and banked in excess of 235,000 specimens from more than 16,200 patients. These samples are of numerous tissue types from patients and their family members located all over the world. The GMB has managed specimens that have resulted in more than 300 original peer-reviewed articles and greater than $25 million total direct costs in extramural funding over the last 7 years.
Samples received by the GMB are processed into a wide range of biomaterials using standardized laboratory techniques and quality control practices. Our services include the isolation of DNA and RNA for genetic studies, isolation of plasma or extraction of protein for proteomic studies, creation of immortalized cell lines from blood lymphocytes for biochemical research, and more. All sample information is entered into a laboratory information management system database (BSI) for cataloguing, coding, and storage as well as integration of additional research data. The GMB works closely with investigators and is committed to meet their comprehensive study goals.

Services & Fees

The Genomic Medicine Biorepository offers the following services to the members of the Genomic Medicine Institute, our collaborators, and members of the Cleveland Clinic family. Those outside of the Cleveland Clinic who may be interested in our services are encouraged to contact us for information.

All projects are subject to review by the GMB and our staff is available for individual consultation and experimental design upon request.

DNA Isolation
(Blood, paraffin-embedded tissue, frozen tissue, cell lines, and others)
This is the mainstay of genomics research and is used for many different investigations.

RNA Isolation (from various sources)
(Blood, cell lines, and others)
This allows for expression research, and combined with rtPCR (cDNA) offers a starting point for micro-array studies.

Spectrofluorometric Quantification of DNA
This differs from spectrophotometric (NanoDrop) analysis in that it specifically quantifies double-stranded DNA and is highly sensitive for quantifying small amounts of DNA.

Normalization of DNA
Preparation of DNA normalized to a specific concentration and volume.

Lymphoblastoid Cell Line Initiation
Initiation of lymphoblastoid cell lines provides a perpetual source of high molecular weight genetic material as well as protein, and opens the door to in vitro studies that cannot be done with primary cells.

Plasma or Serum Processing
This is a low-cost sample that is banked as a by-product when blood is submitted. This has tremendous potential with the emergence of proteomics as a new and exciting research tool.

Urine Processing
This is a standard diagnostic resource. As well, it has significant research value.

Cell Line Revival, Backfreeze, & Transfer
This process allows us to distribute cell lines that have been placed in cryogenic suspension without depleting potentially irreplaceable resources.

Sample Storage
This service is reserved for samples prepared by the GMB. These annual fees will be prospectively assessed at the beginning of each calendar year.

Biomaterial Transfer (other than cell lines or)
This service provides the mechanism to get samples to the investigator. This fee covers the administrative costs associated with preparing and documenting sample transfers.

Shipping
We can directly ship your samples to any lab domestic or international, for further analysis after processing.

Database Integration (BSI)
This is critical in the management of a modern biorepository - not only for sample management, but also for large-scale investigations involving clinical and research data.

Please contact the GMB at [email protected] for specific pricing.

Methods & Procedures

The methods implemented have been developed using standard protocols in the individual fields and following International Society for Biological and Environmental Repositories (ISBER) best practices. All protocols are subject to rigorous validation testing and strict quality assurance standards. Click on any of the below links to download the protocol in PDF form.

  • Plasma Isolation
  • DNA Isolation
  • RNA Isolation
  • Lymphblastoid Cell Line Initiation
  • Protein Isolation from Viable Cells
  • Collection of Small Tissue Biopsies for Frozen Sectioning
  • Preparation of EBV for Lymphoblastoid Initation
  • Placing Viable Cells in Cryogenic Suspension
  • Spectrofluorometric Quantification of dsDNA
  • Care of Lymphoblastoid Cell Lines
Forms

Click on any of the below links to download the document in PDF form.

  • Service Request
  • Transfer Request Form
  • Material Transfer Agreement – Incoming
  • Material Transfer Agreement – Outgoing
  • Shipping Form – Domestic
Facilities

The Genomic Medicine Biorepository is located in the Genomic Medicine Institute in the Center for Genomics Research, the latest addition to the Lerner Research Institute at The Cleveland Clinic. To ensure long-term reliability, samples received or processed by the GMB are stored in research-grade freezers and immortalized cell lines are indefinitely preserved in cryogenic suspension. All storage equipment is kept fail-safe through electrical backup circuits, alarm systems and temperature monitors.

Contact

For information regarding the services and operation of the Genomic Medicine Biorepository, please contact us:

  • GMB Lab
  • (216) 444-4731
  • [email protected]

Genomic Medicine Biorepository
Genomic Medicine Institute
Lerner Research Institute / R4
The Cleveland Clinic
9500 Euclid Avenue
Cleveland, Ohio 44195
Fax: (216) 636-0009

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