Genetic Diagnostic Laboratory
The Genetic Diagnostic Laboratory (GDL) is a molecular genetics laboratory at The University of Pennsylvania that provides diagnostic testing for seven genetic disorders. The laboratory was established in 1994 under the directorship of Haig Kazazian, MD, and is currently directed by Arupa Ganguly, PhD.
The GDL trains fellows who participate in the Clinical Molecular Genetics fellowship program run by the American Board of Medical Genetics (ABMG). The training provides the fellows with an opportunity to learn, understand, and obtain hands-on training in the daily proceedings of a high-throughput molecular genetic diagnosis laboratory.
Individuals trained in this laboratory learn the intricacies of directing a high complexity laboratory. Special emphasis for "high complexity" laboratories include:
- Personnel qualifications including education, training and experience
- Performing and documenting quality control of re-agents, equipment and the environment
- Internal quality assurance including personnel competency, communication, problem solving and ongoing monitoring of the quality of testing
- Confidentiality issues
The laboratory trains fellows in the following aspects of clinical molecular genetics testing:
- Diagnostic evaluation of cases submitted for genetic testing. Specially ensuring that the requested gene testing is appropriate for the conditions pertaining to the tested individual
- Carrier testing for mothers and female relatives of an affected person with hemophiliac
- Prenatal diagnosis for hemophilia A and retinoblastoma disease
- Presymptomatic testing of individuals with a family history of cancer or other genetic diseases
Genetic testing procedures and volume
Specific genetic testing techniques fellows will learn include:
- Mutation analysis
- Southern blot
- PCR fragment or ASO analysis
- Sequence analysis
The GDL offers testing for 300-400 cases a year and covers all the different aspects of genetic testing listed above. New tests are being developed and the total number of tests performed changes every year.
Goals and objectives
- To provide training to molecular genetics fellows
- To provide genetic testing and interpretation of test results at the request of physicians or genetic counselors for the purpose of disease diagnosis, carrier status determination, risk assessment, prenatal testing, or presymptomatic testing
Biochemical Genetics Laboratory
The Biochemical Genetics Laboratory is a full-service clinical laboratory offering a wide range of metabolic tests appropriate for a tertiary care pediatric facility.
- Metabolite measurements for plasma
- Urine and cerebrospinal fluid amino acids using ion exchange chromatography
- Urine organic acids using gas chromatography/ mass spectrometry
- Total and free carnitine levels
- Quantitative acylcarnitine profiles using electrospray tandem mass spectrometry.
Trainees will be exposed to these methods and the interpretation of laboratory results for a wide range of amino acid, organic acid and fatty acid oxidation defects. A critical new facility is our triple-stage tandem mass spectrometry unit which allows for the mass screening of dozens of different inherited metabolic disorders. This technology has become the mainstay of virtually all state newborn screening programs.
Goals and objectives
Trainees will learn the basics of:
- Amino acid quantitation
- Gas chromatography-mass spectrometry
- Thin-layer chromatography
- Gel electrophoresis, including isoelectric focusing
- Enzyme analysis (i.e. Galactosemia, biotinidase and lysosomal storage diseases)
- Carnitine-ester analysis by tandem MS
- Metabolite analysis in blood and urine such as galactose-1-phosphate and sialic acid
Fellows learn to appreciate the limitations of these tests, what is significant, and how to interpret the results. Oftentimes, fellows are required to convey the significance of metabolic test results to outside physicians who are usually non-specialists in this field.
Fellows should be able to convey the following to other healthcare professionals:
- The nature of the patients' inborn error
- The gene involved and its chromosomal location (if known)
- The treatment plan
- The analytes to follow to assure adequacy of therapy (if possible)
- The prognosis
In addition, the laboratory offers a specialist expertise in the diagnosis of lysosomal, galactosemia and fatty acid oxidation enzyme defects for which diseases the laboratory has a National and International reputation. The trainees will have an opportunity to learn these techniques, which include spectrophotometric, fluorescent, and radioisotopic enzyme assays and metabolic flux measurement using isotopic tracers.
Molecular Biology Lab
Directed by Catherine Stolle, PhD, the Molecular Biology Lab rotation helps clinical genetics fellows:
- Develop their abilities to understand and clinically interpret laboratory data
- Develop an understanding of the appropriate use of laboratories during diagnosis, counseling, and management of patients with genetic disorders
Toward this end, fellows must spend a minimum of two continuous weeks in the laboratory. The lab experience must include participation in the working conferences of the lab as well as discussions of lab data.
Proposed participation in lab activities
In conjunction with the director, the fellow will select from the following list those activities most suited to achieve the purposes described above.
- Review of selected protocols from the Molecular Genetics Lab Manual ( i.e., sample handling, a typical Southern blot protocol, a typical PCR protocol)
- Familiarization with Lab Procedures
- Direct observation of sample accessioning, Southern blotting, PCR, and DNA sequence analysis
- Review of key disease related references from the Disease Reference Notebook
- Review of lab data with the director
- Search of current literature for updates on genetic testing for a selected disease
- Use of the Meditech database to access patient reports
- Joint presentation with the director of an In-Service Seminar on a genetic disease from the clinic and benchside perspectives
- Other activities by mutual agreement
Potential topics for didactic session(s)
Didactic sessions will be arranged at the request of the fellow and at the mutual convenience of the director and fellow. Didactic sessions are intended to enrich the fellow’s appreciation of topics or issues arising during participation in lab activities.
- Sample handling, sample tracking, and patient identification
- Molecular diagnostic techniques
- Submitting a sample for testing; the importance of:
- Test request
- Informed consent
- Clinical indication for testing
- Pedigree (if pertinent)
- Clinical data; lab results
- Relationship to proband tested previously
- Type of testing requested
- Name, DOB, gender
- Testing minors for adult onset disease
- Testing female children for X-linked disease
- Clinical utility / validity of test
- Confidentiality, HIPAA
- Mandatory informed consent – prenatal, Huntington, and CADASIL testing; cancer predisposition testing?
- Use of lab data in publications
- Test sensitivity vs. mutation detection rate
- Clinical indications / counter indications for testing
- Reading a lab report
- Research vs. clinical lab testing
- Genetic diseases and molecular testing
- Other topics of interest
Documentation of participation
At the end of the two-week period, the director will provide written documentation the fellow’s participation.