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Lab Manual for UCSF Clinical Laboratories

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ABMGG Laboratory Fellowship Program:
Clinical Biochemical Training Overview

For More Information

Program Coordinators

  • University of California, San Francisco
  • Departments of Pathology and Laboratory Medicine
  • 185 Berry Street, Suite 100
  • Campus Box 0506
  • San Francisco, CA 94107

Training in the Biochemical Genetics Laboratory consists of ongoing exposure to, and involvement with, laboratory testing, interpretation and reporting, with increasing levels of involvement and responsibility as the training period progresses. Trainees first observe testing performed by licensed technologists, and then perform parallel testing of patient samples. Following a period of detailed instruction on results interpretation (including amino acid, organic acid and acylcarnitine data) and practice with archived abnormal samples, trainees provide preliminary interpretations of patient runs, integrate results of multiple tests, and incorporate the clinical history into a final interpretation. These cases are then discussed in detail with the laboratory director at regular sign-out meetings and revisions to the trainee’s interpretations are reviewed. The trainee is expected to learn the basic principles and implementation of each test, so as to fully appreciate the complexities and pitfalls that are part of biochemical testing. For select cases, trainees communicate laboratory results directly to clinical geneticists and/or other physicians and health care providers. Feedback for improving communication performance is discussed.

Training is focused in modules in the Stanford Biochemical laboratory including:

Module 1: GC/MS Methods (Organic Acids).
Each fellow is expected to process and /interpret cases during this training module. The fellow should document his/her roles in every case that he/she is involved.

Module 2: HPLC Methods (Amino Acid Analysis).
Each fellow is expected to process, analyze and interpret cases during this training module. The fellow should document his/her roles in every case that he/she is involved.

Module 3: Tandem Mass Spectrometry Methods (Acylcarnitines, Carnitine, Other Single Analytes).
Each fellow is expected to process, analyze and interpret cases during this training module. The fellow should document his/her roles in every case that he/she is involved.

Module 4: Other Biochemical Genetics Methods (Enzyme Assay, TLC Procedures).
Each fellow is expected to process, analyze and interpret cases during this training module. The fellow should document his/her roles in every case that he/she is involved.

(Insert Schedule Here)

Conferences & Clinics

In addition to laboratory activities, trainees attend the Biochemical Genetics Teaching Conference, the General Genetics Clinical Conference, and all other required seminars, conferences, and courses. Finally, trainees attend the Neurometabolic Clinic.   In these clinics, trainees are assigned patients and are involved with the delivery of test results, either as full participants in the clinical diagnosis, treatment, and genetic counseling of patients and families [physician trainees], or as observers and discussion participants [PhD trainees].

Clinical Genetics Patient Conference
This conference is held weekly under the direction of Dr. Wynshaw-Boris and attended routinely by Drs. Jeng, Nussbaum, Packman, Rauen, and Slavotnek. The conference is a formal review of the patients evaluated that week in various Genetics Clinics and in-house consultations. The clinical fellows present the patients with the history and pertinent physical findings (including photographs when appropriate). Interesting cytogenetic and prenatal diagnosis results of the past week are also discussed, and the clinical fellow for the month is responsible for presenting and leading the discussion on recent inpatient consultations of note. The subsequent discussion is rigorous, and includes issues of differential diagnosis, disease biology, diagnostic testing, treatment, genetic counseling and basic science correlates. In this forum, the trainee gains experience in organizing and more formally presenting medical genetic information, in leading the interactive discussions that ensue, and in addressing the questions and problems that arise in these discussions. Over the years, this conference has been a hub for medical care providers interested in clinical genetics, from UCSF and nearby medical centers. Full and part-time members of the core clinical genetics faculty, physician and non-physician post-doctoral trainees, genetic counselors, interested graduate students, and medical students and house officers rotating through medical genetics all attend this conference. An additional half-hour each week is devoted to didactic presentations on topics or journal articles of particular interest to attendees. All attendees (residents, fellows, faculty, genetics counselors, and students) make presentations. 

Biochemical Genetics Conference
This weekly conference is led by Dr. Packman and attended by all fellows and residents, genetic counselors of the Biochemical Genetics Service, genetic nutritionists, and members of the Medical Genetics faculty [including Dr. Tina Cowan].  All attendees contribute presentations including didactic lectures, journal club presentations, and case presentations with discussion of the biology, genetics, and medical aspects of the disorder.  The conference schedules for the academic years 2009-2010 and 2010-2011 are appended. 

Genetics and Neurology Resident and Fellow Conference
This is a monthly conference attended by faculty, fellows and resident from Medical Genetics, including the laboratory specialties, and Pediatric Neurology.  Trainees present a neurogenetic or neurometabolic topic of interest to the entire group, in the form of a didactic presentation, a journal club presentation, or a case presentation and discussion.

Additional Available Conferences & Seminars

NF/RAS Clinic Conference
Trainees in medical genetics attend the NF/RAS clinic, led by Dr. Kate Rauen. Dr. Rauen holds this conference, which discusses patients from that clinic that interfaces with the Cancer Risk Program, and meets every 2-3 months.

Trainees in medical genetics participate in biweekly tutorials in biochemical genetics, led by Dr. Packman. The format is interactive, and includes didactic presentations (by the trainees and by the preceptors), discussions of important topics or concepts, and journal club presentations.

Prenatal Diagnostic Meeting
This weekly meeting is led by Dr. Rauen, and is attended by faculty, residents and fellows of the Reproductive Genetics Group, genetic counselors, and medical genetics trainees during their Prenatal Diagnostic rotation. At this meeting, recent complicated cases are reviewed.

Fetal Treatment Meeting
Neonatologists, surgeons, radiologists, perinatologists, and geneticists attend this daily meeting. Medical genetics trainees who are in their Prenatal Diagnostic rotation may attend this meeting, at which complicated ultrasonographic findings are reviewed, and prenatal treatment options and protocols are discussed.

Seminars and Conferences of Subspecialty Rotations
Rotations in Cancer Genetics, Reproductive Genetics (Prenatal Diagnostics), Adult Nuerogenetics, Ophthalmology Genetics, Dermatology Genetics are required for physician trainees (Clinical Genetic Residents). Laboratory Subspecialty trainees may avail themselves of the clinical conferences and seminars held during these rotations. The frequency of these seminars and conferences varies with rotation, over one month per rotation.

Research Lectures and Seminar Series
Fellows avail themselves of the opportunity to attend regularly scheduled lecture and seminar series on campus. Of particular interest to those working in basic, human, and medical genetics are the weekly Seminars in Biomedical Science (sponsored by the Biomedical Sciences Program): the weekly Seminar series  of the Department of Biochemistry and Biophysics; the weekly Journal Club of the Program in Biological Sciences; the lecture series  and the monthly seminars of the Institute for Human Genetics; the lecture series sponsored by the Cardiovascular Research Institute; and the Monthly Pediatrics Faculty Research Conference.

Molecular Sign-Out Conference
This is a bi-weekly conference led by Farid Chehab, PhD and Linda Jeng, MD, PhD and is attended by residents and fellows from Pathology, Laboratory Medicine, and Medical Genetics including the Laboratory Specialties.  Trainees give short presentations on laboratory techniques, disease entities or interesting cases during the course of case review and sign-out.

Clinical Biochemical Courses

Specialty Director
Tina Cowan, PhD,  FACMG

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