Note: The contents of the AMP Newsletter and Website (www.ampweb.org) may not be reproduced for distribution of any kind without the express, specific, written permission of the AMP. Thank you for your cooperation. Contact AMP at 301.571.1880 or amp@pathol.faseb.org with any questions.

It was the best of times. It was the worst of times. Some things are eternal, or at least recur with amazing regularity. The molecular pathology community should be thrilled with the recent announcements of completion of two human chromosome sequences, chromosomes 21 and 22. Even better is the recent announcement in the San Francisco Chronicle that DoubleTwist.com of Oakland, CA, is giving Celera a run for their money, by announcing that it has a rough draft of approximately 105,000 human genes. The genes were identified by computer analysis of the 85% of the raw human genome sequence data in the public domain. The data analysis was supported by Sun Microsystems, which provided a $9 million supercomputer network of 300 Sun workstations to separate genes from junk. DoubleTwist plans to distribute the database for a yearly fee of about $10,000 with a discount for academic investigators. The company has no intention of patenting the genes it has identified. We should all be so lucky to have research colleagues who are so reasonable.

On the other hand, the gene patenting issue rages on. The Gene Patent Working Group has finalized a position statement, which is posted on the AMP web site (www.ampweb.org). Based on the position statement, a proposed resolution has been drafted for discussion at the June meeting of the American Medical Association. The goal is to have a unified position that conveys the negative impact of gene patents on the present and future practice of medicine, initially for diagnostics but eventually for therapeutics and preventive medicines, which can be used to back legislative initiatives on Capitol Hill. The debate is heating up as the Biotechnology Industry Organization (BIO) is weighing in on the argument with strong opposition to legislative changes. Only one thing is certain; that the debate will get hotter before anything is achieved to give us relief from the threats and realities of gene patent enforcement.

On another note, several government agencies are looking to make our lives more interesting. The Secretary’s Advisory Committee on Genetic Testing (SACGT) has recently issued a set of Preliminary Recommendations for regulation and monitoring of genetic testing in the US. The Clinical Practice Committee and the AMP President-Elect, Karl Voelkerding, have been working with the College of American Pathologists to respond to the recommendations, some of which have very serious implications for molecular pathology (see article by Wayne Grody, chair of the Clinical Practice Committee). Comments are due to the SACGT by the end of May, so by the time you read this newsletter, the response will likely have been submitted. The response from AMP will be posted on the AMP web site when completed. The Clinical Practice Committee will also be working on the AMP response to the Center for Disease Control and CLIA Advisory Committee recommendations for modification of the CLIA regulations, particularly focused on new regulations for genetic testing. If you thought our testing was already high complexity, just wait!

The 2000 AMP Annual Meeting in November promises to be outstanding. The preliminary meeting schedule is in this Newsletter, as well as registration and abstract information (see article by Linda Wasserman, Program Committee Chair and www.ampweb.org). We already have commitments from several companies for corporate workshops the Thursday before the official start of the meeting, which have been of great interest to our members in years past. In addition the site for the 2001 Annual Meeting has been chosen: Philadelphia. It really was a decision of the entire AMP Council, even though I am delighted that the meeting will be in my hometown!

The AMP Council revisited the issue of authorship for AMP committee publications, and has approved authorship for the major contributors to manuscripts. The Publication Guidelines have been revised accordingly (see article immediately below by Cathy Leiendecker Foster, Chair of the Publications Committee).

The Call for Nominations is also in this issue of the AMP Newsletter (see article by Karl Voelkerding, President Elect). I strongly urge each of you to step forward and offer your services to AMP, by nominating yourself or other worthy members for the open positions on the ballot. These interesting times, in which we live and practice molecular pathology, require many dedicated individuals to be the hands, eyes, ears and voice of our organization.

Many scientific updates are also available in this issue. Many thanks to all who contributed [Ed. Note: I second the thanks]. I am ever amazed at the remarkable group of individuals I have the privilege to work with through AMP. Together we will continue to move the practice of molecular pathology forward, with the challenge of maintaining the high standards of our profession while effectively and efficiently making more and better molecular testing available for the benefit of patients. Thank you all for the opportunity to serve this year as the President of AMP.

-Debra G. B. Leonard, MD, PhD, AMP President, e-mail: debraleo@mail.med.upenn.edu

Council has approved a change to the guidelines for publications allowing individual authorship of AMP position papers. The decision to allow authorship was based on providing the author(s) with credit for time and effort required to publish these position papers. It was determined that authorship is important especially to junior faculty. According to AMP Publication Guidelines (and representing no change), members from each subdivision, the Publications Committee, and Council, will review all position papers prior to acceptance and publication. These revised guidelines will be available in the near future on the AMP web site (www.ampweb.org).

-Cathie Leiendecker Foster, MS, CLSp(MB), AMP Secretary-Treasurer, e-mail: foste011@tc.umn.edu

The Clinical Practice Committee (CPC) continues to be active on a number of fronts of direct interest to the AMP membership. The most important of these are developing official AMP responses (which then must be approved by Council) to a number of government initiatives in the area of genetic testing.

This government-appointed committee of scientific and lay representatives (but including woefully few laboratorians) has recently issued its first set of Preliminary Recommendations and invited public comment before they are finalized. After that the recommendations will be submitted to HHS Secretary Donna Shalala and could become the basis for new regulations and/or legislation. The CPC is particularly concerned about the proposed heightened role of FDA as the lead agency in oversight of genetic tests, the broadening of FDA’s traditional purview to encompass evaluation of individual laboratories’ in-house testing procedures ("home brews"), and the proposal to require informed consent for all predictive genetic tests (targeting the laboratory as gatekeeper) with the option open to consider this a requirement for all genetic tests in the future. The latter recommendation becomes especially problematic when genetic tests are defined so broadly as to include many routine and relatively innocuous procedures. Because our concerns are shared by a number of other organizations such as the College of American Pathologists (CAP) and the American College of Medical Genetics, we are considering working together with these other groups to craft a coordinated response. In particular, we are utilizing the resources of CAP’s seasoned Washington office of Government and Professional Affairs to develop an effective response in a timely manner.

A series of recommendations resulting from the CLIA Advisory Committee’s deliberations over strengthening CLIA regulations in the area of genetic testing has now been published in the Federal Register (Vol. 65, No. 87, pp 25928-25934, May 4, 2000). In contrast to the SACGT recommendations, which are at this point just a "wish list" with no certainty about the form of eventual implementation, the CDC Notice of Intent represents a definitive first step toward revision of the CLIA regulations. As such, it would soon have a powerful and enforceable effect on the way all of us practice molecular pathology. Our major concerns over these recommendations center on their very broad definition of genetic tests (even including tests for somatic mutations), informed consent requirements for re-use of specimens for quality control purposes, and some of the recommendations for laboratory assurance of informed consent. As for the SACGT recommendations, public comments are invited, and we will again be working in concert with other groups, especially the CAP Washington office, in crafting our response.

This consortium of professional and government stakeholders has been put together by CDC in response to a sentiment that has arisen at the SACGT meetings that the individuals and organizations actually involved in genetic testing needed a forum to voice and exchange ideas for quality assurance in the area based on their own first-hand knowledge and experience. AMP has been a primary participant in this consortium (recently renamed as a "Forum") since the very first meeting in January 2000. President-Elect Karl Voelkerding has been designated as our official representative for upcoming meetings of the group, with input from the CPC, AMP Council, and other AMP members attending in different capacities. Although the details remain to be worked out, in general we view the establishment of this public-private-professional consortium to monitor and evaluate developments in the field as a positive step, and one, which could serve as an appropriate venue for deliberating how to implement or modify the SACGT and CLIAC recommendations.

The CPC continues to be the focal point for updating the AMP Test Directory and developing options for an on-line version. In the latter regard, we are continuing our exploration about potential inclusion or linkage of the AMP directory with the NIH/NLM-funded GeneTests website (formerly Helix). Though this database has listed only genetic testing laboratories until now, the directors have expressed enthusiasm about broadening the listings to include all areas of molecular diagnostics, with AMP’s help. This would also provide much wider exposure for AMP’s member laboratories. The next step will be for one or two members of the CPC to visit GeneTests’ headquarters at the University of Washington to begin working out the logistics required for coalescence of the two databases. As pointed out in this column previously, the discussions with GeneTests are still preliminary, no actual commitments have yet been made by either side, and if we do choose to move forward, AMP members would be given the option to be listed only in the AMP Directory and not in the GeneTests directory. For the time being, though, we are putting on hold the next revision of the AMP Test Directory until we see what sort of database might be required for the potential collaboration with GeneTests.

As always, the Clinical Practice Committee welcomes input from AMP members on any of these or other issues.

-Wayne W. Grody, MD, PhD, Chair, Clinical Practice Committee, e-mail: wgrody@mednet.ucla.edu

The sixth annual AMP meeting will be held November 9-12, 2000, in Denver, Colorado at the Hyatt Regency Hotel (1750 Welton Street; phone: 303.295.1234). The Hyatt Regency is a large, modern hotel, conveniently located just a block from the 16^th Street Mall, a pedestrians-only street filled with restaurants and shops in downtown Denver.

The meeting program is posted on the AMP web site (www.ampweb.org). A June mailing to all AMP members will include registration and program information as well as information about and forms for abstract submission. Abstract forms can also be downloaded from the AMP web site. Abstracts are due in the AMP office by July 28^th. Pathology residents, fellows and other trainees are urged to submit abstracts. As in prior years, abstracts submitted by trainees will be reviewed and judged by the Training and Education Committee. Three cash prizes will be awarded to the winners of the best poster presentation at the AMP Business meeting on November 11^th.

The Program Committee has worked very hard to develop a series of plenary sessions and workshops, which include the elements we hope, will lead to a successful AMP meeting. The meeting will officially start on Friday morning, November 10^th with the AMP Award for Excellence lecture by this year’s recipient, Henry Ehrlich, PhD. The program to follow will include a broad mix of scientific lectures, results of sample exchanges, discussions of proficiency testing and laboratory quality control requirements, clinical applications of recent technological developments, including real time PCR and the use of microarrays, and two special topics sessions devoted to the clinical implications of the SACGT and CLIAC committee deliberations and to gene patenting (Ed. Note: learn more above in Dr. Grody’s report). As you read through the schedule of events, we hope you will be as excited as we are about the program.

We look forward to seeing you all in November in Denver!

-Linda Wasserman, MD, PhD, Program Chair

e-mail: lwasserman@ucsd.edu

THURSDAY, NOVEMBER 9, 2000

FRIDAY, NOVEMBER 10, 2000

7:00-7:50 Registration and Continental Breakfast

9:30-10:00 Break

12:00-1:00 Lunch/ Visit Posters and Exhibits

Hemepath Subdivision Business Mtg/Lunch

Inf. Dis. Subdivision Business Mtg/Lunch

1:00-2:30 WORKSHOPS SESSION A

HEMATOPATHOLOGY WORKSHOP 1

2:30-3:00 Break

3:00-4:00 Medical technology selected technical topics

4:00-4:30 Break

4:30-6:00 WORKSHOPS SESSIONS B

6:00-7:00 WELCOMING RECEPTION

7:00-10:00 AMP Council Meeting

SATURDAY, NOVEMBER 11, 2000

7:00-7:55 Breakfast. Put up posters/exhibits

8:00-9:45 PLENARY SESSION II: GENETICS and ID

8:00-8:45 Genetics of Obesity

Rudi Leibl, PhD, Columbia University

9:45-10:15 Break

10:15- 11:45 PLENARY SESSION III: SOLID TUMORS

10:15-11:00 Title to be announced

Dennis J. Slamon, MD, UCLA

12:00-1:00 Lunch/Visit Posters and Exhibits

Genetics Business Meeting and Lunch

Solid Tumors Business Meeting and Lunch

1:00-2:30 WORKSHOPS SESSION C

SOLID TUMORS 2

2:30-3:00 Visit Exhibits, Posters

3:00-4:30 WORKSHOPS SESSION D

4:30-5:00 Break

5:00-6:00 AMP BUSINESS MEETING

6:30-8:00 Canadian Pathologists Meeting

SUNDAY, NOVEMBER 12, 2000

7:00-7:50 Continental Breakfast

9:30-10:00 Break

11:45 Adjourn

We have begun to compile a list of participants for our exhibit area and workshops at the Annual Meeting. This list will expand over the summer and will be finalized in September. Workshops are scheduled for Thursday Nov. 9, the day before the official meeting starts. Qiagen plans a workshop on "Sample Stabilization & Processing for Molecular Diagnostics, Biochip, & SNP Analysis." Roche Molecular Biochemicals is planning a workshop on the "LightCycler System for Molecular Pathology." Third Wave Technologies will present "Clinical Applications of Invader Analyte Specific Reagents in Hemostasis & Other Disciplines." InVivoScribe Technologies will present "Standardized Commercial Assays for Hematopathology Testing." Gentra Systems will offer a workshop on "Automated Nucleic Acid Purification: Anticipating the Demands of the Future".

The exhibit program will include:

-Mark Sobel, AMP Past-president, molpath@helix.nih.gov

At the 1999 AMP Annual meeting, attendees at the Technical Topics sessions evaluated the session and provided excellent suggestions for the topics and the format for this year’s meeting. We will have two Technical Topics sessions covering topics suggested by members and both sessions will incorporate more time for participant questions and perspectives.

In Thursday’s session, entitled "Comparison of Methods for Real Time PCR", Elaine Lyon,. PhD, (ARUP Laboratories, Utah) and Anami Patel, PhD, (St. Jude Children’s Research Hosp., Tennessee), will address advantages and disadvantages of the different real time PCR methods. They will also lead participant discussion. Drs. Lyon and Patel have worked extensively with the Light Cycler and the TaqMan Systems, respectively. They will each prepare a handout and encourage discussion of the experiences of other AMP members.

In Friday’s session, entitled "Quality Control & Test Validation - A Panel Discussion", Lars Mouritsen, BS (ARUP), Roberta Madej, MS MBA, (Roche Molecular Systems California), James Bowden, BA, (Univ. of VA), and Qi Wei, BS, (Children’s Hospital, Colorado) will lead a panel discussion on quality control and test validation in molecular diagnostics laboratories. To stimulate the panel discussion, the panel members have created a Quality Control Survey (see immediately below) to be completed by AMP members by July 31, 2000. Please respond to the survey by fax to Barbara Griffith at 505.272.9038 or by e-mail to Kent.Williams@stjude.org (Ed. Note: remember that the newsletter is available in hard copy or on line at www.ampweb.org). The survey results will be analyzed and shared with the attendees at the Technical Topics session, as well as being the focus of the panel discussion. Panel discussion topics will include assay controls, contamination control, new test validation, proficiency testing, specimen acceptability, and IRB approval for controls.

At the end of each Technical Topics session, attendees will have the opportunity to complete an evaluation form to share their ideas to improve future Technical Topics sessions and to suggest topics for future meetings. We look forward to more interactive sessions and to meeting many AMP members at the sessions. Please bring your excellent ideas, technical problems, and questions to the Technical Topics sessions.

-Barbara B. Griffith, MS, CLSp (MB), University of New Mexico Health Sciences Center, 505.272.4385/e-mail: bgriffit@salud.unm.edu AND Kent Williams, MT CLSp(MB), St. Jude Children’s Research Hospital, 901.495.2680 or 2667/e-mail: kent.williams@stjude.org

Data gathered from this survey will be collated and discussed at the Technical Topics Session on QC at the Annual Meeting. We would appreciate your response to the survey independent of your plans to attend. Please focus your responses on tests performed in Genetics, Hematopathology and Solid Tumors only. A separate workshop will focus on QC for Infectious Disease assays.

Please submit by fax to 505.272.9038 (attention: Barbara Griffith) before 7.31.00. This survey will also be available on CHAMP and at www.ampweb.org for electronic responses (kent.williams@stjude.org). Thank you!

What are the areas of emphasis in your laboratory & which assays are performed in your lab? Check all that apply.

_____ Genetics

_____ Hematopathology

_____ Solid Tumors

1. What controls do you use in your in-house¹ assays? Please check all that apply.

2. What do you use as positive controls in your in-house assays? Please check all that apply.

3. Do you include an internal standard in your in-house assays, for extraction, amplification or hybridization? When do you add the internal standard?

4. When RT-PCR or PCR amplification has failed what do you normally do?

5. For genetic or hematopathology assays, does your lab perform an extraction of a known control(s) that is positive (contains the specific rearrangement, translocation, or is homozygous or heterozygous for a particular mutation) for that disorder, each time the assay is performed?

6. When using a molecular assay from a purchased kit that contains controls, do you also use independent controls?

7. When developing a methodology for testing that utilizes RE digestion of PCR amplified portions of genes (e.g., factor V Leiden, Prothrombin 20210 G® A), it is essential to ensure that complete digestion has occurred. Failed/partial digestions may lead to diagnostic errors. How does your lab control for completeness of restriction digestion? Check all that apply.

____Design method to include constitutive enzyme site on amplified product to serve as control

____Add internal control to each sample, either commercial (e.g., Custom Cuts) or homemade templates

____Use external controls.

____Don’t control restriction analysis portion of procedure.

____Other

Comments:

8. How do you test new lots of molecular reagents before beginning general laboratory use?

9. Do you use biochemical controls for contamination (e.g., UNG, isopsoralen) in your in-house PCR?

10. Which physical controls for contamination are used in your lab? Please mark all that apply.

11. For a new test validation, does your laboratory.……

12. When adding a new test to your lab for which you have no prior methodology in your lab, how many samples do you run in parallel with another lab in order to validate the new test in your lab? Please circle one choice.

Comments:

13. When evaluating the inter-assay (between run) reproducibility of a new test method, how many sample replicates are tested and over how many different runs?

14. When evaluating the intra-assay (within 1 run) reproducibility of a new test method, how many sample replicates are tested and over how many different runs?

15. When using a purchased complete kit for a molecular test, do you ever change any of the procedures or reagents?

15a. Does kit FDA status have bearing on this decision?

16. If Yes to #15, what type of validation do you perform?

17. Does your lab have test performance evaluation methods when there is no other proficiency program available e.g., CAP, New York State, CDC, etc?

18. For in-house assays lacking commercially available proficiency surveys, e.g., CAP, how many blinded samples do you exchange with another lab every 6 months?

19. If you are involved in an internal proficiency testing program, which of the following samples do you use?:

20. When samples fail to meet minimum criteria for acceptance do you reject?

21. If patient samples are used as control specimens in your laboratory, do you obtain permission or proper authorization to use these specimens as control reagents?

___Always ___Sometimes ___Never ___Other

Comments:

The AMP Nominating Committee (NC) is entertaining suggestions for nominees for the open positions listed below. Please e-mail or call suggestions for nominees for Council-level positions to Karl Voelkerding. Please e-mail or call suggestions for the Subdivision positions to relevant members of the NC. Contact information for NC members is provided below.

Self-nominations are welcomed. We encourage your active participation in the governance of AMP, and hope that individuals who have not had an opportunity to serve in an elected position will be included in this year’s ballot. We also welcome incumbents who can lend an experienced hand! On behalf of the Nominating Committee, I thank each of you in advance for your thoughtful consideration and your nomination suggestions.

AMP elections for terms beginning January 2001:

Council: Karl V. Voelkerding; 608.233.6090; voelker@geneinsight.org

Genetics Subdivision: Diane Persons; 913.588.1728; dpersons@kumc.edu

Myra J Wick; 612.273.2441; wickx011@gold.tc.umn.edu

Hematopathology Subdivision: Maher Albitar; 713.794.1292; malbitar@mdacc.tmc.edu

Margaret L Gulley; 210.567.3100; GulleyM@uthscsa.edu

Infectious Disease Subdivision: Deborah Payne; 409.772.9129; dpayne@utmb.edu

D. Wiedbrauk; 248.551.8026; dwiedbrauk@beaumont.edu

Solid Tumor Subdivision: Frederic G Barr; 215.898.0884

Elizabeth R Unger; 404.639.3533; eru0@cdc.gov

1. President-elect automatically becomes the President and Past President in the subsequent two years.

2. The primary responsibility as President-elect is to Chair the Nominating Committee, working with representatives from the subdivisions to organize and administer the nomination and election process. The Nominating Committee is also responsible for nominating awardees of the AMP Award for Excellence in Molecular Pathology.

3. As a member of Council, the President-elect participates in the monthly Council calls and e-mail discussions, and may choose to work on specific projects of AMP.

4. The President is Chair of Council and works with members of Council to facilitate projects and other efforts. The President sets the goals and agenda for AMP, in collaboration with Council and the AMP membership. The President is the elected representative of AMP.

5. The primary responsibility of the Past President is to work with representatives from industry with interests in supporting AMP or participating in the annual meeting as a vendor. The Past President works with the AMP office to coordinate the workshops before the annual meeting and the exhibits during the meeting.

1. The Chair-elect automatically becomes Chair of the Program Committee in the following year.

2. The Program Chair-elect is a member of the program committee and provides input into the planning of the annual meeting. As a program committee member, the Program Chair-elect gains experience and insight that facilitates his/her transition to program chair in the subsequent year.

3. The Chair-elect is responsible for oversight of the portion of the annual meeting devoted to abstract and poster presentations.

4. The Program Chair is responsible for overall planning and organization of the AMP annual meeting. The Program Chair meets with the program committee through monthly conference calls that serve as a forum for updates, discussion and planning for the annual meeting.

5. The Program Chair works in conjunction with the program committee members to identify topics and speakers for plenary sessions and workshops. Subdivision chairs and chairs-elect recruit speakers and organize workshops for their respective subdivisions.

6. The Program Chair serves as the direct link to the AMP central office that administers the annual meeting. The Program Chair is responsible for providing the AMP Council with monthly updates on meeting planning.

1. The Chair-elect automatically becomes Subdivision Chair in the following year.

2. Since the Program Committee is comprised of the Chairs and Chairs-elect of the Subdivisions, a primary responsibility of this job is to represent the Subdivision’s interests in programming speakers and workshops at the Annual Meeting for the next two years. As a Program Committee member, there are monthly conference calls to discuss progress on planning plenary and workshop sessions. Program Committee members assist the Program Chair in contacting speakers and writing confirmation letters.

3. The Chair-elect and Chair work together to assure good communication with the Subdivision members so that issues under discussion by the Society leadership receive appropriate input from each Subdivision.

4. The Chair-elect and Chair serve as primary points of communication with Council to assure that Subdivision activities and concerns are addressed by the Society.

5. The Chair-elect is responsible for development and oversight of the Subdivision’s section of the AMP website.

6. The Chair (or Chair-elect in the Chair's absence) will participate in monthly Council conference calls.

7. The Chair and Chair-elect assist the Nominating Comm. in developing a slate of candidates for the next election.

8. The Chair submits an article to the AMP newsletter three times a year providing membership with an update of Subdivision activities or the relevant topic of choice.

9. At the Annual Meeting, chair the annual business meeting of the Subdivision.

1. The term of office is two years. The Chair of the Committee is a Council member.

2. The Clinical Practice Committee meets monthly by conference call and in person at the annual meeting to address issues pertaining to the clinical practice of molecular pathology. There are also frequent communications by e-mail.

3. Issues of the last 3 years included:

d. Practice guidelines for molecular pathology tests.

1. The term of office is two years. Associate and Regular members are eligible to hold this office. The Chair of the Committee is a Council member.

2. The representative is expected to interact with members of the Subdivision but also serves all AMP members.

3. Representatives are responsible for bringing member concerns on T&E issues to the Committee for discussion.

4. Members will work with the Chair and Chair-elect of the Subdivision to provide feedback to Subdivision members and to help coordinate T&E projects.

5. In past years, the T&E Committee has addressed important issues including training guidelines, compilation of curricular materials, suggestions for new workshops and outreach programs, surveys of educational offerings in molecular pathology, and communication with the American Board of Pathology.

6. The Committee meets approximately 3 times a year by conference call, once in person at the annual meeting, and there is frequent e-mail communication.

1. The term of office is two years. The President-elect chairs the Committee.

2. Members of the Committee work with the Chair and Chair-elect of the Subdivision to develop a slate of candidates for the next election., including Subdivision representatives & suggestions for Council-level positions.

3. The Committee meets by conference call at least once a month from Apr.-Sept. to develop the ballot. In addition, the Committee meets in person at the Annual Meeting.

4. Members of the Committee assist the President-elect in contacting potential nominees and evaluating candidates for nomination.

5. The NC also is responsible for nominating awardees of the AMP Award for Excellence in Molecular Pathology.

-Karl V. Voelkerding, MD, President-elect. 608.233.6090 (P); 608.236.4090 (F)/e-mail: voelker@geneinsight.org

As we work on the sessions for the Annual Meeting, I want to update you on plans for the Infectious Diseases subdivision. The Infectious Diseases plenary session will be combined with Genetics this year to cover the topic of the Genetic Basis of Disease. Dr. Emile Skamene of McGill University will speak on the genetics of mycobacterial infections and Dr. Rudi Leibl will review the genetics of obesity. The combination of plenary session for Genetics and Infectious Diseases provides the time needed for a Special Topics Plenary session, which is very important for the membership. The combined plenary session is planned for this year only, next year we will return to the format of two plenary speakers for both Infectious Diseases and Genetics.

Since the interactive workshop was well received last year, we will keep this format for one of the workshops for the Annual Meeting. The interactive workshop will be a discussion of the NCCLS Proposed Guideline "Quantitative Molecular Methods for Infectious Diseases". Roberta Madej, MS is chairing the committee that has been working on this document for the past two years. Members of the committee include Angela Caliendo, Stephen Day, Andrea Ferreira-Gonzalez, Mel Krajden, Michael Loeffelholz, Rick Nolte, Larry Pope, and John Ticehurst. The document will provide guidelines for quantitative molecular testing in much the same way MM3 provided guidelines for qualitative molecular testing. Many members of the NCCLS committee are also members of AMP and have agreed to be present for an open discussion of the document. Each panel member will briefly present a portion of the document, which will be followed by lively discussion. It is not the intent of the committee to present the entire document, but rather focus on specific areas of interest or controversy. We are very interested in obtaining feedback from the "end users" prior to putting the final draft together and feel that the membership could provide valuable insight into the document. Before the workshop we will provide a general list of topics that will be covered, so that participants will have time to organize their thoughts. We encourage other subdivisions’ members to participate as many of the assay design and QC issues that apply to infectious diseases testing also apply to other types of molecular testing.

In response to the request for a workshop covering genotypic and phenotypic testing, Dr. Tim Alcorn will discuss HIV resistance testing and Dr. Rick Nolte will review HCV genotyping. We look forward to seeing you in Denver.

-Angela M. Caliendo, MD, PhD, Subdivision Chair, e-mail: acalien@emory.edu

The genetics (and infectious diseases) subdivision will have just one rather than the usual two plenary presentations at the Annual Meeting. We are fortunate to have Dr. Rudi Liebel (Columbia University) give a talk on the "Genetics of Obesity". The first genetics workshop, "Biomolecular Research Tools on the Web", will be split into two halves. The first will be led by Dr. Peter Cooper from NCBI who will present "A Field Guide to GenBank and NCBI Resources" (Outline at

http://www.ncbi.nlm.nih.gov/Class/FieldGuide/).

Dr. Nanbert Zhong (NY State Institute for Basic Research) will present "ExPASy Proteomics Tools". If anyone knows of interesting/useful sites please bring the URL (and brief description) with you to share with others. The second workshop will be a chance to get some feedback from (and see the faces behind) the CAP molecular genetics proficiency testing surveys, focusing on fragile X and cystic fibrosis, by Dr Tim Stenzel et al.

Myra Wick will be stepping down from running the genetics subdivision homepage and one or preferably two replacements/volunteers are needed. Apparently a knowledge of web pages is not required and Myra will help through July. Please let me know if you are interested in volunteering.

-Antony E. Shrimpton, PhD, Subdivision Chair, e-mail: shrimpta@mailbox.hscsyr.edu

The Solid Tumor Subdivision website is being updated to include links relevant to diagnostics, education and research. The operational plan is to develop a flexible outline of topics, which can be expanded and updated as needed. Currently, the major sections include database collections, diagnostic labs and tests, education, images, and microarrays / gene expression.

A great number of databases have emerged recently. Keeping track of them is a major challenge. Nucleic Acids Research has made a significant contribution by dedicating its first issue of each year to articles reviewing databases old and new (access

for the table of contents). The January 2000 issue included two collections aimed at compiling and organizing all useful biological websites and providing direct links to each. For the statistics fans, these listings include about 500 sites. The Molecular Biology Database Collection is curated by AD Baxevanis from the National Human Genome Research Institute at NIH, and the databases are listed by name and category at

http://nar.oupjournals.org/cgi/content/full/28/1/1/DC1.

At present, most sites will be useful primarily for research projects, though diagnostic tests will surely continue to emerge from investigational efforts. The categorical listing uses 17 major headings, which are merely highlighted here. All the Major Sequence Repositories (i.e., American, European and Japanese) are listed as well as 14 sites, described as Comparative Genomics, which catalog gene expression in a variety of organisms and specific tissues, e.g., kidney, prostate and dental tissues. Gene-Hunters will be interested in the Gene Identification and Structure collection, which includes eukaryotic gene regulatory regions as well as exon-intron structures, and the Genomic Databases has collections from bacteria and plants to mice. Mutation-Hunters will like the listing of 31 Mutation Databases which includes p53, RB, and some other cancer-related genes, though the BRCA1/2 database is conspicuously absent. Three sections are devoted to proteins including Protein Databases from several structural families, e.g., G protein-coupled receptors, the steroid hormone receptor superfamily; a Protein Sequence Motifs section which compiles motifs, alignments and clusters providing clues to protein function; and a collection of Proteome Resources which includes a site with 2D-PAGE images and reference maps. Similarly, there are two sections on RNA Sequences and RNA Structure, and there is an assembly of miscellaneous sites including a link to DBcat which is a European collection of 500 biological databases available at

http://www.infobiogen.fr/services/dbcat.

The most educational site I’ve seen is described as a "free site designed by a pathologist, for pathology education..." which now features "2100+ links and a greatly expanded and recategorized surgical pathology subdivision" at http://www.pathmax.com. This is an amazing collection of links relevant to many areas of pathology: clinical, anatomic, forensic, and on and on. The site’s creator, Dr. SE Cowper, has a strong interest in bioinformatics, and the interface is fast, smooth and easily navigated through banks of buttons. The surgical pathology section is sub-divided among all major organ systems. As an example, the pulmonary/mediastinal button produces links to six pulmonary pathology resources including the University of Iowa’s Virtual Hospital course on lung tumors. This remarkable site has several case studies abundantly illustrated with X-rays, CT and MRI scans, bronchoscopy images as well as photomicrographs of diagnostic biopsies. The educational opportunities of this single site are remarkable, but then there’s a list of 24 recent text books with links to Amazon.com ready for your "one-click" purchase. All the surgical pathology organ systems are organized in this fashion, and you really must browse this site for a good while to appreciate the breadth of resources at your fingertips. I’ll mention only one more gem that I found in the "Autopsy/Gross" section under the internet links: the Johns Hopkins Database of Autopsy/Gross images has more than 5,000 JPEG-compressed versions of images reproduced from the Armed Forced Institute of Pathology (AFIP) Electronic Fascicles. As compressed JPEG images, they lack some of the detail of the original AFIP images which are available on a CD-ROM series. To investigate the image quality, I downloaded into PowerPoint a gross photograph of a lung tumor which illustrated a mass lesion but was significantly lacking in crisp detail. As U.S. government publications, this collection is in the public domain and not subject to copyright restrictions.

Two additional sections need some further development, and your input is welcome. Diagnostic Labs & Tests is not my main arena of activity, so I’ve listed only the GeneTests site (see http://www.genetests.org/) which replaces the old Helix database (Ed. Note: The CP Committee is investigating partnering GeneTests with the AMP Test Directory). You must complete a free registration, but then you can search for tests by gene or disease name, laboratory, laboratory director or clinical genetics clinic. In addition, there is a downloadable PowerPoint presentation which illustrates the wide range of clinical issues which commonly arise during even routine genetic testing situations. Finally, the arena of Microarrays & Gene Expression will grow rapidly over the next year, so I’ve made a section for it. At this point, I’ve only found sites for breast and prostate cancers, so let me know when and where you find more. I’m hopeful that these studies will lead to truly "tumor-specific antigens" for diagnostic and therapeutic applications. Please contact me directly (bbennett@coh.org) to make suggestions and comments or to volunteer your time and expertise.

-William P. Bennett, MD, Subdivision Chair-elect, e-mail: bbennett@smtplink.coh.org

Although the Annual Meeting is still months away, the AMP program committee has been hard at work and has a great meeting planned. In the hematopathology subdivision, we are looking forward to two excellent plenary speakers. Pier Paolo Pandolfi, MD, PhD, from the Department of Human Genetics, Memorial Sloan-Kettering Cancer Center will speak on the "Molecular Biology of Acute Promyelocytic Leukemia". Dr. Pandolfi is a world recognized expert on this topic. Lawrence M. Weiss, MD from the Division of Pathology, City of Hope National Medical Center will speak on the "Role of the Epstein Barr Virus in Malignancies". Dr. Weiss has published extensively on multiple topics in pathology, including the molecular biology of malignant lymphomas and the detection of the EBV in various neoplasms.

Planning for the hematopathology workshops is also underway. Adam Bagg, MD, Hospital of the Univ. of PA, and Janina Longtine, MD, Brigham and Woman’s Hospital will moderate a workshop on the clinical significance of minimal residual disease detection and quantitative PCR. Rita Braziel, MD, Oregon Health Sciences University, and I will moderate a sample exchange workshop. Samples for a follow up bcl-2/J_H exchange should be mailed by the time this newsletter is published.

I hope that this will be a useful and educational program for not only the hematopathology subdivision members, but also the AMP membership at large. I encourage you to start making your plans now to join us in Denver.

The hematopathology subdivision needs your participation. If you or someone you know would like to be more involved in AMP, contact our nominations committee members to see what is the best position for you. We always need good candidates, and self-nominations are encouraged. The hematopathology Nominating Committee members are Maher Albitar, MD, MD Anderson Cancer Center (malbitar@mdacc.tmc.edu) and Margaret L. Gulley, University of Texas Health Sciences Center, San Antonio (GulleyM@uthscsa.edu).

The recently proposed World Health Organization (WHO) classification of neoplastic diseases of the hematopoietic and lymphoid tissues (J Clin Oncol 17:3835, 1999) includes classification schemes for malignant lymphomas and myeloid neoplasms. The lymphoma classification proposed by the WHO is similar to the previously proposed REAL classification which recognizes recurring cytogenetic and molecular genetic abnormalities associated with some types of lymphomas, but the detection of those abnormalities is not required for diagnosis.

The WHO proposal for myeloid neoplasms, however, has a distinct category of acute myeloid leukemias (AMLs) with recurrent cytogenetic translocations. These include disease groups of AMLs with t(8;21)(q22;q22), AML1(CBFa )/ETO; acute promyelocytic leukemia [AML with t(15;17)(q22;q11-12 and variants, PML/RARa ]; AML with abnormal bone marrow eosinophils [inv(16)(p13q22) or t(16;16)(p13;q11), CBFb /MYH11]; and AML with 11q23 (MLL) abnormalities. Presumably, cytogenetic or molecular genetic confirmation of the translocation would be necessary to make these diagnoses. Although morphologic and immunophenotypic features are recognized to suggest some of these diagnoses, confirmation would be needed. The significance of cytogenetic abnormalities in AML has been recognized for some time now, and the inclusion of molecular genetic and cytogenetic data in the diagnostic criteria represents a major change in the pathologic classification of acute leukemia. The most striking example of the impact of molecular changes in AML is in the acute promyelocytic leukemias (APL). Most have an associated PML/RARa translocation and respond to chemotherapeutic regimens that include all-trans-retinoic acid (ATRA). Cases with morphologic features of APL that do not have abnormalities involving RARa or the rare cases with t(11;17)(q23;p21), PLZF/RARa AML are usually non-responsive to ATRA and require other therapeutic approaches. The leukemias with t(8;21) or inv(16) have abnormalities of the core binding factor, involved in normal hematopoiesis, and tend to have an improved prognosis when compared to other AML types. AMLs with MLL rearrangements have a generally worse prognosis than many other AML types, but this may not be true for the t(9;11)(p22;q23) cases with AF9/MLL translocations. Therefore, even this improved classification scheme might not provide the essential details for a given case of AML with an MLL rearrangement. In addition, many other significant molecular genetic changes are now well recognized in AML but are not included in the WHO proposal.

The proposed WHO classification of AMLs will apparently increase the need for confirmation of suspected molecular genetic abnormalities in these diseases, even though only a limited number of abnormalities are included. More details of the proposal will be presented in the WHO monograph that should be published this year. Although the WHO proposal is limited in regard to the molecular changes in acute leukemia, it will hopefully set the stage for more molecularly-oriented classification systems in the future.

-Daniel A. Arber, MD, Subdivision Chair, e-mail: darber@coh.org

I want to share with my AMP colleagues an interesting sequence of events and important breakthroughs in molecular pathology. At our recent Beaumont DNA Symposium, April 13-15, 2000, the keynote address was given by Dr. Robert L. Strausberg, Director of the Cancer Genome Anatomy Project (CGAP) of the National Cancer Institute. This project started in 1997 with the overall goal of building a new information and technology platform for cancer research and achieve the comprehensive molecular characterization of normal, precancerous and cancerous cells. Among the different facets of CGAP that Dr. Strausberg discussed, were the new technologies for comprehensive molecular analysis, ranging from oligonucleotide and cDNA arrays on various types of solid supports, to serial analysis of gene expression (SAGE) and derivatives of the differential display approach. These technologies have expedited the process of detecting differences in gene expression in a variety of cell types and physiological or pathologic conditions.

The SAGE technology was developed by Dr. Victor Velculescu in the laboratory of Drs. Bert Vogelstein and Ken Kinzler at Johns Hopkins Oncology Center. Victor was one of our guest speakers at the Beaumont DNA Symposium in 1997, shortly after his publications on SAGE appeared in Science, Cell, and Molecular Cell Biology. His presentation addressed the principles and the current and potential applications to provide both quantitative and qualitative data about gene expression. Briefly, the two principles on which SAGE is based are: (i) a short nucleotide sequence tag of 9-14 bp contains sufficient information to uniquely identify a transcript, provided it is isolated from a defined position within the transcript, (ii) concatenation of short sequence tags allows for efficient analysis of transcripts in a serial manner by the sequencing of multiple tags within a single clone. SAGE can be used to characterize the entire set of genes expressed from a eukaryotic genome. The global pattern of gene expression is represented by a "transcriptome" encompassing the identity and level of expression for a certain cell population. In comparison to the genome, transcriptomes are not static entities, being modulated by a variety of internal and external factors.

The number of transcripts analyzed by SAGE world wide has increased explosively over the past three years, reaching 5x10⁶ during 1999. The sheer numbers are staggering. For example, Dr. Velculescu, in his studies on human cancer cells, analyzed 3.5 million transcripts from 19 normal and diseased tissues, identifying expression of 84,000 genes and thus providing an estimate of the minimum number of genes in the human genome. His work showed that more than 43,000 genes can be expressed in a single cell type. Using SAGE, it was possible to identify (i) specific genes expressed in individual cell types (ii) the set of genes expressed in all cell types, and (iii) the small number of genes uniformly expressed at high levels in many cancers, compared to the normal cell counterparts. For this work on SAGE Dr. Velculescu received the 1999 grand prize for young scientists awarded by Amersham Pharmacia Biotech and Science.

Another important development was the creation of a public database, SAGEmap, as a component of CGAP to provide a central location for depositing, retrieving and analyzing human gene expression data, in both malignant and normal tissues. This is the first completely public database for quantitative gene expression comparisons and a repository for SAGE data.

SAGEmap makes it possible for any researcher to access large-scale expression data, comparisons between malignant and normal cell types, candidate tumor-specific genes for immune-based cancer therapy. SAGEmap can be accessed at http://w

w

-Domnita Crisan, MD, PhD, William Beaumont Hospital; e-mail: dcrisan@beaumont.edu

Could someone in your laboratory benefit from a hands-on training course in Molecular Diagnostics techniques for the clinical lab? Promega’s Molecular Diagnostics Business Unit has collaborated with the BioPharmaceutical Technology Center Institute and the Medical Technology Program, Department of Pathology and Laboratory Medicine at the University of Wisconsin-Madison to develop an accredited, week-long workshop entitled "Molecular Technologies for the Clinical Laboratory". The course will cover nucleic acid purification, amplification, mutation detection and other frequently used techniques. It is a week-long course held at the BioPharmaceutical Technology Center Institute in Madison. The next session being offered is July 10-14, 2000. View our brochure and use on-line registration at: http://www.btci.org/courses/CoursesList/courses.htm or call 800.356.9526 ext. 2508 for more information.

The National Committee for Clinical Laboratory Standards or NCCLS (www.nccls.org), a globally recognized, voluntary consensus standards-developing organization, is pleased to announce the availability of two new guidelines for molecular methods.

MM1-A, Molecular Diagnostic Methods for Genetic Diseases; Approved Guideline. Member, $35; Nonmembers, $85. This document provides consensus recommendations for all phases of the operation of a molecular genetics diagnostic lab related to nomenclature for human pedigrees, lab safety, "front-end" activities, and results reporting. MM1-A provides new updates on:

• Nomenclature for designation of mutations
• Intake information
• Specimen identification and accessioning
• Sample preparation and processing
• Test validation and characterization
• Quality assurance/Quality control guidelines

MM4-A, Quality Assurance for Immunocytochemistry; Approved Guideline. Member, $35; Nonmembers $85. This document provides consensus recommendations for the performance of immunocytochemical (also referred to as immunohistochemical) assays to promote a better understanding of the requirements, capabilities, and limitations of these diagnostic methods; to improve their intra- and inter-laboratory reproducibility, and to improve their positive and negative predictive values in diagnosis of disease. MM4-A provides new updates on:

• Tissue collection and sample handling
• Fixation, antigen retrieval methods, staining protocols
• Formats for reporting of test results
• Automated, rapid, and other new technologies

Please contact Marc R. Schlank, MT (ASCP), MS at the NCCLS Executive Offices for ordering information, and to learn more about participation on related projects (mschlank@nccls.org or 610.688.0100 x 123).

NCCLS Announcement List: If you are interested in receiving current information from the "NCCLS Electronic Announcement List," please link to the NCCLS website www.nccls.org and "subscribe".

AMP member Dr. Fahd Al-Mulla of Kuwait reports identification of novel function for a protein called carbonyl reductase. Dr. Al-Mulla’s group is currently looking at expression of the gene in human tumors. Learn more in the reference in Cancer Research (2000), March 1;60(5):1173-6.

-Fahd Al-Mulla BSc, MB, ChB, PhD; e-mail: fahd@al-mulla.org

Expression array analysis has recently become one of the catch phrases of biomedical research. Microarrays promise to provide a picture of how cells differ with regards to their developmental program and their response to environmental cues through differences in global gene expression patterns. In a clinical setting, molecular pathologists are beginning to ask the question of whether this technique can be useful in understanding disease pathogenesis or in facilitating definitive diagnosis. A recent paper spearheaded by the groups of Lou Staudt, Pat Brown, David Botstein, Ron Levy and others provides strong evidence that gene expression analysis can yield important prognostic information in the clinic (Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling, AA Alizadeh et al. Nature 403, 503-511, 2000). Here, I will summarize the relevant data from this paper, and speculate on how this information might be used in the diagnostic laboratory in the future.

The sub-classification of human lymphoma based on histology and cell morphology has been invaluable in predicting patient prognosis and therapeutic response. However, it is also clear that tumors placed in the same category can behave differently in individual patients. For example, although most patients diagnosed with diffuse large B-cell lymphoma (DLBCL) respond to standard multi-agent chemotherapy, durable remission is achieved in fewer than half. It has been hypothesized that these differences in response relate to phenotypic and genotypic differences between individual tumors that are not reflected in morphology. To investigate this possibility, Alizadeh et al. evaluated if gene expression microarray analysis could be used to sub-classify individual B cell malignancies in a way that has clinical significance.

The DNA microarray technique is conceptually simple. cDNA clones specific for individual genes are spotted in an array on glass [or other substrate] slides; as a result of advances in the automation and miniaturization of this process, thousands of cDNAs can be spotted on the same slide. RNA is then isolated from the cell source of interest and converted into a cDNA probe incorporating a fluorescent label. A reference cDNA probe is also prepared by labeling with a different fluorochrome. A mixture of the two cDNA probes is hybridized to the cDNAs immobilized on the glass slides and the fluorescence signals from the two fluorochrome probes compared. In this paper about 18,000 different cDNA clones were used. Two-third were derived from a germinal center B-cell library; the rest were chosen based on their involvement in lymphocyte development or function, cell cycle regulation or cancer etiology, or were derived from lymphoid malignancy cDNA libraries. The reference cDNA probe was synthesized from a pool of RNA samples isolated from eleven different lymphoid cell lines. Hybridization of this probe was compared with cDNA prepared from a panel of different DLBCLs, follicular lymphomas (FL) and chronic lymphocytic leukemias (CLL), and a panel of different normal lymphoid cells and lymphoid cell lines.

The major challenge with this kind of experimental approach is how to make any sense of the massive amount of data generated. The key advance in this field has been the application of cluster analysis to the data to help reveal global trends in gene expression. Remarkably, genes involved in the same cellular process are usually clustered together by this analysis, without any preliminary categorization of the genes or the samples.

By applying cluster analysis to the expression data derived from this panel of malignancies, three key findings can be distilled. First, FL and CLL samples were easily distinguished from DLBCL based on the expression of genes associated with proliferation. As might be expected based on their indolent nature, FL and CLL expressed relatively low levels of "proliferative" genes, including cell cycle control and replication genes. FL could also be distinguished from CLL based on the relatively high level expression of genes specific for germinal center B cells.

Second, variable expression of genes specific for other types of hematopoietic cells, e.g., CD14, NK4, CD3, could be found in individual samples, especially in DLBCL. The authors speculated that this probably reflects the variable presence of non-malignant cells in the biopsy sample and could be used to estimate the contribution of non-malignant cells to the total sample pool.

The third, and perhaps most important finding came from a re-clustering of the DLBCL data based on the expression of B-cell signature genes. The authors found that the DLBCL samples clustered into two groups, one group with similarities in gene expression to germinal center B cells and another with similarities in expression to activated peripheral blood B cells. Most importantly, these phenotypic differences translated into prognostic differences; the average five-year survival for germinal center-type and activated B-cell-type DLBCL was 76% and 16%, respectively.

These studies provide one of the first published demonstrations that global expression analysis can be used to categorize malignancies into clinically relevant subdivisions. But, what does this mean for the diagnostic molecular pathologist? Will we be expected to perform microarray analysis on tens of thousands of genes for every biopsy sample submitted for diagnosis? I would argue that the answer to this question is no (thankfully). As a result of the excellent research study published in this paper, not only do we know that DLBCL describes two different entities (at least), but we also know which genes are differentially expressed in the two groups. I would propose that through the analysis of as few as ten of these genes, these two categories of DLBCL could be objectively and reproducibly distinguished. The table lists a set of genes identified in this study that might serve this purpose, and how frequently they are differentially expressed. Perhaps a simple, robust, cheap, semi-quantitative multiplex PCR (or some other detection method) could be developed that would give a rapid distinction based on the relative intensities of ten signals rather than needing to rely on the elaborate, finicky, expensive microarray analysis in the clinical diagnostic lab. Any fellows out there interested in a project?

* * * * * * *

* The proportion of biopsies in which the indicated gene is expressed at either higher or lower levels in comparison with the reference sample. This information is derived from Supplemental Figure 3 that can be found at http://llmpp.nih.gov/lymphoma.

-Richard H. Scheuermann, PhD, University Texas Southwestern Medical Center, AMP Program Chair-elect. E-mail: scheuerm@utsw.swmed.edu