|Scientific Subdivisions | The Journal of Molecular Diagnostics
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Documents arise both formally and informally within the structure of AMP and are generally of three types:
The result of projects that originate within AMP, i.e. as Subdivision, Committee, or Working Group projects, and therefore are "AMP-Owned Documents," subject to the process outlined in the "Guidelines for Publication of AMP-Owned Documents" section below.
The result of projects that arise within an organization outside of AMP, but that eventually involve an AMP committee or subdivision by invitation of one of the original authors or project organizers.
The result of an invitation by the Publications Committee for an AMP member(s) to write an article for a non-peer reviewed journal or magazine as part of an agreement or understanding established between AMP and a Publisher.
1. Documents that are generated by AMP committees should be considered as AMP-owned manuscripts. Substantial contributors will be named as authors or appropriately acknowledged.
2. When a project that originates within AMP intends to have as a product a report or manuscript, the following considerations should be understood and the following steps should be taken at the outset:
a. The project is the responsibility of the AMP group (i.e. Committee or Subdivision) and not the responsibility of individual members.
b. Non-AMP members should not be involved in AMP Committee or Subdivision Reports or Position Statements without the approval of the Board of Directors. Committees or subdivisions may involve non-AMP members in manuscripts that report a scientific study (e.g. manuscript from an AMP Working Group).
c. The Committee or subdivision Chair should designate a specific member to be in charge of the project ("Project Coordinator"), which can be him/her self.
d. The Project Coordinator should predict the length of the document and recommend whether it will be sent to AMP members as a membership benefit or whether it is intended for publication.
e. If the document is intended for publication as a manuscript, the Project Coordinator should ascertain whether it should be submitted to JMD, and if not, why not. The final decision on journal choice will be approved by the Board of Directors.
f. The Project Coordinator should compile estimated costs associated with the report, e.g., data analysis, data collection, and publication costs, i.e., page, reprint charges, if applicable.
g. The Project Coordinator should prepare a total budget and abstract or project description and submit it to the Committee or subdivision Chair, who will submit it to the Executive Committee for approval. Approval from the Executive Committee should be obtained before proceeding with development of the document or manuscript. The Executive Committee should consider the proposal at its next scheduled meeting.
3. Should the Project Coordinator's term of office terminate before completion of the project, the current Committee Chair will determine if it is appropriate for the Project Coordinator to become an ad hoc member of the Committee or if a new member should be designated as the Project Coordinator. The Committee Chair will also determine if other committee members who have been involved in the project and whose terms of office are completed should become ad hoc members to continue working on the project, or whether new committee members should be assigned.
4. Title / Author list / Disclaimer Guidelines:
a. Manuscripts that are Committee Reports or Position Statements should have "Association for Molecular Pathology Report (or Statement):" at the beginning or the end of the title.
b. Authors should be listed as members of the Working Group or Committee and with their primary institutional affiliation.
c. Working Group manuscripts should list the names of the sponsoring committee for the time period encompassing the project, e.g., Clinical Practice Committee, immediately below the list of Working Group authors.
d. All manuscripts relating to clinical practice, including Practice Guidelines, should contain the disclaimer in a footnote on the first page, "Standard of practice is not being defined, and that there may be alternatives."
CpG Methylation Analysis - Current Status of Clinical Assays and Potential Applications in Molecular Diagnostics: A Report of the Association for Molecular Pathology
Antonia R. Sepulveda1,2, Dan Jones1,3, Shuji Ogino1,4, Wade Samowitz1,5, Margaret L. Gulley1,6, Robin Edwards1,7, Victor Levenson1,8, Victoria M. Pratt1,9, Bin Yang1,10, Khedoudja Nafa1,11, Liying Yan1,12, and Patrick Vitazka1,13
1 The Methylation Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee*
2 University of Pennsylvania School of Medicine, Philadelphia, PA
3 University of Texas M.D. Anderson Cancer Center, Houston, TX
4 Brigham and Women's Hospital and Harvard Medical School, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA
5 ARUP Laboratories, University of Utah, Salt Lake City, UT
6 University of North Carolina, Chapel Hill, NC
7 Oncology Wyeth Research, Collegeville, PA
8 Rush University Medical Center, Chicago, IL
9 Quest Diagnostics, Nichols Institute, Chantilly, VA
10 Cleveland Clinic Foundation, Cleveland, OH
11 Memorial Sloan-Kettering Cancer Center, New York, NY
12 EpigenDx, Worcester, MA
13 Virginia Commonwealth University/MCV, Richmond, VA
*The Methylation Working Group is a subcommittee of the AMP Clinical Practice Committee.
The 2006- 2008 AMP Clinical Practice Committee consisted of Aaron Bossler, Deborah Dillon, Michelle Dolan, William Funkhouser, Julie Gastier-Foster, Dan Jones, Elaine Lyon (Chair 2005-2006),Victoria M. Pratt (Chair 2007-2008), Daniel Sabath, Antonia R. Sepulveda, Kathleen Stellrecht, and Daynna A. Wolff.
Disclaimer: Clinical Practice Guidelines are developed to be of assistance to laboratory and other health care professionals by providing guidance and recommendations for particular areas of practice. The Guidelines or Report should not be considered inclusive of all proper approaches or methods, or exclusive of others. The Guidelines or Report cannot guarantee any specific outcome, nor do they establish a standard of care. The Guidelines or Report are not intended to dictate the treatment of a particular patient. Treatment decisions must be made based on the independent judgment of health care providers and each patient’s individual circumstances.
The Association for Molecular Pathology (AMP) makes no warranty, express or implied, regarding the Guidelines or Report and specifically excludes any warranties of merchantability and fitness for a particular use or purpose. AMP shall not be liable for direct, indirect, special, incidental, or consequential damages related to the use of the information contained herein.
5. Upon completion of the document, the Project Coordinator should:
a. Recommend whether specific contributors should have authorship or be acknowledged, and, if so, in what order.
b. Draft a cover letter to the Editor of the Journal. The cover letter should designate the person who will correspond with the editor. This person ("corresponding author") may be (but does not have to be) the Project Coordinator, the Committee or subdivision Chair, or the Publications Committee Chair. The address for reprints should be the AMP Office.
6. The Project Coordinator should initiate a review process by contacting the Committee or subdivision Chair and the appropriate AMP staff contact.
a. It should be clearly understood that the review process will involve approval by more than one group of AMP members and that all AMP reviewers should treat the document as confidential. Internal AMP reviewers should understand that they are not "substantial contributors" and that they will not receive any particular recognition or acknowledgment upon publication.
b. The following steps should be taken in sequential order:
1. A copy of the document should be sent to the appropriate AMP staff contact, who will distribute and track the manuscript through the AMP internal approval process. The AMP staff member will also ensure that the title page correctly acknowledges AMP and AMP contributors.
2. AMP staff will forward the manuscript to the Publications Committee Chair, and if received from a Working Group, to the appropriate Committee Chair. A committee review may take place concurrently with the AMP internal review. The AMP internal review group consists of the Publications Chair, the appropriate Committee Chair, and the appropriate Subdivision Chair. The Publications Committee Chair is in charge of the internal AMP review and can enlist the assistance of any expert in addition to this review group. The Project Coordinator's response to comments will be returned to the Publications Committee Chair, who acts in the role of Editor, with a copy to the AMP staff contact for tracking purposes.
3. It should be understood that reviewers have a maximum of 2 weeks to provide their review comments to the Publications Committee Chair. Failure to do so will imply tacit approval of the manuscript.
4. The Project Coordinator should make any recommended revisions / generate a response, and send an explanatory note with the revised manuscript to the Publications Committee Chair and AMP staff contact.
5. The Publications Committee Chair will make a recommendation to the Project Coordinator concerning when the document is ready for final review, at which time the AMP staff contact will distribute the manuscript and cover letter to each Executive Committee member.
6. Final review and approval of the manuscript and letter is by the AMP Executive Committee. The Executive Committee should return a decision within 2 weeks. Executive Committee members should understand that failure to respond within the designated time frame means implicit acceptance without revision. Any exception to publication in JMD shall be approved by the Executive Committee.
7. AMP staff will keep the JMD Editor-in-Chief and Managing Editor informed of manuscripts in process as well as the identity of AMP internal reviewers should the Editor choose to select different reviewers for the JMD review.
8. The Project Coordinator is responsible for submitting the approved manuscript and cover letter to the journal.
c. During peer review by the journal, suggested revisions may be required by the reviewers. The corresponding author should keep the Project Coordinator, the Publications Committee Chair, and the AMP staff member informed of all correspondence with the Editor. Journal staff will send a copy of the submitted manuscript to the AMP staff member who will forward it to the Publications Committee Chair. The Publications Committee Chair may require that the revised manuscript receive approval from the Publications Committee Chair before resubmission to the journal for final acceptance.
7. AMP should be considered as the "owner" of the manuscript. If copyright privileges are signed over to a journal, the Executive Director, COO, President, or Publications Committee Chair of AMP should sign on behalf of the AMP.
8. For published manuscripts in journals, as the "owner", AMP should pay for any page charges and should purchase sufficient reprints for its main office as well as to distribute a reprint to each author and members who made a substantial contribution to generate the report. Reprints will be provided from the AMP Office.
9. Documents that are not to be published in peer reviewed journals will be distributed to the AMP membership in a manner to be determined by the Publications Committee.
10. After publication, should any AMP member be critical of an AMP-owned document, the Publications Committee should be contacted so that such criticisms can be adequately addressed, and corrections should be made when appropriate.
AMP and AMP members contributing to this effort should be acknowledged in a footnote to the title of the publication. This acknowledgement of AMP is appropriate because the project involves the resources of AMP, including but not limited to, completion of a survey, contribution to or discussion of the project during committee conference calls, or provision of specific information. Any use of the AMP name requires approval by the association; therefore, these publications require the review of the Publications Committee Chair in order to ensure AMP's protection from liability or other problems due to the publication's content. The Publications Committee Chair may enlist the assistance of any Subdivision or Board member in this review. These articles do not require review by the Executive Committee. Preferential consideration of submission to The Journal of Molecular Diagnostics is encouraged but is not required.
AMP members may be invited by the Publications Committee to submit articles for non-peer reviewed journals or magazines as part of an agreement or understanding established between AMP and a Publisher. Such articles are reviewed by the Publications Committee Chair or designee and at least one other member of the Publications Committee. The Publications Committee Chair, or designee, will communicate suggested revisions, if any, to the author(s). The Publications Committee Chair will make the final determination when the document is ready to be sent to the Editor of the journal/magazine. Review by the Editor may occur simultaneously or subsequent to the Publications Committee review process. These non-peer reviewed articles do not require review by the Executive Committee. Long-term agreements entered between AMP and a Publisher to provide suitable AMP-member authorship for a series of articles must be pre-approved by the Executive Committee.
Approved by AMPCouncil December 11, 2008