Last updated: December 01, 2005
Report to the National Advisory Council for - Human Genome Research - on the Status of Single Chromosome Workshops
Report to the National Advisory Council for
Human Genome Research
on the Status of Single Chromosome Workshops
January 30, 1995
The National Human Genome Research Institute (NHGRI) helped to initiate and continues to participate in the support of the international single chromosome workshop (SCW) program. The purposes of these workshops are to assemble up-to-date consensus maps, to collect state-of-the-art mapping data, and to provide those maps and the data to the general scientific community. During the early years of the Human Genome Project (HGP), the success of the SCWs in meeting the community's needs was highly variable. As a result, the funding agencies worked with HUGO to develop and refine a set of guidelines designed to increase the consistency and productivity of the workshops. There has been considerable acceptance of these guidelines and the SCW program, as a whole, has been improved (see attached HUGO reports).
The SCW program was created for a specific purpose, to address what was, at the time, a uniform need of individual chromosome communities to come together to work toward meeting the mapping goals of the HGP. Progress toward these goals has been rapid. The initial goal of a 2 to 5 cM human genetic linkage map has been reached and rapid progress is being made on the physical maps of human chromosomes through both individual chromosome and genome-wide efforts. In light of the progress, it is appropriate to assess the continuing need for SCWs.
This report consists of a brief summary of the current state of the SCW program and several long-term and short-term recommendations.
Summary of Recommendations
Long-Term
- Support for the SCW program, as an entity, should be terminated by the end of FY 1996.
- Applications for individual meetings that address the evolving needs of the genome community should be encouraged and considered.
Short-Term
- The National Institutes of Health (NIH) and the Department of Energy (DOE) should expend a maximum of $20,000 per workshop.
- Restriction of travel funds pending the submission of the workshop report should be increased to 50 percent and all participants should be notified of this policy prior to the meeting.
- Terms and conditions should be added to awards stating that organizers would have to require that GDB data submission forms be submitted at the same time as abstracts as a condition of reimbursement.
Nature of Single Chromosome Workshop Program
Budgets
The NIH and the DOE share equally in the U.S. contribution to the SCWs, which provides support for the travel of U.S. participants to the meetings as well as support for local arrangements for those meetings that are held in the United States. The NIH and DOE spent $345,786 and $443,045 for SCWs held in calendar years 1993 and 1994, respectively [n.b.: these numbers do not correspond completely to FY1993 and FY1994 expenditures]. The average cost per meeting to the U.S. agencies for the 1993 and 1994 meetings was $31,435 and $26,061, respectively. The average number of participants per meeting was 45 and 43, for 1993 and 1994, respectively, and the average number of U.S. participants (excluding HUGO, NIH and DOE staff) per meeting was 20 and 18, for 1993 and 1994, respectively. [n.b.: Not all of the participants in a meeting receive funding from the workshop grants because some are local participants who are not supported while others pay their own way.]
Analysis of the expenditures indicates that the workshops were significantly over-funded. In 1993, approximately 50 percent, on average, of awarded NIH funds were expended and the situation appears to be similar for 1994. The causes of this over-budgeting were over-estimation of the number of participants and/or over-estimation of the travel costs. Whenever possible, the excess funds are used for subsequent meetings.
Dissemination of Information
In principle, the rapid publication of a workshop report is an essential outcome of the SCWs, as the reports are one of the major means of disseminating the information collected and generated at the meeting. In the early years, not all SCWs even produced reports while some reports were submitted for publication well after the workshop was held. To address this problem, the HUGO guidelines called for the submission of a report within 30 days of the SCW. As an attempt at enforcement, beginning in March, 1993, the NHGRI restricted 25 percent of the awarded funds until a report was submitted for publication.
As a result, the situation seems to have improved markedly. Information on the publication of reports from meetings held in 1993 and 1994 are presented in Table 1. Reports were published for all workshops held in 1993 while, for meetings held in 1994, nearly all have already published reports or have submitted them for publication. For the most part, reports were submitted and accepted for publication within a few months of the meeting and contained consensus maps. However, not all SCWs produced timely reports. The restriction of 25 percent of the awarded funds has not proven to be an incentive in many cases because of the overfunding of the workshops. The time taken to publish a report is a review criterion for subsequent grant applications and should have an effect on the funding of subsequent meetings; however, this has not proven to be a major factor in such reviews. In addition to publication, at least one workshop report has been made available electronically, and some data from several other reports are available via chromosome-specific ftp sites.
Submission of Data to GDB
In discussions with GDB staff, it appears that more data are getting submitted to GDB from the workshops than in the past. However, it is difficult to attribute most data submission directly to a workshop because, for the most part, SCW participants submit their data directly to GDB. According to the HUGO Guidelines, participants are required to submit an abstract prior to the meeting and data and abstracts are to be entered in GDB prior to the workshop. There appears to be great variability in compliance with this guideline for submission of data and abstracts to GDB.
Frequency of Meetings
Despite significant progress in mapping, the community continues to call for additional (or, for chromosome 10, the first) SCWs. In fact, plans are underway for at least 21 SCWs in 1995 and early 1996. Several chromosome communities have begun to question the need for future meetings (in some cases as a result of strong prompting from funding agencies); however, no previously held nor planned meeting has publicly been declared to be any chromosome's last. At least one chromosome community plans to hold its next SCW as a short satellite meeting to the American Society of Human Genetics annual meeting. There also seems to be a trend toward less frequent meetings. In 1993, the meetings were held an average of 13 months after the previous meeting. In 1994 and 1995/6 (planned), the intervals rose to 16 and 18 months, respectively. The latter interval will likely turn out to be even longer because meetings often take place later than initially projected.
Long-Term Recommendations
There is a wide range of opinion within the genome community regarding the appropriate future of SCWs. Some of this comes from variability in the maturity of maps of different chromosomes, but there also are fundamental differences in philosophy regarding the benefit of actual face-to-face meetings versus reliance on electronic means of communication for data sharing and consensus-map building. It is also the case that, over time, some of the research community has come to presume that each chromosome is entitled to its own set of meetings.
In staff's opinion, the SCW program, as currently configured, is becoming obsolete. Large amounts of mapping data are coming from projects that are not chromosomally-based. The integration of mapping information from chromosome-specific efforts with genome-wide efforts is imperative, yet it is unclear whether the SCW setting is the most practical venue for this to occur. Further, the mapping goals of the HGP are rapidly being approached. From a practical point of view, the number of individuals contributing a significant amount of data on each chromosome is relatively small and the current capability for rapid world-wide electronic communication is quite high. In the context of competing priorities for limited funding, the SCWs may not be the most efficient vehicle for helping to meet the goals of the HGP. Staff therefore recommends that support for the SCW program, as an entity, be terminated by the end of FY 1996 and that short-term changes be made to the program in the interim to make the remaining workshops more effective (see below).
It is unlikely, however, that the physical maps of all chromosomes will be completed by the end of FY 1996. There will be a continuing need, in some cases, for data collection, map construction, map integration, annotation and quality control. Further, as the HGP evolves, new issues and needs will emerge, e.g., the lines between high resolution physical mapping and DNA sequencing are rapidly becoming blurred. Staff recommends therefore that applications for individual meetings that address the evolving needs of the genome community should be encouraged and considered. Specifically, applications for additional chromosome-specific meetings would still be considered if adequately justified.
The SCWs have played an important role in facilitating map construction and integration, quality control, and data submission to GDB. It is unclear what effect the demise of the SCW program will have on these vital activities. It may be necessary to put other mechanisms into place to ensure that data entry and consensus map building continues. One option would be to encourage journal editors to require the submission of data to GDB as a condition of publication.
Short-Term Recommendations
In the interim, there are several changes to the SCW program that need to be made to make it more effective.
Budgets
As mentioned above, the NIH funding level has been considerably more than what was necessary to run the meetings or to support foreign travel. The workshop budgets need to be much more closely scrutinized by the IRG, Council and staff. Staff recommends that the NIH and DOE together expend a maximum of $20,000 per workshop (waivers from this ceiling will be considered and allowed if a strong justification is presented; this waiver must be recommended by the IRG, Council and staff). The DOE has already established an informal policy of limiting its contribution to SCWs to $10,000 with some allowance for extenuating circumstances.
Dissemination of Information
The rapid dissemination of information from the SCWs is of vital importance to the genome and genetics communities. Most meeting reports are now published in a reasonably rapid fashion. Rapid reimbursement of travel funds is also of vital importance to the participants. Staff recommends that the restriction of travel funds pending the submission of the report should be increased to 50 percent and all participants should be notified of this policy prior to the meeting. This recommendation has the potential to cause problems for meetings held outside of the United States because the U.S. principal investigator is not always a co-organizer of the SCW and may not have control over the report. This situation needs to be addressed with HUGO.
Organizers of the meeting should be encouraged to have a draft of the meeting report prepared in time for the meeting such that its completion could be rapidly accomplished. In addition, an ftp server should be set up (through GDB?) and all workshop reports should be available through this mechanism.
Submission of Data to GDB: In order to increase observance of these guidelines, the NHGRI should add terms and conditions to the awards stating that organizers would have to require that GDB data submission forms be submitted at the same time as abstracts as a condition of reimbursement.
Table 1: Publication of SCW Reports
January 30, 1995
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[1] Date accepted for publication
[2] Number of months from meeting to date accepted for publication
[3] Date of publication
[4] Number of months from meeting to date of publication
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[5] Number of months from meeting to date of submission for publication
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