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Summary of the Report of the Second International
Strategy Meeting on Human Genome Sequencing
(Bermuda, 27th February - 2nd March, 1997)
as reported by HUGO
Summary
- The principles enunciated at the first International Strategy meeting,
of rapid data release and public access to the primary genomic sequence, were
reaffirmed.
- Scientists and funding agencies should take the necessary steps to ensure
that the principles are adhered to by all participating organisations.
Sequence Quality Standards
The following standards were agreed:
- The nucleotide error rate should be 1 error in 10,000 bases or less for
most sequence.
- Assemblies should be verified by restriction digest using two or more restriction
enzymes.
- Gaps in sequence. The agreed long term goal is no gaps, recognising that
this is not yet routine.
- Closing gaps is the responsibility of the original sequencer.
The following proposals were endorsed by the participants:
- It was agreed that a useful trial to assess sequence accuracy would be
to perform a data exchange exercise. Raw sequence data would be exchanged
among sequencing centres, centres would reassemble the data and identify outright
discrepancies or ambiguities with reference to the sequence submitted to the
database. These would be resolved by further consultation or resequencing.
The same data sets would be sent to two centres which would hopefully engender
competition to detect errors.
- All sequence reads should be archived in a retrievable form.
- Sequencing centres should define explicitly how error rates and costs have
been calculated.
Sequence Submission and Annotation
Sequence data should be classified simply as "finished" or "unfinished" and should
be stored in distinct databases; consideration should be given to establishing
a public database for unfinished sequence data.
Sequence annotation should be standardised if possible, and include the following
information:
- Error estimation such as PHRED AND PHRAP data.
- Enzymes used to verify assemblies, and sizes of fragments produced.
- Exact details on how to assemble adjacent clones, with a minimum of 100
bp of overlapping (preferably unique) sequence between clones for verification.
- Gaps must be sized and the surrounding sequence oriented and ordered. The
methods used for sizing, and reasons for not closing the gap should be stated.
- If features such as coding sequence and splice sites are included in the
annotation, it should be stated if they were identified experimentally or
by computer predictions.
- Unfinished sequence; it should be stated how near the sequence is to completion.
Potential development of a database listing all gaps in 'finished' sequence.
Sequence Claims and Etiquette
Mapping investment does not automatically entitle sequencing claims over the
same region until a sequence ready map has been generated.
Potential conflicts with other sequencers to be resolved by early communication.
Collaborations with groups with a biological interest in a region should be
subject to the same principles of data release and communication.
Investigate whether the Human Sequence Map Index should be relocated to be
more closely associated with the other major human sequence databases.
Claims allowed on the Index:
- Duration - maximum 1 year.
- Size of region - minimum 1 Mb; regions to be defined by Généthon
markers if possible, other agreed and available markers if not.
- Maximum amount - in the order of three times the sequence released by the
centre in the preceding year.
- Sequence claims must span the entire region between, and including, the
delimiting markers.
Summary of Principles Agreed at the First International
Strategy Meeting on Human Genome Sequencing
(Bermuda, 25-28 February 1996)
as reported by HUGO
The following principles were endorsed by all participants. These included officers
from, and scientists supported by, the Wellcome Trust, the UK Medical Research
Council, the NIH NCHGR (National Center for Human Genome Research) , the DOE (U.S.
Department of Energy), the German Human Genome Programme, the European Commission,
HUGO (Human Genome Organisation) and the Human Genome Project of Japan. It was
noted that some centres may find it difficult to implement these principles because
of legal constraints and it was, therefore, important that funding agencies were
urged to foster these policies.
Primary Genomic Sequence Should be in the Public Domain
It was agreed that all human genomic sequence information, generated by centres
funded for large-scale human sequencing, should be freely available and in the
public domain in order to encourage research and development and to maximise its
benefit to society.
Primary Genomic Sequence Should be Rapidly Released
- Sequence assemblies should be released as soon as possible; in some centres,
assemblies of greater than 1 Kb would be released automatically on a daily
basis.
- Finished annotated sequence should be submitted immediately to the public
databases.
It was agreed that these principles should apply for all human genomic sequence
generated by large-scale sequencing centres, funded for the public good, in order
to prevent such centres establishing a privileged position in the exploitation
and control of human sequence information.
Coordination
In order to promote coordination of activities, it was agreed that large-scale
sequencing centres should inform HUGO of their intention to sequence particular
regions of the genome. HUGO would present this information on their World Wide
Web page and direct users to the Web pages of individual centres for more detailed
information regarding the current status of sequencing in specific regions. This
mechanism should enable centres to declare their intentions in a general framework
while also allowing more detailed interrogation at the local level.
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