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Processing Batches Of Mutation Data Trace Files

It is not clear which is the best way of organising the data for the simplest and most efficient processing using the current programs, but for now we make the following suggestions.

We assume that the region of the DNA being studied has a standard set of forward and reverse primer pairs covering all segments of interest and that a standard reference sequence in EMBL format is available.

We recommend that batches of data from single primer pair combinations are processed separately, using separate temporary gap4 databases. For example, exon 11 of BRCA1 can be covered by five pairs of forward and reverse primers and we suggest that batches of traces obtained from each of these primer pairs should be processed using five gap4 databases.

Each processing run should create a new database and should enter, not only the new sets of patient data for that particular primer pair, but also the corresponding reference sequence and reference traces.

Obviously when several primer pairs are needed to cover a given region of the DNA (eg for BRCA1) the same reference sequence would be used for all the primer pairs.

An alternative to the above is to create a template database for each primer pair which contains the data for the corresponding forward and reverse reference traces plus the fully annotated reference sequence. These template databases are copied to create a temporary database for each new batch of data for the given primer pair.

Whichever of these two strategies is adopted each batch of new data is processed, analysed and assembled into these temporary databases, inspected visually, and a mutation report generated.

The use of separate temporary databases simplifies the assignment of reference traces and the use of the report generation function.

(Click for full size image)

Figure 9. An overview of a database containing data for only one primer pair of BRCA1

For long term storage and to facilitate larger studies, the content of each of these temporary databases is then transferred to archive databases, after which the temporary databases are no longer needed. The archive databases could be restricted to individual primer pairs or could accommodate data covering the whole of the reference sequence.

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