PCR primers and hybridization probes

Linda J. Carter ljc55 at cas.org
Wed Sep 29 14:12:05 EST 1993

      - Summary- Responses to questions about whether PCR primers and
hybridization probes should be included in general sequence databases and, if
so, what kind of information is valuable in searching for them.

	I received replies from 29 people and will share their responses with
you here.  I sincerely thank all of you who took the time to respond, and I
apologize to anyone I may have inconvenienced.  I am a novice at using the NET
and appreciate the advice several of you offered me.  I am a Ph.D. molecular
geneticist employed in the biochemistry department of CAS as a document analyst.
I chair a committee involved with resolving biosequence-related issues, and I
felt we needed some input from researchers active in the field.

	Here is my summary of the 28 responses to one or more of my original

1) Should primers and probes be included in a general nucleic acid sequence
   database?  (No - 16, Yes - 2.  Four additional responses were a qualified
   yes, provided the primers and probes were both useful and that there was
   some mechanism to exclude them from a search.  One person felt that they
   should only appear as annotations and/or features of the naturally
   occurring sequence from which they are derived.)

   Do primers and probes clutter up the database or create confusion or
   difficulty during searching?   (Yes - 11, No - 3, Possibly - 1.
   One person reported they had no difficulties with GenBank searches.)

2) Do primers and probes represent useful information in a sequence database?
   (Yes - 12, No - 3).  One of the people who said no expressed concern that
   their widespread availability might encourage sloppy use, especially in
   the area of clinical diagnosis, where the PCR reaction criteria often need to
   be clearly defined to avoid false-positives.

   Eighteen people responding felt that primer databases separate from general
   sequence databases would be helpful and desirable.

3) What applications warrant the inclusion of primers and/or probes in a
   biosequence database?

    a) Clinical diagnosis, taxonomy, evolution, gene mapping, or methods
       development  (Four people believed all these were appropriate,
       and taxonomy received one additional reply.)

    b) Their mere existence warrants their inclusion; there should be no
       restriction to particular applications (2 replies).  Comments included:
       "How can one predict what someone else may need?" and "This implies
       that one area of research is more important than another."

    c)  Only applications of widespread utility (1 reply).

    d)  Any application for a given organism (1 reply).

    e)  Satellite primers (1 reply).

4) What information (descriptive or other) should be available for primer
   searching in addition to the sequence itself?

    a) Cross-references to larger naturally occurring sequences from which the
       primers were derived, including information with respect to organism,
       gene, and product, as well as application (8 replies).

    b) Detailed PCR reaction conditions including annealing temperatures and
       substrates (7 replies).

    c) Application (3 replies).

    d) Other desirable information requested:

       - who made the primers, when, and why?
       - primer purification procedure and storage conditions
       - product detection method
       - if the application is taxonomy, a list of all organisms
	 for which the primers have been used successfully

  For those of you interested in primer databases, I did find out (via
information posted on the NET) that the genome database at John Hopkins
currently includes specific information regarding primers and probes useful for
clinical diagnosis, taxonomy, evolution, and gene mapping.  In addition, Benny
Shomer at Tel-Aviv University and Dan Jacobson from John Hopkins University GDB
are now working to establish a primer database, including detailed descriptive
information, as a gopher server.  There is also a directory of sequence tagged
sites maintained as part of the Human Genome project.

  Thanks again to all who responded.  I hope this information is useful.

				Sincerely, - Linda Carter


More information about the Bioforum mailing list