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Incyte Corporation Message Board

  • pain_webber pain_webber Feb 11, 1999 12:43 AM Flag

    Very Interesting Article

    Read DECODING ICELAND in the 1/18/99 issue of the
    New Yorker magazine, "There are three billion pairs
    of chemical bases--the building blocks of DNA--in
    each person's body and as many as a hundred thousand
    genes in the human genome" "The process of deducing the
    causes of a common illness is one of the most daunting
    ever faced by medicine" After reading the article, I
    can see how INCY's data-base could be considered a
    gold mine !!!

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    • SmithKline Beecham Clinical Laboratories and
      diaDexus Announce
      Exclusive Licensing Agreement for
      Novel Prostate Cancer Test

      Thursday February 25,
      8:32 am Eastern Time

      Company Press
      Release

      SANTA CLARA, Calif.--(BW HealthWire)--Feb. 25,
      1999--SmithKline Beecham Corporation's (NYSE:SBH - news) clinical
      laboratories unit (SBCL)
      and diaDexus LLC, a privately-held
      molecular diagnostics company, today announced that SBCL
      has exclusively licensed rights from diaDexus to
      develop
      and perform a proprietary blood test that measures
      stages of development of prostate cancer.


      Preliminary studies indicate that the diaDexus proprietary
      test, called PLA2, is able to determine whether an
      individual's prostate cancer has spread to other
      parts of
      the body. While the prostate-specific antigen (PSA)
      blood test has been credited with increasing the
      detection rate of prostate cancer, it provides
      limited
      information regarding the stage of the cancer.

      more
      at the
      link:

      http://biz.yahoo.com/bw/990225/ca_diadexu_1.html
      >>>>>>>>>>

      So of course even though INCY owns half of diaDexus,
      and this news went out this morning, the stock went
      down quite a bit today. The markets are either blind
      or have no appreciation for progress.

    • Not sure if they are only doing cDNA, but I think
      so, at least in human DNA. I think they are doing
      some shotgun full genome sequencing in microbial
      genomes. I wouldn't be surprised if they did some selected
      shotgun stuff in human too, at least to test the waters
      ala. Celera.

    • >>>Also, keep in mind that INCY's
      clients are contracturally obligated to INCY, not just
      held by patent law. I'm not sure where you see the
      patent difficulties ahead
      though?<<<

      ExIncy makes a very important point. The patents are
      important in many ways including a "cover-your-backside"
      concept, but remember the future revenues in their
      sequencing capabilities, contracts with other pharms, and
      Incyte's products that they are developing on their own.

    • I'm a biologist, and *I'm* finding some of this
      patenting intron/exon talk confusing, so I took the liberty
      of quoting from Molecular Cell Biology by Darnell,
      Lodish and Baltimore, 1990, pg. 287-288. If this adds to
      the confusion, my apologies in advance, but I hope it
      helps.

      "Walter Gilbert suggested the term intron to refer to a
      part of a primary transcript (or the DNA encoding it)
      that is not included in a finished mRNA, rRNA, or
      tRNA. An exon is a primary transcript region (or,
      again, the DNA encoding it) that exits the nucleus and
      reaches the cytoplasm as part of an RNA molecule. The
      terms intron and exon are clear when they are applied
      to a primary transcript that gives rise to only one
      mRNA molecule. However, in the case of transcription
      units like that for the adenovirus late genes, which
      can give rise to many different mRNAs, the
      definitions of intron and exon can become blurred. A sequence
      that is an intron (i.e., that is destroyed in the
      nucleus) in the processing of one RNA transcript may
      become an exon (i.e, may become part of the mRNA) in the
      processing of another primary transcript from the same
      transcription. Nonetheless, the terms intron (or intervening
      sequence) and exon are commonly used."

      I had thought
      that INCY was only sequencing cDNA? Has that changed?

    • >>>>But I'd say it is very likely
      that a very different DNA sequence may produce exactly
      the same protein in
      another cell since there are
      large numbers of variable introns/extrons existing in
      the genome.>>>>>

      I think you
      have the introns/exons confused with the codons. There
      are 64 codons (3 base pair combos of 4 bases to
      choose from), but only about 21 amino acids, so some
      amino acids have more than one codon. Thus, you can get
      the same amino acid sequence in a protein out of
      varying DNA sequences. The intron/exon refers to splicing
      of RNA transcribed from the DNA to make the mRNA.
      The spliced out pieces are thought to be involved in
      regulatory and feedback mechanisms or just even may be junk
      in some cases. Since INCY sequences primarily cDNA
      which is made from the mRNA, this is post splicing and
      the intron/exon issues are pretty irrelevant here. I
      believe that INCY also files patents on the proteins. It
      would also be easy enough to make claims on the various
      codon permutations in the sequences, but I'm not sure
      if this is being done. I'm trying to get some more
      info from someone who REALLY knows this subject well.
      I will post what I find out if I can find out
      more.

      While no patents are set in stone, they are more in
      pencil and can be erased by challenges, they are better
      than no protection at all. As far as having a great
      intellectual property strategy, INCY has a very large in-house
      patent group which is very competent in this field. Rest
      assured that they are using whatever means are available
      to protect the information.

      Also, keep in
      mind that INCY's clients are contracturally obligated
      to INCY, not just held by patent law. I'm not sure
      where you see the patent difficulties ahead
      though?

      By the way, Znutar knows this subject well and works
      in the patent field - thanks for the great postings.

    • Thanks Znutar, this is really great. I can't
      remember the last time I actually learned something off of
      a YAHOO message board...

      Anyway, combining
      Exincytes post with various aspects of your posts, I can
      see patent difficulties ahead.

      INCY may
      produce a sequence for a gene that produces a certain
      useful protein, and patent its originating DNA sequence.
      But I'd say it is very likely that a very different
      DNA sequence may produce exactly the same protein in
      another cell since there are large numbers of variable
      introns/extrons existing in the genome. How is INCY dealing with
      that in their patent applications?!

      Just to be
      sure, my investment thesis in INCY is not that it will
      make money on patented DNA sequences but instead that
      it will earn royalties from pharmas creating new
      drugs today using its databases.

    • My last post was dinged for excessive length.
      Here's the rest of it, the part pertaining to
      patents...

      OK, so back to patents. Exincy did a nice job of
      pointing out the usefulness of the DNA sequences INCY has
      patent protection on. I question, though, what copyright
      protection INCY might have. Perhaps the software INCY has
      developed is what is being referred to. Anyway, patent
      protection only extends as far as you enable your claims in
      the written description you supply to the Patent
      Office. A good example is an early case involving
      plastics. A claim was granted to a formulation of a
      plastic. Later it was discovered that the same plastic
      could be made as much longer chains than previously
      thought possible with correspondingly higher molecular
      weights. The patent's written description didn't make
      mention of high molecular weights and the examples cited
      were all of low molecular weight compounds. The patent
      was held, therefore, not to cover the high molecular
      weight compounds even though the claim language itself
      was broad enough to encompass the higher molecular
      weight compounds. So by analogy, INCY would not
      necessarily have patent protection over any later discovered
      uses unless the patent application mentioned that they
      were somehow anticipated.

    • Sorry, folks, for the long-windedness. read on
      only if you're interested in copyrights and
      patents.

      Lets start with patents vs. copyrights. Patents are
      granted for a term of 20 years from the application date
      on inventions that are novel, useful, and
      non-obvious. Copyrights are granted for a term of either 70
      years beyond the life of the author, or for a "work for
      hire" either 75 years from the publication date or 100
      years from the date of creation. Copyright covers
      original works of authorship fixed in a tangible medium of
      expression. Copyright adheres automatically in all
      copyrightable works, but you have to register your copyright in
      order to enforce it. Some examples of things
      copyrightable are books, scultpure, choreography, computer
      programs, buildings, a haiku done in chalk on the sidewalk,
      etc. The problem with copyright on DNA is who's the
      author? One who writes on paper the string of letters
      that corresponds to the series of base pairs in a
      segment of DNA has authored a work of authorship fixed in
      a tangible medium, but it still may not be
      "original" and the protection doesn't go to the DNA itself.
      The arrangement of the base pairs is a fact, and
      copyright does not protect facts, only how they are
      expressed by an author. The problem with "originality" has
      to do with the question of whether one who sought to
      write on a sheet of paper the base pair sequence of a
      segment of DNA had much choice in how the writing
      ultimately turned out. Sometimes there's only one good way
      to express something, like in a telephone directory.
      The courts have held that there is no originality in
      a telephone directory that lists names and phone
      numbers alphabetically because it is the only reasonable
      way to order the information. On the other hand,
      there's an infinite number of ways to tell the story of a
      man lost at sea. The copyright laws will protect the
      way you chose to tell the story of a man at sea
      because it doesn't preclude anyone else from telling the
      same story a little differently or much differently.
      The law will not protect your alphabetical telephone
      directory because it would preclude others from doing the
      same in the only reasonable way the information can be
      expressed. I think that writing the series of base pairs for
      a segment of DNA is more like a telephone directory
      than a man at sea. Although you could arguably
      reletter all of the base pairs to be Q, W, K, and X, for
      example, their very arrangement is dictated by the
      underlying fact of the arrangement of the base pairs in the
      DNA itself. In fact, if you did reletter the base
      pairs you'd probably be able to claim a copyright
      because it took some small measure of originality to
      choose 4 other letters, but the copyright protection
      would not extend to the arrangement of the letters,
      which is really what you're trying to protect.

    • INCY attempts to figure out by analogy to what is
      known, what the DNA sequence encodes for and includes
      that in the patent claims. For example the 44 ESTs
      patented last year were for protein kinases (if I recall
      correctly). Also, ESTs are useful for finding the full length
      gene, as probes on things like GEM chips, for mapping
      chromosomes and for some other purposes. One of the problems
      with the first attempt to patent ESTs by the NIH
      (which was later withdrawn) was that they didn't make
      claims to utility. The full length genes are definitely
      useful to make the proteins, which are typically
      described in some manner, also for mapping, making probes,
      gene therapy, etc... I think (but am not positive)
      that INCY also files copyright claims on the DNA
      sequences too. Copywrites are much longer lived than
      patents.

    • Applying your info to INCY seems to indicate that
      they need to know more about a piece of DNA than just
      its sequence to be able to patent it. But how much
      more is not really clear to me.

      Regarding your
      aswer about the purified compound which you suppose to
      be patentable: do I assume correctly that such a
      patent would extent only to the substance in its
      purified form? Or also to (perhaps naturally ocurring,
      pre-existing, already elsewhere in use) mixtures of the
      substance?
      Such details could somehow be important in
      the INCY case...

      I'm a bit confused about the
      (legal) differences between a copyright and a patent.
      E.g. could copyright be extended to a nucleotide
      sequence?

      Finally - I'm just thinking, does anyone here know how
      many/what kind of patents INCY has actually received so far
      in this critical area?

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