`Myriad Genetics, Inc. et al. (Petitioners) v. The Johns Hopkins University (Patent Owner)
`IPR For USPN 7,824,889
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`Page 1 of 7
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`IIN THE CLAIMS:
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`Please substitute the following claim set for those currently of record.
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`1.
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`(Original) A method for determiningan allelic imbalancein a biological
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`sample, comprisingthe steps of:
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`amplifying template molecules within a set comprising a plurality of assay samples to
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`form a population of amplified molecules in each of the assay samples of the set, wherein the
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`template molecules are obtained from the biological sample;
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`analyzing the amplified molecules in the assay samples ofthe set to determinea first
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`numberof assay samples which contain a first allelic form of a marker and a second numberof
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`assay samples which contain a secondallelic form of the marker, wherein between 0.1 and 0.9
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`of the assay samples yield an amplification product;
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`comparing the first numberto the second numberto ascertain an allelic imbalance in
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`the biological sample; and
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`identifying an allelic imbalance in the biological sample.
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`2.
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`(Original) The method of claim 1 wherein the step of amplifying employsreal-
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`time polymerase chain reactions.
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`3.
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`(Original) The method of claim 2 wherein the real-time polymerase chain
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`reactions comprise a dual-labeled fluorogenic probe.
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`4.
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`(Original) The method of claim 1 wherein between 0.1 and 0.9 of the assay
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`samples yield an amplification product as determined by amplification ofthefirst allelic form
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`of the marker.
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`5.
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`(Original) The method of claim 1 wherein between 0.1 and 0.9 of the assay
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`samples yield an amplification product as determined by amplification of the secondallelic
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`form of the marker.
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`6.
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`(Original) The method of claim 1 wherein the amplified molecules in each of
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`the assay samples within the first and second numbers of assay samples are homogeneous such
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`that the first number of assay samples do not contain the secondallelic form of the marker and
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`the second numberof assay samples do not contain thefirst allelic form of the marker.
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`7.
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`8.
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`(Original) The method of claim 1 wherein the sample is from blood.
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`(Previously presented) A method for determining an allelic imbalance in a
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`biological sample, comprising the stepsof:
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`distributing nucleic acid template molecules from a biological sample to form a set
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`comprising a plurality of assay samples;
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`amplifying the template molecules within the assay samples to form a population of
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`amplified molecules in the assay samplesoftheset;
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`analyzing the amplified molecules in the assay samples of the set to determinea first
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`numberof assay samples which contain a first allelic form of a marker and a second numberof
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`assay samples which contain a secondallelic form of the marker;
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`comparing the first number of assay samples to the second numberof assay samples to
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`ascertain an allelic imbalance betweenthefirst allelic form and the secondallelic form in the
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`biological sample.
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`9.
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`(Original) The method of claim 8 wherein the sample is from blood.
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`10.
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`(Previously presented) The method of claim 1 or 8 wherein between 0.1 and 0.6
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`of the assay samples yield an amplification product.
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`11.
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`(Previously presented) The method of claim 1 or 8 wherein between 0.3 and 0.5
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`of the assay samples yield an amplification product.
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`12.
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`(Previously presented) The method of claim 1 or 8 wherein the set comprises at
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`least 500 assay samples.
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`13.
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`(Previously presented) The method of claim 1 or 8 wherein the set comprises at
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`least 1000 assay samples.
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`14.
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`(New) The method of claim 8 wherein the step of amplifying employsreal-
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`time polymerase chain reactions.
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`15.
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`(New) The method of claim 14 wherein the real-time polymerase chain
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`reactions comprise a dual-labeled fluorogenic probe.
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`16.
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`(New) The method of claim 8 wherein between 0.1 and 0.9 of the assay
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`samples yield an amplification product as determined by amplification ofthefirst allelic form
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`of the marker.
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`17.
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`(New) The method of claim 8 wherein between 0.1 and 0.9 of the assay
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`samples yield an amplification product as determined by amplification of the secondallelic
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`form of the marker.
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`18.
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`(New) The method of claim 8 wherein the amplified molecules in each of the
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`assay samples within the first and second numbers of assay samples are homogeneoussuch that
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`the first number of assay samples do not contain the secondallelic form of the marker and the
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`second numberof assay samples do not contain the first allelic form of the marker.
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`Remarks
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`New dependentclaims on claim 8, claims 14-18, are supported inter alia by original
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`dependent claims on claim 1, claims 2-6.
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`Applicant notes the reconsideration of the issue of new matter and appreciates the
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`conclusion that the subject matter of claim 1 wasdisclosedin the earliest priority application as
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`well as in the particular application as originally filed.
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`Claims 1 and 6-13 stand rejected for non-statutory double patenting over claims 3, 7-11,
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`19, 24, and 31 of parent patent U.S. 6,440,706. Similarly, claims 2 and 3 stand rejected over the
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`same set of issued claims combined with claims 12 and 13 of the ‘706 patent and combined with
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`the Marrasliterature reference. Applicants submit a terminal disclaimer over the “706 which
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`obviates these rejections.
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`If all issues are resolved, we request that the U.S. Patent and Trademark Office process
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`this application for grant.
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`Respectfully submitted,
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`By: /Sarah A. Kagan/
`Sarah A. Kagan
`Registration No. 32,141
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`Date: October 6, 2010
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`Banner & Witcoff, Ltd.
`Customer No. 22907
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`001107.00794
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`In re Application of: VOGELSTEIN ET AL.
`
`Application No.: 12/617 ,368
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`Filed: November 12, 2009
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`The undersigned is an attorney or agent of record. Reg. No._ 32,141
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`/Sarah A. Kagan/
`06 October 2010
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`Sarah A. Kagan
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