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Excerpts from the Main ATI Request

Below are excerpts from material returned to date from the main Access to Information request. These are presented in chronological order. Each excerpt is linked to the page of the PDF reproduction on which it appears to provide the best context possible.

These reproductions are copies of official works published by the Government of Canada.  The reproductions have not been produced in affiliation with, or with the endorsement of the Government of Canada. They are reproduced in accordance with the terms and conditions of Innovation, Science and Economic Development Canada.

Excerpts from 2011 Documents:

From a French language “Rapport de la formation sur les directives suit a la decision” (Report on training on the guidelines following the decision) dated November 2011:






Excerpts from 2012 Documents:

From an undated document entitled “Diagnostic Methods as Patentable Subject Matter in Canada” attached to emails of January 2012:



From an email of January 6, 2012 6:31 PM:


From an email of January 9, 2012 11:27 AM:


 From an email of January 9, 2012 12:17 PM:


From an email of January 9, 2012 1:33 PM:


From an email of the Assistant Commissioner of Patents of February 2, 2012 2:34 PM:


From a “rough guide to applying purposive construction” dated February 9, 2012:


From an email of February 20, 2012 12:04 PM:


From an email of February 20, 2012 1:44 PM:


From one version of a revised document entitled “Diagnostic Methods as Patentable Subject Matter in Canada” dated February 27, 2012:



From a “Patent Branch Newsletter” dated March 30, 2012 2:14 PM:


From an email to the Assistant Commissioner of Patents of April 20, 2012 9:04 AM:


From an email of May 1, 2012 8:13 AM:


From an email that prompted the reply of June 19, 2012 excerpted below:


From the reply email of June 19, 2012 8:21 AM:



From a further reply email of June 19, 2012 10:19 AM:


Excerpts from 2013 Documents:

Dramatis Personæ

Sylvain Laporte – Commissioner of Patents
Agnès Lajoie – Assistant Commissioner of Patents
Chris Evans – Chair of the Patent Appeal Board
Michael Gillen – Division Chief, Biotechnology
Katrina Campsall – Senior Patent Examiner*
Scott Vasudev – Division Chief, Patent Policy and International Affairs*
Konstantinos Georgaras – Director General, Corporate Strategies and Services
Marc de Vleeschauwer – Program Manager, Patent Branch Training
Isabelle Robert – Section Head, General Chemistry and Organic Chemistry Division
Nicholas Ohan – Section Head, Biotechnology Division
Robert Rymerson – Section Head, Biotechnology Division
Shirley Arpin – Section Head, General Chemistry and Organic Chemistry Division*
Xiao-Ying Ma – Senior Patent Examiner
Maria Mill – Patent Examiner, Biotechnology Division
Sophie Beaudoin – Senior Patent Examiner, General Chemistry and Organic Chemistry*
Josée Pharand – Program Manager, Examination Practice

*current (2013 information unavailable)

Act 1: “…Sylvain needs to be educated”

The year began, appropriately enough, with media lines for the release of post-Amazon practice, and with the Canadian College of Medical Geneticists forwarding its statement on gene patents (not included in the ATI material) to then Commissioner of Patents, Sylvain Laporte, and Assistant Commissioner, Agnès Lajoie.  Mr. Laporte solicited input on this document from Ms. Lajoie and Patent Appeal Board Chair, Chris Evans:


(page 332)

Mr. Evans’ response of February 13, 2013 mentioned the debate raging over gene patents in the U.S. at the time.  Mr. Evans stated that CIPO must weigh in on the patentability of diagnostics pursuant to the Amazon FCA decision (2011 FCA 328):


(pages 7-8)

At a time when examination practices were still to be discussed, the Fly is intrigued by reference to a “current position of the Office”.

In reply, Mr. Laporte stated that he did not understand the issues:


(page 7)

Ms. Lajoie then asked for input from Dr. Michael Gillen, then Division Chief of Biotechnology, noting Mr. Laporte’s indication that he “needs to be educated”:


(page 20)

Mr. Gillen replied on February 18, 2013 with point-form (page 23) and written (page 24) summaries, the latter noting with respect to diagnostics that “A tremendous amount of effort is needed to associate a particular gene with a medical condition”.  Notably absent from these documents is mention of the “current position of the Office” referred to by Mr. Evans.

“Do we want the CoP to get briefed by the US on how they handle these types of applications and why?”

On March 18, 2013, Katrina Campsall wrote to Scott Vasudev, referring to an upcoming meeting between Mr. Laporte and his USPTO counterpart, and asking if “we want the [Commissioner of Patents] to get briefed by the US on how they handle these types of applications and why”:


(page 36)

On March 26, 2013, Konstantinos Georgaras noted that Mr. Laporte had mentioned that post-Amazon practice would permit the patenting of personalized health diagnostics. Mr. Georgaras asked if this was true:


(page 41)

Mr. Georgaras explained that his question was prompted by government investment in the area:


(page 40)

Mr. Evans ultimately answered the question.  He stated that the subject was contentious, and equated the patenting of a diagnostic to the patenting of new information:


(page 40)

On June 17, 2013, Mr. Laporte emailed to ask for information pursuant to U.S. Supreme Court decision in Myriad:


(page 59)

“It remains to be seen… whether applications in Canada will reflect the subject-matter restrictions imposed by the US Supreme Court”

Ms. Campsall’s reply noted that the Myriad decision “has no legal impact on the patenting of DNA in Canada”, and later stated, “It remains to be seen… whether applications in Canada will reflect the subject-matter restrictions imposed by the US Supreme Court”. An excerpt reads:


(page 58)

Act 2: “The intention is to present some examples to the Commissioner so that he may become better informed on how diagnostic methods may be construed in light of PN2013-02.”

Returning to June 6, 2013, Ms. Campsall reported that she had drafted Example scenarios, each presented with both a “broad and narrow approach to framing the problem and solution”:


(page 48)

The Examples themselves begin on page 49 and are worth reading to understand what was later to be debated. Example 3 (“Old diagnostic marker for new condition”) proved most contentious. To avoid confusion over numbering, the Fly points out that an analogous scenario was presented as Example 4 (“New meaning attributed to acquired data”) in a later set of discussion material (see August 15, 2013 and page 149).

The broad and narrow approaches were referred to again by Ms. Campsall in an email of June 27, 2013, and the explanation of these two approaches appears in an out-of-order document entitled “Considerations for Diagnostic Methods”, dated June 23, 2013, and bearing the initials “KC”.  This document indicates that taking the “broad approach” will result in most diagnostic method claims being statutory.  Under “Approaches” we find the following:


(page 42)

The alternative “narrow approach” – said to be undertaken “when an examiner seeks a deeper understanding” – leads to a conclusion of non-statutory subject matter when the solution resides in new meaning for data:


(page 42)

The Fly notes that it is quite untenable that claim interpretation should hinge on an examiner’s desired level of understanding.  The requirement for a new “step needed to acquire the data” is very much like contribution analysis. The implication that common general knowledge is the “converse” of novelty is also not exactly correct.

The conclusion to this document indicates “Thus, a determination of whether or not a claim is statutory may be influenced by which approach is preferred”:


(page 43)

Ms. Campsall sent a draft Practice Notice and Examples to Marc de Vleeshauwer on July 16, 2013, in advance of a meeting on diagnostics planned for the following week:


(page 64)

The draft Practice Notice indicated that a claim involving “first use” of a diagnostic tool or “discovery of a new physical means to acquire data” would generally result in a finding of statutory subject matter.  On the other hand, when the physical steps were part of the common general knowledge, “the method intrinsically cannot be part of the problem or its solution, and thus, cannot be essential elements of the claim”.  An excerpt appears below:


(page 66)

We see here, in 2013, much of what underpins PN2015-02, albeit not yet couched in terminology that superficially disguises the persisting contribution approach or the direct involvement of prior art; we find “first use”, “newly-discovered”, “known”, and “discovery” as considerations in the above.

Act 3: “The group discussing diagnostic methods has hit an impasse…”

A revised set of Examples was circulated by Ms. Campsall on July 25, 2013, just in advance of the planned meeting:


(page 76)

Very quickly, on July 29, 2013, it was noted by multiple individuals in attendance that an “impasse” had been reached at the meeting in the diagnostic discussion:


(page 100)

Mr. Evans attempted to clarify matters with a further question involving a new Example in which a marker indicative of one disease is later found to be indicative of another:


(pages 101-102)

Isabelle Robert, noted the conflation of subject matter eligibility and prior art issues in this Example and stated that it did not help matters.  Noting the “circular discussion at those meetings now”, she asked for the question of how to proceed to be put directly to the Commissioner:


(page 101)

Ms. Campsall provided an explanation to Mr. Vasudev in an email of July 30, 2013. Noting the impasse, she indicated that consensus had been reached for claims involving an essential physical step, but stated there was a divergence of opinion when the physical data acquisition steps were part of the “common general knowledge”:


(page 103)

Given the later misunderstanding of common general knowledge and the above suggestion that common general knowledge may simply be the converse of what is new, it is unclear exactly how the term “CGK” is being applied here.

“Chris mentioned to me that he is convinced that we don’t need to go to Sylvain for a decision…”

On August 1, 2013, the Assistant Commissioner also suggested bringing two options to the Commissioner for a decision:


(page 103)

Mr. Laporte had already admitted to Ms. Lajoie that he lacked understanding of the subject (see his email of February 13, 2013).  On what basis could such a decision be rendered?

In any case, Ms. Lajoie reported on August 6, 2013 that Mr. Evans did not believe involvement of the Commissioner was necessary:


(page 110)

This is not the last time that Mr. Evans would advise against taking the matter to the Commissioner.

In the above email, and in one sent by Ms. Campsall on August 5, 2013, we see the first suggestions that “this is a prior art issue, not a subject matter issue”.  Ms. Campsall suggested stepping away from the contentious question of statutory subject matter, and instead looking at other issues such as “inherent anticipation”:


(page 108)

This is mirrored in her comments to Mr. Vasudev on August 7, 2013:


(page 110)

Act 4: “It seems that our task here is to keep analyzing diagnostic claims until we find a reason to reject some or all of them… or until those in favour of allowing these claims give up.”

Following this suggestion, Mr. Gillen wrote to a group of Biotechnology Section Heads on August 7, 2013 noting the impasse.  He stated that “Chris [Evans], and to some extent Katrina [Campsall], are on one side of the fence and everyone else is on the other side”.  Noting the shift away from subject matter eligibility and towards the new issue of inherent anticipation, Mr. Gillen remarked that the exercise appeared to be aimed at invalidating diagnostic claims or at wearing down the resolve of those in opposition to this outcome:


(page 112)

Following this impasse, Isabelle Robert solicited input from her colleagues on August 9, 2013 (page 124), as did Shirley Arpin (page 127), and Mr. Gillen (page 125).  Mr. Gillen set out his view that neither inherent anticipation nor subject matter eligibility were concerns for the contentious Examples (see paragraph 9 below):


(page 125)

In one discussion thread, Biotechnology Examiner Maria Mill wrote to express her view that “diagnostic methods are the practical application of the correlation. You need to consider both the data acquisition step and the data analysis/correlation step”:


(page 118)

Nicholas Ohan expressed agreement with Ms. Mill’s reasoning, indicating “For me, it all comes down to Shell Oil.” (page 118).

Another commonly expressed view was that the Examples provided for discussion were somehow flawed.  Mr. Ohan noted this on August 9, 2013:


(page 128)

Robert Rymerson agreed on August 12, 2013:


(page 138)

Mr. Rymerson also pointed out the urgency of the situation later in the same email:


“Chris and Katrina are on the other side of the fence!”

Mr. Gillen agreed that the Examples were problematic.  He explained that only Mr. Evans and Ms. Campsall were of the opinion that a per se known detection step was non-essential.  He noted that Mr. Evans had drafted new Examples for the discussion of “inherent anticipation”:

2013-144 - important.PNG

(page 144)

On August 15, 2013, Ms. Campsall forwarded the revised Examples to Ms. Lajoie, who forwarded them on to the Chief of the Electrical Division, Nathalie Tremblay.


(page 148)

These examples are lengthy and appear beginning on page 149.  The titles provide useful orientation, but do not speak to the details:


Act 5: “…we are back to “contribution” and the Federal Court told us to stop doing this!”

In mid-August 2013, a draft interim notice to diagnostic examiners was prepared by Ms. Campsall, with the apparent aim of getting non-contentious patent applications moving in the examination process.  We do not appear to have the earliest version of this, but Mr. Evans provided his comments to Ms. Campsall on August 16, 2013,  and suggested using a set paragraphs, conceding that they “may still need much polishing”:


(page 159)

The focus on prior art and reference to contribution analysis are unfortunate here.  It is also curious that, in the last paragraph, examination may proceed “If the claimed diagnostic method may be credibly addressed on the basis of prior art, sufficiency, utility, or statutory subject matter defects”.  Does “credibly addressed” mean “rejected to for some other reason”?

The document prepared by Ms. Campsall and Mr. Evans was edited by Mr. Gillen on August 22, 2013, although we do not appear to have his version:


(page 162)

A subsequent email from Ms. Campsall of August 28, 2013 to Mr. de Vleeshauwer stated “I think the final draft will be closer to our document than his”:


(page 166)

Ms. Robert expressed concern about the delay on the interim guidance on August 29, 2013:


(page 167)

The revised interim guidance appears on pages 180-182, an excerpt of which is reproduced below. At this stage, contribution analysis is mentioned and the assessment relies on an examiner’s search of prior art:


(page 180)

Patent applications were to be divided into three categories:


(page 181)

The idea was apparently that all but Category 3 could proceed in examination to clear out a portion of the backlog.

The interim guidance capped examiner time for considering such to that of a “complex examination” case:


(page 181)

“…I think it is unfortunate any reference is made to contribution analysis – isn’t this completely irrelevant now?” 

The mention of contribution in the interim guidelines was noted by Mr. Ohan in an email of September 17, 2016, and excerpt of which is presented:


(page 204)

“We purposively (!) stayed away from purposive construction because that is one of the main source of disagreement.”

On September 17, 2013, Mr. de Vleeschauwer indicated that the interim guidance had stayed away from the subject of purposive construction, and reported that the discussion of interim guidance had near become protracted itself:


(page 209)

On September 18, 2013, Mr. Ohan questioned the value of the interim guidance, noting that few applications in the backlog would actually move forward in examination:


(page 219)

On September 19, Mr. de Vleeschauwer wrote to Mr. Evans and Ms. Campsall to say that direction from the Commissioner was required:


(page 231)

Mr. Evans replied, asking how Mr. Laporte could be advised without the “inherent anticipation” question being addressed:


(page 239)

Here, the notion of discretional “construction options” is troubling.

Mr. de Vleeschauwer then proposed to call the next meeting on the subject “inherent anticipation of diagnostic methods” in order to “make it a little more appealing” (page 239).

On October 4, 2013, when Ms. Campsall circulated a list of cases for a planned discussion of “reverse infringement, mere discovery or inevitable result, and of course diagnostic methods”:


Discussion at this point had apparently moved from “inherent anticipation” on to something termed “reverse infringement”, under which a later diagnostic method involving measurement of an analyte was somehow deemed to infringe an earlier-claimed method involving measurement of the same analyte to diagnose a different disease.  This apparently indicated to some that the later diagnostic may be a “mere discovery”.  Senior Patent Examiner, Xiao-ying Ma (a recipient of the above email from Ms. Campsall) explained this approach in an email of October 16, 2013, though it is clear from her other comments that she was not in support of it:


(page 249)

The example provided for this discussion was evidently the one drafted by Mr. Evans (see Mr. Gillen’s email of August 12, 2013), which appears below:


(pages 250-251)

The Fly finds a marker indicative of two diseases to be an interesting choice for discussion. Such “extreme case” examples may be useful for making philosophical points, but seem to be of rather limited real-world relevance.

Mr. Gillen replied on October 16, 2013, expressing concern about this approach, and about the persistence of contribution analysis:


(page 252)

The Examples were again criticized by Mr. Ohan and Mr. Rymerson.  Mr. Ohan wrote on October 16, 2013:



(page 254)

Mr. Rymerson agreed, and also questioned the foray into questions of infringement during examination:


(page 262)

On October 17, 2013, Xiao-Ying Ma forwarded an email from Examiner Sophie Beaudoin (pages 264), the latter pointing to a 1957 CIBA Ltd. vs. Canada decision of the Exchequer Court (27 CPR 82) in which the Court found that claims involving the reaction of known materials by known methods to make a new product were patentable.  Ms. Ma replied the same day, referencing the Calgon Carbon v. North Bay decision of the Federal Court of Appeal (2005 FCA 410) with its finding (in deference to the Supreme Court in Shell Oil) that a new use of an old method is not a “mere discovery”:


(page 264)

“It sounds like they simply do not understand Shell Oil.”

This led to a discussion of the Shell Oil decision of the Supreme Court, with Mr. Ohan expressing the opinion that the decision was not understood:


(page 266)

Mr. Ohan’s full comments on the subject (page 267) and Ms. Ma’s (page 268) are worth reading. To quote a particularly poignant passage:


(page 267)

On October 18, 2013, Mr. Gillen discussed purposive construction, stating emphatically “This is the only legal basis going forward!”  He then discussed the problem and solution approach, stating that claim elements that solve the identified problem are the ones that are essential:


(page 272)

Readers wary of “problem and solution” post-PN2015-02 must remember these comments were prior to CIPO’s problematic “building blocks” approach to diagnostics, under which diagnostic claims are said to address either a “data acquisition problem” or a “data analysis problem”, but never both.  Mr. Gillen does not hold this view, and hence the problem and solution approach was not one that necessarily read out data acquisition features.

Mr. Gillen again expressed concern about contribution analysis in brief message sent two minutes later:


(pages 277-278)

“…and hopefully we choose wisely”

Mr. Ohan agreed, but also expressed concern about “crippled” examination.  He stated that a “consistent and clear approach” was required, conceding that “The rest will have to work itself out in the courts (and hopefully we choose wisely)”:


(page 277)

Ms. Ma expressed agreement with Mr. Gillen and Mr. Ohan, and stated that the two camps construed claims differently:


(page 277)

Act 6: “Did the inventor do her own work or did she simply look at a database exploiting the work of others?”

Ms. Campsall set out her view of one example scenario in an email exchange with Ms. Ma in October, including emails of October 17 (page 289) and October 25, 2013 (page 286). It is worth reproducing the former.  The Fly notes Ms. Campsall’s concern over the question “what do you get?” from a diagnostic:


(pages 289-290)

The suggestion that databases could exploit the work of others is startling.  Does this refer to a database of public information? It is quite normal to use such information in the course of research.  Such is the nature of innovation, which does not occur in a vacuum.  The Patent Act expressly permits the patenting of improvements in Section 2 and Section 32.  Such a view would be difficult to square with the fundamental role of disclosure in the quid pro quo at the heart of the patent system.

“…I feel we are starting to discuss whether or not a diagnostic method is a patentable subject matter. We all know it is…”

Ms. Ma replied on October 18, 2013:


(page 288)

Later in this message, Ms. Ma returned to a discussion of the Calgon Carbon v. North Bay decision (2005 FCA 410).

On November 18, 2013 Mr. Evans circulated news of the U.S. District Court Ariosa decision (page 314).

Discussion in December 2013 turned to a planned update of MOPOP Chapter 17.  Josée Pharand  indicated in an email of December 9, 2013 that diagnostics were being discussed with senior management:


(page 329)

And so ends the year 2013 according to ATI.


Excerpts from 2014 Documents:


Excerpts from 2015 Documents:


Excerpts from 2015 Advice to the Deputy Minister: