Category: Amberblog

Was the outcome of the CRISPR patent dispute predictable from advanced patent analytics?

CRISPR, which is short for Clustered Regularly Interspaced Short Palindromic Repeats, are segments of DNA containing repetitive base sequences. A simple version of CRISPR, known as CRISPR/Cas9 has been modifed to allow addition or removal of genes, so editing the genome of a cell. This ability to edit a genome is a big deal, and not surprisingly was the choice of Science magazine for the Breakthrough of the Year in 2015.


Not surprisingly with such a potentially important invention, there have been disputes over ownership. In particular there has been a high profile dispute between the Broad Institute (MIT) and University of California.  The University of California had filed first, with a priority of date of May 2012 for their published application US20140068797, which is yet to be granted.

 The Broad Institute first filed a little later in December 2012, but then pushed the examination process so that the first of their patents was granted in April 2014. Since then the Broad Institute has gone onto to receieve more than 50 granted patents for this technology.

In response, the University of California launched a patent interference process to determine who was the first inventor of this technology.  Given the nature of patent litigation in the US, and the commercial value of this technology, it is more than than possibloe that several million dollars might have been spent collectively by the parties in legal fees in relation to this case.

On 15th February the USPTPO handed down its decision on this case, finding that there was no intererence-in-fact between the patents, namely US20140068797 and a group of patents filed by the Broad Institute in December 2012:

..we conclude that the parties’ claims are not drawn to the same patentable subject matter and that there is no interference-in-fact between them.

There is a 51 page judgment to this effect, and here at Ambercite we will leave ithe judgement and others to explain the reason for this.

But we were curious – what would advanced patent analytics tell us about this case? 

To answer, we will use our the Family Cluster Searching patent analytics tool. This can find similar patents to one or more ‘seed patents’. Essentiallly all of the patent citaitons in the area of a patent or a group of patents are combined together to identify these similar patents. Because every patent in this area may have its own search report, this network represents the opinion of every applicatn and every examiner in this area about which individual patents are similar. 

We call it ‘Family Cluster Searching’ because each patent in our network is  in fact a family of patents. And so even a single point in the network can combine the opinions of say the PCT patent examiner, the US examiner, the EP, JP and even Chinese examiners. A lot of data is combined in this ‘collective wisdom approach, and this helps to produce a statistical robust approach. 

So what can advanced patent analytics tells us about this case?


Was the potential for ligitation predictable?

Family Cluster Searching comes with the ability to identify similar patents to one or more starting patents. To answer this question, we took the Broad Instittute patents mentioned in the litigation, and ran a search for the most similar patents.

This query looked like this:



Note that we had changed the application # 14,704,551 to its published version US2015024710 – and that we had requested the most similar 2000 patents

And what did we find?

Not suprisingly, the three most similar patents found were are filed by the Broad Institute



And this continued down to the 9th position. But in this list of 2000 patents, there are many other similar patents, such as these ones:


And this list goes all the down to position #1993



But the real question is, as hinted by the image above, is ‘does this list include the University of California patent?


To answwer this questoin run a filter for patents filed by the University of California:


Which produces this list of patents:


In fact the full list is somewhat longer than this, but at  the top is the entry WO2013176772.

This is in the same family as US20140068797, which is the  published form of the litigated patent 13/842,859. And according to this analysis, there is a total similarity score of 102.5 to the Broad Institute patents shown/ This is a relatively high figure, and suggest strong similarity between the Broad Institute patents and the University of California patent. 

So no surprises about the litigation then – they are in very similar fields. The University of California patents was the 15th most similar patent, and in fact the second most similar non-Broad patent filed, with only US9023649 filed by Harvard in December 2012 only being ranked higher 11th place, with a slightly higher score of 106.5.

Of course, this is a bit of a ‘so-what’ analysis – a number of different pathways would have produced a similar outcome, including the litigation history itself. But – this analysis was quick and simple, and so a useful example of the potential of patent analysis to at least identify the potential for litigation (or licensing), based on patent numbers alone. This can reduce the time and cost needed for other, more time-consuming and expensive forms of analyis

So who else filed the most similar non-Broad Institute patents?

To answer this question, we can filter out the Broad patents:



Which leads to the following list:



So a big range of applicants. From these results as a whole, we can make a range of analysis

Who has the most commercially similar patent portfolio?


We can predict this from our Licensing Potential metric, again which is based on the Broad Institute patents listed in the ligitation:



Sangemo Therapeutics describes itself as “Developing the most advanced and precise genomic medicines“, while Arbustus Biopharma is primarily focused on Hepatitus B, that is also  developing a pipeline of Non-HBV Assets that leverage our expertise in RNA interference (RNAi) therapeutics

Perhaps what is most surprising is that the the patents belonging to the University of California have a comparably low Licensing Potential compare to some other companies.

We should note that this analysis, like any analysis, is limited by the assumptions used. In this case one of the key assumptions is that the Broad Institute portfolio is the patents listed in the litigation. These were all the early patents filed by the Broad Institute, and they have filed many since. Ideally we would rerun this analysis with the more recent Broad Institute patents, but such an analysis would sit outside the scope of this blog.


What are the most similar prior art patents? 

By looking for earlier priority date patents filed prior to December 2012, and say looking for patents filed after 2002 to allow for the rapid advances in this field, we would suggest that the most similar prior art patents would be:

Patent family (representative patent)





Priority date






Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription







Transgenic animals secreting proteins into milk







solation of exogenous recombinant proteins from the milk of transgenic mammals







N[ omega ,( omega -1)-dialkyloxy]- and N-[ omega ,( omega -1)-dialkenyloxy]-alk-1-yl-N,N,N-tetrasubstituted ammonium lipids and uses therefor







RNA-directed dna cleavage by the Cas9-crRNA complex







Targeted genomic modification with partially single-stranded donor molecules







CRISPr-based genome modification and regulation







Methods and compositions for delivery of biologics







Multiple domain proteins







Methods and compositions for targeted cleavage and recombination




Not surprisingly, the litigated University of California patent was at  the top of the list, but there were many others – and this is only a top 10 list. 

Note too that the list comprised a mixture of ‘Known’ and ‘Unknown’ citations. An unknown citaiton is a patent family which has never been cited against the patent family being examined. While not all unknown citations in a Family Cluster search are relevant, many are


Next steps?

This is what we could learn from just Family Cluster Search. Just like any other searching system, we recommend running a range of different queries to end up a range of different results – you may be suprised what you can find. 

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Citations vs Citations – How to get an accurate list of forward and backward citations – and without double counting


Patent citations and citation data is available from a number of different sources. But how reliable is this data? Are citation links double counted? What about the effect of family members?

In this blog we look at these questions and compare the Ambercite approach to some other well known databases – and show how Ambercite can give both more direct citation links that these other sources – and yet avoid the errors and extra time caused by the double counting of citations links seen in these other database.


Patent citations are increasingly being recognised as a key set of data for a patent. Many people judge the quality of a patent by its forward citation count, while backward citations are carefully reviewed to see if the patent is truly valid. Reviewing forward citations can help identify monetization options. And reviewing both can quickly help similar patents to relevant patents you have found.

In addition, the Ambercite patent search tool Cluster Searching goes one step further and uses citation data to find similar patents not already listed as citations, and then all ranking all citations found.

Given this importance of patent citations, you would think that there would be some sort of agreement of what the citations are for a given patent.

One would think that, but the reality is there can be a surprising range of opinions, depending on the patent database you use.

To demonstrate this , we have prepared four cases studies for some represenative patents, both US and non-US.  We have chosen an older patent as this would have been around long enough to accumulate a reasonable number of citations.


Case study #1 – US granted patent, filed by US applicant.

The first patent to be considered is US6212066, filed by Apple in 1999 for a Portable computer with removable keyboard.


I looked up this patent in the following range of patent databases, and recorded the prior art and forward citations. For these citations, we also recorded if the citation was a US record or an international record

The databases we looked at were:

  • Ambercite Cluster Searching
  • Google Patent
  • Espacenet
  • Patentlens

The results are shown in the table below. The number of prior art citations is consistent at 9 from every data source.  But the number of forward citations ranged from 35 up to 63.

Known citation search based on US6212066

Ambercite Cluster Searching

Google Patent




# of prior at citations (number of non-US citations)

9 (0)



9 (0)

9 (0)

# of forward citations (number of non-Us)


63 (5)

46 (1)

63 (5)

35 (0)


So what is causing this big variation in forward citation count?

There are two factors affecting the number of citations shown in this example:

1) The first factor is the jurisdictions of the citations found.  The USPTO database shows backward citations to other jurisdictions, but not forward ciations.  In contrast, the remaining databases do show citation connections to patents in other jurisdictions.

As an example of the effect of this, the forward citations CN10220082, filed for a Notebook computer with detachable keyboard and movable host. This was identified as a forward citaiton by Cluster Searching, Google, Espacenet and Patentlens, but not by the USPTO.

2) The second factor is the concept of a ‘patent’ record. Google, Patent Lens and sometimes Espacenet treat a patent application and its granted version as being separate records – but self-evidently they are the same patent. So for example Google lists US patent application 20080030934 amd US7643278 as being separate records, but in fact the second patent is the granted form of the first patent. 

Ambercite Cluster Searching goes further. The data is this database is further deduplicated by combining all of the members of a EPO “simple family” (a group of patent sharing the same priority documents) into a single record. We do this because we believe that this leads to a higher quality of analysis by avoiding counting the same invention (because a simple family is one invention) more than once. 

This can have a surprising impact on the results. For example, in the Espacenet results the forward citations W02014164470 and US9229486 are counted as separate records. But in fact they are not – the are simply different members of the same patent family.

This can also affect the number of non-US patents shown. For example, the Google patent forward citations includes the record EP2631753 – but the Ambercite data does not recognise this is as a separate records as this is in the same patent family as US9025323, which is in the list of Ambercite forward citations. Ambercite is very careful to avoid double counting – thereby providing more accurate records as well as removing the need to review what turn out to be seperate members of the same patent family

Of interest though, neither the family member US9025323 or its application number US20130222993 are recognised as forward ciations in the Google list. 

So this is one example of how different patent databases can give different citation records from a given patent, in this case from a US patent filed by a US company.


Case study #2 – US granted patent, filed by non-US applicant

But what a US patent filed by a non-US applicant, for example a Japanese company?  The next example is US6520045 which was filed by Toyota in 2001 for a the arrangement of pedals in a car. 


Of note, this patent has other family members filed in Japan and Germany.

We will apply the same analysis as before:

Known citation search based on US6520045

Ambercite Cluster Searching

Google Patent




# of prior art citations (number of non-US citations)

9 (1)

10 (0)

10 (1)


10 (1)

# of forward citations (number of non-US citations)

28 (8)

26 (0)

11 (4)

27 (1)

10 (0)


Again we see big differences, and in some cases for the same reasons as before. But in this data, we see an additional factor come in.

This third factor is that the Ambercite results include a much higher number of non-US forward citations. An example of such a citation is DE202005004272, filed for a Adjustable position pedal mechanism for motor vehicle… This patent is not found in the list of Google forward citations, for example, because it is a forward citation in fact from the German family member of the Toyota patent.

There are similar reasons for the other additional non-US citations found in the Ambercite data, including patents filed in China,Korea and Japan.


Case study #3 – Patent families without US family members 

What if a patent family has no US family members? An example of this, consider EP0741529B1, filed by Adidas in 1995 for a Elastomer midsole shoe structure.



This has recognised family members in Australia and Germany, a WO patent application, but no US family member.  Its citation count from different databases is shown below:

Known citation search based on EP0741529B1

Ambercite Cluster Searching

Google Patent



# of prior art citations


None listed



# of forward citations


None listed



The * on the backwards citation count is because if you were search in Espacenet for patents linked to the patent application EP0741529 A1, it would have 8 backward citations. But no forward citations. 

So in this case, Ambercite provides citation links unavailable from these other databases.


Case study #4 – Patent families with US family members, but from the perspective of  non-US patents 

The final example concerns a patent family with a combination of US and non-US family members  – but this time from the perspective of a non-US family member. We might choose EP0879230, filed by GlaxoSmithKline for a Optically Active Phenyl Pyrimidine Derivative As Analgesic Agent.



Known ciitation search based on EP0879230B1

Ambercite Cluster Searching

Google Patent



# of prior art citations


None listed



# of forward citations


None listed




So again a big difference between the Ambercite results, and those available from the data sources. 

I should note that, for example, if we instead looked the granted US family member US6124308 Espacenet would show 3 backward citations (2 in one patent family) and 7 forward citations. This is useful to know – but not as useful, if for example you are one of our many clients who use Cluster Searching outside of the US, as being able to run such a search from any family member and end up with the same result, regardless of the family member searched on. 


Discussion – Confirming the benefits of the Ambercite approach

These are some great case studies of the benefits of the Ambercite approach to finding citatons, namely that

  • It finds citations missed by other services, particuarly non-Us citaitons 
  • It does so without double counting citations, providing more accurate citations counts and avoiding the need to review the same patent family more than once – saving you time
  • It can be searched from any family member.

Also, unlike these other services the Ambercite citaitons are ranked in terms of order of likely similarity.

But this is regarding direct citaitons, or as we like to say ‘known citations’ because in theory these citations are known to other databases – although this example shows that this is not always the case. 

Ambercite also, within the same results, also supplies a long list of ‘unknown’ or indirect citaitons, and these can also be highly relevant. And again these unknown citations  also have exactly the same benefits as above,

All of which can improve the results of your patent searching while reducing the time spent on it


I should note that this blog was catalysed by a comment by a contact along the lines of ‘I can get citation data in other sources‘. Hopefully this blog has instead shown you that is not always the case, not by a long way in some of the above case studies. 


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How much money can Family Cluster Searching save you?

Patent searchers have many options for patent searching, including a number of free patent search databases, or they already have subscription to other patent search databases. Given this, why should you invest in a subscription to Ambercite Family Cluster Searching

There are many good reasons for this – all which add up to significant cost savings for your organisation. These cost savings include:

  1. Saving valuable time spent on patent searching
  2. Finding otherwise hidden patents that can save your organisation signficant amounts of money in project and legal costs
  3. Avoiding outsourcing patent searching
  4. Corporate cost savings from running more searches prior to projects and patent filings,  since they are more cost effective
  5. Reducing subscriptions to other patent search databases


1) Saving valuable time spent on patent searching

Even if using a free search engine, a patent search using conventional processes can take a lot of time, firstly to formulate the query, and then review what could be hundreds of relevant results. Your time is not free – most patent searchers work in environments where they are expected to deliver something for a fixed budget.

In contrast, a Family Cluster Search can take seconds to run, and because the results are ranked for relevancy, can be reviewed in minutes. This can save you hours and hours of searching time saved, up to 90% of the total search time in some cases.  Or in the words of our users:

I can not appreciate how much work and time this program has saved us. Its capability to analyse all possible relevant patents in accordance to timeline, key words and other means are a great filtering tool. The degree of relevance highlighted by the thickness and type of arrows are even more helpful in eventually pinpointing a possible IP area to target the new technology”. – Kishan Nawzidh, Monash University

“Ambercite is a leap forward in efficiency and organization. I work very fast, through a number of patents with this platform, and it has significantly improved my patent research workflow. … Thank you for giving me the gift of time.” – Mark Hunter, M.D.,Director of Gynecologic Oncology, Ellis Fischel Cancer Center, University of Missouri

The top ranked patent, USxxxxxxx, was very good because it found an element that is hard to search for, i.e. ‘independent power settings’.  The ‘independent power settings’ are hard to search for because searching for something like “power near2 settings” would return several thousand hits ….  And it’s amazing that it came up first in your search…”  – Patent Examiner of a world leading patent office.

“I was able to uncover significantly more patents that were relevant to my topic, … much more quickly than when compared to a text based site.  I found the graphical representation very intuitive and easy to use.  It also opened up relevant areas that I would not have otherwise considered. – Mechanical Engineering Consultant, for a new product engineering company.

In just a few minutes I was able to find several relevant documents additional to International Search Reports”. Mr. Tudor Jovmir, Patent examiner

“I spent two days looking for a relevant patent for a client using a conventional search. The second patent took me 30 minutes to find with AmberScope” – R.W., Patent Attorney.


2) Finding otherwise hidden patents that can save your organisation signficant amounts of money in project and legal costs

The unique algorithms in Family Cluster Searching can find patents missed by conventional techniques – would this help your project?

A fantastic tool for technical/IP folk in terms of opportunity finding and to establish the landscape”. IP manager, global manufacturing company.

In 33% of our test cases with AmberScope we were able to find ‘X’ citations, i.e. patents highly relevant to novelty, that we did not find through any other search process we applied. Patent office.

“I was able to find a patent I had not seen before, even after 20 years in the technical area” – G.S, Patent Attorney

“I was looking for a prior art patent to invalidate a granted patent that was blocking a client’s product coming to market. I had tried a conventional patent search, and even a conventional citation search, but without luck. So I ran the search in AmberScope – and .. was able to find a prior art patent that essentially discloses the blocking patent. My client is now in a much better position to bring a product to market..” Gennaro Simonetta – Patent attorney, IP consultant – Griffith Hack

My role is more directly analyzing patents including claims, infringement and prior art. AmberScope appears exceptional for identifying prior art from anything else I’ve seen.” – Paul Morinville, CEO at OrgStructure, US


3) Avoiding outsourcing patent searching

Yes, there are some very low cost patent searcher out there, but the payment is only part of the cost. It takes time to instruct outsourced searchers, and time to review the results, and all of this time costs money.

But there is an additional cost to oursourcing. Outsourcing inevitably involves a delay – which means putting down the file, and picking up it again at a later date, and refreshing your memory. Maybe it would be easier to deal with the matter immediately.


4) Corporate cost savings of running more searches,  since they are more cost effective

All of these costs mean that sometimes patents searches are avoided when perhaps they could have been done – and could have found patents that might have had a real impact on projects, perhaps avoiding an expensive project when the prior art was not found, or avoiding filing a patent for the same reason.


5) Reducing subscriptions to other patent search databases

We actually encourage our users to use Ambercite along other patent search engines – a hybrid approach can be very effective.  And we know that many of our users do use a variety of search databases. However given the speed and unique of Cluster Searching, it might be possible to reduce your overall expenditure of patent search databases if you replace some of the seats on other patent search database with access to Cluster Searching. 



So there is the potential for significant cost savings when using Ambercite Cluster Searching, and this is Ambercite why developed this tool in the first place – because an associated patent law firm recognised the need to improve on current search processes. Cluster Searching is available for corporate or individual subscriptions at very competitive annual packages, much more cost effective than some other, more conventional patent search databases that we are aware of. API options are also available. 

Please contact us for further details of these subscription packages, and you too can be on your way to achieving these significant cost savings. 


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