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__NOTOC__
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==Sample of the RNAi Database Dashboard==
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===1. [[#Intellectual Property (IP) Services|Intellectual Property(IP) Services]]===
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[http://client.dolcera.com/dashboard/dashboard.html?workfile_id=587 RNAi Database]
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===2. [[#Business and Information Research Services|Business and Information Research Services]]===
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===3. [[#Dolcera Technology Platform|Dolcera Technology Platform]]===
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== Intellectual Property (IP) Services ==
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==Overview==
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{| style="border:1px solid #AAA; background:#E9E9E9;width:100%" align="center"
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|-
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! style="background:lightgrey;width:50%" valign = "top" |
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===Life Sciences and Chemistry===
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! style="background:lightgrey;width:50%" valign = "top" |
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===Technology===
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|-
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=== Landscape reports ===
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* [[Alopecia - Hair Loss]] | ([http://www.youtube.com/watch?v=jAIoyKuKQ6o Video])
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* [[Inflammation and cardiovascular drugs]]
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* [[Hormone Sensitive Lipase]]
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* [[RNA Interference]]
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* [[RNAi Database sample wiki]]
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* [[Choline Bitartarate]]
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* [[Non-wovens]]
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* [[Pressure sensitive adhesives]] | ([http://www.youtube.com/watch?v=plP3TzjYsiQ Video])
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* [[Ureteral Stent]]
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* [[Smart miniature drug delivery systems]]
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* [[Silicone Hydrogel contact lens]]
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* [[Bio-fuels database sample wiki]]
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* [[SC Johnson]]
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| valign = "top" |
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=== Landscape Reports ===
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[[Image:rnai1.jpg|250 px|right|thumb|RNA Interference [http://www.sciencemag.org/feature/e-market/prodlink/qiasihp.jpg Source]]]
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* [[Hybrid Electric Vehicle Battery System]]
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* [[Supply Chain RFID Applications]]
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* [[Insurance sector]]
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* [[CDMA Basics]]
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* [[Quality of Service on CDMA platforms]]
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* [[OLED - Organic Light Emitting Diode]]
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* [[Carbon Nanotubes (CNT)]]
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* [[Metallic and Ceramic construction materials]]
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* [[Transactional memory]]
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* [[Invalidation Search on a patent in the semiconductors space]]
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|-
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| valign = "top" |
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=== Licensing ===
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* '''RNA interference (RNAi)''', is a technique in which exogenous, double-stranded RNAs (dsRNAs) that are complimentary to known mRNAs, are introduced into a cell to specifically destroy that particular mRNA, thereby diminishing or abolishing gene expression.
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* [[Environment Friendly Technology to Replace Cadmium Coatings]]
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* This technology considerably bolsters functional genomics to aid in the identification of novel genes involved in disease processes and thus can be used for medicament and for delivery as therapeutics. [http://www.bmj.com/cgi/content/full/328/7450/1245 Source]
 +
* RNA interference was known by other names, including post transcriptional gene silencing and quelling. [http://en.wikipedia.org/wiki/RNA_interference Source]
  
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===STN Search Reports===
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===Effector RNA molecules===
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* [[Markush Search Report]]
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RNAi pathways are guided by small RNAs that include
  
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=== Dashboard ===
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'''SiRNA:'''
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* [http://client.dolcera.com/dashboard/dashboard.html?workfilegroup_id=10 Alopecia areata dashboard - live]
+
* Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of 20-25 nucleotide-long double-stranded RNA molecules.  
−
** ([[Alopecia Areata Dashboard Screenshots|Screenshots only]])  
+
* SiRNAs can also be exogenously (artificially) introduced into cells by various transfection methods to bring about the specific knockdown of a gene of interest. [http://en.wikipedia.org/wiki/SiRNA Source]
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* [http://www.dolcera.com/ipmapdemo/stent_model.swf Stent dashboard]
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* [http://www.dolcera.com/website/demos/dna/main.html Sequence dashboard]
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* [[Legal Updates Demo|Legal updates dashboard]]
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* [http://client.dolcera.com/dashboard/dashboard.html?workfile_id=587 RNAi Dashboard]
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| valign = "top" |
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=== Dashboard ===
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'''miRNA:'''
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* [http://client.dolcera.com/dashboard/dashboard.html?workfilegroup_id=27 Automotive dashboard - live]
+
* microRNAs (miRNA) are single-stranded RNA molecules of about 21–23 nucleotides in length, which regulate gene expression.  
−
** [[Automotive Dashboard Screenshots|Screenshots only]]
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* miRNAs are encoded by genes from whose DNA they are transcribed but miRNAs are not translated into protein (non-coding RNA); instead each primary transcript (a pri-miRNA) is processed into a short stem-loop structure called a pre-miRNA and finally into a functional miRNA.
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* [http://client.dolcera.com/dashboard/dashboard.html?workfile_id=54 WiMAX dashboard - live]
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* Mature miRNA molecules are partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to down-regulate gene expression. [http://en.wikipedia.org/wiki/MicroRNA Source]
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** [[WiMAX Dashboard Screenshots|Screenshots only]]
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* [http://www.dolcera.com/ipmapdemo/rfid_model.swf RFID dashboard]
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−
|-
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| valign = "top" |
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=== Prior Art / Invalidation / FTO Search ===
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'''shRNA:'''
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* [http://dolcera.com/client/d8r3/hairloss_map.htm Alopecia/Hair loss IPMap]
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* A small hairpin RNA or short hairpin RNA (shRNA) is a sequence of RNA that makes a tight hairpin turn that can be used to silence gene expression via RNA interference.
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* [[Markush Structure Search Sample]]
+
shRNA uses a vector introduced into cells and utilizes the U6 promoter to ensure that the shRNA is always expressed. This vector is usually passed on to daughter cells, allowing the gene silencing to be inherited.
−
==== Study: In re Bilski Impact ====
+
The shRNA hairpin structure is cleaved by the cellular machinery into siRNA, which is then bound to the RNA-induced silencing complex (RISC). This complex binds to and cleaves mRNAs which match the siRNA that is bound to it. [http://en.wikipedia.org/wiki/Small_hairpin_RNA Source]
−
* [[In re Bilski Impact assessed from US PAIR Information]]
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| valign = "top" |
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=== Prior Art / Invalidation / FTO Search ===
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'''Others:'''
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* [http://www.dolcera.com/ipmapdemo/satellite_antenna/ipmap.html Satellite Antenna IPMap]
+
* In addition to miRNAs and siRNAs, other innate RNAi effectors have been identified.
−
* [http://www.dolcera.com/ipmapdemo/rfid/ipmap.html RFID IPMap]
+
** One class of these is the Piwi-interacting RNAs (piRNAs). piRNAs seem to be uniquely expressed in the mammalian germline, particularly in the testes. The functional role of piRNAs is currently unclear, but a role in spermatogenesis is likely.  
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* [http://www.dolcera.com/ipmapdemo/multimodal_apps/ipmap.html Multimodal Applications IPMap]
+
** A number of other small RNAs associated with RNAi have been identified in different species, including trans-activating siRNAs (tasiRNAs), studied in plants and nematodes, and small scan RNAs (ScnRNAs), found in Tetrahymena. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genom.8.080706.092424?cookieSet=1&journalCode=genom Source]
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* [http://www.dolcera.com/ipmapdemo/Invalidation_US4825448.htm Invalidation Claim Map Sample]
+
 
−
|-
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==Cellular Mechanism==
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|}
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 +
'''The RNA interference pathway:''' Long double-stranded RNA (dsRNA) or small hairpin RNA (shRNA) is processed by Dicer to form a small interfering RNA (siRNA), which associates with RNA-induced silencing protein complex (RISC) and mediates target sequence specificity for subsequent mRNA cleavage leading to gene silencing.
 +
 
 +
[[Image:mech1.jpg|450 px|center|thumb|RNA Interference mechanism [http://arthritis-research.com/content/figures/ar1168-1.jpg Source]]]
 +
 
 +
==Cancer specific Targets==
 +
[[Image:genes1.jpg|700px|center|thumb|'''Cancer specific Targets [http://journals.prous.com/journals/servlet/xmlxsl/pk_journals.xml_summaryn_pr?p_JournalId=3&p_RefId=985937 '''Source]]]
 +
 
 +
=='''Intellectual property'''==
 +
 
 +
=== Search Strategy===
 +
 
 +
Effective search strategy ensures that all key words covering the technology are adequately covered. IPC class limitations help in removing the unwanted patents.
  
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===Clinical Trial Database===
+
The search strategy was employed to extract patents disclosing  RNAi agents against disease causing target genes. Table below summarizes an exemplary search strategy used to extract patents for BCL2, a target gene for curing cancer.
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*[[Clinical Trial Database]]
+
  
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== Business and Information Research Services ==
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{|border="2" cellspacing="0" cellpadding="4" width="100%"
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{| style="border:1px solid #AAA; background:#E9E9E9;width:100%" align="center"
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|align = "center" bgcolor = "#CCFFCC"|'''S.No.'''
 +
|align = "center" bgcolor = "#CCFFCC"|'''Concept'''
 +
|align = "center" bgcolor = "#CCFFCC"|'''Search scope'''
 +
|align = "center" bgcolor = "#CCFFCC"|'''Query'''
 +
|align = "center" bgcolor = "#CCFFCC"|'''No. of Hits'''
 
|-
 
|-
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! style="background:lightgrey" valign=top width=50%|  
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|align = "center" bgcolor = "#CCFFCC"|'''1'''
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===Life Sciences and Chemistry===
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|align = "center"|RNAi
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! style="background:lightgrey" valign=top width=50%|
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|align = "center"|Claims,Title, Abstract
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===Technology===
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|align = "center"|(siRNA<nowiki>*</nowiki>1 OR (short ADJ1 interfering ADJ1 RNA<nowiki>*</nowiki>1) OR (short ADJ1 interfering ADJ1 nucleic ADJ1 acid<nowiki>*</nowiki>1) OR (short ADJ1 interfering ADJ1 NA<nowiki>*</nowiki>1) OR siNA OR siNAs OR (si ADJ1 RNA<nowiki>*</nowiki>1) OR (Small adj1 interfering adj1 RNA<nowiki>*</nowiki>)OR miRNA or (microRNA<nowiki>*</nowiki> or micro adj1 RNA<nowiki>*</nowiki>)OR shRNA or (small adj1 hairpin adj1 RNA<nowiki>*</nowiki>)OR piRNA or (Piwi adj1 interacting adj1 RNA<nowiki>*</nowiki>)OR tasiRNAs or (trans adj1 activating adj1 siRNA<nowiki>*</nowiki>) OR ScnRNAs or (small adj1 scan adj1 RNA<nowiki>*</nowiki>)OR RNAi or(RNA adj1 interference))
 +
|align = "center"|12729
 
|-
 
|-
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| valign=top |
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|align = "center" bgcolor = "#CCFFCC"|'''2'''
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* [[Diabetes products and services]]
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|align = "center"|IPC
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* [[Osteoporosis]]
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|align = "center"|
−
* [[Oral Diabetes Drugs]]
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|align = "center"|a61k or c12q or c12n or c07k or c07h
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* [[Ureteral Stent]]
+
|align = "center"|1688146
−
* [[Premium Coffee Consumers Market Segmentation|Premium Coffee - Market Positioning]]
+
−
* [[Dolcera's Poster on Industrial Biotechnology|Industrial biotechnology]]
+
−
* [[OTC products for acne treatment]]
+
−
* [[Botox - from Medical Procedure to Household Word]]
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| valign=top |
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* [[4G wireless technology developments]]
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* [[HDTV in the US]]
+
−
* [http://www.dolcera.com/ipmapdemo/innovation_explorer/innovation_explorer.html Household robotics Innovation Explorer]
+
−
* [[Web video]]
+
−
* [[OLED Mobile Phones Market Research and Analysis Report]] | ([http://www.viddler.com/explore/dolcera/videos/6/ Video])
+
−
* [[Virtualization]]
+
−
* [[Cloud Computing]]
+
−
* [[Estimation of liquid carrying vehicles in USA]]
+
−
* [[A market study on Hybrid vehicles and the concept of V2G]]
+
 
|-
 
|-
−
! style="background:lightgrey" valign=top colspan=2 |
+
|align = "center" bgcolor = "#CCFFCC"|'''3'''
 +
|align = "center"|'''BCL2'''
 +
|align = "center"|Full Patent Spec
 +
|align = "center"|(Bcl2 OR (Bcell ADJ1 CLL) OR (Bcell ADJ1 Lymphoma2 ) OR DKFZp781P2092) and Current IPC-R a61k or c12q or c12n or c07k or c07h
 +
|align = "center"|3890
 +
|-
 +
|align = "center" bgcolor = "#CCFFCC" rowspan = "2"|'''4'''
 +
|align = "center" rowspan = "2"|BCL2 <nowiki>+</nowiki> RNAi <nowiki>+</nowiki>IPC
 +
|align = "center" rowspan = "2"|
 +
|align = "center" rowspan = "2"|'''1 AND 3'''
 +
|align = "center" rowspan = "2"|'''633<br>(293 unique records)'''
  
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===Finance===
 
 
|-
 
|-
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| valign=top colspan=2 |
 
−
* [[Innovative personal finance products]]
 
−
* [[Life Insurance Industry in US]]
 
 
|}
 
|}
  
−
== Dolcera Technology Platform ==
+
==Interactive Taxonomy==
−
{| style="border:1px solid #AAA; background:#E9E9E9;width:100%" align="center"
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−
|-
+
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| align = "top" |
+
−
==== IP and Products dashboard ====
+
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* [http://client.dolcera.com/dashboard/dashboard.html?workfilegroup_id=10 Alopecia areata dashboard]
+
−
* [http://www.dolcera.com/ipmapdemo/stent_model.swf Stent dashboard]
+
−
* [[Legal Updates Demo|Legal updates dashboard]]
+
−
* [http://client.dolcera.com/dashboard/dashboard.html?workfile_id=54 4G wireless product and patent dashboard]
+
  
−
==== Patent-pathway mapping ====
+
Grouping specific elements into more general categories is conceptually easier and cleaner than is entertaining hundreds of specific elements separately. We categorize the information from analyzed patents and scientific literate into four levels of taxonomy which allow both “bird’s-eye view” and “in-depth views” of  scientific technologies.
−
* [[Inflammation and cardiovascular drugs#Interactive signaling pathways and patents|Patent-pathway mapping]]
+
−
==== Sequence dashboard ====
+
−
* [http://www.dolcera.com/website/demos/dna/main.html Sequence dashboard]
+
  
−
==== Design analysis ====
 
−
* [http://www.dolcera.com/website/demos/dental/main.html Dental Implant Design Analysis]
 
  
−
==== Innovation explorer ====
+
[[Image:tax2.jpg|800px|center|thumb| '''Interactive Taxonomy''']]
−
* [http://www.dolcera.com/ipmapdemo/innovation_explorer/innovation_explorer.html Household robotics innovation explorer]
+
−
==== KPort ====
+
−
* [http://dolcera.com/website/demos/kport/main.html Collaboration Portal]
+
  
−
|-
+
=='''Top Players and Patenting Activity'''==
−
|}
+
 
 +
[[Image:bcl2.jpg|800px|center|thumb| '''Bcl-2''']]
 +
 
 +
==RNAi Database Dashboard==
 +
 
 +
RNAi database dashboard:
 +
 
 +
*Categorize and organize large sets of product, patent, and scientific literature
 +
*Analyze client’s competitive position and that of key competitors
 +
*Identify licensing opportunities
 +
*Make build-vs.-buy decisions in new product areas
 +
*Predict product features based on technology and market trends
 +
 
 +
 
 +
 
 +
[[Image:dash1.jpg|1000px|center|thumb| '''Patent Dashboard''']]
 +
 
 +
==RNAi Sequence Dashboard==
 +
 
 +
Sequence dashboard allows comparison of siRNA agents extracted from patents and scientific literature to the consensus sequence. Since not all the documents disclose the target sequence, the consensus sequence has to be identified and used for sequence dashboard. For example for Bcl-2, consensus sequence is retrieved from NCBI having seq. id [http://www.ncbi.nlm.nih.gov/nuccore/179370 '''M14745'''].
 +
 
 +
The dashboard also depicts the associated information with RNAi agent on the click of your mouse such as patent number, patent title, length of RNAi agent (siRNA), identity score etc.
 +
 
 +
[[Image:seq1.jpg|1000px|center|thumb| '''Sequence Dashboard''']]
 +
 
 +
==Experimental data comparison matrix==
 +
 
 +
Experimental data may be qualitative or quantitative, each being appropriate for different investigations.
 +
 
 +
 
 +
Quantitative data  was captured from following RNAi experiments for patent focusing on therapeutic application and compared.
 +
 
 +
*  % inhibition of target mRNA expression
 +
*  % encapsulation efficiency
 +
*  % transfection efficiency
 +
*  % tumor volume reduction
 +
*  % cell count reduction
  
−
=== Dolcera Offerings summary ===
+
More such comparison matrix can be prepared for patent having varied focus such as on delivery vehicle, nature of RNAi agents, target gene source, system used to test RNAi etc.
−
* [[Dolcera Offerings|Dolcera offerings summary]]
+
  
−
=== [[Technology Support]] ===
+
==='''Patent Focus- Therapeutic Application'''===  
  
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==<span style="color:#C41E3A">Like any of these sample reports?</span>==
+
{|border="2" cellspacing="0" cellpadding="4" width="100%"
−
<p align="center"> '''These are sample reports with brief analysis''' <br>
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|align = "center" bgcolor = "#C0C0C0" rowspan = "2"|'''Sr. No.'''
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'''Dolcera can provide a comprehensive report customized to your needs'''</p>
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|align = "center" bgcolor = "#C0C0C0" rowspan = "2"|'''Patent/Publication No.'''
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{|border="2" cellspacing="0" cellpadding="4" align="center" "
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|align = "center" bgcolor = "#FFCC99" colspan = "2"|'''Target gene'''
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|style="background:lightgrey" align = "center" colspan = "3"|'''[mailto:info@dolcera.com <span style="color:#0047AB">Buy the customized report from Dolcera</span>]'''  
+
|align = "center" bgcolor = "#FF99CC" colspan = "7"|'''Experimental Details'''
 +
|align = "center" bgcolor = "#99CCFF" rowspan = "2"|'''RANK'''
 
|-
 
|-
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| align = "center"| [http://www.dolcera.com/website_prod/services/ip-patent-analytics-services Patent Analytics Services]
+
|align = "center" bgcolor = "#FFCC99"|'''BCL-2'''
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|align = "center"| [http://www.dolcera.com/website_prod/services/business-research-services Market Research Services]
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|align = "center" bgcolor = "#FFCC99"|'''Others'''
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|align = "center"| [http://www.dolcera.com/website_prod/tools/patent-dashboard Purchase Patent Dashboard]
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|align = "center" bgcolor = "#99CC00"|<font color="#000000">'''Test Model'''</font>
 +
|align = "center" bgcolor = "#99CC00"|<font color="#000000">'''Inhibition of Target mRNA Expression (%)'''</font>
 +
|align = "center" bgcolor = "#99CC00"|<font color="#000000">'''Encapsulation Efficiency'''</font>
 +
|align = "center" bgcolor = "#99CC00"|<font color="#000000">'''Transfection efficiency Increase (%)'''</font>
 +
|align = "center" bgcolor = "#99CC00"|<font color="#000000">'''Tumor Volume Reduction (%)'''</font>
 +
|align = "center" bgcolor = "#99CC00"|<font color="#000000">'''Cell Count Reduction (%)'''</font>
 +
|align = "center" bgcolor = "#99CC00"|<font color="#000000">'''Other Remarks'''</font>
 
|-
 
|-
−
|align = "center"| [http://www.dolcera.com/website_prod/services/ip-patent-analytics-services/patent-search/patent-landscapes Patent Landscape Services]
+
|align = "center" bgcolor = "#C0C0C0"|'''1'''
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|align = "center"| [http://www.dolcera.com/website_prod/research-processes Dolcera Processes]
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|align = "center"| [http://appft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PG01&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.html&r=1&f=G&l=50&s1=%2220070298056%22.PGNR.&OS=DN/20070298056&RS=DN/20070298056 US20070298056A1]
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|align = "center"| [http://www.dolcera.com/website_prod/industries Industry Focus]
+
 
 +
|align = "center"|Yes
 +
|align = "center"|
 +
|align = "center"|Human colon cancer (Caco-2) xenografts in nude mice
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center"|90.08%<br>Day 25 <br>(Fig 2)
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center" bgcolor = "#99CCFF"|'''1'''
 +
|-
 +
|align = "center" bgcolor = "#C0C0C0"|'''2'''
 +
|align = "center"| [http://appft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PG01&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.html&r=1&f=G&l=50&s1=%2220080038296%22.PGNR.&OS=DN/20080038296&RS=DN/20080038296 US20080038296A1]
 +
|align = "center"|Yes
 +
|align = "center"|
 +
|align = "center"|In vivo (Mice)
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center"|61.29%<br>Day 13<br>(Fig 3)
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center" bgcolor = "#99CCFF"|'''2'''
 +
|-
 +
|align = "center" bgcolor = "#C0C0C0"|'''3'''
 +
|align = "center"| [http://appft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PG01&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.html&r=1&f=G&l=50&s1=%2220070258952%22.PGNR.&OS=DN/20070258952&RS=DN/20070258952 US20070258952A1]
 +
|align = "center"|Yes
 +
|align = "center"|
 +
|align = "center"|Human pancreatic carcinoma H79 xenografts
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center"|49.23%<br>Day 25<br>(Fig 4)
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center" bgcolor = "#99CCFF"|'''2'''
 
|-
 
|-
−
|align = "center"| [http://www.dolcera.com/website_prod/services/ip-patent-analytics-services/patent-search/patent-landscapes Patent Search Services]
+
|align = "center" bgcolor = "#C0C0C0"|'''4'''
−
|align = "center"| [http://www.dolcera.com/website_prod/services/ip-patent-analytics-services/alerts-and-updates Patent Alerting Services]
+
|align = "center"| [http://appft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PG01&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.html&r=1&f=G&l=50&s1=%2220070172847%22.PGNR.&OS=DN/20070172847&RS=DN/20070172847 US20070172847A1]
−
|align = "center"| [http://www.dolcera.com/website_prod/tools Dolcera Tools]
+
|align = "center"|Yes
 +
|align = "center"|  
 +
|align = "center"|Ramos cells
 +
|align = "center"|80%<br>(Fig 4. B)
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center"|No
 +
|align = "center" bgcolor = "#99CCFF"|'''2'''
 
|-
 
|-
 
|}
 
|}
−
<br>
 
  
−
----
+
'''Ranking of patents''' can be done on the basis of focus of the study, experimental data disclosed, effectiveness of RNAi agent, type of model used to test the RNAi agent, etc.
−
{| style="border:1px solid #AAA; background:#E9E9E9" align="center"
+
 
 +
Advantages:
 +
*Information disclosure wise sorting available.
 +
*Efficiency of different RNAi agent against target gene can be compared.
 +
*Different models used to test cell line and the efficiency can also be compared.
 +
 
 +
===Qualitative Data from Patent Documents===
 +
 
 +
Experiments yielding qualitative  data, mentioned below, can’t be compared but are equally important. We did not miss them!
 +
 
 +
* Gel electrophoresis
 +
* Gel blots
 +
* Tissue section* Cell staining
 +
* RNAi agent construction
 +
 
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{|border="2" cellspacing="0" cellpadding="4" width="100%"
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|align = "center" bgcolor = "#C0C0C0"|'''Patent/ Publication No.'''
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|align = "center" bgcolor = "#FFCC99"|'''Gel blots'''
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|align = "center" bgcolor = "#FFCC99"|'''Gel Electrophorosis'''
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|align = "center" bgcolor = "#FFCC99"|'''Tissue section micrograph'''
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|align = "center" bgcolor = "#FFCC99"|'''Cell staining micrograph'''
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|align = "center" bgcolor = "#FFCC99"|'''RNAi Agent Construction'''
 
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! style="background:lightgrey" | Contact Dolcera
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|align = "center" bgcolor = "#C0C0C0"|'''US20080021205A1'''
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|align = "center" bgcolor = "#C0C0C0"|Yes
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|align = "center" bgcolor = "#C0C0C0"|Yes
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! style="background:lightgrey" | Samir Raiyani
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|align = "center" bgcolor = "#C0C0C0"|'''US20070275465A1'''
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|align = "center" bgcolor = "#C0C0C0"|Yes
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| '''Email''': [mailto:info@dolcera.com info@dolcera.com]
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|align = "center" bgcolor = "#C0C0C0"|'''WO2007013575A2'''
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|align = "center" bgcolor = "#C0C0C0"|Yes
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|align = "center" bgcolor = "#C0C0C0"|Yes
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| '''Phone''': +1-650-269-7952, +91-40-2355-3493
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|align = "center" bgcolor = "#C0C0C0"|'''US20070081982A1'''
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|align = "center" bgcolor = "#C0C0C0"|Yes
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|-
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|align = "center" bgcolor = "#C0C0C0"|'''WO2007013575A2'''
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|align = "center" bgcolor = "#C0C0C0"|Yes
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|align = "center" bgcolor = "#C0C0C0"|Yes
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|align = "center" bgcolor = "#C0C0C0"|'''US20050266561A1'''
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|align = "center" bgcolor = "#C0C0C0"|Yes
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|}                                                                                                                                                 *Mathematically incomparable data disclosed in patents

Revision as of 06:08, 13 October 2009

Sample of the RNAi Database Dashboard

RNAi Database

Overview

RNA Interference Source
  • RNA interference (RNAi), is a technique in which exogenous, double-stranded RNAs (dsRNAs) that are complimentary to known mRNAs, are introduced into a cell to specifically destroy that particular mRNA, thereby diminishing or abolishing gene expression.
  • This technology considerably bolsters functional genomics to aid in the identification of novel genes involved in disease processes and thus can be used for medicament and for delivery as therapeutics. Source
  • RNA interference was known by other names, including post transcriptional gene silencing and quelling. Source

Effector RNA molecules

RNAi pathways are guided by small RNAs that include

SiRNA:

  • Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of 20-25 nucleotide-long double-stranded RNA molecules.
  • SiRNAs can also be exogenously (artificially) introduced into cells by various transfection methods to bring about the specific knockdown of a gene of interest. Source

miRNA:

  • microRNAs (miRNA) are single-stranded RNA molecules of about 21–23 nucleotides in length, which regulate gene expression.
  • miRNAs are encoded by genes from whose DNA they are transcribed but miRNAs are not translated into protein (non-coding RNA); instead each primary transcript (a pri-miRNA) is processed into a short stem-loop structure called a pre-miRNA and finally into a functional miRNA.
  • Mature miRNA molecules are partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to down-regulate gene expression. Source

shRNA:

  • A small hairpin RNA or short hairpin RNA (shRNA) is a sequence of RNA that makes a tight hairpin turn that can be used to silence gene expression via RNA interference.

shRNA uses a vector introduced into cells and utilizes the U6 promoter to ensure that the shRNA is always expressed. This vector is usually passed on to daughter cells, allowing the gene silencing to be inherited. The shRNA hairpin structure is cleaved by the cellular machinery into siRNA, which is then bound to the RNA-induced silencing complex (RISC). This complex binds to and cleaves mRNAs which match the siRNA that is bound to it. Source

Others:

  • In addition to miRNAs and siRNAs, other innate RNAi effectors have been identified.
    • One class of these is the Piwi-interacting RNAs (piRNAs). piRNAs seem to be uniquely expressed in the mammalian germline, particularly in the testes. The functional role of piRNAs is currently unclear, but a role in spermatogenesis is likely.
    • A number of other small RNAs associated with RNAi have been identified in different species, including trans-activating siRNAs (tasiRNAs), studied in plants and nematodes, and small scan RNAs (ScnRNAs), found in Tetrahymena. Source

Cellular Mechanism

The RNA interference pathway: Long double-stranded RNA (dsRNA) or small hairpin RNA (shRNA) is processed by Dicer to form a small interfering RNA (siRNA), which associates with RNA-induced silencing protein complex (RISC) and mediates target sequence specificity for subsequent mRNA cleavage leading to gene silencing.

RNA Interference mechanism Source

Cancer specific Targets

Cancer specific Targets Source

Intellectual property

Search Strategy

Effective search strategy ensures that all key words covering the technology are adequately covered. IPC class limitations help in removing the unwanted patents.

The search strategy was employed to extract patents disclosing RNAi agents against disease causing target genes. Table below summarizes an exemplary search strategy used to extract patents for BCL2, a target gene for curing cancer.

S.No. Concept Search scope Query No. of Hits
1 RNAi Claims,Title, Abstract (siRNA*1 OR (short ADJ1 interfering ADJ1 RNA*1) OR (short ADJ1 interfering ADJ1 nucleic ADJ1 acid*1) OR (short ADJ1 interfering ADJ1 NA*1) OR siNA OR siNAs OR (si ADJ1 RNA*1) OR (Small adj1 interfering adj1 RNA*)OR miRNA or (microRNA* or micro adj1 RNA*)OR shRNA or (small adj1 hairpin adj1 RNA*)OR piRNA or (Piwi adj1 interacting adj1 RNA*)OR tasiRNAs or (trans adj1 activating adj1 siRNA*) OR ScnRNAs or (small adj1 scan adj1 RNA*)OR RNAi or(RNA adj1 interference)) 12729
2 IPC a61k or c12q or c12n or c07k or c07h 1688146
3 BCL2 Full Patent Spec (Bcl2 OR (Bcell ADJ1 CLL) OR (Bcell ADJ1 Lymphoma2 ) OR DKFZp781P2092) and Current IPC-R a61k or c12q or c12n or c07k or c07h 3890
4 BCL2 + RNAi +IPC 1 AND 3 633
(293 unique records)

Interactive Taxonomy

Grouping specific elements into more general categories is conceptually easier and cleaner than is entertaining hundreds of specific elements separately. We categorize the information from analyzed patents and scientific literate into four levels of taxonomy which allow both “bird’s-eye view” and “in-depth views” of scientific technologies.


Interactive Taxonomy

Top Players and Patenting Activity

Bcl-2

RNAi Database Dashboard

RNAi database dashboard:

  • Categorize and organize large sets of product, patent, and scientific literature
  • Analyze client’s competitive position and that of key competitors
  • Identify licensing opportunities
  • Make build-vs.-buy decisions in new product areas
  • Predict product features based on technology and market trends


Patent Dashboard

RNAi Sequence Dashboard

Sequence dashboard allows comparison of siRNA agents extracted from patents and scientific literature to the consensus sequence. Since not all the documents disclose the target sequence, the consensus sequence has to be identified and used for sequence dashboard. For example for Bcl-2, consensus sequence is retrieved from NCBI having seq. id M14745.

The dashboard also depicts the associated information with RNAi agent on the click of your mouse such as patent number, patent title, length of RNAi agent (siRNA), identity score etc.

Sequence Dashboard

Experimental data comparison matrix

Experimental data may be qualitative or quantitative, each being appropriate for different investigations.


Quantitative data was captured from following RNAi experiments for patent focusing on therapeutic application and compared.

  •  % inhibition of target mRNA expression
  •  % encapsulation efficiency
  •  % transfection efficiency
  •  % tumor volume reduction
  •  % cell count reduction

More such comparison matrix can be prepared for patent having varied focus such as on delivery vehicle, nature of RNAi agents, target gene source, system used to test RNAi etc.

Patent Focus- Therapeutic Application

Sr. No. Patent/Publication No. Target gene Experimental Details RANK
BCL-2 Others Test Model Inhibition of Target mRNA Expression (%) Encapsulation Efficiency Transfection efficiency Increase (%) Tumor Volume Reduction (%) Cell Count Reduction (%) Other Remarks
1 US20070298056A1 Yes Human colon cancer (Caco-2) xenografts in nude mice No No No 90.08%
Day 25
(Fig 2) 		No No 1
2 US20080038296A1 Yes In vivo (Mice) No No No 61.29%
Day 13
(Fig 3) 		No No 2
3 US20070258952A1 Yes Human pancreatic carcinoma H79 xenografts No No No 49.23%
Day 25
(Fig 4) 		No No 2
4 US20070172847A1 Yes Ramos cells 80%
(Fig 4. B) 		No No No No No 2

Ranking of patents can be done on the basis of focus of the study, experimental data disclosed, effectiveness of RNAi agent, type of model used to test the RNAi agent, etc.

Advantages:

  • Information disclosure wise sorting available.
  • Efficiency of different RNAi agent against target gene can be compared.
  • Different models used to test cell line and the efficiency can also be compared.

Qualitative Data from Patent Documents

Experiments yielding qualitative data, mentioned below, can’t be compared but are equally important. We did not miss them!

  • Gel electrophoresis
  • Gel blots
  • Tissue section* Cell staining
  • RNAi agent construction


Patent/ Publication No. Gel blots Gel Electrophorosis Tissue section micrograph Cell staining micrograph RNAi Agent Construction
US20080021205A1 Yes _ _ _ _ Yes _ _
US20070275465A1 _ _ Yes _ _ _ _ _ _
WO2007013575A2 _ _ Yes Yes _ _ _ _
US20070081982A1 _ _ _ _ _ _ _ _ Yes
WO2007013575A2 Yes _ _ Yes _ _ _ _
US20050266561A1 _ _ _ _ _ _ _ _ Yes
*Mathematically incomparable data disclosed in patents
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