DNA Microarray A Focus of Sales Growth

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1 DNA Microarray A Focus of Sales Growth February 2013 Biopharm Reports, Tamarisk House, High Street, Colne, Cambridgeshire PE28 3ND United Kingdom, 1

2 The Author John Bates is a market consultant in the life science industry. After a degree in biochemistry and chemistry (1978) and a Ph.D in cancer research in 1981, John joined Upjohn Ltd (now Pfizer), where he managed a team of scientists in the department of biopharmaceutical sciences and drug metabolism. In 1985 he took a similar role with Glaxo Group Research (now GSK), in the department of Biochemical Pharmacology. In 1989 he co founded Melbourn Scientific Ltd, a CRO operating in the pharmaceutical field, later moving to Acumen Bioscience (drug discovery instrumentation) as Technical Director. John has over twenty years laboratory experience and has worked as a market consultant since 2003, covering many areas of laboratory technology in the fields of molecular biology, bioanalysis, drug discovery and diagnostics. Copyright 2013 Biopharm Reports This Report is published by Biopharm Reports. All Rights Reserved. The reproduction or redistribution of this Report is prohibited, without the prior permission of Biopharm Reports. The information in this report and the opinions, views and conclusions contained herein, are those of the author and publisher. While the information contained in this report is believed to be accurate at the time of publication, Biopharm Reports accepts no liability for the information contained herein, nor for its completeness in any respect. Biopharm Reports accepts no liability for any decisions or actions that are taken, based on the content, views or conclusions contained in this report. 2

3 INDEX Page 1. Conduct of Study Study Participants DNA Microarray Methods DNA Microarray Applications DNA Microarray Company Suppliers Preferred Company Suppliers and Products Expenditure and Budgets Purpose Samples Sample Preparation Therapeutic Area Disease Biomarkers Bioinformatics Software Challenging Applications Innovation Quality Control DNA Microarray Consumables Discussion 177 3

4 DNA Microarray A Focus of Sales Growth 1. Conduct of Study 4

5 1. INTRODUCTION Between July 2012 and January 2013, Biopharm Reports carried out a global study of DNA microarray (hereafter referred to as DNA Microarray 2013). The findings of this study are presented in this report THIS STUDY Microarray 2013 is an independent global study of DNA microarray and investigated current and evolving markets in the DNA microarray field. Focussed on individuals who use DNA microarray in the laboratory, this study examined current DNA microarray end user practices, preferences, developments and emerging applications, together with market considerations, areas of sales growth and future use. This study was carried out to assist DNA microarray developers and vendors to better understand and support current and evolving needs in this field, and to help scientists compare their own practices with others, and gain insights into emerging technologies and applications. This DNA microarray study was designed for scientists or managers who use DNA microarray in their everyday activities, but excluding DNA microarray commercial developers and vendors (for the avoidance of bias). Overall, 480 individuals took part, of whom 201 were selected as qualifying participants. 1.2 DATA MINING Microarray 2013 generated more than 250,000 end user data points and market related information on the DNA microarray field. This database allows data mining to answer specialised questions. To discuss an interest to explore the use of the DNA Microarray 2013 database, contact John Bates (jbates@biopharmreports.com). 1.3 MICROARRAY SURVEY QUESTIONS 1. MICROARRAY TECHNIQUES Do you use microarray techniques, either as a laboratory scientist, laboratory manager or clinician? Options: Yes or No) 2. MICROARRAY ACTIVITIES Please estimate (as a %) how much of your microarray activities are spent in the 5

6 following areas. Options1: Running routine (developed and validated) microarray tests ; The development or validation of microarray tests; The qualitative discovery of molecules using microarray methods;. If other, please indicate. Options2: 0% 1% 2% 5% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 3 PARTICIPANTS DETAILS: Name, Organisation, Department, Job Title, Address and Country. As it is not possible to verify participants using personal addresses (e.g. hotmail, gmail etc.), please use the address of the organisation (e.g. company, university etc.) to which your activities relate. 4 ORGANISATION TYPE Please select your organisation type. Options: University, Research Institute, Small or Medium Sized Company, Large International Company, Clinic or Hospital, Government Organisation, Veterinary Organisation,. If other, please indicate 5 FIELDS Please select the main field in which you use microarray methods. Options: Biotechnology, Chemicals, Clinical or Hospital, Defense, Energy, Environmental, Food and Drink, Forensics, Geology, Government, Healthcare, Natural Products, Pharmaceuticals, Research Institute, Security, University, If other, please indicate. 6 PURPOSE: Please estimate (as a %) how much of your microarray activities relate to the following purposes (more than one option can be selected). Options1: Biotechnology, Chemicals, Clinical or Hospital, Defense, Energy, Environmental, Food and Drink, Forensics, Geology, Government, Healthcare, Natural Products, Pharmaceuticals, Research Institute, Security, University or [NB: as the purposes for which microarray could potentially be used varies with the field, this questions presented different potential purposes for each field (see tabulated options below). Options2: 0% 1% 2% 5% 10% 20% 30% 40% 50% 60% 70% 80% 90% or 100% (this allowed the % associated with these activities, to be selected). 6

7 Biotechnology options: Preclinical research Clinical research Routine diagnostics Routine screening Clinical trials Treatment monitoring Diagnostics research Disease research Drug R&D Drug targets Pathology Toxicology Defence options: Improvised Explosive Devices (IEDs) Chemical weapons Battlefield threats Early warnings Chemical Warfare Agents (CWAs) Toxic Industrial Chemicals (TICs) Explosives Contraband Chemicals: options Purity Assessment Structural determination Contaminants Quality control Stability Reaction kinetics Reactants Environmental Energy options: Agricultural biomass Electricity Fossil fuels Fusion Gas Geothermal Hydroelectric Mining Nuclear Petroleum Solar Tidal Clinical/Hospital options: Clinical research Routine diagnostics Routine screening Clinical trials Treatment monitoring Diagnostics research Disease research Drug R&D Drug targets Pathology Toxicology Environmental options: Marine water River water Land water Soil Environmental Impact Analysis Environmental monitoring Heritage sites Wetlands Ecological communities Migratory regions Nuclear sites National Heritage sites Industrial developments Natural landscape 7

8 Food and Drink options: Food Drink Ingredients Additives Government options: Preclinical research Clinical research Routine diagnostics Routine health screening Clinical trials Treatment monitoring Diagnostics research Disease research Drug R&D Drug targets Pathology Toxicology Forensics options: Criminal Pathology Toxicology Civil Military Healthcare options: Clinical research Routine diagnostics Routine screening Clinical trials Treatment monitoring Diagnostics research Disease research Drug R&D Drug targets Pathology Toxicology Geology Options: Climate Change Engineering Environmental Mining Energy Hydrology Natural hazards Palaeontology Natural Products options: Plants Animals Marine Aquatic Prokaryotes Fungi Soil 8

9 Pharmaceuticals options: Preclinical research Clinical research Routine diagnostics Routine screening Clinical trials Treatment monitoring Diagnostics research Disease research Drug R&D Drug targets Pathology Toxicology University options: Preclinical research Clinical research Routine diagnostics Routine screening Clinical trials Treatment monitoring Diagnostics research Disease research Drug R&D Drug targets Pathology Toxicology Research Instit options: Preclinical research Clinical research Routine diagnostics Routine screening Clinical trials Treatment monitoring Diagnostics research Disease research Drug R&D Drug targets Pathology Toxicology Security options: Early Warning Systems Forensic analysis Chemical threats Rapid Response Narcotics Contraband 7 GENERAL MICROARRAY TECHNIQUES Please select the main microarray technique you use in the laboratory or clinic. Options: Antibody Microarray*, DNA Microarray, Protein Microarray**, Tissue Microarray,. [* Antibodies attached to microarrays, as capture molecules, ** A variety of different proteins (other than antibodies) attached to microarrays as capture molecules (e.g. enzymes, receptors etc)]. Please note, the set of questions presented to participants after questions 7 were determined by which of the array techniques were selected in this question. This report only presents those findings relating to the use of DNA microarrays, which was by far the dominant groups (see Chapter 2). 9

10 8 THERAPEUTIC AREAS Please estimate (as a %) how much of your DNA microarray activities relate to the following therapeutic areas (more than one option can be selected). If not applicable, please select "Not Applicable". Options2: 0%, 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% Options1: Arthritis Autoimmune Diseases Bone Metabolism Cancer Cardiovascular Central Nervous System Dermatology Endocrine Gastrointestinal Genitourinary System Haematology Infections Inflammation Metabolic Disorders Musculoskeletal Disorders Nutrition Obstetrics and Gynaecology Ophthalmology Pain Respiratory Skin Not Applicable 9 SAMPLES Please estimate (as a %) how much of your DNA microarray activities are applied to the following sample types (more than one option can be selected). Options2: 0%, 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% Animal tissues Cell isolates Cells Cerebrospinal fluid Genetic material Human tissues In Vitro biological solutions Microbiological materials Pathology samples Plasma Saliva Serum Urine Whole blood If other, please indicate 10 SAMPLE PREPARATION Please estimate how much (as a %) of your DNA microarray applications use the following sample preparation methods (more than one option can be selected). 0%, 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% Options1: 10

11 Automated sample preparation Solid Phase Extraction (SPE) Liquid Liquid Extraction (LLE) Size Exclusion Organic solvent precipitation Direct injection Dialysis Affinity methods Filtration If other, please indicate 11 CURRENT METHODS Please estimate how much (as a %) of your current DNA microarray activities, are based on the following methods (more than one option can be selected). Options2: 0%, 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% Options1: Chromatin Immunoprecipitation on Chip (ChlP Chip) Comparative Genomic Hybridization Array CpG island custom Array DamID Array DNA methylation Array Exon Junction Array Gene Array Gene copy number Array Gene Expression Profiling (cdna) Array GeneID Array mirna Array Proximity Ligation Array SNP Detection Array Tiling Array If other, please indicate 12 FUTURE METHODS Please estimate how much (as a %) your DNA microarray activities, based on these methods, will change (increase or decrease), over the next 3 years (more than one option can be selected). Options2: > 50%, 50%, 40%, 30%, 20%, 10%, 5%, 0, +5%, +10%,+20%,+30%,+40%,+50%, > +50% Chromatin Immunoprecipitation on Chip (ChlP Chip) Comparative Genomic Hybridization Array CpG island custom Array DamID Array DNA methylation Array Exon Junction Array Gene Array Gene copy number Array Gene Expression Profiling (cdna) Array GeneID Array mirna Array Proximity Ligation Array SNP Detection Array Tiling Array If other, please indicate 13 CURRENT APPLICATIONS Please estimate how much (as a %) of your current DNA microarray activities, are used in the following applications (more than one 11

12 option can be selected). Options1: 0%, 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% Options2: Alternative Splicing Comparative Genomic Hybridization (DNA Arrays) DamID (Protein Binding site Occupancy) Fusion Gene Transcripts Protein Binding Site Occupancy (by ChlP) DNA Capture DNA Copy Number Epigenetic analyses For FISH assays For PCR Gene Expression Gene Identification GeneID (e.g. Pathogens) Identify mirna Mutation Identification SNP detection Whole Genome Analysis (DNA Array), If other, please indicate 14 FUTURE APPLICATIONS Please estimate how much (as a %) your use of DNA microarray methods for the following applications, will change (increase or decrease) over the next 3 years (more than one option can be selected). Options2: > 50%, 50%, 40%, 30%, 20%, 10%, 5%, 0, +5%, +10%,+20%,+30%,+40%,+50%, > +50% Alternative Splicing Comparative Genomic Hybridization (DNA Arrays) DamID (Protein Binding site Occupancy) Fusion Gene Transcripts Protein Binding Site Occupancy (by ChlP) DNA Capture DNA Copy Number Epigenetic analyses For FISH assays For PCR Gene Expression Gene Identification GeneID (e.g. Pathogens) Identify mirna Mutation Identification SNP detection Whole Genome Analysis (DNA Array), If other, please indicate 15 CURRENT COMPANIES Please estimate how much (as a %) of your current DNA microarray methods, are based on products supplied by the following companies (more than one option can be selected). Options2: 0%, 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% Options1: 12

13 Affymetrix Agilent Amersham Pharmacia Applied Biosystems Aushon Biosystems BD Beecher Biacore Biochip Clontech CombiMatrix EMBL Genomics Fortebio Hitachi HTG Illumina Invitrogen Life Technologies Luminex Molecular Devices MSD Nimblegen Systems Pharmagen Randox RayBiotech Roche Applied Sciences Samsung Sequenom Toshiba Self Made (In House) If other, please indicate 16 FUTURE COMPANIES Please estimate how much (as a %) your DNA microarray methods based on products supplied by these companies, will change (increase or decrease) over the next 3 years (more than one option can be selected). Options2: > 50%, 50%, 40%, 30%, 20%, 10%, 5%, 0, +5%, +10%,+20%,+30%,+40%,+50%, > +50% Affymetrix Agilent Amersham Pharmacia Applied Biosystems Aushon Biosystems BD Beecher Biacore Biochip Clontech CombiMatrix EMBL Genomics Fortebio Hitachi HTG Illumina Invitrogen Life Technologies Luminex Molecular Devices MSD Nimblegen Systems Pharmagen Randox RayBiotech Roche Applied Sciences Samsung Sequenom Toshiba Self Made (In House) If other, please indicate 13

14 17 PREFERRED COMPANY Who is your preferred company supplier in the DNA microarray field? 18 PREFERRED PRODUCT What is your preferred product (from your preferred supplier) in the DNA microarray field? 19 STRENGTHS What are the strengths of your preferred product in the DNA microarray field (how is it meeting your needs in this area)? 20 WEAKNESSES What are the weaknesses of your preferred product in the DNA microarray field (how is it failing to meet your needs in this area)? 21 BIOINFORMATICS SOFTWARE What is your preferred bioinformatics software in the DNA microarray field? 22 BIOMARKERS Do you use DNA microarray methods to discover or measure disease Options1: Yes or No 23 BIOMARKER TYPES : Relating to your use of DNA microarray methods for the study of disease biomarkers, please estimate (as a %) how much of your work in this area relates to the following genetic variations (more than one option can be selected). Options2: 0%, 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% Options1: Gene variations (mutations/polymorphisms) DNA methylation Gene copy number Gene expression SNPs mirna Alternative splicing variants If other, please indicate 24 CLINICAL UTILITY Relating to your use of DNA microarrays for the study of disease biomarkers, please estimate (as a %) how much of these activities relate to the following biomarker clinical utilities. Options2: 0%, 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% Options1: 14

15 Disease prognosis Disease susceptibility or risk Disease stage or severity Drug discovery Early detection of disease Clinical trial endpoint Guiding treatment Response to therapy Safety or toxicity factors If other, please indicate 25 CHALLENGES Please indicate the molecule type or parameter that present the greatest technical challenge or difficulty (qualitatively or quantitatively) in your laboratory or clinic, relating to your use of DNA microarray methods. Please indicate molecule type, sample type (matrix) and microarray method used. REASONS: What are the principal technical challenges or difficulties in the study of this molecule type, using the DNA microarray method indicated above? 15

16 26 REQUIRED INNOVATION On a scale of 1 to 10 (where 1 = least important and 10 = most important), please indicate which of the following areas you believe innovation is most required, relating to DNA microarray methods? Options2: 1 to 10; Options1: Sample preparation Ancillary techniques Array (qualitative) selectivity Array (quantitative) sensitivity Array reproducibility Array qualitative/quantitative capability Array robustness (ruggedness) Detection methods Automation Speed or sample throughput Specialist data control systems Specialist bioinformatics systems 27 RECENT INNOVATION In your own area, what has been the most important laboratory or clinical innovation over the last three years, relating to DNA microarrays? 28 FUTURE INNOVATION From what is currently in development or emerging in your own area, what do you anticipate will be the most important innovation over the next three years, relating to DNA microarrays? 29 FINANCIAL BUDGET Please estimate your annual financial budget (and financial currency) relating to your DNA microarray activities. 30 CURRENT BUDGET BREAKDOWN Please estimate how much (as a %) of your financial budget for DNA microarrays, is used in the following areas. Options2: 0% 1% 2% 5% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Options1: Consumables System control software Specialist bioinformatics software Microarrays/instruments Sample preparation/related instrumentation Ancillary systems/instrumentation General overheads Staff salaries 16

17 31 FUTURE BUDGET BREAKDOWN Please estimate by how much (as a %) your financial budget breakdown for DNA microarrays will change, either increase or decrease, over the next three years. Options2: > 50%, 50%, 40%, 30%, 20%, 10%, 5%, 0, +5%, +10%,+20%,+30%,+40%,+50%, > +50% Options1: Consumables System control software Specialist bioinformatics software Microarrays/instruments Sample preparation/related instrumentation Ancillary systems/instrumentation General overheads Staff salaries 32 OVERALL FINANCIAL BUDGET Please estimate by how you anticipate your overall annual financial budget for the use of DNA microarrays will change, either increase or decrease, over the next three years. Options1: > 50%, 50%, 40%, 30%, 20%, 10%, 5%, 0, +5%, +10%,+20%,+30%,+40%,+50%, > +50% 33 CONSUMABLES In terms of overall costs to your laboratory or clinic, what are the top three consumables directly associated with your microarray work? 34 QUALITY CONTROL GUIDELINES OR PROCEDURES Please indicate the main quality control guidelines or procedures relating to your work in the DNA microarray field. 1.4 QUALIFYING PARTICIPANTS In total, 440 DNA Microarray end users participated in this study, of which 201 contributed to the findings presented in this report. Participants were excluded if they: a) answered No to question Q.1 of this study b) provided incomplete personal contact details, which prevented them from being tracked to the organisation in which they carry out DNA microarray c) were developers or vendors, operating in the DNA microarray field (this exclusion was necessary for the avoidance of bias) 17

18 DNA Microarray A Focus of Sales Growth 2. Study Participants 18

19 SUMMARY In total, 201 individuals participated in the DNA microarray 2013 study described in this report. These individuals work in 37 countries, of which the USA, Italy, Germany and the UK were the largest participants. Regionally, European countries were the greatest contributors to this study and together they represented 55% of participants. Participants in DNA Microarray 2013 indicated three general areas of activity in the DNA microarray field, namely the conduct of routine tests, the development and validation of DNA microarray tests and the use of DNA microarray in qualitative studies. Together, these three areas represented around 87% of all DNA microarray activities, almost one third of which are associated with routine testing. More than 88% of participants in DNA Microarray 2013 are employed by seven different organisation types, namely universities, research institutes, SMEs (small and medium sized enterprises), large companies, government, clinics/hospitals and veterinary organisations. Participants from research institutes, universities, clinics/hospitals and the healthcare field were the largest contributors and together represented 85% of participants. Commercial insights in this report relating to marketing and sales in the DNA microarray field are of particular relevance to these groups. The findings of DNA Microarray 2013 provide insights and indicate sales opportunities, areas of growth and need, as well as potential threats to innovators and vendors in the DNA microarray field. This global DNA microarray study involved the participation of a substantial number of DNA microarray end users and its findings provide both depth and breadth of technical and market related information, relevant to developers and vendors in this field. 19

20 2.1 THIS CHAPTER This chapter presents background information relating to DNA microarray endusers, who participated in DNA Microarray PARTICIPANTS In total, 440 individuals participated in the DNA microarray study described in this report. Of these, 180 were excluded either because they said that they did not confirm that they used microarray as part of their everyday activities, or because they failed to provide sufficient information to confirm their position and organisation. Of the remaining 260 participants, 194 said they carried out DNA microarray and 7 reported that they use arrays to study other polynucleotides, such as mrna. The combined disclosures of these two groups are the subject of this report (n = 201). The remainder of the study participants used antibody microarrays (n=12), protein microarray arrays (n = 24), tissue microarrays (n = 11) or other microarrays (n= 12). See Figure 2.1 Figure 2.1 Microarray activities of individuals who participated in DNA Microarray 2013 DNA: (43%) polynucleotides: (2%) Tissue: (3%) : (3%) Antibody: (3%) Excluded: (40%) Protein: (6%) 20

21 2.3 COUNTRIES Qualifying individuals (n=201) who participated in DNA Microarray 2013, work in 37 countries. Of these, USA, Italy, Germany and the UK were the largest participant countries (see Figure 2.2 and Table 2.1). Figure 2.2 Countries and numbers of individuals who participated in DNA Microarray 2013 Italy: (9%) Germany: (8%) USA: (27%) UK: (6%) Finland: (4%) Canada: (4%) Spain: (4%) Sweden: (4%) France: (3%) : 30.3 (31%) Table 2.1 Countries and numbers of individuals who participated in DNA Microarray 2013 Country % Participants USA Italy Germany United Kingdom Finland Canada Spain Sweden France Switzerland Belgium

22 Table 2.1 Countries and numbers of individuals who participated in DNA Microarray 2013 Country % Participants Australia India China Japan Norway Austria Brazil Czech Republic Denmark New Zealand Slovenia The Netherlands Argentina Colombia Croatia Greece Hong Kong Hungary Israel Mexico Portugal Puerto Rico Romania South Africa Taiwan Uruguay

23 2.4 REGIONS Regionally, European countries were the greatest contributors to DNA Microarray 2013 and together represented 55% of participants (see Figure 2.3). Figure 2.3 Global regions of individuals who participated in DNA Microarray 2013 Europe: 110 (55%) Rest of World: 30 (15%) North America: 61 (30%) 2.5 DNA MICROARRAY ACTIVITIES Participants in DNA Microarray 2013 indicated three general areas of activity in the DNA microarray field, namely the conduct of routine tests, the development and validation of DNA Microarray tests and the use of DNA Microarray in qualitative studies. Together, these three areas represented around 87% of all DNA Microarray activities, almost one third of which are associated with the routine testing (see Figure 2.4). Figure 2.4 DNA Microarray activities of individuals who participated in DNA Microarray 2013 Routine Tests: (31%) Development and/or Validation: (29%) : (13%) Qualitative: (27%) 23

24 2.6 ORGANISATIONS More than 88% of participants in DNA Microarray 2013 are employed by seven different organisation types, namely universities, research institutes, SMEs, large companies, government, clinics/hospitals and veterinary organisations (see Figure 2.5). Figure 2.5 Organisation types of individuals who participated in DNA Microarray 2013 Clinic/ Hospital: (55%) Government: (16%) : (12%) Veterinary: (1%) SMEs: (2%) Res Institutes: 2.0 (2%) Universities: 2.0 (2%) Large Companies: (10%) Table 2.2 Organisation types of individuals who participated in DNA Microarray 2013 Organisation Type % Clinic/ Hospital 55.2 Government 16.4 Large Companies 10.0 Universities 2.0 Res Institutes 2.0 SMEs 1.5 Veterinary

25 2.7 FIELDS DNA Microarray 2013 participants reported that they worked in 1o fields, of which research institutes, universities, clinical and hospital and healthcare fields were the largest contributors and together these groups represented 85% of participants (see Figure 2.6 and Table 2.3). Figure 2.6 Fields of individuals who participated in DNA Microarray University: (36%) : (5%) Research Institute: (33%) Biotechnology: 1.0 (1%) Food and Drink: 1.3 (1%) Government: (2%) Healthcare: (12%) Environmental :(3%) Pharmaceuticals: (3%) Clinical or Hospital: (4%) Table 2.3 Fields and percentage of individuals who participated in DNA Microarray 2013 Fields % University 35.7 Research Institute 32.6 Healthcare 12.0 Clinical or Hospital 4.4 Pharmaceuticals 3.1 Environmental 2.6 Government 1.9 Food and Drink 1.3 Biotechnology 1.0 Natural Products 0.6 Chemicals 0 Defense 0 25

26 Table 2.3 Fields and percentage of individuals who participated in DNA Microarray 2013 Fields % Energy 0 Forensics 0 Geology 0 Security Discussion This global DNA microarray study involved the participation of a substantial number of DNA microarray end users and its findings provide both depth and breadth of technical and market related information, relevant to end users, and developers and vendors in this field. Notably, participants from research institutes, universities, clinical and hospital and healthcare fields were the largest contributors and together these groups represented 85% of participants. Commercial insights in this report relating to markets and sales in the DNA microarray field, are therefore of particular relevance to these groups. As will be seen later in this report, the findings of DNA Microarray 2013 provide insights and indicate sales opportunities, areas of growth and need, as well as potential threats to innovators and vendors in the DNA microarray field. In particular, these relate to European and North American end users. 26

27 DNA Microarray A Focus of Sales Growth 3. DNA Microarray Methods 27

28 SUMMARY Participants reported on the current use of around 20 DNA microarray methods, of which the top five were gene expression profiling array, gene array, comparative genomic hybridization array, SNP detection array and mirna array. Together, these five methods represented almost 80% of those cited, of which gene expression profiling was the most important. This technique represented one third of DNA microarray methods cited. DNA microarray methods that are anticipated to be of greatest importance over the next three years are mirna array methods, followed by DNA methylation array, SNP detection, comparative genomic hybridization and gene copy number array. These data probably reflect the growing importance of these methods in disease research and in the advancement of diagnosis and treatment. In particular, these changes reflect the growth of interest in the study of epigenetics through a better understanding of gene methylations, the role of mirnas amongst other things, and their impact on gene expression patterns. Notably, a number of DNA microarray end users also reported an anticipated switch from array methods to next generation sequencing, which identifies a potential threat to companies operating in the DNA microarray field. 28

29 3.1 This Chapter This chapter presents findings on the current use of specific DNA microarray methods in the laboratory or clinic, reported by individuals who participated in DNA Microarray Findings are also presented on the anticipated use of specific DNA microarray methods over the next three years ( ). 3.2 Current DNA Microarray Methods Participants reported the current use of around 20 DNA microarray methods, of which the top five were [Edited]. Together, these five methods represented almost 80% of those cited, of which [Edited] was the most important. This technique represented one third of current DNA microarray methods cited. See Figure 3.1 and Table 3.1. Where participants selected [Edited]. Figure 3.1 Top currently used DNA microarray methods (% used), reported by individuals who participated in DNA Microarray

30 Table 3.1 Top currently used DNA microarray methods (% used), reported by individuals who participated in DNA Microarray 2013 Current DNA Microarray Methods % Edited 33.5 Edited 15.9 Edited 12.6 Edited 8.8 Edited 6.7 Edited 5.1 Edited 3.4 Edited 3.2 DNA methylation Array 2.3 Edited 1.8 Edited 1.7 Edited 1.3 Edited 1.0 Edited Future DNA Microarray Methods Calculations Findings relating to the future use of DNA microarray methods were calculated using two versions (A and B) of the so called User Ratio (UR). User Ratio A (UR A) was calculated using the formula below: UR A = np(0 >+50%)/nP(> 50% 0) where np(0 >+50%) is the number of participants who indicated that their future use of a particular method will be either the same or increased (from +5% to >+50%) and where AP(> 50% 0) is the number of participants who indicated that their future use of a particular method will be either the same or decreased (from > 50% to 0). UR A is therefore a simple ratio of the number of participants who said that their anticipated use of a method would stay the same or increase (at any percentage) 30

31 to the number of participants who said that their anticipated use of a method would stay the same or decrease (at any percentage). This ratio is therefore an average value in respect of the percentage that individuals indicated their use of a particular method would either increase, or decrease. A UR A of > 1 therefore suggests that a method is anticipated to be used by more individuals over the next three years, whereas a UR A of < 1 suggests that a method is anticipated to be used by fewer individuals over the next three years. It also follows that the greater the value if UR A above 1, the greater the number of individuals anticipated to use a method over the next three years, and the reverse for UR A of <1. In contrast, User Ratio Method B (UR B) was calculated using the formula below UR B = np**(+5 >+50%)/ np** (> 50% 5%) where np**(0 >+50%) is a numerical value calculated from the number of participants who indicated that their future use of a particular method will either increase (from +5% to >+50%) and which mathematically takes into account the % increase indicated (0 +50), and where AP%(> 50% 0) is the number of participants who indicated that their future use of a particular method would decrease (from > 50% to 0) and which also mathematically takes into account the % decrease (0 50). UR B is therefore a ratio of the number of individuals who said that their anticipated use of a method would increase (taking into account the percentage) to the number of individuals who said that their anticipated use of a method would decrease (taking into account the percentage). This ratio is therefore an average value in respect of the percentage that individuals collectively indicated their use of a particular method would either increase or decrease, but excludes individuals who indicated their use of a method would stay the same over the next three years. A UR B of > 1 therefore suggests that a method is anticipated to be used more by individuals (or at a higher % increase, or both) over the next three years, whereas a UR B of < 1 suggests that a method is anticipated to be used by fewer individuals (or at a higher % decrease,or both) over the next three years. It also follows that the value if UR B above 1, the greater the number of individuals who are anticipated use of that method over the next three years, and the reverse for UR B of <1. 31

32 In answer to this question, where data analysis was based on the UR A ratio, Edited were anticipated to be of greatest importance over the next three years, followed Edited, Edited, Edited and Edited arrays. Where data analysis was based on the UR B ratio, Edited was anticipated to be of greatest importance to end users over the next three years, followed by Edited, Edited, Edited and Edited. Where participants selected other relating to future anticipated DNA microarray methods over the next three years, participants indicated: Edited Edited Edited Edited Edited Edited Edited Edited Edited Figure 3.2 The top DNA microarray methods that study participants indicated they will be using over the next three years ( ), expressed by the User Ratio A (UR A) method

33 Table 3.2 The top DNA microarray methods that study participants indicated they will be using over the next three years ( ), expressed by the User Ratio A (UR A) method. DNA Microarray Method UR A Edited 2.1 Edited 1.9 Edited 1.7 Edited 1.7 Edited 1.6 Edited 1.5 Edited 1.4 Edited 1.3 Edited 1.2 Tiling Array 1.2 Edited 1.2 Edited 1.2 Edited 1.1 Edited 1.1 Edited 0.9 Figure 3.3 The top DNA microarray methods that study participants indicated they will be using over the next three years ( ), expressed using the User Ratio B (UR B) method

34 Table 3.3 The top DNA microarray methods that study participants indicated they will be using over the next three years ( ), expressed using the User Ratio B (UR B) method. DNA Microarray Method UR B Edited 3.7 Edited 3.6 Edited 3.2 Edited 2.9 Edited 2.9 Edited 2.4 Edited 1.7 Edited 1.6 Edited 1.5 CpG island custom Array 1.2 Edited 1.1 Edited 1.0 Edited 1.0 Edited 0.9 Edited Discussion Edited 34