Biochips and Microarrays - Technologies,markets and companies

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Biochips and Microarrays - Technologies,markets and companies
Published on September 2011

Report Summary

This report is an analysis of biochip/microarray markets based on technologies and applications. The report starts with a description
of technologies as a basis for estimation of markets. Technologies include array comparative genomic hybridization (CGH), copy
number variation (CNV), DNA methylation, ChIP-Chip, RNA splice variants, and microRNA. Separate chapters are devoted to protein
biochips/microarrays, microfluidics and nanobiotechnology-based nano-arrays.

Various applications of biochips and microarrays are described throughout the report. Areas of application such as point-of-care,
genetic screening, cancer, and diagnosis of infections are included. Separate chapters are devoted to applications in drug discovery
and development as well as personalized medicine

The report provides current share of each segment: market size in 2010 and projected value for the years 2015 and 2020. Gene
expression has the largest share and is an established market. Share of microarray technologies in other areas will grow with the
maximum growth in RNA splice variants followed by epigenetics. The growth in protein microarrays is somewhat less, partly because
it is more mature than the other submarkets and has already shown considerable growth in the past. Impact of next generation
sequencing on segments of microarray markets is identified. Customer requirements and unmet needs are described. Markets are
also analyzed according to geographical areas.

Brief profiles of companies involved in biochip/microarray technologies are provided. Currently selected 74 companies are included
along with listing of 92 collaborations between companies. The text is supplemented by 17 tables, 8 figures and 100 references to
literature.

Table of Content

TABLE OF CONTENTS

0. Executive Summary 9
1. Introduction 11
Definitions of biochips/microarray 11
Terms used for biochips 11
Historical aspects of biochip/microarray technology 12
Relation of microarrays to other technologies 13
Applications of biochips/microarrays 13
2. Biochip and Microarray Technologies 15
Introduction 15
Nucleic acid amplification and microarrays 15
PCR on a chip 15
Fast PCR biochip 15
Multiplex microarray-enhanced PCR for DNA analysis 16
Universal DNA microarray combining PCR and ligase detection reaction 16

Biochips and Microarrays - Technologies,markets and companies (From Slideshare) Page 1/9


NASBA combined with microarray 17
Rolling circle amplification on microarrays 17
LiquiChip-RCAT 17
Multiplexed Molecular Profiling 17
Genomewide association scans 18
Whole genome microarrays 18
GeneChip Human Genome Arrays 19
Arrayit's® H25K 20
Transposon insertion site profiling chip 20
Standardizing the microarrays 20
Optical Mapping 21
Microarrays based on ENA detection by physico-chemical methods 21
Electrochemical detection of DNA 21
Photoelectrochemical synthesis of DNA microarrays 22
Microchip capillary electrophoresis 23
Strand displacement amplification on a biochip 23
Biosensor technologies for biochips 23
DNA-based biosensors 24
Phototransistor biochip biosensor 24
Microarrays for cytogenetics 25
Comparative genomic hybridization 25
Array-based CGH 25
NimbleGen CGH arrays 26
Single-cell array CGH 27
Regulatory requirements for array CGH 27
Agilent CGH+SNP microarray platform 27
SignatureChip® 27
Tissue microarrays 28
Pathology tissue-ChIP 28
Carbohydrate microarrays 29
RNA profiling 29
RNA splice variants 29
miRNAs 30
Microarrays for miRNAs 30
Microarrays vs quantitative PCR for measuring miRNAs 31
Exon microarrays 32
Microarrays & DNA sequencing 32
Microarray-based emerging DNA sequencing technologies 32
Exome sequencing for study of human variation 33
High-throughput array-based resequencing 33
Sequencing by hybridization 33
SOLiD-System based ChIP-Sequencing 34
Next generation sequencing vs microarrays for expression profiling 35
Microarray-based gene synthesis 35
3. Microfluidics-based Biochips and Microarrays 37
Introduction 37
Fish-on-chip 37
Lab-on-a-chip 38



LabCD 38
Micronics' microfluidic technology 38
Rheonix CARD technology 39
Microfluidic chips/arrays using PCR 39
Digital PCR Array 39
Digital PCR on a SlipChip 39
Microfluidic automated DNA analysis using PCR 40
Microfluidic single-cell RT-qPCR on a chip 40
Microfluidic chips integrated with RCAT 40
Microfluidic chips integrated with PET 41
Companies developing microfluidic technologies 41
4. Protein Biochips 43
Introduction 43
Protein biochip technologies 43
Protein microarrays 43
Antibody microarrays 44
Aptamer-based protein biochip 44
High-density protein microarrays 45
HPLC-Chip for protein identification 45
LabChip for protein analysis 45
Multiplexed Protein Profiling on Microarrays 46
ProteinChip 46
Protein chips for antigen-antibody interactions molecular diagnostics 48
Proteomic pattern analysis 48
Single molecule array 48
TRINECTIN proteome chip 49
New developments in protein chips/microarrays 49
Microfluidic devices for proteomics-based diagnostics 49
Viral protein chip 49
Use of microarray technologies in human protein atlas initiative 50
Applications of protein biochip/microarrays 51
Biosensor protein chip 51
Proteome Identification Kit 52
Protein nanobiochip for diagnosis 52
Protein biochips/microarrays for personalized medicine 52
Companies involved protein biochips/microarrays 53
5. Nanobiotechnology-based Biochips & Microarrays 57
Introduction 57
Nanotechnology-based biochips 57
Fullerene photodetectors for chemiluminescence detection on microfluidic chip 57
Nanotechnology on a chip 57
Nanogen's NanoChip 58
Use of nanotechnology in microfluidics 58
Construction of nanofluidic channels 59
NanoAnalyzer® chip 59
Nanoscale flow visualization 60
Moving (levitation) of nanofluidic drops with physical forces 60
Electrochemical nanofluid injection 61



Nanofluidics on nanopatterned surfaces 61
Nano-interface in a microfluidic chip 61
Nanofluidic channels for study of DNA 62
Nanofluidic/nanoarray devices to detect a single molecule of DNA 62
Nanoarrays 63
Dip Pen Nanolithography for nanoarrays 63
NanoPro' System 64
Nanosensors 65
Cantilever arrays 65
Nanotechnology-based protein biochips/microarrays 66
AFM for immobilization of biomolecules in high-density nanoarrays 66
Nanoparticle protein chip 67
Protein biochips based on fluorescence planar wave guide technology 67
Self-assembling protein nanoarrays 67
6. Biochips & Microarrays for Epigenetics 69
Introduction 69
Epigenomic technologies 69
Epigenomics Digital Phenotype 69
Global methylation analysis 70
Illumina's assays for analysis of methylation sites 70
GenomicTree's MDScan' technology 70
Orion's MethylScope® technology 70
ChIP-chip 70
Microarray for immunogenetic testing 71
Applications for study of DNA methylation 71
7. Applications of Microarrays in Drug Discovery & Development 73
Introduction 73
Drug discovery 73
Finding lead compounds 73
High-throughput cDNA microarrays 73
Use of gene expression data to find new drug targets 74
Investigation of the mechanism of drug action 74
Cellular microarrays 74
Peptide microarrays for high-throughput screening 75
Biochips for toxicology studies 75
Gene expression studies for toxicology using microarrays 75
MetaChip/Datachip 75
Testing drugs in organ-on-a-chip microdevices 76
ADME-on-a-chip 76
Liver-on-a-chip 76
Lung-on-a-chip 77
SmartChip for cancer drug discovery 77
Drug development 77
Use of microarrays in clinical trials 77
Reverse phase protein microarrays 78
Controlled-release microchip for drug delivery 78
8. Biochips for Biomarkers, Molecular Diagnostics & Personalized Medicine 79
Introduction 79



Applications of biochip technology in personalized medicine 79
AmpliChip P53 as companion diagnostic for cancer 80
Application of microarrays for discovery of biomarkers 80
Antibody-based biomarker discovery 80
Discovery of biomarkers by MAb microarray profiling 81
Gene expression microarray data as a source of protein biomarkers 81
Peptide array technology for detection of biomarkers 81
Protein microarrays for discovery of biomarkers 81
Tissue microarrays for study of biomarkers 82
Biochip and microarray-based detection of SNPs 83
Affymetrix Variation Detection Arrays 83
Biochip combining BeadArray and ZipCode technologies 83
NanoChip for detection of SNPs 83
SNP genotyping by MassARRAY 83
SNP-IT primer-extension technology 84
Copy number variations in the human genome 84
Agilent 2x105K microarray 85
Affymetrix's chromosome copy number analysis 86
Infinium's CNV and SNP lines 87
HD Human660W-Quad BeadChip 87
Roche NimbleGen's CGH and CNV product line 87
TaqMan® Copy Number Assays 87
Innovations in CNV and CGH microarrays 88
Bioinformatic tools for analysis of CNV data 88
Microarrays for Pharmacogenetics 89
AmpliChip CYP450 89
Commercial development of biochip technologies for diagnostics 90
9. Markets 93
Introduction 93
Methods for estimation of markets 93
Microarray markets 93
Market share of microfluidics-based microarrays 94
Gene expression microarray markets 94
Array CGH markets 94
CNV markets 95
Markets for RNA splice variants 95
Markets for microarray relevant to miRNA 95
Epigenetic markets 96
ChIP-Chip 96
Markets for protein microarrays 96
Role of scientists' attitudes on the evolution of protein microarray markets 97
Market share of microarray technology in protein biomarkers 97
Geographical distribution of microarray markets 97
Currents trends 97
Types of arrays used 98
Tiling array 98
Exon array 98
Reaction specifics 99



Pre-amplification use 99
Reagents from array vendor or other sources 99
Dual versus single color array preference 99
Oligo versus BAC preference 100
Cost per sample or cost per array 100
Preference for single versus multiplex sample arrays 101
Current and future throughput in samples per week 101
Use in niche markets 101
Diagnostics 101
Drug discovery 102
Therapeutics 102
Research 102
Screening assays versus whole genome aCGH 103
Effect of next generation sequencing on microarray markets 103
Impact of next generation sequencing on microarray markets for diagnostics 104
Impact of next gen sequencing on microarray markets for drug discovery 104
Resequencing 104
RNA profiling 105
Transcriptome sequencing for mRNA Expression 105
Applications of next generation sequencing in basic research 105
Mapping and sequencing of structural variation from human genomes 105
Identifying protein-coding genes in genomic sequences 106
Applications in clinically relevant areas 107
Genetic disorders 107
Cancer research 108
Management of HIV/AIDS 109
Customer requirements and unmet needs 109
Concluding remarks on microarray markets 109
Future of biochip technology for molecular diagnostics 110
Impact of next generation sequencing on microarray markets in the future 110
Effect on CNV market 110
Effect on RNA profiling 110
Screening samples 111
10. Companies 113
Profiles of companies 113
Collaborations 202
11. References 207

List of Tables
Table 1 1: Various terms used for biochips, microarrays and microfluidics 11
Table 1 2: Historical landmarks relevant to the development of biochip technology 12
Table 1 3: Applications of microarrays 13
Table 2 1: Companies developing whole genome chips/microarrays 18
Table 2 2: Microarray/biochip-based technologies for cytogenetics 25
Table 2 3: Companies developing whole genome chips/microarrays 32
Table 2 4: ChIP detection platforms for sequencing 34
Table 3 1: Companies developing microfluidic technologies 41
Table 4 1: Applications of protein biochips/microarrays 51



Table 4 2: Selected companies involved in protein biochip/microarray technology 53
Table 5 1: Companies with nanoarray and nanofluidic technologies 63
Table 8 1: Applications of biochip technology relevant to personalized medicine 79
Table 8 2: Companies involved in biochips for molecular diagnostics 90
Table 9 1: Growth of markets for microarray technologies from 2010 to 2020 93
Table 9 2: Geographical distribution of biochip/microarray markets 2010-2020 97
Table 9 3: Global markets for sequencing services according to applications 103
Table 10 1: Collaborations 202

List of Figures
Figure 1 1: Relation of microarrays to other technologies and applications 13
Figure 2 1: Affymetrix GeneChip technology 19
Figure 2 2: Basic principle of a biosensor 24
Figure 2 3: Construction of SOLiD fragment library using DNA enrichment by ChIP 34
Figure 4 1: ProteinChip System 47
Figure 5 1: Schematic representation of Dip Pen Nanolithography (DPN) 64
Figure 8 1: Role of biochips/microarrays in personalized medicine 80
Figure 8 2: Role of CYP450 genotyping in development of personalized medicine 90


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