Molecular Diagnostics in Genetic Testing

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Molecular Diagnostics in Genetic Testing
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Molecular diagnostics in genetic testing brings advanced analytical techniques to the diagnosis and treatment of genetic disorders. The confluence of breakthroughs in genomics and proteomics and the development of microarray devices to measure analytes in the blood and various body tissues are driving significant growth in the segment. Major developments include the integration of specialty labs and gene expression profiling into clinical practice, the introduction and rapid growth of cell-free fetal DNA prenatal testing, the advancement of companion diagnostics for drug development, the widespread installed base of automated instruments for molecular testing and the development of personalized medicine. The genetic testing space is one of the most profitable sectors of molecular diagnostics and is expected to be an area of high growth and corporate change throughout the forecast period. This TriMark Publications report describes the emerging field of molecular diagnostics in genetic testing.

This review analyzes the size and growth of the molecular diagnostics in genetic testing market, including the factors that influence the various market segments within it and the dollar volume of sales, both in the United States and worldwide. Moreover, this analysis profiles the leading companies focused on the molecular diagnostics for genetic testing sector.



1. Overview 8

1.1 Statement of Report 8
1.2 About This Report 8
1.3 Scope of the Report 9
1.4 Objectives 11
1.5 Methodology 11
1.6 Executive Summary 12

2. Role of Molecular Diagnostics and Opportunities in the Genetic Testing Sector 15

2.1 Introduction to Molecular Diagnostics for Genetic Testing 15
2.1.1 Definition and Scope of Molecular Genetic Testing within this Report 15
2.1.2 Key Functions of Molecular Genetic Testing 15
2.1.3 Overview of Molecular Genetic Testing Laboratories 16
2.2 Diagnostic Testing of Genetic Disorders 16
2.2.1 Review of Genetic Disorders: Characterizations of Abnormalities and Patterns of Inheritance 17
2.2.2 Common Genetic Disorders 19
2.3 Carrier Testing for Genetic Disorders 20
2.4 Preimplantation Genetic Diagnosis and Preimplantation Genetic Screening 20
2.5 Prenatal/In utero Genetic Testing 21
2.6 Newborn Genetic Screening Tests 23
2.6.1 Molecular Diagnostics for Newborn Genetic Testing 25
2.7 Pre-symptomatic and Predictive Testing for Adult Onset Disorders 26
2.8 Pharmacogenetics and Pharmacogenomics 26
2.8.1 Current Applications for Pharmacogenetics and Pharmacogenomics 28
2.8.1.1 Warfarin and VKORC1 and CYP2C9 Testing 29
2.8.1.2 Trastuzumab and Lapatinib and HER2 Overexpression Testing 31
2.8.1.3 Clopidogrel and CYP2C19 Testing 32
2.8.1.4 Thiopurines and TPMT Testing 32
2.8.1.5 Cetuximab and EGFR Expression and KRAS Mutation Testing 33
2.8.1.6 Irinotecan and UGT1A1*28 Testing 33
2.8.1.7 Abacavir and HLA-B*5701 Testing 34
2.8.1.8 Carbamazepine and HLA-B*1502 Testing 34
2.9 Tissue and Blood Typing 34
2.9.1 HLA Determination 34
2.9.2 Rhesus D Factor Determination 37
2.10 Parentage/Relationship Testing (Paternity Testing) 38
2.11 Genealogical DNA Testing 38
2.12 Criminal and Forensics Testing 39

3. Introduction to Molecular Diagnostics Technology for Genetic Testing 40

3.1 Introduction to Genomics and Its Opportunity 40
3.1.1 Science Background: Structures and Functions of Nucleic Acids and Proteins 40
3.1.2 The Human Genome 40
3.1.3 Genomics: Opening up of Opportunities in Molecular Diagnostics 41
3.2 Genetic Variability and Disease 42
3.3 Impact of the Human Genome Project on Molecular Diagnostics 43
3.4 Key Considerations for Molecular Diagnostics 44
3.5 Molecular Diagnostics in the Post-Genomic Era 45
3.6 Advances in Molecular Diagnostics Technologies 48
3.7 Molecular Diagnostics Testing Technologies and Platforms 50
3.7.1 Amplification Technologies 50
3.7.1.1 PCR and PCR Derivative Platforms 50
3.7.1.2 Multiple Displacement Amplification (MDA) 55
3.7.1.3 Multiple Annealing and Looping-based Amplification Cycles (MALBAC) 56
3.7.1.4 Whole Genome Amplification 57
3.7.1.5 Nucleic Acid Sequence-based Amplification (NASBA) 57
3.7.2 Detection of Amplified Gene Products 57
3.7.2.1 High Resolution Melting Analysis 58
3.7.2.2 Microparticle-based Flow Cytometry 59
3.7.3 DNA and Oligonucleotide Microarrays and Chips 59
3.7.3.1 Array Comparative Genomic Hybridization (aCGH) 62
3.7.4 Gene Sequencing 62
3.7.4.1 Sanger Sequencing 62
3.7.4.2 Next Generation Sequencing 63
3.7.5 Fluorescence In situ Hybridization (FISH) 68

4. Business Landscape for Molecular Diagnostics in Genetic Testing 69

4.1 Market Analysis: Size, Growth, Share and Competitors 69
4.1.1 Worldwide Genetic Testing Markets 69
4.1.2 Market Structure and Competitive Situation 73
4.1.3 Primary Competitors 74
4.1.4 Commercialization Strategies for Molecular Diagnostic Products 74
4.1.5 Market Penetration Strategies for Genetic Testing 74
4.2 Growing Genetic Testing Market Segments 75
4.2.1 Personalized Medicine and Companion Diagnostics Market 75
4.2.2 Predictive Molecular Diagnostics Market 76
4.2.3 Parallel Genetic Tests for Drug Development 77
4.2.4 Direct-to-Consumer Genetic Testing Market 78
4.2.5 Detecting Genetic Disorders 79
4.2.6 Pre-natal Screening 79
4.2.7 Neonatal Screening 79
4.2.8 Forensic Testing 80
4.2.9 Blood and Tissue Typing 80
4.2.10 Parentage Testing 80
4.2.11 DNA Sequencing 80
4.3 Market Drivers and Restraints 82
4.3.1 Market Drivers 82
4.3.2 Market Restraints 83
4.4 Market and Technology Trends 84
4.4.1 Market Trends 84
4.4.2 Technology Trends 84
4.5 Industry Challenges and Strategic Recommendations 85
4.6 Recent Industry Activity 87
4.6.1 M&A Activity 87
4.6.2 License Agreements and Partnerships 88
4.7 Business Models and Requirements for Successful Products in the Genetic Testing Industry 89
4.7.1 Commercial Manufacturing of Genetic Testing Products: Requirements 89
4.7.1.1 Regulatory Requirements 89
4.7.1.2 Manufacturing Process Scale 89
4.7.1.3 In-House Manufacturing 89
4.7.1.4 Contract Manufacturing: Commercial and Academic 90

5. Molecular Diagnostic Assays and Select Laboratories for Genetic Testing on the Market 92

5.1 Select Diagnostic Tests for Genetic Disorders 92
5.1.1 CombiMatrix DiagnosticsÕ DNAarrayª Pediatric Microarray Oligo 105K 92
5.1.2 GeneDxÕs Genetic Testing for Hereditary Disorders 92
5.1.3 HologicÕs Factor V Reagents 92
5.1.4 ProgenikaÕs FH Test 92
5.2 Carrier Tests for Genetic Disorders 93
5.2.1 Abbott MolecularÕs Cystic Fibrosis Genotyping Assay 93
5.2.2 CounsylÕs Universal Genetic Test 93
5.2.3 GenPathÕs InheriGen and InheriGen Plus 94
5.2.4 Good Start GeneticsÕ Good Start Select 94
5.2.5 HologicÕs InPlex¨ CF Molecular Test 94
5.2.6 Integrated GeneticÕs InheritestSM Carrier Screen 94
5.2.7 LuminexÕs xTAG Cystic Fibrosis (CFTR) v2 Assays 95
5.2.8 NateraÕs Natera Oneª Multi-Disease Genetic Carrier Screening Panel 95
5.2.9 SequenomÕs Heredi-Tª Cystic Fibrosis Carrier Screen Test 96
5.3 Pre-implantation Genetic Tests 96
5.3.1 NateraÕs Preimplantation Genetic Diagnosis (PGD) Test 96
5.4 Prenatal/In utero Molecular Genetic Screening Tests 97
5.4.1 Cell-free Fetal DNA Testing 97
5.4.1.1 Ariosa DiagnosticsÕ Harmonyª Prenatal Test 97
5.4.1.2 NateraÕs Panorama 98
5.4.1.3 SequenomÕs MaterniT21 PLUS Test 98
5.4.1.4 Verinata HealthÕs verifi¨ Prenatal Test 99
5.4.2 Molecular Cytogenetic Tests 99
5.4.2.1 Abbott MolecularÕs AneuVysion (Vysis CEP 18/X/Y-alpha satellite/LSI 13/21) Multicolor
DNA Probe Panel 99
5.4.2.2 CombiMatrix DiagnosticsÕ DNAarrayª Prenatal Microarrays 100
5.4.2.3 Signature GenomicsÕ Signature Precision Panelª I Prenatal 101
5.4.2.4 Signature GenomicsÕ Signature PrenatalChip¨TE (Targeted Enhanced) Microarray 101
5.4.2.5 Signature GenomicsÕ Signature PrenatalChip¨OS Microarray 102
5.5 Newborn Genetic Screening Tests 102
5.5.1 Screening for Cystic Fibrosis with Molecular Diagnostic Assays 102
5.5.2 Screening for SCID with the TREC Assay 102
5.5.2.1 PerkinElmer Genetics 103
5.6 Predictive and Presymptomatic Tests for Adult Onset Disorders 103
5.6.1 SequenomÕs RetnaGeneª AMD Test for Age-Related Macular Degeneration 103
5.7 Pharmacogenomics and Pharmacogenetics 103
5.7.1 Warfarin Sensitivity 104
5.7.2 EntroGenÕs Mutation Analysis and Genotyping Kits 104
5.7.3 QiagenÕs therascreen¨ KRAS RGQ PCR Kit 105
5.7.4 RocheÕs COBAS¨ AmpliPrep/COBAS¨ TaqMan¨ HLA-B*5701 Screening Test 105
5.7.5 Genomic Health Oncotype Tests 106
5.7.6 Life Technologies 106
5.7.6.1 Life TechnologiesÕ Pervenioª Lung RS Test 107
5.7.7 NanosphereÕs Veragene¨ Human Genetic Tests 107
5.7.8 AgendiaÕs SYMPHONYª Personalized Breast Cancer Profile 108
5.7.9 CardioDxÕs Corus CAD 109
5.7.10 VeracyteÕs Afirma Thyroid FNA Analysis 109
5.8 Tissue and Blood Typing Tests 109
5.8.1 ImmunocorÕs LIFECODES HLA Typing Kits 109
5.8.1.1 LIFECODES HLA SSO Typing Kits 109
5.8.1.2 LIFECODES HLA SSP Typing 110
5.8.2 Life Technology/InvitrogenÕs AllSet+ª Gold HLA Typing Kits 111
5.8.3 Life Technology/InvitrogenÕs SeCore¨ HLA Sequence-Based Typing Kits 111
5.8.4 One LambdaÕs LABType¨ SSO 111
5.8.5 ProgenikaÕs BLOODchipª 112
5.8.6 SequenomÕs SensiGene¨ Fetal RHD Genotyping Test 112
5.9 Paternity Tests 113
5.9.1 NateraÕs Non-Invasive Prenatal Paternity Test 113
5.10 Criminal and Forensics Tests 113
5.10.1 IntengenXÕs RapidHITª 200 Human DNA Identification System 113
5.10.2 NetBioÕs and GE Healthcare Life SciencesÕ DNAscan Rapid DNA Analysis System 113
5.10.3 Sorenson Forensics 114
5.11 Direct to Consumer Genetic Tests 114
5.11.1 23andMe 114
5.11.2 Lumigenix 115
5.11.3 DNA DTC 115
5.11.4 Family Tree DNA 115
5.11.5 Gene by Gene 115
5.11.6 AncestryDNA Test 116
5.12 Select Laboratories Providing Genetic Testing Services 116
5.12.1 Ambry Genetics 116
5.12.2 ARUP Laboratories 117
5.12.3 GeneDx 117
5.12.4 LabCorp and Integrated Genetics 119
5.12.5 Mayo Medical Laboratories 119
5.12.6 Medical Genetics Laboratory at Baylor College of Medicine 120
5.12.7 Pathway Genomics 121
5.12.8 Quest Diagnostics 121
5.13 Major Technology Platforms for Genetic Testing on the Market 121
5.14 Product Launches and Introductions 122
5.14.1 Ariosa Diagnostics Introduces Y-Chromosome Analysis Test Option 122
5.14.2 Ariosa Diagnostics Expands Harmony Prenatal Test to Twin Pregnancies and Launches New X,Y
Analysis Test 122
5.14.3 Natera Launches Panoramaª 123
5.14.4 Rubicon Genomics Launched Its New ThruPlex Technology and Partners with Agendia 123
5.14.5 Sequenom Center for Molecular Medicine Launches New Cystic Fibrosis Carrier Screen Test 123
5.14.6 Sequenom Launches the MaterniT21 PLUS 123
5.14.7 Next Generation Sequencing with RocheÕs GS Junior System Approved for Tissue Typing 124

6. Reimbursement and Billing Landscape for Molecular Diagnostic Genetic Testing 125

6.1 Overview 125
6.2 Trends in Healthcare Reimbursement Practices 126
6.2.1 Molecular Genetics Testing Reimbursement 127
6.3 Medicare Reimbursement Program 128
6.4 Medicare Billing Procedure 129
6.5 CPT Coding Rules for Molecular Diagnostics 131
6.5.1 Former Coding Rules for Molecular Diagnostics 132
6.5.2 Current Coding Rules for Molecular Diagnostics 132
6.5.2.1 Gapfilling 132
6.5.2.2 Reimbursement Delays for Molecular Diagnostics 133
6.6 Revenue Threats 134
6.6.1 Medicare Payment Exceptions 136
6.6.2 Three Areas for Denial of Claims 136
6.7 Bundled Payments for Care Improvement (BPCI) Initiative 137

7. Regulatory Issues for Genetic Testing 138

7.1 U.S. Food and Drug Administration 139
7.1.1 FDA Labeling Requirements 139
7.1.2 U.S. Government Regulation of Medical Devices 139
7.1.3 FDAÕs Qualification of Biomarkers 140
7.1.4 FDAÕs Voluntary Genomic Data Submission 141
7.2 Clinical Laboratory Improvement Act (CLIA) 142
7.3 CLIA Regulations 143
7.4 State Licensing for Service Laboratories 143
7.5 Multivariate Index Assays (IVDMIAs) 144
7.6 FDA Draft Guidance on In Vitro Companion Diagnostic Devices 145
7.7 Pre-Market Approval (PMA) 145
7.7.1 510(k) Clearance 145
7.8 De Novo Classification 146
7.9 Laboratory Developed Tests 147
7.9.1 Analyte Specific Reagents (ASRs) 149
7.10 U.S. Patent and Trademark Office (USPTO) 150
7.11 IRB Approval in Clinical Trials 150
7.12 CE marking and IVDD (European In Vitro Diagnostic Device Directive) 150
7.13 Research Use Only Reagents 150
7.14 Regulatory Issues for Direct to the Consumer Genetic Tests (DTC) 151
7.15 The Genetic Information Nondiscrimination Act of 2008 152
7.16 Genetic Tests and Medical Records 152
7.17 Recommendations by the American College of Medical Genetics and Genomics (ACMG) 153

8. Business Decisions, Strategic Outlook and Recommendations Using Molecular Diagnostic Tests in
Genetic Testing 154

8.1 Key Opportunities in Genetic Testing Development and Commercialization 154
8.2 What are the Current Obstacles in Molecular Diagnostic Genetic Testing Implementation? 154
8.3 How are Genetic Testing Products Driven by Business Strategies? 155
8.4 How might Novel Genetic Test Development Lead to Acquisition Strategies? 155
8.5 How can Genetic Tests Increase Value in Associated Drug Marketing Plans? 156
8.6 What Steps can be Taken in the Clinical Phases to Improve the Success Rate of Genetic Tests in Development? 156
8.7 How can Regulatory Oversight Drive Approval and Adoption of New Technologies? 156
8.8 What are the Noteworthy Deals? 157
8.9 How will Platform Technology Companies Enter the Space and Position Themselves for Diagnostic Development? 158
8.10 Will Pharma Integrate with Diagnostics? 158
8.11 How will Partnering and M&As Alter the Competitive Landscape? 159
8.12 How will FDA Regulations Impact New Diagnostic Tests? 159
8.13 What is Necessary for Incorporating Promising Molecular Tests into Clinical Practice 160
8.14 What is the Best Type of Business Model for Developing Genetic Testing Biomarkers? 161
8.15 How have Genetic Biomarkers Provided the Most Benefit in Genetic Testing? 161
8.16 What are the Most Innovative Methods in Development of Molecular Diagnostic Biomarkers? 162
9. Company Profiles 163

9.1 Abbott Laboratories 163
9.2 Beckman Coulter 166
9.3 CombiMatrix 169
9.4 EntroGen, Inc. 170
9.5 Genmark Diagnostics, Inc. 170
9.6 Genomic Health 170
9.7 Hologic, Inc. 171
9.8 Illumina, Inc. 175
9.9 IntegenX 176
9.10 Laboratory Corporation of America Holdings 176
9.11 Life Technologies Corporation 177
9.12 Luminex Corporation 179
9.13 Myriad Genetics, Inc. 179
9.14 Natera 181
9.15 NetBio 181
9.16 PerkinElmer Genetics 181
9.17 Progenika, Inc. 182
9.18 Roche Diagnostics 182
9.19 Sequenom, Inc. 183
9.20 Signature Genomics 184
9.21 Spartan Bioscience, Inc. 184
9.22 Transgenomic, Inc. 184

INDEX OF FIGURES

Figure 3.1: Segment of Double-Stranded DNA Showing the Base-Pair Relationship 40
Figure 3.2: Schematic of Molecular Diagnostics for Studying Gene Expression in Patients 47
Figure 3.3: The PCR Cycle 50
Figure 3.4: Multiple Displacement Amplification 56
Figure 3.5: Using DNA Microassays to Measure Gene Expression 61
Figure 4.1: Overall Structure of Nucleic Acid Testing Market 70
Figure 4.2: Segmentation of the Biomarker Development Market 76
Figure 6.1: Reimbursement for Diagnostics in Healthcare Decision Making 127
Figure 6.2: MAC Jurisdiction Map, 2012 133
Figure 7.1: Current Regulations for Laboratory Testing 138
Figure 7.2: Existing Regulatory Framework for LDTs 149

INDEX OF TABLES

Table 2.1: Common Genetic Disorders 19
Table 2.2: Recommended Uniform Screening Panel of the U.S. SecretaryÕs Advisory Committee on Heritable Disorders in Newborns and Children 24
Table 2.3: Potential Benefits of Pharmacogenetics 28
Table 2.4: Select Drugs with Commercially Available Pharmacogenetic Tests 29
Table 2.5: HLA Allele Nomenclature 36
Table 2.6: Comparison of HLA Typing Methods 37
Table 3.1: Key Assay Technologies for Molecular Diagnostics 49
Table 3.2: Emerging Molecular Diagnostic Technologies 49
Table 3.3: DNA Microarray Applications 60
Table 3.4: Companies Involved in Next Generation Sequencing Platforms 64
Table 3.5: Desired Characteristics for Clinical Versus Discovery Next Generation Sequencing 66
Table 4.1: Summary of Molecular Diagnostics Testing Sectors 70
Table 4.2: Global Market for Molecular Diagnostics Testing, 2008-2018 71
Table 4.3: Global Market for Molecular Genetic Testing, 2008-2018 72
Table 4.4: U.S. Market for Molecular Diagnostics Testing, 2008-2018 72
Table 4.5: U.S. Market for Molecular Genetic Testing, 2008-2018 73
Table 4.6: Diagnostic Companies with Existing Pharma Relationships 75
Table 4.7: Use of Cancer Biomarkers in Drug Development 77
Table 4.8: Utility of Biomarkers as Companion Diagnostics to Drug Development 77
Table 4.9: Competitors in the Field of Forensic Testing 80
Table 4.10: Competitors in the Field of Identity, Family and Paternity Testing 80
Table 4.11: Comparison of Current Genetic Testing Protocols and Potential Use of Whole Genome
Sequencing 81
Table 4.12: Molecular Diagnostics Market: Market Drivers Ranked in Order of Impact 83
Table 4.13: Drivers of the Genetic Analysis Market 83
Table 4.14: Molecular Diagnostics Market: Market Restraints Ranked in Order of Impact 84
Table 4.15: Total Molecular Genetic Testing Market: Impact of Top Industry Challenges (U.S.) 86
Table 4.16: The Required Elements of a Manufacturing Facility 90
Table 4.17: CMO Qualification Audit: Points to Investigate 91
Table 6.1: Factors Determining Third-Party Payment for Molecular Diagnostic Tests 134
Table 7.1: Regulatory Rules that Affect the Ability of a Diagnostic Testing Reagent Company to
Conduct Business 138
Table 7.2: Strengths of the 510k Process 146
Table 7.3: Drawbacks of the 510k Process 146
Table 8.1: Effect of Regulation on MD Infectious Disease Market Technology Platforms, 2007 and 2015 156
Table 8.2: Impediments to Incorporating Promising Molecular Tests into Clinical Practice 160

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In_Vitro_Diagnostic Industry: Molecular Diagnostics in Genetic Testing

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