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===Introduction to Genetic and Genomic Diagnostics===
===Introduction to Genetic and Genomic Diagnostics===


The field of Biotechnology is a critical US industry, by some estimates approaching 2% of the US GPD and growing 15% per year. Genetic and Genomic research represent a core focus of research and development in the biotechnology industry.  Over the last 30 years, improvements in sequencing technology have led to massive increases in test precision and overall throughput capacity.  These advances have bolstered the breadth of genetic and genomic research, and have allowed these fields to transcend from mere laboratory concepts to a number of practical, real world applications.  
The field of Biotechnology is a critical US industry, by some estimates approaching 2% of the US GPD and growing 15% per year. Genetic and Genomic research represent a core focus of R&D in the biotechnology industry.  Over the last 40 years, improvements in sequencing technology have led to massive increases in test precision and overall throughput capacity.  These advances have bolstered the breadth of genetic and genomic research, and have allowed these fields to transcend from mere laboratory concepts to a number of practical, real world applications.  


Today, these research efforts have contributed clinical diagnostic methods of testing that are capable of providing information specific to the genetic characteristics of an individual. The logical core of diagnostics is the link between a health state, such as a disease or drug response, and particular genetic sequence (often a mutation therein).  Once this link is clinically established, a test can readily be developed based on existing techquies.  Thus, the acutal methods that are developed are not often based on new measurement or sampling techniques, but rather, newly discovered links between genotype and phenotype.
Today, these research efforts have contributed clinical diagnostic methods of testing that are capable of providing information specific to the genetic characteristics of an individual. The logical core of diagnostics is the link between a health state, such as a disease or drug response, and particular genetic sequence (often a mutation therein).  Once this link is clinically established, a test can readily be developed based on existing techniques.  Thus, the actual methods that are developed are not often based on new measurement or sampling techniques, but rather, newly discovered links between genotype and phenotype.


Through these tests a clinician can perceive a wealth of information, including an individual's disposition to develop complex diseases over time, such as cancer, heart disease, asthma, and diabeties, and allow the clinician to advise practical changes in lifestyle to minimize health future health risks or maximize preventative medical care.  In cases where disease may already be present, some tests are useful for determining more efficient methods of treatment that are specific to that individual.  The diagnostic tests range from single tests which evaluate a single gene and its affects to others, which are more comprehensive, and can evaluate samples on the genomic level, which are capable of analyzing multiple genetic factors.   
Through these tests a clinician can perceive a wealth of information, including an individual's disposition to develop complex diseases over time, such as cancer, heart disease, asthma, and diabetes, and allow the clinician to advise practical changes in lifestyle to minimize health future health risks or maximize preventative medical care.  In cases where disease may already be present, some tests are useful for determining more efficient methods of treatment that are specific to that individual.  The diagnostic tests range from single tests which evaluate a single gene and its affects to others, which are more comprehensive, and can evaluate samples on the genomic level, which are capable of analyzing multiple genetic factors.   


These tests represent valuable assets to the companies who develop them and bring them to market in the form of consumer product offerings. Currently, diagnostic tests are being marketed to the public in a three different ways: Laboratory Developed Test Services, In Vitro Diagnostic Kits, and Tests Sold Directly to Consumers.  It should be no suprise that these companies seek robust legal protection for their investments in the form of intellectual proeprty ("IP"). For instance, many companies obtain patents for their inventions that grant them a legal mechanism to exclude others from utilizing their research and development efforts.  However, these protections occasionally affect research and development efforts of others in these fields negatively.
These tests represent valuable assets to the companies who develop them and bring them to market in the form of consumer product offerings. Currently, diagnostic tests are being marketed to the public in a three different ways: Laboratory Developed Test Services, In Vitro Diagnostic Kits, and Tests Sold Directly to Consumers.  It should be no surprise that these companies seek robust legal protection for their investments in the form of intellectual property ("IP"). For instance, many companies obtain patents for their inventions that grant them a legal mechanism to exclude others from utilizing their research and development efforts.  However, these protections occasionally affect research and development efforts of others in these fields negatively.


Emerging research in genetic and genomic diagnostics presents unique challenges for IP considerations.  Changes in laboratory research due to actual or anticipated patent or license enforcement could signal the failure of protections secured through intellectual property to spur the innovations such protections are intended to promote.  These issues are at the center of our research efforts under the Industrial Cooperation Project at the Harvard University's Berkman Center for Internet & Society.  This research is part of a broader project beind led by Professor Yochai Benkler.  Through the research, we seek to understand the approaches to innovation with genetic diagnostic kits, and look specifically to the barriers to use and innovation.   
Emerging research in genetic and genomic diagnostics presents unique challenges for IP considerations.  Changes in laboratory research due to actual or anticipated patent or license enforcement could signal the failure of protections secured through intellectual property to spur the innovations such protections are intended to promote.  These issues are at the center of our research efforts under the Industrial Cooperation Project at the Harvard University's Berkman Center for Internet & Society.  This research is part of a broader project being led by Professor Yochai Benkler.  Through the research, we seek to understand the approaches to innovation with genetic diagnostic kits, and look specifically to the barriers to use and innovation.   


==Resources==
==Resources==
Line 21: Line 21:


==Defining Genetics and Genomics==
==Defining Genetics and Genomics==
Understanding the definitions of "Genetics" and "Genomics" and how these terms are used in practice is a helpful precursor to discussing the broader issues presented in the diagnostics sector.  These terms are often confused because the distinctions between "genetic" and "genomic" diagnostics are rarely delineated well, if at all. Consequently, discussions of their market, innovation cycles and the impact of intellectual property in the emergence of open or closed arrangements of cooperation is less than precise.  For instance, in a 2008 report, The Secretary’s Advisory Committee on Genetics, Health, and Society (pg. 17) defined this class of tests as those that involve generally the analysis of human DNA, RNA, genes, or gene products to detect mutations, genotypes, and phenotypes related to disease and health. As of 10/22/2009, http://genetests.org lists 1557 disease conditions for which clinical genetic tests are commercially available, and the number is growing by at least 7% per year. However, despite this growth, fewer tests and therapeutics are reaching the market than would be expected based on major scientific achievement and investment in the field. This phenomenon is termed the "pipeline problem" in the literature. We will explore this phenomeon under the Section XXX
Understanding the definitions of "Genetics" and "Genomics" and how these terms are used in practice is a helpful precursor to discussing the broader issues presented in the diagnostics sector.  These terms are often confused because the distinctions between "genetic" and "genomic" diagnostics are rarely delineated well, if at all. Consequently, discussions of their market, innovation cycles and the impact of intellectual property in the emergence of open or closed arrangements of cooperation is less than precise.  For instance, in a 2008 report, The Secretary’s Advisory Committee on Genetics, Health, and Society (pg. 17) defined this class of tests as those that involve generally the analysis of human DNA, RNA, genes, or gene products to detect mutations, genotypes, and phenotypes related to disease and health.  


A more rigorous definition can be done by approaching this challenge from a [technology-historical] perspective we may find some guidance. For instance, "The invention of the [[A_brief_history_of_license_practices_in_BGP_-_the_case_of_PCR PCR -  Polymerase Chain Reaction]], back in 1985, and the rapid pace at which novel genetic defects have been identified since 'positional cloning' came of age in the early 1990s, have greatly increased the possibilities for genetic diagnosis. Over the past two decades, the number of diagnostic tests has steadily increased." [2]
[Q:  what is the problem with the SACGHS definition of "tests" and what class of tests are they referring to? No distinctions at all? Over/under inclusive?]
===Understanding Genetic and Genomic Diagnostic Distinctions===
In simple terms, "Genetics" can be defined as the scientific study of single genes and their effects. Genes are units of heredity that carry the instructions for making proteins, which direct the activities of cells and functions of the body. Genetics is also term that refers to the study of genes and their role in inheritance - the way certain traits or conditions are passed down from one generation to another. Genes influence traits such as hair and eye color as well as health and disease development. Genetics determines much, but not all, of a person's appearance and health status. Environmental factors also play a part. Many disorders of the human body, such as disease and illness, are linked to abnormal gene function.    For example, single gene disorders include cystic fibrosis and PKU (phenylketonuria).   For more examples, see [http://www.Genome.gov Genome.gov] and [http://www.CDC.gov CDC.gov Genetics].


==Understanding Genetic and Genomic Diagnostic Distinctions==
Thus, "Genetic Diagnostics" is clinical testing of ''singular genes'', by assaying a relatively small sample containing DNA, to determine genotype and identify genetic abnormalities known to be link to disease. Additionally, these tests can determine the prognosis of disease, potential responses to drug treatment, and other factors related to the state of health of the sample provider.  
Genetics involves scientific studies of single genes and their effects. Genes (units of heredity) carry the instructions for making proteins, which direct the activities of cells and functions of the body. Genetics is also term that refers to the study of genes and their role in inheritance - the way certain traits or conditions are passed down from one generation to another.  Genes influence traits such as hair and eye color as well as health and disease development. Genetics determines much (but not all) of a person's appearance and health status, but environmental differences also play a part. Examples of single gene disorders that would be considered as "genetics" include cystic fibrosis and PKU (phenylketonuria). More at Genome.gov and at CDC.gov Genetics.  


Thus, genetic diagnostics (or "GDx") assay a relatively small piece of DNA and/or make a relatively small number of measurement to determine genotype and identify genetic variation known to be related to disease, it's prognosis, drug response, and other heath states. [1]. Over the last 30 years, improvements in sequencing technology have led to massive increases in test throughput, resulting in an accelerating discovery of new genetic targets for diagnostics and a new class diagnostics, genomic diagnostics, based themselves on the high-throughput techniques.
On the other hand, "Genomics" is a relatively new term that describes the study of all of a person's genes including interactions of those genes with each other and the person's environment. Genomics involves the scientific study of complex diseases such as heart disease, asthma, diabetes and cancer because they are caused more by a combination of genetic and environmental factors. Genomics is offering new possibilities for therapies and treatment of some diseases, as well as new diagnostic methods. The major tools and methods related to Genomics studies are bioinformatics, genetic analysis, measurement of gene expression, and determination of gene function. More at Genome.gov and at and at CDC.gov Genomics and Health Resources and CDC.gov Genomics Translation Resources


Genomic diagnostics are capable of many more measurements than genetic diagnostics, often the complete sequence of several genes to the entire genome, or of hundreds of thousands of SNPs from a genomic sample. In this sense, genomic tests "provide comprehensive genetic risk profiles for many diseases or targeted genetic risk profiles for specific conditions (e.g., breast cancer)" (Scientific Foundations for Personal Genomics paper) and are often based on microarrays (sometimes called SNP chips or gene chips) or second generation (still called "next-generation" sequencing circa 2010), high-throughput DNA sequencing.  Microarrays are widely used in direct-to-consumer genomic diagnostics designed to provide risk profiles for many genetic diseases at once (see DTC+Genomics cell in the table for examples). For instance, Myriad Genetic's BRCAanalysis diagnostic is based on direct sequencing of BRCA1 and BRCA2 genes.  
However, the phrase "Genomic Diagnostic" tends to be used differently than the scientific meaning of "Genomics."  The majority of Genomic Diagnostics that are available today are based on second generation sequencing platforms. Today, this type of diagnostic refers to the testing of fractions of the complete human genome of a person. These tests evaluate mutiple genes and are significantly larger than what is typically analyzed in a typical "Genetic Diagnostic." Although whole genome sequencing is possible, these tests are quite expensive and the term "Genomic Diagnostic" is used to refer to the tests of portions, or fractions, of the entire genome. Perhaps, a more apt term to define this type of diagnostic, is "multiplex genetic tests," because they represent genetic diagnostics that are highly parallelized and have a relatively high-throughput, but are not based on a complete genome sequence.    


Direct sequencing of whole genes is thus the preferred technique for providing comprehensive risk profiles for specific diseases. Genomics involves the scientific study of complex diseases such as heart disease, asthma, diabetes and cancer because they are caused more by a combination of genetic and environmental factors. Genomics is offering new possibilities for therapies and treatment of some diseases, as well as new diagnostic methods. The major tools and methods related to genomics studies are bioinformatics, genetic analysis, measurement of gene expression, and determination of gene function. More at Genome.gov and at and at CDC.gov Genomics and Health Resources and CDC.gov Genomics Translation Resources
"Genomic Diagnostics", as in the popular usage of the term, are capable of many more measurements than genetic diagnostics. Often these tests completely sequence several genes to the entire genome, or of hundreds of thousands of SNPs from a genomic sample and tend to use microarrays (sometimes called SNP chips or gene chips) or second generation (still called "next-generation" sequencing circa 2010), high-throughput DNA sequencing.  Microarrays are widely used in direct-to-consumer genomic diagnostics designed to provide risk profiles for many genetic diseases at once (see DTC+Genomics cell in the table for examples). These tests are highly useful for more complex diseases that caused by ''multiple'' genetic abnormalities, rather than single abnormal genes.  In this sense, Genomic diagnostics "provide comprehensive genetic risk profiles for many diseases or targeted genetic risk profiles for specific conditions." (Scientific Foundations for Personal Genomics paper)  Examples of disease caused by multiple genetic disorders include asthma, heart disease, autism, cancer, and hypertension.  
 
However, in practice, "Genomic Diagnostics" still is something of a misleading term, because the genomic diagnostics that are available today are based on second generation sequencing platforms on which whole-genome sequencing is still quite expensive.  Consequently, "genomic diagnostics" today refers to tests that involve the measurement of fractions of the complete genome of a person that are significantly larger than what is typically analyzed with typical genetic tests, although that fraction may be much less than the complete genome. A more accurate term would be "multiplex genetic tests": genetic diagnostics that are highly parallelized and have a relatively high-throughput, but are not based on a complete genome sequence.
 
In-Vitro Diagnostic Multivariate Index Assays (IVDMIA) are a specific class of diagnostic in which multiple data points, for instance from a variety of mutations in a set of genes or the expression levels of those genes, are measured and then combined into a single score or metric by an (often proprietary) algorithm.  The FDA defines IVDMIAs as "test systems that employ data, derived in part from one or more in vitro assays, and an algorithm that usually, but not necessarily, runs on software to generate a result that diagnoses a disease or condition, or is used in the cure, mitigation, treatment, or prevention of disease."(FDA 1610). Note that an IVDMIA could be based around a microarray or direct sequencing; they defining characteristic is the combination of the multiple measurements into a single score by a cryptic algorithm.
 
Ultimately, manufacturers would like to develop, and clinicians would like to use, diagnostics based on multiplex genetic measurements or whole genome sequencing (link to "two types of genomics"), which would be more cost-effective than multiple single tests. (SACGHS Patents line 1459)


==Understanding the Diagnostics Market==
==Understanding the Diagnostics Market==
Although market data is readily available for molecular / esoteric diagnostics, it usually is not broken into further sub-categories, making it difficult to find market information specifically for genetic tests.   
Although market data is readily available for molecular / esoteric diagnostics, it usually is not broken into further sub-categories, making it difficult to find market information specifically for genetic tests.  According to [http://genetests.org genetests.org], there are genetic tests for more than 1,574 diseases. Generally speaking, genomic and genetic diagnostic tests are available to the public in three different ways: Laboratory Developed Tests services (LDT), In Vitro Diagnostics Kits (IVD), and Direct to Consumers (DTC) as "over the counter" kits.   


In-Vitro Diagnostic Multivariate Index Assays ("IVDMIAs") are another specific class of diagnostics which expound on Genetic and Genomic diagnostics as discussed above.  These tests utilize multiple data points from a variety of mutations in a set of genes, or the expression levels of those genes, and then combined the results into a single score or metric by an (often proprietary) algorithm.  The FDA defines IVDMIAs as "test systems that employ data, derived in part from one or more in vitro assays, and an algorithm that usually, but not necessarily, runs on software to generate a result that diagnoses a disease or condition, or is used in the cure, mitigation, treatment, or prevention of disease."(FDA 1610).  Note that an IVDMIA could be based around a microarray or direct sequencing; they defining characteristic is the combination of the multiple measurements into a single score by a cryptic algorithm.


Generally speaking, these two kind tests - genomics and genetics -  are delivered to users in three different ways: Laboratory Developed Tests services (LDT), In Vitro Diagnostics Kits (IVD), Direct to Consumers (DTC) or Over the Counter Diagnostic Kist (OTC) The table below provide a general framework for this categorization.
The table below provide a general framework for this categorization.


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===Market Participants in Personal Genomics===
==== Sequencer Manufacturers ====
* Illumina
* Solexa
* 454
* CompleteGenomics.com
* PacificBio
* Helicos
==== Full Genome Sequencing providers ====
* [http://knome.com/home/ Knome.com]: full genomic sequencing and 2 years research updates; personal genetic counseling.  Only $68,500.
* [http://everygenome.com/ EveryGenome.com]: $48,000 full genome sequencing by Illumina. Requires physician request.
* [http://www.personalgenomes.org/ PersonalGenomes.org]: Plans to offer free genomic sequencing to 100,000 volunteers.  Currently working on the first 100.  Jason Bobe works here.
==== Recreational and Clinical Genomic diagnostics ====
* Coriell Personal Medicine Collaborative - [http://cpmc.coriell.org/ cpmc.coriell.org]: Free Affymetrix GeneChip SNP sequencing, but only for "potentially medically actionable" conditions. Currently this list includes 10
conditions, and will grow as the Informed Cohort Oversight Board approves more conditions.
* [http://www.23andme.com/ 23andMe.com]: Offers ancestry and health genomic analysis with an Illumina 550,000 SNP chip for between $399-$499.  Results are not clinically useful.
* [http://www.decodeme.com/ DeCODEme.com]: $195 - $985 for up to 48 genetic conditions using a 100,000 SNP chip.  In Bankruptcy proceedings.
* [http://www.counsyl.com/ Counsyl.com]: offers a (I presume) a chip-based screen for 100 genetic disease markers, including some for cystic fibrosis. Trying to sell both direct to consumers and clinically and aiming for insurance coverage.  DTC costs $349.  Not sure how they ensure the results are clinically useful.
* [http://www.navigenics.com/ Navigenics.com]: offers chip-based testing for 28 different conditions along with personal genetic counseling for $999.  Not sure how they ensure the results are clinically useful.  Want to be clinically used.
* [http://www.pathway.com/ PathwayGenomics.com]: offers carrier testing for 61 genetic diseases, metabolism genes for 9 different drugs, as well as ancestry analysis for $199-$399. Not sure how they ensure the results are clinically useful.
* [http://www.dnadirect.com/web/ DNADirect.com] - not sure what their product is.
* [http://genomichealth.com/ GenomicHealth.com] / [http://oncotypedx.com/ OncotypeDX.com] : 21-gene expression assay that predicts recurrence of certain kinds of breast cancer. Considered a multivariate assay and regulated by the FDA; has more clinical data than most other genetic diagnostics demonstrating it's clinical validity and utility.  Covered my insurance more often than other tests.
==== Reference labs ====
"The major national reference labs including Quest, LabCorp, Specialty/Ameripath, Mayo and others account for at least 60% of the market for esoteric test services.  The remaining 40% is shared by a group of some 3000 small, local market laboratories.  The major reference labs have built a comprehensive menu of specialized test services and continue to expand their offerings via collaborations with leading medical research centers.  They offer a huge presence in the market and manage distribution networks that touch just about every medical specialty.  Thus many CLIA-registered company sponsored test services avail themselves of the marketing resources offered by the national reference labs."
Quest and Labcorp are the two most dominant national reference labs.  Financial information can be gotten from the SEC by using the ''Standard Industrial Classification'' [http://www.sec.gov/cgi-bin/browse-edgar?action=getcompany&SIC=8071 8071: Services - medical laboratories], which includes Quest, Lab-Corp, Bio-Reference, Athena, and ~120 others.
* [http://en.wikipedia.org/wiki/Quest_Diagnostics Quest] (wikipedia) [http://www.wikinvest.com/stock/Quest_Diagnostics_(DGX) DGX] stock symbol. (SEC CIK#: [http://www.sec.gov/cgi-bin/browse-edgar?action=getcompany&CIK=0001022079&owner=include&count=40 0001022079] )
** [http://www.sec.gov/Archives/edgar/data/1022079/000093041309000848/c56618_10-k.htm 2008 10-K - Annual Report]
***  Net Sales of gene-based & esoteric tests: $1,400 Million (20% of total revenue).
* [http://en.wikipedia.org/wiki/LabCorp LabCorp] wikipedia. [http://www.wikinvest.com/stock/Laboratory_Corporation_of_America_Holdings_%28LH%29?ref=topnav LH] stock symbol. (SEC CIK# [http://www.sec.gov/cgi-bin/browse-edgar?action=getcompany&CIK=0000920148&owner=include&count=40 0000920148])
** [http://www.sec.gov/Archives/edgar/data/920148/000092014809000015/labcorp10k.htm 2008 10-K - Annual Report]
*** Net Sales of Genomic & Esoteric tests: $1,478.3 Million (+5.9% from 2007)
*** Volume of Genomic & Esoteric tests: 23.7 Million
*** Patents, licences, and technology "2008 gross carrying amount": 94.7 million
* Bio-Reference Laboratories INC (SEC CIK# [http://www.sec.gov/cgi-bin/browse-edgar?action=getcompany&CIK=0000792641&owner=include&count=40 0000792641])
** [http://www.sec.gov/Archives/edgar/data/792641/000110465909002204/a09-3066_110k.htm 2008 10-K - Annual Report]
*** Net revenue from esoteric tests (50%): $150.5 Million
* Athena Diagnostics INC (SEC CIK# [http://www.sec.gov/cgi-bin/browse-edgar?action=getcompany&CIK=0001161704&owner=include&count=40 0001161704])
==Regulation of Diagnostics==


==Navigation==
==Navigation==

Revision as of 18:12, 30 April 2010

Introduction to Genetic and Genomic Diagnostics

The field of Biotechnology is a critical US industry, by some estimates approaching 2% of the US GPD and growing 15% per year. Genetic and Genomic research represent a core focus of R&D in the biotechnology industry. Over the last 40 years, improvements in sequencing technology have led to massive increases in test precision and overall throughput capacity. These advances have bolstered the breadth of genetic and genomic research, and have allowed these fields to transcend from mere laboratory concepts to a number of practical, real world applications.

Today, these research efforts have contributed clinical diagnostic methods of testing that are capable of providing information specific to the genetic characteristics of an individual. The logical core of diagnostics is the link between a health state, such as a disease or drug response, and particular genetic sequence (often a mutation therein). Once this link is clinically established, a test can readily be developed based on existing techniques. Thus, the actual methods that are developed are not often based on new measurement or sampling techniques, but rather, newly discovered links between genotype and phenotype.

Through these tests a clinician can perceive a wealth of information, including an individual's disposition to develop complex diseases over time, such as cancer, heart disease, asthma, and diabetes, and allow the clinician to advise practical changes in lifestyle to minimize health future health risks or maximize preventative medical care. In cases where disease may already be present, some tests are useful for determining more efficient methods of treatment that are specific to that individual. The diagnostic tests range from single tests which evaluate a single gene and its affects to others, which are more comprehensive, and can evaluate samples on the genomic level, which are capable of analyzing multiple genetic factors.

These tests represent valuable assets to the companies who develop them and bring them to market in the form of consumer product offerings. Currently, diagnostic tests are being marketed to the public in a three different ways: Laboratory Developed Test Services, In Vitro Diagnostic Kits, and Tests Sold Directly to Consumers. It should be no surprise that these companies seek robust legal protection for their investments in the form of intellectual property ("IP"). For instance, many companies obtain patents for their inventions that grant them a legal mechanism to exclude others from utilizing their research and development efforts. However, these protections occasionally affect research and development efforts of others in these fields negatively.

Emerging research in genetic and genomic diagnostics presents unique challenges for IP considerations. Changes in laboratory research due to actual or anticipated patent or license enforcement could signal the failure of protections secured through intellectual property to spur the innovations such protections are intended to promote. These issues are at the center of our research efforts under the Industrial Cooperation Project at the Harvard University's Berkman Center for Internet & Society. This research is part of a broader project being led by Professor Yochai Benkler. Through the research, we seek to understand the approaches to innovation with genetic diagnostic kits, and look specifically to the barriers to use and innovation.

Resources

The following resources may helpful for understanding key concepts discussed in our research:

Research Vocabulary

Bibliography by Resource Type

Bibliography by Research Question

Defining Genetics and Genomics

Understanding the definitions of "Genetics" and "Genomics" and how these terms are used in practice is a helpful precursor to discussing the broader issues presented in the diagnostics sector. These terms are often confused because the distinctions between "genetic" and "genomic" diagnostics are rarely delineated well, if at all. Consequently, discussions of their market, innovation cycles and the impact of intellectual property in the emergence of open or closed arrangements of cooperation is less than precise. For instance, in a 2008 report, The Secretary’s Advisory Committee on Genetics, Health, and Society (pg. 17) defined this class of tests as those that involve generally the analysis of human DNA, RNA, genes, or gene products to detect mutations, genotypes, and phenotypes related to disease and health.

[Q: what is the problem with the SACGHS definition of "tests" and what class of tests are they referring to? No distinctions at all? Over/under inclusive?]

Understanding Genetic and Genomic Diagnostic Distinctions

In simple terms, "Genetics" can be defined as the scientific study of single genes and their effects. Genes are units of heredity that carry the instructions for making proteins, which direct the activities of cells and functions of the body. Genetics is also term that refers to the study of genes and their role in inheritance - the way certain traits or conditions are passed down from one generation to another. Genes influence traits such as hair and eye color as well as health and disease development. Genetics determines much, but not all, of a person's appearance and health status. Environmental factors also play a part. Many disorders of the human body, such as disease and illness, are linked to abnormal gene function. For example, single gene disorders include cystic fibrosis and PKU (phenylketonuria). For more examples, see Genome.gov and CDC.gov Genetics.

Thus, "Genetic Diagnostics" is clinical testing of singular genes, by assaying a relatively small sample containing DNA, to determine genotype and identify genetic abnormalities known to be link to disease. Additionally, these tests can determine the prognosis of disease, potential responses to drug treatment, and other factors related to the state of health of the sample provider.

On the other hand, "Genomics" is a relatively new term that describes the study of all of a person's genes including interactions of those genes with each other and the person's environment. Genomics involves the scientific study of complex diseases such as heart disease, asthma, diabetes and cancer because they are caused more by a combination of genetic and environmental factors. Genomics is offering new possibilities for therapies and treatment of some diseases, as well as new diagnostic methods. The major tools and methods related to Genomics studies are bioinformatics, genetic analysis, measurement of gene expression, and determination of gene function. More at Genome.gov and at and at CDC.gov Genomics and Health Resources and CDC.gov Genomics Translation Resources

However, the phrase "Genomic Diagnostic" tends to be used differently than the scientific meaning of "Genomics." The majority of Genomic Diagnostics that are available today are based on second generation sequencing platforms. Today, this type of diagnostic refers to the testing of fractions of the complete human genome of a person. These tests evaluate mutiple genes and are significantly larger than what is typically analyzed in a typical "Genetic Diagnostic." Although whole genome sequencing is possible, these tests are quite expensive and the term "Genomic Diagnostic" is used to refer to the tests of portions, or fractions, of the entire genome. Perhaps, a more apt term to define this type of diagnostic, is "multiplex genetic tests," because they represent genetic diagnostics that are highly parallelized and have a relatively high-throughput, but are not based on a complete genome sequence.

"Genomic Diagnostics", as in the popular usage of the term, are capable of many more measurements than genetic diagnostics. Often these tests completely sequence several genes to the entire genome, or of hundreds of thousands of SNPs from a genomic sample and tend to use microarrays (sometimes called SNP chips or gene chips) or second generation (still called "next-generation" sequencing circa 2010), high-throughput DNA sequencing. Microarrays are widely used in direct-to-consumer genomic diagnostics designed to provide risk profiles for many genetic diseases at once (see DTC+Genomics cell in the table for examples). These tests are highly useful for more complex diseases that caused by multiple genetic abnormalities, rather than single abnormal genes. In this sense, Genomic diagnostics "provide comprehensive genetic risk profiles for many diseases or targeted genetic risk profiles for specific conditions." (Scientific Foundations for Personal Genomics paper) Examples of disease caused by multiple genetic disorders include asthma, heart disease, autism, cancer, and hypertension.

Understanding the Diagnostics Market

Although market data is readily available for molecular / esoteric diagnostics, it usually is not broken into further sub-categories, making it difficult to find market information specifically for genetic tests. According to genetests.org, there are genetic tests for more than 1,574 diseases. Generally speaking, genomic and genetic diagnostic tests are available to the public in three different ways: Laboratory Developed Tests services (LDT), In Vitro Diagnostics Kits (IVD), and Direct to Consumers (DTC) as "over the counter" kits.

In-Vitro Diagnostic Multivariate Index Assays ("IVDMIAs") are another specific class of diagnostics which expound on Genetic and Genomic diagnostics as discussed above. These tests utilize multiple data points from a variety of mutations in a set of genes, or the expression levels of those genes, and then combined the results into a single score or metric by an (often proprietary) algorithm. The FDA defines IVDMIAs as "test systems that employ data, derived in part from one or more in vitro assays, and an algorithm that usually, but not necessarily, runs on software to generate a result that diagnoses a disease or condition, or is used in the cure, mitigation, treatment, or prevention of disease."(FDA 1610). Note that an IVDMIA could be based around a microarray or direct sequencing; they defining characteristic is the combination of the multiple measurements into a single score by a cryptic algorithm.

The table below provide a general framework for this categorization.

Diagnostic Kits Available on Market
Marketing Method Examples of Genetic Tests Examples of Genomic Kits
Products sold in Kits ? Myriad, oncotypeDX,
LDTS genetests.org deCodeMe, navigenics, DNA Direct, pathway, counsyl
DTC (clinical) DNA Direct http://www.dnapolicy.org/news.release.php?action=detail&pressrelease_id=137
DTC (recreational) ? 23andme

Market Participants in Personal Genomics

Sequencer Manufacturers

  • Illumina
  • Solexa
  • 454
  • CompleteGenomics.com
  • PacificBio
  • Helicos

Full Genome Sequencing providers

  • Knome.com: full genomic sequencing and 2 years research updates; personal genetic counseling. Only $68,500.
  • EveryGenome.com: $48,000 full genome sequencing by Illumina. Requires physician request.
  • PersonalGenomes.org: Plans to offer free genomic sequencing to 100,000 volunteers. Currently working on the first 100. Jason Bobe works here.

Recreational and Clinical Genomic diagnostics

  • Coriell Personal Medicine Collaborative - cpmc.coriell.org: Free Affymetrix GeneChip SNP sequencing, but only for "potentially medically actionable" conditions. Currently this list includes 10

conditions, and will grow as the Informed Cohort Oversight Board approves more conditions.

  • 23andMe.com: Offers ancestry and health genomic analysis with an Illumina 550,000 SNP chip for between $399-$499. Results are not clinically useful.
  • DeCODEme.com: $195 - $985 for up to 48 genetic conditions using a 100,000 SNP chip. In Bankruptcy proceedings.
  • Counsyl.com: offers a (I presume) a chip-based screen for 100 genetic disease markers, including some for cystic fibrosis. Trying to sell both direct to consumers and clinically and aiming for insurance coverage. DTC costs $349. Not sure how they ensure the results are clinically useful.
  • Navigenics.com: offers chip-based testing for 28 different conditions along with personal genetic counseling for $999. Not sure how they ensure the results are clinically useful. Want to be clinically used.
  • PathwayGenomics.com: offers carrier testing for 61 genetic diseases, metabolism genes for 9 different drugs, as well as ancestry analysis for $199-$399. Not sure how they ensure the results are clinically useful.
  • DNADirect.com - not sure what their product is.
  • GenomicHealth.com / OncotypeDX.com : 21-gene expression assay that predicts recurrence of certain kinds of breast cancer. Considered a multivariate assay and regulated by the FDA; has more clinical data than most other genetic diagnostics demonstrating it's clinical validity and utility. Covered my insurance more often than other tests.

Reference labs

"The major national reference labs including Quest, LabCorp, Specialty/Ameripath, Mayo and others account for at least 60% of the market for esoteric test services. The remaining 40% is shared by a group of some 3000 small, local market laboratories. The major reference labs have built a comprehensive menu of specialized test services and continue to expand their offerings via collaborations with leading medical research centers. They offer a huge presence in the market and manage distribution networks that touch just about every medical specialty. Thus many CLIA-registered company sponsored test services avail themselves of the marketing resources offered by the national reference labs."

Quest and Labcorp are the two most dominant national reference labs. Financial information can be gotten from the SEC by using the Standard Industrial Classification 8071: Services - medical laboratories, which includes Quest, Lab-Corp, Bio-Reference, Athena, and ~120 others.

  • LabCorp wikipedia. LH stock symbol. (SEC CIK# 0000920148)
    • 2008 10-K - Annual Report
      • Net Sales of Genomic & Esoteric tests: $1,478.3 Million (+5.9% from 2007)
      • Volume of Genomic & Esoteric tests: 23.7 Million
      • Patents, licences, and technology "2008 gross carrying amount": 94.7 million

Regulation of Diagnostics

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