DNAPrint Genomics

Last updated
DNAPrint Genomics
Company type Public
Expert Market :  DNAG
Industry Genomics, Forensic Science
Headquarters Sarasota, Florida
Key people
 Richard Gabriel (CEO)
Hector J. Gomez, Chief Medical Officer
Tony Frudakis, Co-Founder & Chief Scientific Officer
Products Pharmacogenomics, Genomic profiling, Genotyping
Website www.dnaprint.com

DNAPrint Genomics was a genetics company with a wide range of products related to genetic profiling. They were the first company to introduce forensic and consumer genomics products, which were developed immediately upon the publication of the first complete draft of the human genome in the early 2000s. They researched, developed, and marketed the first ever consumer genomics product, based on "Ancestry Informative Markers" which they used to correctly identify the BioGeographical Ancestry (BGA) of a human based on a sample of their DNA. They also researched, developed and marketed the first ever forensic genomics product - DNAWITNESS - which was used to create a physical profile of donors of crime scene DNA. The company reached a peak of roughly $3M/year revenues but ceased operations in February 2009. [1] [2]

Contents

Consumer applications

DNAPrint Genomics' flagship product was "AncestryByDNA", a DNA test for its consumers that breaks down the percentage ancestry of a client, based on Ancestry Informative Markers (SNP polymorphisms) their DNA. AncestryByDNA was a historical product, representing the first consumer genomics product ever developed and marketed in the US and probably world-wide. It was marketed as a tool for personal genealogical research, and for adoptees looking to learn more about their genealogy. [3]

Forensic applications

DNAPrint's most controversial offering was "DNAWitness", a product that uses the same Ancestry Informative Markers for a forensic purpose, as well as polymorphisms in the human OCA2 gene and others to make inference about iris (eye), hair and skin color. DNAPrint was the first to research and publish the linkages between OCA2 polymorphisms and human eye color and by integrating these with the same ancestry informative markers used with its consumer BGA tests for analysis with DNA evidence from crime scenes, DNAPrint Genomics was able to help narrow down suspects based on the construction of an "in-silco constructed, database driven" physical trait or phenotype profile. [4] [5]

In 2006, Scotland Yard and London's Metropolitan Police announced that they would be investigating the use of DNAWitness to narrow suspects in the search for a long-standing effort to capture a serial rapist known as the Minstead Rapist. [6]

DNAWitness was used in 2007 to help narrow down suspects in the investigation into the 2002 murder of Pam Kinamore. Though the police dragnet was initially looking for white suspects based on an early eyewitness, DNAPrint Genomics was later contracted to test the DNA sample, and concluded that the suspect was of "substantial African ancestry". [7] Investigators redirected their investigation to focus on individuals fitting this description and shortly thereafter identified Derrick Todd Lee, who was subsequently convicted of the crime as well as a series of other similar murders in the Baton Rouge, Louisiana, area. This application of forensic phenotyping, where physical characteristics were inferred from crime scene DNA and used to redirect, and help solve a crime, was covered by The New York Times, Wired magazine, Popular Science, U.S. News & World Report, Sarasota Herald Tribune, ABC and CBS Evening News programs, Australian and German News programs and in a Forensic Files episode entitled "Tight Fitting Genes" [8] as a historical first.

Since the Lee case, the product was used on dozens of other serial homicide cases with successful results.

AncestrybyDNA

AncestrybyDNA was invented by Dr. Tony Frudakis in 2002 through DNAPrint Genomics. AncestrybyDNA is an online DNA testing service for the average person—it determines the biogeographical ancestry of an individual through autosomal DNA testing. [9] DNA testing is a process that uses DNA information to determine someone's ancestry accurately up to about 10 generations. After that point, the amount of shared DNA is so little that it is considerably more difficult to identify. [10] Autosomal DNA testing is a specific type of genetic testing that is done by looking at a subset of DNA regions in the autosomal chromosomes (the non-sex chromosomes) that make up the vast majority of the genome. Most autosomal DNA tests examine about a million genetic markers in order to gather information about the DNA donor's ancestry and relatedness. Genetic markers are genes or DNA sequences whose location on the chromosome is known. Genetic markers and genes that are close to each other on a chromosome tend to be inherited together; therefore, genetic markers can help identify a nearby gene. Genetic markers in humans include single polymorphism nucleotides (SNPs), restriction fragment length polymorphisms (RFLPs), variable number of tandem repeats (VNTRs), microsatellites, and copy number variants (CNVs). [11]  Because of their known locations, markers can be used to identify individuals or species, as well as determine relatedness between and among species. Typically, these markers are considered "observable variations" due to the fact that the variations can be located on the DNA. [12]

Autosomal DNA tests like AncestrybyDNA are used to identify people with whom the DNA donor shares ancestors. The process involves identifying large, shared chunks of DNA between individuals. These "shared chunks'' are indicators of some kind of relatively-recent shared inheritance. [10] It is rare that a DNA chunk is conserved in two individuals from a common ancestor who lived more than ten generations (around 300 years) in the past. Beyond ten generations, the fraction of ancestors who contributed directly to the DNA being tested is incredibly small due to genetic crossing-over events and the inherent randomness in the process of transferring DNA from parent to offspring. [10] While shared DNA chunks are strong indicators of relatedness, determining the exact age of the DNA donor's ancestors beyond four generations is difficult. [10] Additionally, there is no definitive way to determine the exact relationship between the DNA donor and the perceived ancestor. [10] While DNA genetic testing is often a good approximation of relatedness to older ancestors, it is hardly definitive.

Both AncestrybyDNA and DNAPrint Genomics are elements of a larger conversation about the genetic basis of race. In particular, the delivery of the information to the average consumer in the form of percentages of racial background has proved to be somewhat misleading. Several companies offer similar genetic testing services as AncestrybyDNA, such as CRI Genetics, AncestryDNA (not to be confused with AncestrybyDNA), and 23andMe. [13] Each of these companies returns varying genetic results in the form of percentages. This occurs for a few reasons. Firstly, each company uses different genetic databases for genetic comparison. [10] Secondly, the DNA samples used in the databases are categorized in different ways. [10] Finally, each company uses unique algorithms to make the time estimates and the approximate amount of relatedness of the DNA donor to their ancestors. [10]   Quantifying the racial compositions of a DNA donor's DNA suggests that distinct divisions exist between human populations. [14] Simply put, patterns of relatedness are flexible estimates. To assume that people are easily categorizable is inaccurate.

Aside from the percentage problem, genetic testing processes such as AncestrybyDNA—especially in the context of uncovering a racial background—is connected to the perpetuation of the myth of race. As stated by the National Human Genome Research Institute,

"Race is a fluid concept used to group people according to various factors including, ancestral background and social identity. Race is also used to group people that share a set of visible characteristics, such as skin color and facial features. Though these visible traits are influenced by genes, the vast majority of genetic variation exists within racial groups and not between them. Race is an ideology and for this reason, many scientists believe that race should be more accurately described as a social construct and not a biological one. [15] " All in all, race has proven over and over to be a social construct rather than a biological fact. [14]

Historical relevance

In the early 2000s, under the leadership of founder and then CEO Tony N. Frudakis, Ph.D., DNAPrint forged a nascent consumer genetics/genomics and forensic phenotyping marketplace. In the mid to late 2000s many journalists and academics harshly criticized DNAPrint's application of genomics research for consumer and forensic purposes but by the early 2000-teens, the forensic science applications of BioGeographical Ancestry (BGA) admixture analysis for the inference of BGA and certain anthropometric phenotypes such as skin shade, eye/hair color, had become well established and by 2019 the market for these types of products had grown to over $500M/year in size. As of 2019, various capillary electrophoresis (e.g. Applied Biosystems) and next generation sequencing platform and consumable manufacturers have introduced human identity products combining classical (CODIS eligible) STR profiling marker sets with unique SNP based AIMS for the inference of BGA and phenotype (e.g. ForenSeq, from Illumina's Verogen). Various private and public laboratories had also emerged to provide forensic phenotyping services (e.g. Parabon Nanolabs).

In the mid-2000s, Frudakis wrote the seminal textbook introducing the forensic and consumer market application of genome-derived marker panels. [16]

In the mid-to late 2000s, before it had fully developed these new markets, the hedge fund supporting DNAPrint liquidated the company and sold its intellectual property and know-how to DNA Diagnostics Company (DDC). Just prior to the company's liquidation, other companies launched similar products in the consumer genomic genealogy market (e.g. 23andMe and Ancestry.com). By 2018, these companies had extended the science significantly, building even larger genomic databases and enabling finer level and even entirely new inferences. For example, in forensics, over 70 serial homicide cases (including the Golden State Killer) having been solved through genetic genealogy hits enabled by the types of consumer genomics databases DNAPrint was the first to introduce. In these cases, potential relatives of individuals that donated DNA to crime scenes are identified. With consumer genealogy, family members can now be identified and reconnected through database matching, and customers can now pinpoint even intracontinental and regional family origins using the types of consumer genomics databases DNAPrint was the first to introduce.

Related Research Articles

<span class="mw-page-title-main">Genetic testing</span> Medical test

Genetic testing, also known as DNA testing, is used to identify changes in DNA sequence or chromosome structure. Genetic testing can also include measuring the results of genetic changes, such as RNA analysis as an output of gene expression, or through biochemical analysis to measure specific protein output. In a medical setting, genetic testing can be used to diagnose or rule out suspected genetic disorders, predict risks for specific conditions, or gain information that can be used to customize medical treatments based on an individual's genetic makeup. Genetic testing can also be used to determine biological relatives, such as a child's biological parentage through DNA paternity testing, or be used to broadly predict an individual's ancestry. Genetic testing of plants and animals can be used for similar reasons as in humans, to gain information used for selective breeding, or for efforts to boost genetic diversity in endangered populations.

A genetic screen or mutagenesis screen is an experimental technique used to identify and select individuals who possess a phenotype of interest in a mutagenized population. Hence a genetic screen is a type of phenotypic screen. Genetic screens can provide important information on gene function as well as the molecular events that underlie a biological process or pathway. While genome projects have identified an extensive inventory of genes in many different organisms, genetic screens can provide valuable insight as to how those genes function.

<span class="mw-page-title-main">Haplotype</span> Group of genes from one parent

A haplotype is a group of alleles in an organism that are inherited together from a single parent.

Genetic genealogy is the use of genealogical DNA tests, i.e., DNA profiling and DNA testing, in combination with traditional genealogical methods, to infer genetic relationships between individuals. This application of genetics came to be used by family historians in the 21st century, as DNA tests became affordable. The tests have been promoted by amateur groups, such as surname study groups or regional genealogical groups, as well as research projects such as the Genographic Project.

Researchers have investigated the relationship between race and genetics as part of efforts to understand how biology may or may not contribute to human racial categorization. Today, the consensus among scientists is that race is a social construct, and that using it as a proxy for genetic differences among populations is misleading.

Genetics, a discipline of biology, is the science of heredity and variation in living organisms.

A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change, or a long one, like minisatellites.

A genealogical DNA test is a DNA-based genetic test used in genetic genealogy that looks at specific locations of a person's genome in order to find or verify ancestral genealogical relationships, or to estimate the ethnic mixture of an individual. Since different testing companies use different ethnic reference groups and different matching algorithms, ethnicity estimates for an individual vary between tests, sometimes dramatically.

<span class="mw-page-title-main">Ancestry-informative marker</span>

In population genetics, an ancestry-informative marker (AIM) is a single-nucleotide polymorphism that exhibits substantially different frequencies between different populations. A set of many AIMs can be used to estimate the proportion of ancestry of an individual derived from each population.

<span class="mw-page-title-main">Human genetic variation</span> Genetic diversity in human populations

Human genetic variation is the genetic differences in and among populations. There may be multiple variants of any given gene in the human population (alleles), a situation called polymorphism.

<span class="mw-page-title-main">Family Tree DNA</span> Commercial genetic testing company

FamilyTreeDNA is a division of Gene by Gene, a commercial genetic testing company based in Houston, Texas. FamilyTreeDNA offers analysis of autosomal DNA, Y-DNA, and mitochondrial DNA to individuals for genealogical purpose. With a database of more than two million records, it is the most popular company worldwide for Y-DNA and mitochondrial DNA, and the fourth most popular for autosomal DNA. In Europe, it is the most common also for autosomal DNA. FamilyTreeDNA as a division of Gene by Gene were acquired by MYDNA, Inc., an Australian company, in January 2021.

During the latter half of the 20th century, the fields of genetics and molecular biology matured greatly, significantly increasing understanding of biological heredity. As with other complex and evolving fields of knowledge, the public awareness of these advances has primarily been through the mass media, and a number of common misunderstandings of genetics have arisen.

<span class="mw-page-title-main">23andMe</span> American personal genomics company

23andMe Holding Co. is a publicly traded personal genomics and biotechnology company based in South San Francisco, California. It is best known for providing a direct-to-consumer genetic testing service in which customers provide a saliva sample that is laboratory analysed, using single nucleotide polymorphism genotyping, to generate reports relating to the customer's ancestry and genetic predispositions to health-related topics. The company's name is derived from the 23 pairs of chromosomes in a diploid human cell.

The following outline is provided as an overview of and topical guide to genetics:

Personal genomics or consumer genetics is the branch of genomics concerned with the sequencing, analysis and interpretation of the genome of an individual. The genotyping stage employs different techniques, including single-nucleotide polymorphism (SNP) analysis chips, or partial or full genome sequencing. Once the genotypes are known, the individual's variations can be compared with the published literature to determine likelihood of trait expression, ancestry inference and disease risk.

Diversity Arrays Technology (DArT) is a high-throughput genetic marker technique that can detect allelic variations to provides comprehensive genome coverage without any DNA sequence information for genotyping and other genetic analysis. The general steps involve reducing the complexity of the genomic DNA with specific restriction enzymes, choosing diverse fragments to serve as representations for the parent genomes, amplify via polymerase chain reaction (PCR), insert fragments into a vector to be placed as probes within a microarray, then fluorescent targets from a reference sequence will be allowed to hybridize with probes and put through an imaging system. The objective is to identify and quantify various forms of DNA polymorphism within genomic DNA of sampled species.

Cognitive genomics is the sub-field of genomics pertaining to cognitive function in which the genes and non-coding sequences of an organism's genome related to the health and activity of the brain are studied. By applying comparative genomics, the genomes of multiple species are compared in order to identify genetic and phenotypical differences between species. Observed phenotypical characteristics related to the neurological function include behavior, personality, neuroanatomy, and neuropathology. The theory behind cognitive genomics is based on elements of genetics, evolutionary biology, molecular biology, cognitive psychology, behavioral psychology, and neurophysiology.

Genetic studies on Arabs refers to the analyses of the genetics of ethnic Arab people in the Middle East and North Africa. Arabs are genetically diverse as a result of their intermarriage and mixing with indigenous people of the pre-Islamic Middle East and North Africa following the Arab and Islamic expansion. Genetic ancestry components related to the Arabian Peninsula display an increasing frequency pattern from west to east over North Africa. A similar frequency pattern exist across northeastern Africa with decreasing genetic affinities to groups of the Arabian Peninsula along the Nile river valley across Sudan and the more they go south. This genetic cline of admixture is dated to the time of Arab expansion and immigration to North Africa (Maghreb) and northeast Africa.

<span class="mw-page-title-main">DNA phenotyping</span> DNA profiling technique

DNA phenotyping is the process of predicting an organism's phenotype using only genetic information collected from genotyping or DNA sequencing. This term, also known as molecular photofitting, is primarily used to refer to the prediction of a person's physical appearance and/or biogeographic ancestry for forensic purposes.

Genetic privacy involves the concept of personal privacy concerning the storing, repurposing, provision to third parties, and displaying of information pertaining to one's genetic information. This concept also encompasses privacy regarding the ability to identify specific individuals by their genetic sequence, and the potential to gain information on specific characteristics about that person via portions of their genetic information, such as their propensity for specific diseases or their immediate or distant ancestry.

References

  1. ↑ The Genetic Genealogist | DNAPrint Genomics Ceases Operations
  2. ↑ | GenomeWeb Daily News | GenomeWeb
  3. ↑ Hamilton, Anita (2005-07-05). "Can DNA Reveal Your Roots?". Time. Archived from the original on July 6, 2005. Retrieved 2007-10-05.
  4. ↑ "Molecular Photofitting: Predicting Ancestry and Phenotype from DNA". Elsiever Academic Press. 5 October 2007. Archived from the original on 24 September 2019. Retrieved 7 September 2007. Alt URL
  5. ↑ An Invisible Man: The Hunt for a Serial Killer Who Got Away With a Decade of Murder. Berkley. 6 June 2006. ISBN   0425208877.
  6. ↑ "DNAPrint Genomics Scientist Delivers Presentation to Detectives at New Scotland Yard". Market Wire. 2006-04-05. Retrieved 2007-10-05.
  7. ↑ "The Inconvenient Science of Racial DNA Profiling". Wired Magazine. 5 October 2007. Archived from the original on 25 February 2009. Retrieved 5 October 2007.
  8. ↑ "Forensic Files Season 10, Episode 15 "Tight Fitting Genes"". Forensic Files. 14 September 2005. Archived from the original on 6 November 2019. Retrieved 14 September 2005.
  9. ↑ "AncestrybyDNA - ISOGG Wiki". isogg.org. Retrieved 2022-05-11.
  10. 1 2 3 4 5 6 7 8 UCL (2019-02-13). "Understanding genetic ancestry testing". UCL Division of Biosciences. Retrieved 2022-05-11.
  11. ↑ www.cancer.gov. 2012-07-20 https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/genetic-marker . Retrieved 2022-05-11.{{cite web}}: Missing or empty |title= (help)
  12. ↑ "Genetic marker", Wikipedia, 2022-03-17, retrieved 2022-05-11
  13. ↑ "Free Review of Ancestry DNA Tests | Genetics Digest". geneticsdigest.com. Retrieved 2022-05-11.
  14. 1 2 Chou, Vivian (18 April 2017). "How Science and Genetics Are Reshaping the Race Debate of the 21st Century". Harvard University. Retrieved 11 May 2022.
  15. ↑ "Race". Genome.gov. Retrieved 2022-05-11.
  16. ↑ "Molecular Photofitting: Predicting Ancestry and Phenotype from DNA". Elsiever Academic Press. 5 October 2007. Retrieved 7 September 2007.
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