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Conspiracy Theories and Ebola: How a US Federally Funded Research Facility in the Heart of Sierra Leone’s Ebola Outbreak Acerbated Local Misconceptions about Ebola

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By: Caroline Duncombe

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An inherent distrust follows what one does not understand; scientific endeavors if not explained properly are easily misunderstood. From climate skeptics to CERN’s 666 logo, the world is wrought with conspiracy theories surrounding science. The role of conspiracies should not be underestimated or neglected, especially since such theories are interspersed with layers of truth. Usually conspiracies reside harmlessly on the edge of the web, but during the Ebola outbreak in Sierra Leone an unaddressed rumor resulted in fatal consequences. Rumors revolving around a Tulane University research facility located in Kenema Government Hospital prompted a breakdown in relations between the local populations and international health care workers. This mistrust led to the refusal to permit blood draws for diagnostic purposes during the critical initial stages of the Ebola outbreak. By underestimating the importance of cultural and religious symbolism surrounding scientific research U.S. federal funding agencies, laboratory researchers, and private companies made a crucial mistake. By analyzing this curious conspiracy theory, scientists, funding agencies, and health practitioners can learn from past mistakes and become more aware of the impact of research beyond pure scientific pursuit.

Background

            On May 24th, 2014,a young woman miscarried in Kenema Government Hospital. Given the recent outbreak in nearby Gueckedou, Guinea, Ebola was suspected. A day later, the same hospital reported the first confirmed case of Ebola in Sierra Leone. Soon after, Kenema became a hot zone – the entry point for the Ebola virus to spread throughout Sierra Leone and eventually the world. The repercussions of the Ebola outbreak extend well beyond the 11,310 death count in West Africa to economic, social, medical, and cultural spheres.

The Kenema Government Hospital was not a typical Sierra Leonian public hospital. In fact, the hospital was well-equipped, with the only Lassa fever isolation ward anywhere in the world. The lab dated to 2005, when Tulane University received a $10 million grant from the U.S. National Institutes of Health to study “Diagnostics for Biodefense against Lassa fever”. Since previous investigations of sporadic Lassa fever outbreaks were based out of Kenema, the natural choice for the establishment of first-rate laboratory infrastructure was Kenema Government Hospital.

As the years passed, the Tulane research laboratory acquired more grants and partnerships. One of the principal collaborators was the private for-profit company, Metabiota, which received grants from two U.S. Department of Defense (DoD) agencies – Defense Threat Reduction Agency and Biological Engagement Program – to primarily study the pathogenesis of Lassa fever, a ‘US bioterror threat’. Due to stipulations in NIH grant funding, the substantial amount of money flowing into this “shiny new” research laboratory could not be applied to assisting patients in the “dilapidated, cramped, and poorly resourced Lassa ward only some 50m away” (Bausch). During the Ebola outbreak, the Lassa laboratory’s focus shifted to Ebola, continuing research until the NIH did not renew funding in 2014, primarily due to safety reasons.

The Conspiracy Theory

Following the 2014 outbreak, a conspiracy theory circulating throughout Sierra Leone, essentially claiming that the U.S. created Ebola, or a Lassa-Ebola hybrid, and either intentionally or accidentally released this bioterror weapon from the U.S. NIH and DoD-funded research facility at Kenema Government Hospital. While such a rumor lacked credible evidence, there were specific circumstances surrounding the policies of the research outpost that fed into the narrative – truths that should have been addressed through culturally sensitive policies.

Four main factors converged into a superstitious and suspicious narrative about the Lassa research laboratory. First, by branding the Lassa research facility with a bioterrorism component, the project assisted in drawing out a natural conclusion that bioterror weapons were also present in the laboratory. Tulane University’s initial grant application in 2005 framed Lassa virus as a US biosecurity threat through key words such as “Diagnostics for Biodefense” and “LASV as a biological weapon directed against civilian or military targets necessitates development of… diagnostics.” The framing of the diagnostic development laboratory in terms of a biodefense strategy against the NIAID Category A classification was not an accident, but rather a necessity to gain funding. As Annie Wilkins puts it “whether the prospect of weaponization is regarded as sensationalism or a real concern, all researchers are aware of the utility the bioweapons threat has in obtaining funding.” By emphasizing biodefense and collaborating with the U.S. DoD via Metabiota’s funding stream, a natural linkage between the work of the research outpost and bioweapons developed.

The second factor was out of the control of Tulane University: A suspicious coincidence. Due to its proximity to Guinea, laboratory capacity, and fluidity in movement across the Sierra Leone-Guinea border, the first confirmed case of Ebola in Sierra Leone occurred in Kenema Government Hospital. Although there potentially were other cases of Ebola in Sierra Leone, none of the primary health care clinics in the area had the laboratory capacity to officially diagnose Ebola. A natural speculation ensued: what are the chances that the one Biodefense laboratory in Sierra Leone, where the hemorrhagic Lassa fever virus was located, was also the site of the first confirmed case of a “new” bioterror threat that also causes hemorrhagic fever, Ebola? Money draws attention, and the money flowing into this singular laboratory was substantial when compared with other public hospitals in Sierra Leone. For reference, the Sierra Leone Ministry of Health and Sanitation allocated U.S. $20 million budget to run the entire national health system in 2009.

Third, a nurse from Kenema Government Hospital claimed to an audience at a fish market that “the deadly [Ebola] virus was invented to conceal “cannibalistic rituals”. The statement and an already distrustful community culminated into a riot at the hospital on July 25th, 2014. Such a case further cemented the people’s suspicions that the laboratory was “stealing” the blood of Sierra Leonians. Even though collecting blood is necessary for diagnostic tests, there are many deeply held cultural beliefs about blood in Sierra Leone, and many people are reluctant to participate in blood test as a result.

Fourth, the research facility suspiciously and suddenly shut down right at the beginning of the outbreak without much explanation to the community. Additionally, many of the Sierra Leonian staff who could have addressed the suspicions about the facility pre-outbreak have since died while bravely combatting Ebola. All of these factors accumulated into the conspiracy theory that actors involved with the bio-defense grant and the US government created a bioterror weapon and unleashed it on West Africa.

Policy Considerations

The accumulation of these factors demonstrate the importance of cultural sensitivity and awareness when implementing scientific research policies. In 2018, Tulane University and a variety of partners received a new $15 million federally funded grant to study how Ebola and Lassa survivors fought off the diseases. Hopefully, the researchers are opening this facility with a new awareness and increased precautions on the spiritual and social baggage they bring to Kenema. This is especially important when considering the potential for further stigmatization of Ebola survivors if called to Kenema Government Hospital for research or treatment purposes.

There are several policy considerations that could alter the course of this conspiracy and help acclimate the community to both the presence of a well-equipped laboratory and blood draws for diagnostic purposes. Research institutions should refrain from using vocabulary such as “biodefense” and “bioweapon” to describe the purpose of research. A clinician in the Lassa ward pointed out that “The average Sierra Leonian won’t see Lassa Fever as a bioweapon threat. Only in the Western world do they see it like that.” Since the potential for contracting Lassa and Ebola is an everyday reality for Sierra Leonians, research initiatives on such diseases should be spoken about in terms of their potential for public health. Additionally, universities seeking to do medical research should consider the cultural significance of their location, and contemplate ways, including shifting location, that might reduce any negative connotations. Engaging influential spiritual leaders in productive information partnerships could also assist in assuaging local concerns.

Policy considerations should also be contemplated by grant funding institutions like the NIH and DoD. First, grant stipulations should integrate a layer of flexibility for distributing certain supplies and resources for patient care. Second, the NIH and DoD should be cognizant of their bias in funding grants that are written in terms of biodefense interests of the US, especially when related to countries where such a ‘bioweapon’ is an everyday reality. This is especially important because such bias incentivizes deleterious narratives that invokes cultural, social, and medical consequences.  Lack of funding for neglected infectious diseases that only burden developing countries by the US is a complex and important issue that will require deep structural changes – and would require another blog post to contemplate. Yet, a simple solution would be to require scientific grant applications to contain a section in which the applicant considers the cultural and social impact of the work within the community of interest. In addition, community outreach with intentional dialogue on assuaging concerns about sensitive research activities should made be mandatory.

The conspiracy theory exacerbated the already high level of mistrust in Western interventions during the outbreak. As the Washington Post emphasizes, the lesson from this case study is “that winning the trust of communities at risk is absolutely indispensable to limiting the impact of the inevitable next Ebola epidemic in West Africa.” Hopefully, the Tulane University research center in Kenema Government Hospital has learned from past mistakes, and seeks to engage the community and douse suspicions against their research upon re-opening the laboratory this year. Conspiracy theories usually integrate truth with speculation. The traditional method of ignoring such theories or flat out denying (as was the case with Tulane University) may have detrimental consequences as seen during the Ebola outbreak in Sierra Leone. The power in a conspiracy theory is not necessarily its truth, but it’s power to persuade people that it is true. And as scientists who are often focused on the facts, we often have a hard time understanding that concept. When doing research, it is crucial to be cognizant of the social perception of science and attempt to build bridges between gaps of understanding on cultural practices and scientific endeavors.

 

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January 17, 2019 at 6:34 pm

Vaccination Politics: Exploring the policy measures needed to lower the risk of vaccine-preventable disease outbreaks

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By: Allison Cross, Ph.D.

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Source: Wikimedia

Thanks to modern medicine, many of the diseases that plagued our ancestors can now be prevented by vaccination.  Although there are no federal vaccination laws in the US, there are state laws making vaccination mandatory for children attending public schools. All 50 states require public school children to be vaccinated against diphtheria, tetanus, pertussis, polio, measles, rubella, and varicella (chicken pox). There are exceptions to these requirements, however, with all states allowing medical exceptions, 47 states allowing religious exemptions, and 17 states allowing personal belief exemptions.  A recent study published in PLOS medicine found that in states that allow personal belief exemptions, the rates of these exceptions has increased two-thirds in the last decade.  The study warns that numerous states and large metropolitan centers that have shown increases in non-medical exceptions (NMEs) may become increasingly vulnerable to outbreaks of vaccine-preventable disease.  This raises the question of whether policy measures should be taken to increase rates of vaccination.

Many parents who apply for personal belief exemptions for vaccinations do so because of concerns of vaccine safety and efficacy. The most influential milestone of the current anti-vaccination movement came in 1998 with an article published by Dr. A Wakefield in the Lancet linking the MMR vaccine to autism; the story was later featured on 60 minutes. Dr. Wakefield’s research has since been debunked, his paper has been retracted from the Lancet, and he was stripped of his medical license. Despite this, many parents remain fearful of vaccination and these fears continue to be fueled by the media, celebrities, and politicians.  While safety concerns keeps some parents from vaccinating their children, others choose not to vaccinate because they believe their children have a low risk of contracting vaccine preventable diseases due to their low prevalence.  Still others hold beliefs that natural immunity is better than vaccine acquired immunity.  In addition to personal beliefs against vaccination, some individuals oppose vaccination on the basis of their religious beliefs.

It is critical to maintain high vaccination rates among the population to provide protection to those who cannot be vaccinated or who have not yet developed immunity.This concept is known as herd immunity. There is a very small proportion of children that cannot be vaccinated due to medical reasons, but this small percentage of the population generally does not compromise herd immunity.  However, when parents refuse to vaccinate their children based on religious or personal beliefs, the percentage of unvaccinated children can rise and compromise herd immunity.   The percentage of the population that needs to be vaccinated for herd immunity to be effective depends on how contagious the germ is.  In 2017, the CDC reported that 83.4% of children from 19-35 months were vaccinated against diphtheria, tetanus and pertussis, 91.9% against polio, 91.1% against measles, mumps and rubella, and 90.6% against varicella.  Though these numbers may sound high they may not be high enough; for example the vaccination rate required to achieve herd immunity for measles is believed to be roughly 96% or higher.

Currently there are only three states that solely allow medical exemptions for school vaccination; Mississippi and West Virginia banned NMEs more than 30 years ago while California recently banned NMEs in January of 2016.  The strict rules on vaccination exemptions in Mississippi and West Virginia are linked to increased rates of vaccination.  In the 2014-2016 school year, over 99% of kindergarteners in Mississippi were reported to have received their MMR and DPT vaccines. On the contrary, states that permit both personal belief and religious exceptions are reported to have 2.5 times higher rates of vaccine exemptions.  California passed its statewide ban of NMEs after a 2015 measles outbreak that was linked to the Disneyland Resort in Anaheim, California.  Investigations into the outbreak reported that the exposed population had a vaccination rate of only 50-86%.  After passing the NME ban, California reported a record high level of vaccination with 95.6% of kindergarteners receiving all required vaccinations during 2016-2017.

Considering that the states that allow personal and religious exemptions to vaccination generally have higher levels of vaccine exemptions, one must consider whether more states should act to ban NMEs.   While these policies may increase vaccination rates, they may also come with other undesirable side-effects.  For example, although California reported a dramatic increase in vaccination rates following its ban of NMEs, a study by Mohanty S. et. al. also reported a significant increase (from 0.2% in 2015–2016 to 0.7% in 2017–2018) in medical exceptions, with the strongest increase reported in regions with high rates of personal belief exemptions prior to the NME ban.  This suggests that parents with personal beliefs against vaccination were able to find physicians willing to exercise “broader discretion” in providing medical exceptions.   Even more troubling, the study found that some physicians were charging steep fees to sign off on “medical” exceptions for parents who previously sought non-medical vaccination exemptions.  These findings suggest that the potential long-term benefit of the NME ban in California may not be achieved without further legal changes, including some form of standardized review of medical exemptions.

Though eliminating NMEs may be a successful means of raising vaccination rates to the levels needed to achieve herd immunity, other less drastic legislation changes may have similar results while respecting both the pro- and anti-vaccination viewpoints.  Some proposed alternatives include financial disincentives and stricter exception policies. Navin M.C. and Largent M.A.  proposed an “inconvenience approach”, which allows non-medical exceptions to continue but makes the application process more burdensome. Similarly, Billington J.K. and Omer. S.B. proposed the use of processing fees as a financial disincentive to discourage NMEs.  They suggest that states require annual renewal of NMEs and require a processing fee for each renewal.  They further recommend that these fees be administered in a “sliding-scale” to avoid income-based discrimination.  Billington and Omer argue that these fees will “help tilt the balance of convenience in favor of vaccination”.  Another approach could be requiring parental counseling on vaccine risks and benefits to obtain NMEs. After Washington state passed a law in 2011 requiring counseling intervention for NMEs they reported a relative 40.2% decrease in exception rates, with an absolute reduction of 2.9%.   Although elimination of NMEs is linked to higher vaccination rates, the less drastic proposals above could provide increased rates of vaccination without evoking the public backlash of eliminated NMEs entirely.

In states that allow medical and religious vaccination exemptions, policy makers attempting to crack down on religious exceptions can expect to face a lot of criticism from individuals who hold strong anti-vaccination beliefs.  In April, New Jersey lawmakers faced harsh criticism after advancing a proposal to make it harder for children to receive religious exemptions for vaccinations. New Jersey is among the 33 states that do not allow personal belief exemptions but permit both medical and religious vaccine exceptions.  Lawmakers decided to take action after noticing a dramatic increase in the number of children citing religion as a reason for refusing vaccination, from 1,641 students in the  2005-2006 school year to 10,407 children in 2016-2017. The proposed legislation would require parents to provide a notarized statement about their religious beliefs, including proof that their beliefs are ongoing, and to specifically explain how immunization conflicts with their religious tenets.  The proposed measured are intended to curb the percentage of parents who use the religious exceptions as a way to avoid vaccination due to personal beliefs or fears about vaccination.

Individuals who oppose vaccination, whether for religious or personal reasons, strongly believe that the government should not be able to force vaccination on anyone. However, childhood immunizations prevent serious illness and death along with billions of dollars of costs to society each year.  Furthermore, the choice not to vaccinate does more than effect the unvaccinated individual, as it also puts at risk those individuals who cannot receive vaccinations due to medication reason and those who have not yet developed immunity. Although rates of vaccine preventable diseases are currently very low in the US, the CDC has made it clear that maintaining high levels of vaccination is essential to prevent diseases from making a comeback. Strong anti-vaccination sediments and subpar MMR vaccination rates are being blamed for the current and ongoing measles outbreaks in Romania, France, Greece, and Italy; outbreaks across the EU have resulted in 33 deaths this year. It is clear that policies promoting vaccination are important for disease prevention but determining the best policy measures to increase vaccination rates, while considering the ethical debate of mandatory vaccination, while continue to be a struggle for policy makers.

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December 20, 2018 at 9:37 am

The Impact of Research Funding on Minority Health and Health Disparities

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By: Nancy Chiles Shaffer, Ph.D.

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Source: Maxpixel

Federal agencies have attempted to improve minority health and reduce health disparities since the 1980s, and these efforts have continued through today. To briefly highlight some of the progress that has been made, the Department of Health and Human Services (HHS) initially released a report in 1985, “The Secretary’s Task Force Report on Black and Minority Health (Heckler Report)”, that discussed the state of racial health disparities in the United States1. This report led to the creation of the Office of Minority Health in 19861. Subsequently, the Office of the Director of the National Institutes of Health (NIH) created the Office of Minority Programs2. This began the efforts of NIH to address minority health and health disparities. Additionally, in 1993, HHS founded the Office of Research on Minority Health, which was later reauthorized in 20101,2. The Agency for Healthcare Research and Quality (AHRQ), under the Healthcare Research and Quality Act, was directed in 1999 to monitor racial disparities in health care3.  The National Center on Minority Health and Health Disparities was founded in 2000 and later became an NIH institute in 20102. More recently, in 2011, the HHS Action Plan to End Health Disparities as well as the National Stakeholder Strategy for Achieving Health Equity were created to further reduce health disparities1. Over these 33 years, funding also has been explicitly designated to improve minority health in the United States. While only 427 grants addressing minority health and health disparities were funded in 1985, there are currently 7,958 active grants4. How have health outcomes and health care been impacted by funding for minority health and for addressing health disparities?

One of the markers of national health that can be used to examine the success of these efforts so far is life expectancy. In 1990, life expectancy at birth was 71.8 years for men and 78.8 years for women5. Race-specific life expectancy was 72.7 years and 64.5 years for White and Black men, respectively, and 79.4 years and 73.6 years for White and Black women, respectively5. These data reflect 8.2 years shorter life expectancy for Black men and 5.8 years shorter life expectancy for Black women compared to their White counterparts.  Efforts to increase life expectancy led to a 6% (4.5 years) and 3% (2.3 years) increase in life expectancy by 2015 in men and women, respectively. Additionally, the difference in life expectancy between Black and White individuals decreased by 46% (3.8 years) in men and 52% (3 years) in women.

The National Center for Health Statistics (NCHS), a division of HHS’ Centers for Disease Control and Prevention, produced two data briefs examining racial differences in life expectancy. The first report explored the causes of death related to racial differences in life expectancy in 20106. It was found that there was a Black disadvantage in death rates due to heart disease, cancer, homicide, diabetes, and perinatal conditions. The Office of Minority Health stated in a 2011 press release that the Affordable Care Act provided opportunities for “bringing down health care costs, investing in prevention and wellness, supporting improvements in primary care, and creating linkages between the traditional realm of health and social services”7. The second NCHS brief assessed how decreases in racial disparities in life expectancy in 2013 are attributable to decreases in death rates for conditions among Black people, including heart disease, cancer, HIV, unintentional injuries, and perinatal conditions8. Despite these decreases, AHRQ’s “National Healthcare Quality and Disparities Report” in 2016 stated that most racial disparities in health care still exist9.

Beyond federal funding, private organizations and philanthropic organizations have also committed to reducing health disparities. A 2009 workshop that aimed to determine factors associated with health disparities was funded by the California Endowment, Missouri Foundation for Health, Connecticut Health Foundation, United Health Foundation, and Kaiser Permanente, and the CDC7. The Merck Company Foundation in 2009 provided $15 million to fund their Alliance to Reduce Disparities in Diabetes, focusing on reducing disparities in type 2 diabetes in low-income adults, Blacks, Hispanics/Latinos, and Native Americans7. Aetna Foundation, through their Racial and Ethnic Health Care Equity program, funded a report in 2012 addressing how the Affordable Care Act could be used to “advance health equity for racial and ethnic minorities”7. A brief funded by the California Endowment, California Wellness Foundation, and the San Francisco Foundation concluded that language barriers in California inhibited enrollment in the California Health Benefit Exchange7,10. As a result, funding was provided to increase cultural and linguistic competence for health care providers. The Cigna Foundation funded a $200,000 grant in 2015 for the Health Advocates In-Reach and Research (HAIR) program at the University of Maryland School of Public Health’s Center for Healthy equity to train barbers and hair stylists on health education11.

While funding has resulted in improvements in minority health, there is still more work to be done. The Office of Minority Health states that racial and ethnic minorities “…are less likely to get the preventive care they need to stay healthy, more likely to suffer from serious illnesses such as diabetes or heart disease, and when they do get sick, are less likely to have access to quality health care”12. Many of the areas that require additional attention are the focus of several current funding initiatives. The Office of Minority Health currently has grants to address uninsured men, HIV/AIDS, Lupus, and cultural and linguistic competency13. In addition, AHRQ is currently funding research addressing health disparities among the lesbian, gay, bisexual, transgender, and queer/questioning (LGBTQ) community, as well as mobile technology to improve self-care for HIV/AIDS patients9. Given the improvements that have been observed thus far over the past 33 years, the ongoing continuation of funding to address minority health and health disparities has the potential to help the United States achieve health equity for all.

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December 7, 2018 at 2:41 pm

Publications and Patents: Laying the foundation for future innovation and economic growth

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By: Xavier Bofill de Ros, Ph.D.

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Source: Pixabay

 

Many hours on the laboratory bench made me wonder: What is the real impact of our science? How do the thousands of publications appearing in scientific magazines every month and the funds poured into research benefit our society? We all know history; Fleming’s research on mold resulted in the discovery of penicillin and saved millions of lives ever since, and GPS systems rely heavily on basic trigonometry. These examples embody the power of science as a driver of technological progress and motivates – public policies to support scientific research. For example, NIH receives $37 billion  annually to fund intramural and extramural biomedical research[1]. Some of this investment in research generates intellectual property, bringing back to the system private money derived from license agreements. For instance, the NIH Technology Transfer Office had an income of $138 million from royalties in 2015[2]. However, many critics are quick to point out that basic research rarely pays off in practical R&D.

To understand where we are we need to know where we are coming from. A big part of the current legislation that governs the intellectual property derived from publicly-funded research is inspired from the Patent and Trademark Law Amendments Act, also known as the Bayh–Dole Act passed in 1980. This act established that the ownership of inventions made with federally-funded research projects by universities, small business and non-profit institutions is entitled to them in preference to the government. Prior to that act, the government accumulated ownership to large numbers of patents derived from the $75 billion per year of funding dispersed through different agencies, however fewer than 5% of those patents were licensed[3]. In exchange for this new source of revenue, public money receiving institutions  are required to educate the research community about the patenting procedures and to protect the government’s interests on funded inventions among other requirements. Despite the criticisms for forcing consumers to “pay twice” for patented products, the economic impact of the Bayh-Dole Act has been important. Recent reports suggest that academic licenses to industry contributed between $148 to $591 billion per year to US gross domestic product (GDP)[4].

Besides economic performance, other approaches to assess the impact of scientific publications on intellectual property come from the bibliometric analysis of the prior art on issued patents. A recent study from Kellogg School of Management analyzed the content of 4.8 million patents and 32 million research articles to find out how research is connected to inventions[5]. By analyzing the prior art references of patents, and the references of these references, the authors revealed that 80% of research articles linked to a future patent. This connection is often indirect, since direct citations of research articles in patents only account for about 10%, but it quickly accumulates to 42% and 74% when second degree and third degree citations are included. This indicates that the vast majority of the publication corpus ends up in the pool of knowledge where inventions arise. The analysis of the distance between research articles and patents also revealed differences between fields of research. Areas such as “Computer science”, “Nanotechnology” and “Biochemistry and Molecular Biology” depict a more immediate impact on patents compared to others less easily applicable. The authors of the study also went on to address which institutions yield research articles with a more significant impact on patents. To this aim, they compared the publications from universities, government laboratories and publicly traded firms. Consistent with previous studies, firms’ scientific production is the most directly linked to patent production. However, universities and government publications follow at a very close distance, despite generally engaging with more long-term research goals.

Other less tangible contributions from academic research and industry take place through the open access of data, reagents or knowledge[6]. Examples of these are The Cancer Genome Atlas (TCGA) with genomic data from more than 11,000 patients, the Jackson Laboratory (JAX) collection and distribution of mouse strains of human diseases, or the Addgene repository, with a collection of more than 67.000 plasmids. Similarly, collaboration agreements like CRADAs (Cooperative Research and Development Agreements) allow industry to partner with academic labs[7]. Under such agreements, which can last years, researchers from academic labs and companies can engage with joint ventures by providing each other with resources, skills and funds. In these partnerships the ownership of any coming intellectual property is discussed upfront as well as first option rights for licensing. Such collaboration formulas have a positive impact on the market readiness of the technologies developed, when not directly shortening the pathway to market through the same industrial partner. Similarly, there’s also specific agreements allowing for to joint clinical trials, specifically for rare diseases, or to transfer research materials.

Overall, this illustrates that public investment can be used to generate innovation and economic growth through the right policy measures. Contrary to the belief that technological and scientific advances move independently, there’s a well-connected flow of ideas that permeate between patented inventions and scientific articles. There are already good incentives to the research communities to facilitate the collaboration between academia and industry. However, there’s still room for novel policies to further leverage what can be achieved through the public investment on research.

[1]https://www.nih.gov/about-nih/what-we-do/budget

[2]https://www.ott.nih.gov/sites/default/files/documents/pdfs/AR2016.pdf

[3]GAO/RCED-98-126 Transferring Federal Technology. Page 3.

[4]The Economic Contribution of  University/Nonprofit  Inventions in the United  States: 1996-2015. Biotechnology Innovation Organization and the Association of University Technology Managers

[5]Ahmadpoor M, Jones BF. “The dual frontier: Patented inventions and prior scientific advance”. Science. 2017 Aug 11;357(6351):583-587.

[6]Bubela T, FitzGerald GA, Gold ER. Recalibrating intellectual property rights to enhance translational research collaborations. Sci Transl Med. 2012 Feb 22;4(122).

[7]Ben-Menachem G, Ferguson SM, Balakrishnan K. Beyond Patents and Royalties: Perception and Reality of Doing Business with the NIH. J Biolaw Bus. 2006 Jan 1;24(1):17-20.

 

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November 28, 2018 at 10:41 am

Mapping the Human Exposome: Understanding the “E” after the “G”

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By: Bryan Bassig, Ph.D.

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Source: Pixabay

 

Current efforts to maximize our understanding of the known interplay between genetic and environmental factors in disease etiology have the potential to inform future research priorities and disease management and prevention

Defining the concept of the ‘exposome’

It is now commonly accepted that the etiology of most chronic diseases is a combination of genetics and environmental exposures, and most likely the interaction of these factors (“G” x “E”). The breadth of environmental exposures that have been implicated in chronic disease risk is substantial and includes personally modifiable factors including smoking and dietary choices as well as exposures that likely require policy interventions on a more universal scale, such as reducing air pollution. Substantial investments to map and characterize the human genome have led to an explosion of population-based studies that seek to understand the specific genetic variants that are associated with a wide variety of disease phenotypes. This in turn has generated great enthusiasm in applying these identified variants to personalized disease risk management and treatment. Whereas current discussion of the role of genetics in population-based health has already begun to move from discovery to translation with ongoing personalized medicine initiatives, our understanding of how to comprehensively measure the totality of environmental factors (broadly defined as non-genetic factors) that shape disease risk at a population-based level has generally lagged behind that of genetics.

Given the interplay and contributions of both “G” and “E” in disease processes, research and financial investments in one component but not the other likely lead to less efficiency in capturing the interindividual variation that exists in disease etiology and treatment and survival. An increasing recognition of this point over the last decade has propagated several research initiatives aimed at greater understanding of environmental factors in disease etiology, including efforts to understand the human “exposome.” Investment in these initiatives from a scientific funding standpoint has the potential to significantly improve exposure science and may in theory inform population-based health research strategies.

The concept of the human exposome was first conceived by epidemiologist Dr. Christopher Wild, a former director of the International Agency for Research on Cancer, in 2005. The concept has since gained traction within the research community. The idea behind the exposome is to complement the advances that have been made in understanding the human genome by characterizing the full spectrum of environmental exposures that occur from conception to death with an understanding that these exposures are both dynamic in nature and broad in scope. Indeed, a full “mapping” of the exposome as originally conceived by Dr. Wild and subsequently by others would include an ability to measure all internal (e.g. endogenous hormones and metabolites) factors as well as exogenous exposures that are either specific to the individual (e.g. smoking/alcohol, diet) or more universal in nature (e.g. built environment, climate). These exposures would be captured or measured at various “snap shots” throughout life, ideally corresponding to key time points of biological development such as in utero, childhood, and early adulthood. In contrast to traditional exposure assessment in population-based studies, which rely on questionnaires or targeted biological measurements of a limited number of chemicals that have been selected a priori, innovative technologies that take an agnostic and more comprehensive approach to measuring internal biomarkers (e.g. “omics”) or lifestyle-related factors (e.g. using smart phones to log physical activity patterns) would be needed for full characterization. Ideally, this would represent the “cumulative level of all cumulative exposures” in the human body.

Implementation: Progress, Potential, and Challenges

Implementation of the exposome paradigm is still in its relative infancy and current discussions are primarily focused on the scope of the initiative that is achievable within the parameters of scientific funding and infrastructure. For instance, in the absence of large prospective cohort studies that include collection of repeated samples or exposure information from people over multiple timepoints, application of the exposome paradigm is still possible but may be limited to fully characterizing the internal and external environment using samples or measurements taken at a single timepoint. While the current focus is on scientific implementation of this paradigm, the potential long-term translatable implications of exposome research can be imagined. From the standpoint of environmental regulation, agencies that conduct risk assessments of environmental exposures evaluate a series of questions including the dose-response relationship of these exposures with biologic effects or disease risk, and whether certain factors like age at exposure influence susceptibility. Application of the exposome framework provides a mechanism to potentially better characterize these questions as well as to evaluate multiple exposures or “mixtures” when making regulatory decisions. This potential however would need to be balanced in view of the existing regulatory framework and the need to develop guidelines for interpreting the expansive and complex datasets.   

While any application of the exposome paradigm to public health or clinical utilization would be an incredibly daunting challenge, a 2012 study published in Cell described this theoretical potential. The case study presented findings from a multiomic analysis of a single individual over 14-months in which distinct biologic changes and omic profiles were observed during periods when the individual was healthy relative to periods when he developed viral illness and type 2 diabetes. The authors concluded that the observed profiles were a proof of principle that an integrative personal omics profile could potentially be used in the future for early diagnostics and monitoring of disease states. While the study did not integrate data on external environmental exposures, further incorporation of these factors into the omic framework may provide evidence of distinct signatures that differ according to exposure status.

Current efforts to advance the exposome field have been bolstered by several initiatives including a 2012 report by the National Academies that described the future vision and strategy of exposure science in the 21st Century. Exposome-related research is also a major goal of the 2018-2023 strategic plan offered by the National Institute of Environmental Health Science (NIEHS), and the agency has supported two exciting exposome research initiatives. These include the HERCULES (Health and Exposome Research Center: Understanding Lifetime Exposures Center) research center at Emory University that is on the front lines of developing new technologies for evaluating the exposome, and the Children’s Health Exposure Analysis Resource (CHEAR) to encourage the use of biological assays in NIH-funded studies of children’s health.

As the field of exposomics matures, there will undoubtedly be several issues that arise that intersect both scientific and policy-related considerations as described by Dr. Wild and others involved in this field. These include but are not limited to:

  1. a) Cross-discipline education and training opportunities: The exposome paradigm encompasses multiple scientific disciplines, including laboratory sciences, bioinformatics, toxicology, and public health. Given the traditional model of graduate programs in science, which generally focus on distinct subfields, new educational and/or training programs that provide cross-disciplinary foundations will be critical in training the next-generation of scientists in this field.
  2. b) Data accessibility and reproducibility: Given its expansive nature and the inherent interindividual variation of non-genetic factors, full characterization of the exposome and associations between exposures and disease may require large international teams of researchers that have central access to the expansive, complex datasets that are generated. Unlike the human genome, the dynamic nature of the internal and external environment will require extensive reproduction and validation both within and across different populations.
  3. c) Funding and defining value: Fully implementing the exposome paradigm from an epidemiological research perspective would likely require profound investments in study infrastructure and laboratory technology. The discontinuation of the National Children’s Study, which originally intended to enroll and follow 100,000 children from birth to 21 years of age in the United States, illustrates the challenges associated with conducting large longitudinal research projects. These demands would need to be balanced with justifying the added value and potential for future utility along the same lines as genomics. The comprehensive understanding of non-genetic determinants of disease risk from a research standpoint, however, is the natural precursor to any discussion of utility.
  4. d) Communication of research findings: The field of genomics has matured to the point that consumers can now obtain personalized reports and risk profiles of their genome from companies like 23andMe and Ancestry.com. It is theoretically possible that this commercial model could be extended in the future to other types of biomarkers such as the metabolome, yet the dynamic nature and current lack of clarity regarding the disease relevance of most non-genetic biomarkers would create considerable challenges in interpreting and conveying the data.

Conclusions

The underlying principles of the exposome were originally conceived by Dr. Wild as a mechanism to identify non-genetic risk factors for chronic diseases in epidemiologic studies. While the increasing number of exposome research initiatives are primarily focused on this scientific goal, challenges remain in the implementation. It is likely too early to project what the future public health and/or clinical utility of this paradigm, if any, may be. Nevertheless, continued investments in this area of research are critical to understand the “missing pieces” of disease etiology and to ideally inform preventive measures and/or disease management in the future.  

 

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November 21, 2018 at 9:55 pm

Insect Allies and the role of DARPA in scientific research

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By: Ben Wolfson, Ph.D.

early-heath-dragonfly-2186186_1920

Source: Pixabay

 

Last month, a Pentagon research program called Insect Allies burst into the public conversation after a team of research scientists and legal scholars published an article detailing their concerns and critiques of the project in Science magazine. Insect Allies is run by the Defense Advanced Research Projects Agency (DARPA), and was announced in 2016 with the stated goal of “pursuing scalable, readily deployable, and generalizable countermeasures against potential natural and engineered threats to the food supply with the goals of preserving the U.S. crop system”. As indicated by its eponymous project name, the Insect Allies research program seeks to develop insects that carry gene editing viruses, allowing for rapid genetic modification of plant food sources. The Insect Allies program exemplifies both the pros and cons of DARPA work. The described project leapfrogs current technological paradigms, promoting a next stage of synthetic biology work. However at the same time, it seeks to create a technology with problematic potential military applications. The battle between basic research and the development of military technologies is one that has dogged DARPA since its inception. As the theoretical and empirical knowledge in the fields of genetic modification and synthetic biology improve, it is imperative that novel technologies are developed with the appropriate ethical and moral oversight and that scientists consider the ramifications of their work.

Origins and Changes of DARPA

Science and the military have long been interwoven, a process that was formalized in the U.S. in the past century. In 1947, President Truman created the Department of Defense, in part to fund scientific research. A decade later President Eisenhower highlighted the importance of science in national defense with the creation of the Advanced Research Projects Agency (renamed DARPA in 1972). DARPA’s creation was in direct response to the launch of Sputnik by the Soviet Union, and given the mission statement of “preventing technological surprises like Sputnik, and developing innovative, high-risk research ideas that hold the potential for significant technological payoffs”.

In its early years, DARPA funded significant amounts of basic and foundational research that did not have immediate applications. However, in 1973 Congress passed the Mansfield Amendment, preventing the Defense Department from funding any research without “a direct and apparent relationship to a specific military function or operation”. The amendment was contentious at the time of its passing, with Presidential Science Advisor Lee DuBridge telling a congressional subcommittee that the amendment had negatively affected the quality of research projects because it is not possible to prove the relevance of a project, and therefore it is wrong to prevent an agency from funding basic research it sees as valuable. Passage of the amendment fundamentally reshaped the U.S. research funding landscape, and projects consisting of upwards of 60% of DOD research funds were cancelled or moved to other agencies. In place of basic research DARPA has shifted to funding research with direct military applications. These projects have often fallen into the realm of “dual-use” technologies, having both civilian and military uses. Successful examples of this strategy include funding projects that evolved into the internet and Global Positioning Systems (GPS). Current research span from projects with clear civilian applications, such as a multitude of projects researching the next generation of medical technologies, to those that are weapons research with purely military potential.

The Insect Allies program

Agriculture is one of the predominant industries in the U.S., making the U.S. a net exporter and world’s largest supplier of a variety of agricultural products including beef, corn, wheat, poultry and pork. The importance of American agriculture to both national security and the security of its global allies and trade partners is well recognized by national security officials, especially in the context of climate change and the potential for growing scarcity. The primary threats to agriculture are disease and weather related events. While these can be mitigated through pesticides, clearing of crops, quarantine, and selective breeding, current strategies are both destructive and time consuming.

The Insect Allies program has three focus areas; viral manipulation, insect vector optimization, and selective gene therapy in mature plants. Through application and combination of these technologies Insect Allies would function by genetically modifying already growing plants through utilization of “horizontal environmental genetic alteration agents (HEGAAs). Traditionally, genetic modification involves changing the genes of a parent organism and propagating its offspring. This process is essentially the same as the selective breeding practiced in agriculture for generations. While this is effective, it is a time-consuming practice as you must breed successive generations of your population of interest.

Through HEGAAs, Insect Allies completely revamp the process. Instead of creating a population of interest from scratch, HEGAAs allow scientists to modify an existing population. If you wanted to create a pesticide-resistant crop, the traditional strategy would be to insert the gene for pesticide resistance into one plant and then collect its seeds and use them to grow an entire field of pesticide resistant plants. With HEGAA technology, farmers could make an already grown field resistant by modifying each individual plant on a broad scale.

Criticism of the Insect Allies program

The authors of the Science article critique the Insect Allies program over a variety of issues, ranging from biological to ethical or moral dilemmas. The article raises issue with both the use of wide-scale genetic modification technologies as well as with the application of insects as vectors as opposed to already existing technologies such as overhead spraying. The use of wide-scale genetic modification is a line which has yet to be crossed, and currently lacks a regulatory path. While research into gene modifying technology is ongoing and real-world tests inevitable, these tests are a contentious issue that is currently being debated. Moreover, agricultural products modified by HEGAAs have no current path to the market. The combination of seemingly little thought in the program towards the regulation that would be necessary for the described application of their technology as well as the existence of lead the authors to suspect that Insect Allies is being developed for other means. While a population of gene-modifying insects could be used to help U.S. crops survive weather-changes or pesticides, they could also potentially be applied to crops of other nations in war. Biological Weapons were banned in 1972, and currently no nations have (publicly) developed them.While the technologies being developed by Insect Allies are described as “for peaceful means”, the stated goals are achievable through already existing technologies. Furthermore, international competition with Insect Allies may accelerate crossing the line between wartime and peacetime technology.

Soon after publication of the Science article, Dr. Blake Bextine, program manager for Insect Allies, released a statement refuting many of these points. He stated that DARPA moved into agricultural work as it is an important aspect of both national and international security, and that the work falls under DARPA’s charter to develop fundamentally new technologies that leapfrog existing capabilities. Moreover, he affirmed that Insect Allies has no plan for open release, and that regulatory systems would be developed and had been planned since the start of the program.

What does the future hold

The Science article’s authors note that they would be worried about Insect Allies whether it was under a civilian or military purview, but it is impossible to ignore the implications of synthetic biology and genetic modification research to the military. DARPA’s strategy of generating high-risk, high-reward research is both effective and engrained into the DNA of the organization, however so is the fact that DARPA is a defense organization.

When DARPA was founded (as ARPA), it was to promote high-risk scientific research that would increase U.S. soft power internationally. After the Mansfield amendment, these goals were shifted towards applied research instead of basic, and with them a focus on defense-oriented research. An advantage of basic research is that it takes time to develop, allowing the findings, and their ramifications, to percolate throughout the global scientific community. The quintessential example of this is regulation of recombinant DNA technologies. Soon after recombinant DNA technology was developed, the 1975 Asilomar Conference was held to establish voluntary guidelines that would ensure the safety of a game-changing scientific technology. As synthetic biology technological development has accelerated, the discussion around the regulation of synthetic biology and genetic modification technology has also begun, and is currently ongoing.

While it is impossible to argue with the massive benefits that civilian applications of DARPA developed technologies have provided, synthetic biology and genetic modification technologies have the potential to enact immense changes globally. The environment and application of a technology has a huge potential to influence its use and the way it is viewed by the public for generations. Insect Allies program states that it is focusing on developing insect-based HEGAAs technologies as a means of pushing development of gene-editing technologies to increase food security in a transparent manner that promotes open published research. It is critical that the Insect Allies program is held to this standard, and that regulation by the global scientific community is allowed to impact the direction and application of these potentially game-changing technologies.

 

 

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November 15, 2018 at 11:22 am

Unlinking databases is not enough to unlink identity from genetic profiles

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By: Allison Dennis B.S.

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Source: Pixabay

 

The efficacy of law enforcement is an issue of public safety. Advances in medicine are a matter of personal wellbeing. Knowing more about one’s unique genetic heritage is a point of curiosity. As all of these spheres delve further and further into DNA sequencing, the ubiquity of personal genetic information is increasingly becoming an issue of privacy. The emerging nature of DNA technology has left us with three major types of DNA databases separated by their use: medical, forensic, and recreational. Each is governed by its own sets of rules, set by federal law, state law, and user agreements. Under specific circumstances data can be intentionally shared for other uses. However, the technological limitations that kept these databases separated in the past may be nearing erosion.

Medical

By congregating and comparing the genomes of people with and without a specific disease through DNA databanks, researchers can discover small glitches in the DNA of affected patients. Identifying the genetic changes that disrupt the normal functions of the body allows researchers to begin designing therapeutics to correct deficiencies or developing genetic tests to diagnose specific diseases, possibly before symptoms have appeared. The potential for medical databases have prompted government led initiatives such as All of Us to amass genetic information from a diverse group of 1 million Americans, which will be queried for medical insights. Already, the Cancer Genome Atlas, maintained by the US National Institutes of Health, contains deidentified genetic data from tumor and normal tissues from 11,000 patients and is openly searchable for research purposes. Foundation Medicine, a private company that provides doctors and patients with genomic profiles of tumor samples to inform treatment options, has stockpiled data from over 200,000 samples. Foundation Medicine shares these data through collaborative agreements and business partnerships with members of the oncology research community and pharmaceutical companies.

Medical DNA databanks, while masking a patient’s name, may link to an individual’s medical history. Because researchers often do not know what parts of the genome will reveal key clues, the genetic data contained in these databases is rich. Often researchers look at how the frequency of single nucleotide changes at hundreds of thousands of places in the genome differ between people affected and unaffected by a particular disease.

The medical benefit of compiling and sharing genomic information is carefully balanced against privacy concerns by Federal regulation. The Genetic Information and Nondiscrimination Act of 2008 (GINA) prohibits employers and health insurers from requesting access to an individual’s or family’s genetic information. The Health Insurance Portability and Accountability Act (HIPAA) Privacy Rule mandates that health-care providers not disclose an individual’s genetic information. The NIH Genomic Data Sharing Policy limits access to individual-level genetic information held in their databases, including the Cancer Genome Atlas, to approved scientific researchers. Despite these safeguards, genetic information contained within medical databases can be identified and provided to law enforcement following a court order in extreme cases.

Forensic

Forensic DNA databases contain searchable genomic profiles for the critical task of identification by law enforcement and military experts. U.S. Federal law allows law enforcement officers to collect and store DNA profiles on anyone they arrest, including those detained by immigration enforcement. Since 1998, the Federal Bureau of Investigation has hosted the national Combined DNA Index System (CODIS), which currently contains 16.8 million offender and arrestee profiles. Unlike medical databases, which can contain a wealth of information, CODIS profiles are limited to a set of 20 places in the genome where the number of times a small sequence of DNA is repeated varies between individuals. The unique combination of these 20 lengths place the probability of two unrelated people sharing a profile at roughly 1 in 1 septillion, and were intentionally selected to not reveal any medically relevant parts of the genome.

The creation of CODIS was authorized by Congress through the DNA Identification Act of 1994, which mandated privacy protection standards. As a safeguard, the database profiles are associated with specimen identification numbers rather than any personal information. The system can only be accessed in physically secure spaces and is restricted to use by criminal justice agencies specifically for the purpose of law enforcement. Only after a match has been found from a query and the candidate match has been confirmed by an independent laboratory will the identity of the suspected perpetrator be revealed, and even then only to the agencies involved in the cases. The Scientific Working Group on DNA Analysis Methods (SWGDAM) continues to recommend revisions to these standards for security and confidentiality issues. Despite housing a relatively unrevealing type of genetic information, CODIS goes above and beyond the privacy protections provided by many recreational and medical databases.

Recreational

Individuals are increasingly turning to direct-to-consumer genetics testing, driven by their curiosity to discover their genetic heritage and to gain some insight into their genetic traits. These tests contain a wealth of information drawn from single nucleotide changes across more than 500,000 parts of the genome. The most popular tests are offered by AncestryDNA and 23andMe, who manage data according to Privacy Best Practices established by the industry. These practices include removing names and demographic identifiers from genomic records, storing identifying information separately if retained, using encryption, limiting access, and requiring consent for third party sharing. As the records are presumed to contain medically relevant information, all identified samples are governed by the same HIPAA and GINA regulations that govern medical tests. 23andMe has amassed a database of over 5 million genetics profiles. AncestryDNA has over 10 million, greatly rivaling the size of forensic and medical databases.

Direct-to-consumer genetics testing companies often sell de-identified genetic data to pharmaceutical and diagnostic development companies for research purposes. Those that follow the Privacy Best Practices established by the industry only do so for users who have consented to participate in research, and GINA expressly prohibits these companies from sharing an individual’s genetic information with potential employers or health insurers.

There are also limits to prevent law enforcement from abusing recreational genetics testing companies. While there is the potential for someone to submit a sample that is not their own, the AncestryDNA service agreement stipulates that users only provide their own sample, and 23andMe expressly disallows “law enforcement officials to submit samples on behalf of a prisoner or someone in state custody.” Moreover, their tests have been specifically designed to make collection of a third parties’ sample difficult. For instance, the 23andMe test requires an amount of saliva needing 30 minutes to generate, preventing illicit collection.

While companies go to great lengths to protect the information contained in their databases, most companies will provide individuals with their own complete profiles when requested. The allure of mapping family connections has lead millions of genealogical hobbyists to openly contribute their re-identified genomic DNA to searchable online databases. The most famous searchable database is GEDmatch, which currently contains about one million profiles. The platform allows users to upload their own genome to retrieve high probability matches of other user’s profiles. A level of privacy is maintained by only sharing small pieces of the genome, allowing complete profiles to remain obscured. However, GEDmatch’s user agreement emphasizes that rather than use encryption, they store data in a format that “would be very difficult for a human to read” and allow volunteers access to the data. Additionally, they specifically welcome “DNA obtained and authorized by law enforcement” for inclusion in their database. The wealth of information publicly hosted on sites like GEDmatch have provided a unique opportunity for other types of DNA databanks to share information and blur the lines of privacy.

Database Cross-Linking

The use of GEDmatch by law enforcement marks an important seachange in genetic privacy. In the past, medical and recreational databases were only occasionally queried by law enforcement, who were seeking specific profiles. However in April 2018, in a desperate search for leads to solve a cold case, law enforcement officers utilized a nearly 40-year old rape-kit to develope a genetic profile. While previous searches over the decades had been limited to the FBI database and the perpetrator’s 20 CODIS loci law enforcement officials were able to undertake a blind and expansive search by uploading the complete profile to the GEDmatch database, which ultimately lead to a third cousin of the man who would be charged with 12 murders.

These types of searches have the power to exonerate or implicate criminals, as a 100% match is undeniable. While only just starting to be used, for someone of European ancestry living in the United States the odds are as high as 60% that a genetic relative can be identified from a database similar to GEDmatch. A public opinion poll conducted shortly after April 2018, revealed that the majority of respondents approved of searches of recreational databases by law enforcement, especially to identify perpetrators of violent crimes.

Scientists have already laid the theoretical groundwork that could allow law enforcement to link a suspect’s profile in a medical or recreational database using the limited 20 CODIS markers from a crime-scene sample. Portions of the genome that share close physical proximity along a chromosome are more likely to be inherited together, allowing statistical predictions to be made about which pieces are most likely to occur together. Although the two types of profiles do not contain the same markers, scientists can predict which marker profiles most likely came from the same individual.

While the use of these tactics might be supported for the purpose of identifying violent criminals, it also puts medical privacy at risk. Despite the de-identification of genomic profiles, scientists have demonstrated reasonable success in tracking down a person’s identity given a genetic profile, a genealogical database such as GEDmatch, and information on the internet.

As DNA databases develop in their depth of information and coverage of individuals, the ability to link records to individuals grows. A lack of compatibility will not be enough to keep medical genomic information sequestered from criminal profiles. Industry standards and user agreements must be discussed and strengthened to safeguard the genetically curious.

 

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November 8, 2018 at 10:14 am