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Background: One source of deoxyribonucleic acid (DNA) for genetic studies is the utilization of dried blood spots stored on paper cards (Guthrie cards) collected shortly after birth. These cards represent an important source of material for epidemiologic and population-based genetic studies. Extraction of DNA from these cards can lead to variable amounts of recovered DNA. We report here results of our efforts to maximize yield from this valuable, but nonrenewable, resource., Method: Commercial methods of DNA extraction from blood cards were used, and protocol modifications were introduced that enhanced DNA yield., Results: Use of a commercial solvent prior to DNA extraction steps gave greater yields than extraction without the solvent. Modification of the elution step by use of prewarmed extraction buffer and a soaking step at an elevated temperature increased yield by 6- to 10-fold., Conclusions: The modified DNA extraction method yielded as much as 660 ng of DNA from a single 5-mm-diameter punch of a blood spot card. The DNA performed well in downstream, polymerase chain reaction-based applications., ((c) 2010 Diabetes Technology Society.)

Focuses on a DNA science and technology course which taught at the University of Albany for high school students during the summer of 1998. What was learnt during the course; Details on the use of Escherichia coli in experiments; Information on plasmids; In-depth look at the course.

Forensic Genetic Genealogy (FGG) has fast become a popular tool in criminal investigations since it first emerged in 2018. FGG is a novel investigatory tool that has been applied to hundreds of unresolved cold cases in the United States to generate investigative leads and identify unknown individuals. Consumer DNA testing and the public's increased curiosity about their own DNA and genetic ancestry, have greatly contributed to the availability of human genetic data. Genetic genealogy has been a field of study/interest for many years as both amateur and professional genetic genealogists use consumer DNA data to explore genetic connections in family trees. FGG encompasses this knowledge by applying advanced sequencing technologies to forensic DNA evidence samples and by performing genetic genealogy methods and genealogical research, to produce possible identities of unknown perpetrators of violent crimes and unidentified human remains. This combination of forensic genetics, genetic genealogy, and genealogical research has formed a new subdiscipline within the forensic sciences. This paper will summarize the individual disciplines that led to the emergence of FGG, its practice in forensic investigations, and current/future considerations for its use.

Background: Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with—and potential exchange of—microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter) and June (Summer) 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills. Results: Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea. Eukaryotic assemblages were dominated by human, other metazoan and fungal taxa. The currency investigated harbored a diverse microbial population that was dominated by human skin and oral commensals, including Propionibacterium acnes, Staphylococcus epidermidis and Micrococcus luteus. Other taxa detected not associated with humans included Lactococcus lactis and Streptococcus thermophilus, microbes typically associated with dairy production and fermentation. Culturing results indicated that viable microbes can be isolated from paper currency. Conclusions: We conducted the first metagenomic characterization of the surface of paper money in the United States, establishing a baseline for microbes found on $1 bills circulating in New York City. Our results suggest that money amalgamates DNA from sources inhabiting the human microbiome, food, and other environmental inputs, some of which can be recovered as viable organisms. These monetary communities may be maintained through contact with human skin, and DNA obtained from money may provide a record of human behavior and health. Understanding these microbial profiles is especially relevant to public health as money could potentially mediate interpersonal transfer of microbes. [ABSTRACT FROM AUTHOR]

Buccal cells provide a convenient source of DNA for epidemiologic studies. Mouthwash rinses yield a higher quality and quantity of DNA than cytobrushes but are not practical for collection from infants. Although cytobrushes yield sufficient DNA for most genotyping analyses, human leukocyte antigen (HLA) analysis can require 1,000-fold more DNA. In Iowa City, Iowa, in 2002, the authors tested two cytobrush collection methods to optimize total DNA yield and purity for HLA genotyping in mothers and infants: 1) brushing the left and right inner cheeks (standard method) and 2) brushing the upper and lower “gutters”, that is, the space between the gums and the inner lips/cheeks along the front and sides of the mouth (test method). Storage and mailing experiments were performed to define conditions for optimizing DNA yield and purity. Mothers’ gutter samples yielded significantly higher total amounts of DNA (mean yield = 15.0 µg/two brushes) than cheek samples (mean yield = 7.6 µg/two brushes) (paired t test: p < 0.001), while DNA yields from cheek and gutter collections from infants were equivalent. Cytobrushes stored and/or mailed in paper envelopes yielded significantly more and higher-purity DNA than brushes in plastic bags or tubes. Cytobrush sampling of the mouth’s gutter areas can enhance DNA yield in mothers but not in young infants. DNA yields can be further optimized by controlling mailing and storage conditions. [ABSTRACT FROM AUTHOR]

The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR–findable, accessible, interoperable, and reusable– despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate. [ABSTRACT FROM AUTHOR]

Interlaboratory studies are a type of collaborative exercise in which many laboratories are presented with the same set of data to interpret, and the results they produce are examined to get a "big picture" view of the effectiveness and accuracy of analytical protocols used across participating laboratories. In 2005 and again in 2013, the Applied Genetics Group of the National Institute of Standards and Technology (NIST) conducted interlaboratory studies involving DNA mixture interpretation. In the 2005 NIST MIX05 study, 69 laboratories interpreted data in the form of electropherograms of two-person DNA mixtures representing four different mock sexual assault cases with different contributor ratios. In the 2013 NIST MIX13 study,108 laboratories interpreted electropherogram data for five different case scenarios involving two, three, or four contributors, with some of the contributors potentially related. This paper describes the design of these studies, the variations observed among laboratory results, and lessons learned., (Published by Elsevier B.V.)

This paper discusses the genesis of human DNA patents and the legal confusion and ramifications that ensued. Beginning in the mid-1970s with policymakers and lawmakers in the United States, confronted with an economy impacted by an oil crisis, inflation, growing and persistent unemployment and the fledgling biotechnology industry, this paper tracks the development of the practice until its banning in the US Supreme Court in June 2013. The paper raises serious questions regarding the relevance of a patent system--a system that, as the patenting of naturally occurring biological materials demonstrates, is so easily manipulated through the use of legal contrivances. The paper outlines that potential future manipulation poses as a significant threat to the national economy and security of the United States if history is allowed to repeat itself in the context of biological materials. [ABSTRACT FROM AUTHOR]

The chemical characterization of the substance responsible for the phenomenon of "transformation" of pneumococci was presented in the now famous 1944 paper by Avery, MacLeod, and McCarty. Reception of this work was mixed. Although interpreting their results as evidence that deoxyribonucleic acid (DNA) is the molecule responsible for genetic changes was, at the time, controversial, this paper has been retrospectively celebrated as providing such evidence. The mixed and changing assessment of the evidence presented in the paper was due to the work's interpretive flexibility--the evidence was interpreted in various ways, and such interpretations were justified given the neophytic state of molecular biology and methodological limitations of Avery's transformation studies. I argue that the changing context in which the evidence presented by Avery's group was interpreted partly explains the vicissitudes of the assessments of the evidence. Two less compelling explanations of the reception are a myth-making account and an appeal to the wartime historical context of its publication.

Extensive enthusiasm surrounds the potential for human DNA information to sustain and enhance the pharmaceutical industry's profitability. Nevertheless, persons whose health makes their DNA of commercial interest are routinely expected simply to give their DNA and the information in it to pharmaceutical or genomics companies or their academic intermediaries, voluntarily and without compensation. This state of affairs is increasingly recognized as paradoxical, but it is favored by conventional bioethical opinion. Given that most DNA information is now collected for commercial purposes and is worth considerably more than is generally imagined, bioethical objections to compensation of individuals for their DNA information are inappropriate. This paper suggests approaches by which individuals and representative governments and patient interest groups can negotiate compensation. Appreciable attitudinal change is required if those individuals personally involved are to be included fairly in the commercialization of human DNA information. Ultimately, however, such change is necessary if commercial genetic research is to respect human dignity and human rights.

In 1944, two Canadians, Oswald Avery and Colin MacLeod, and an American, MacLyn McCarty, published a paper in The Journal of Experimental Medicine that demonstrated genes to be the chemical, deoxyribonucleic acid (DNA). Even though this paper is now regarded as the single mos important publication in biology of the 20th century, Avery was not awarded the Nobel Prize. This raises the question as to why his work did not earn him the Prize. These are several possible reasons: the discovery may have been ahead of tis time; all three authors were physician-scientists ans not recognized chemists or geneticists; and Avery, the principal author, had reached an advanced age and characteristically took an extremely cautious and low-key approach to his work. Discussion of these reasons in turn raises other issues surrounding the recognition of the work of celebrated scientist, from Galileo and Copernicus onwards.

This paper considers the potential benefits and harms of DNA patenting for biomedical research and medical practice. It argues that, all things considered, the benefits of patenting DNA outweigh the harms, although societies should adopt policies designed to prevent or mitigate the harms associated with patenting. Some of these policies include: (1) reinforcing the research exemption for academic researchers, (2) raising the "bar" for the criteria of patentability, (3) restricting the scope of patents, (4) disclosing conflicts of interest related to DNA patents, (5) sharing the economic benefits of patenting with patients, and (6) providing insurance coverage for some types of genetic tests.

In countries with multiple racial or ethnic groups, it is not uncommon that contributors to a mixed stain or a DNA mixture belong to different ethnic origins. This paper derives a general formula for evaluating the likelihood ratio in such situations based on the commonly adopted Recommendation 4.1 of the U.S. Second National Research Council Report on the evaluation of DNA evidence. The restrictive Hardy-Weinberg assumption is not taken in this paper. Our formula generalizes the results of Fung and Hu for a single ethnic group, and of Weir et al. under the Hardy-Weinberg law for a single, and Fukshansky and Bär for multiple ethnic groups. The effect of different ethnic groups of contributors to the interpretation of mixtures is illustrated through the analysis of the Simpson case., (Copyright 2002 John Wiley & Sons, Ltd.)

Motivation: Locating the regions of similarity in a genome requires the availability of appropriate tools such as 'Accelerated Search for SImilar Regions in Chromosomes' (ASSIRC; Vincens et al., Bioinformatics, 14, 715-725, 1998). The aim of this paper is to present different strategies for improving this program by distributing the operations and data to multiple processing units and to assess the efficiency of the different implementations in terms of running time as a function of the number of processing units., Results: The new version D-ASSIRCis based on three alternative strategies of task sharing: (1) a distributed search using the splitting of studied sequences into large overlapping subsequences (strategy ASS); (2) two distributed searches for repeated exact motifs of fixed size either managed by a central processor (strategy AGD) or locally managed by numerous processors (strategy ALD). The result is that the strategy ASSis suitable for a large number of processing units (the time was divided by a factor of 12 when the number of processing units was increased from 1 to 16) wheras the strategy ALDis better for a small set of processors (typically for four or six). The different proposed strategies are efficient for various applications in genomic research, particularly for locating similarities of nucleic sequences in large genomes., Availability: D-ASSIRCis freely available by anonymous FTP at ftp://ftp.ens.fr/pub/molbio/dassirc.tar.gz. Sources and binaries for Solaris and Linux are included in the distribution.

The incidence of thyroid cancer is increasing, especially papillary thyroid carcinoma (PTC), making it currently the fastest-growing cancer among women. Reasons for this increase remain unclear, but several risk factors including radiation exposure and improved detection techniques have been suggested. Recently, the induction of chromosomal fragile site breakage was found to result in the formation of RET/PTC1 rearrangements, a common cause of PTC. Chromosomal fragile sites are regions of the genome with a high susceptibility to forming DNA breaks and are often associated with cancer. Exposure to a variety of external agents can induce fragile site breakage, which may account for some of the observed increase in PTC. This paper discusses the role of fragile site breakage in PTC development, external fragile site-inducing agents that may be potential risk factors for PTC, and how these factors are especially targeting women. [ABSTRACT FROM AUTHOR]

Background: In the present paper, we describe the effect of 4', 6-diamidino-2-phenylindole (DAPI) dihydrochloride concentration and pH on the resolution of DNA distribution histograms generated by dual-parametric simultaneous analysis of DNA content and electronic nuclear volume (ENV)., Methods: Nuclei from tissue culture cell lines and frozen human solid tumors were isolated in nuclear isolation media containing different concentrations of DAPI, at various pH levels, and analyzed on a NASA/American Cancer Society (ACS) flow cytometer. Samples stained with propidium iodide/hypotonic citrate and analyzed in a Coulter XL flow cytometer were used for comparison., Results: Nuclei stained with DAPI concentration of 1-3 microg/ml, pH 6.0, gave the best resolution for the detection of the near-diploid and near-tetraploid populations. Simultaneous use of ENV and DAPI/DNA fluorescence under these conditions identified subpopulations that otherwise could not be detected by DNA analysis alone., Conclusions: Staining at 1-3 microg/ml DAPI, pH 6.0, was optimal for the detection of aneuploid populations, especially the near-diploid and/or near-tetraploid populations in human tumors.

This paper focuses on the question of whether DNA patents help or hinder scientific discovery and innovation. While DNA patents create a wide variety of possible benefits and harms for science and technology, the evidence we have at this point in time supports the conclusion that they will probably promote rather than hamper scientific discovery and innovation. However, since DNA patenting is a relatively recent phenomena and the biotechnology industry is in its infancy, we should continue to gather evidence about the effects of DNA patenting on scientific innovation and discovery as well the economic, social, and legal conditions relating to intellectual property in biotechnology. We should give the free market, the courts, researchers, and patent offices a chance to settle issues related to innovation and discovery, before we seek legislative remedies, since new laws proposed at this point would lack adequate foresight and could do more harm than good. However, we should be open to new laws or regulations on DNA patents if they are required to in order to deal with some of the biases and limitations of the free market.

Hepatitis B virus (HBV) is a major cause of chronic liver disease worldwide. Besides genotype, quantitative analysis of HBV infection is extensively used for monitoring disease progression and treatment. Affordable viral load monitoring is desirable in resource-limited settings and it has been already shown to be useful in developing countries for other viruses such as Hepatitis C virus (HCV) and HIV. In this paper, we describe the validation of a real-time PCR assay for HBV DNA quantification with TaqMan chemistry and MGB probes. Primers and probes were designed using an alignment of sequences from all HBV genotypes in order to equally amplify all of them. The assay is internally controlled and was standardized with an international HBV panel. Its efficacy was evaluated comparing the results with two other methods: Versant HBV DNA Assay 3.0 (bDNA, Siemens, NY, USA) and another real-time PCR from a reference laboratory. Intra-assay and inter-assay reproducibilities were determined and the mean of CV values obtained were 0.12 and 0.09, respectively. The assay was validated with a broad dynamic range and is efficient for amplifying all HBV genotypes, providing a good option to quantify HBV DNA as a routine procedure, with a cheap and reliable protocol. [ABSTRACT FROM AUTHOR]

Currently in the United States there is little direction for what constitutes sufficient guidelines for DNA mixture interpretation. While a standardized approach is not possible or desirable, more definition is necessary to ensure reliable interpretation of results is carried out. In addition, qualified DNA examiners should be able to review reports and understand the assumptions made by the analyst who performed the interpretation. Interpretation of DNA mixture profiles requires consideration of a number of aspects of a mixed profile, many of which need to be established by on-site, internal validation studies conducted by a laboratory’s technical staff, prior to performing casework analysis. The relevant features include: criteria for identification of mixed specimens, establishing detection and interpretation threshold values, defining allele peaks, defining nonallele peaks, identifying artifacts, consideration of tri-allelic patterns, estimating the minimum number of contributors, resolving components of a mixture, determining when a portion of the mixed profile can be treated as a single source profile, consideration of potential additive effects of allele sharing, impact of stutter peaks on interpretation in the presence of a minor contributor, comparison with reference specimens, and some issues related to the application of mixture calculation statistics. Equally important is using sensible judgment based on sound and documented principles of DNA analyses. Assumptions should be documented so that reliable descriptive information is conveyed adequately concerning that mixture and what were the bases for the interpretations that were carried out. Examples are provided to guide the community. Interpretation guidelines also should incorporate strategies to minimize potential bias that could occur by making inferences based on a reference sample. The intent of this paper is to promote more thought, provide assistance on many aspects for consideration, and to support that more formalized mixture interpretation guidelines are developed. [ABSTRACT FROM AUTHOR]

Reports that the U.S. Attorney General has submitted a report to Congress based on a nationwide survey on the use of DNA and its utility in Great Britain.

Simple Summary: Increasing threats to wildlife have made assessing their populations, health, and adaptation to stressors ever more important. The use of environmental DNA to make these assessments is relatively new and offers many advantages, such as non-lethal sampling. How novel technologies such as these are framed in the news media is critically important because the general public gathers much of its information about scientific developments from the media, and public perceptions can impact use of technology, responses to data derived from its use, and ethical concerns. To date, media constructions of eDNA and perceptions among the general public have not been examined. The current paper begins to address this gap by undertaking an examination of media coverage of eDNA in Canada and the United States for the past approximately twenty years—likely a critical period in shaping understandings of and responses to eDNA. The findings indicate that eDNA is framed as a powerful tool, yet the social concerns that receive the most attention are those where there are financial interests at play, and these interests have to date eclipsed attending to relevant ethical considerations. Environmental DNA (eDNA) is an emerging technology used for understanding ecosystems, environmental change, and stressors. Cellular and extracellular DNA are collected from environmental samples instead of individual wildlife animals, and as such eDNA comes with associated logistical and ethical benefits. It is increasingly being used, yet to date public knowledge and perceptions of eDNA have not been explored. Given that most of the public gathers scientific information from news media sources, this is a logical first place to start. This paper reports on a framing and agenda-setting analysis of news media coverage of eDNA in Canada and the United States from 2000 to 2020. The findings indicate that eDNA is being framed as an emerging and powerful tool, although questions regarding its validity and reliability are raised vis-à-vis identifying the presence of invasive species. Less than half of the news articles analyzed address broader social or ethical issues in relation to eDNA, and the majority focus on the potential financial impacts of eDNA findings on development projects and business interests. The potential ethical advantages of non-lethal sampling methods used via eDNA sampling are not addressed, nor are the potential ethical issues raised by its potential use in bioprospecting, indicating that the current state of agenda setting regarding eDNA in these newspapers is focused on economic impacts, to the exclusion of potential ethical issues. This unfolding news coverage will likely be key to understanding public perceptions of this novel technology. [ABSTRACT FROM AUTHOR]

Modern chemical control of pests has contributed to a dramatic improvement in public welfare since its introduction 50 years ago. Millions of lives have been saved through the control of disease vectors, and millions more have been improved by the use of chemicals to produce an inexpensive and abundant food supply. Hundreds of pesticidally active ingredients are in commercial use today, and among these are found genotoxic and nongenotoxic carcinogens. In the United States, the Environmental Protection Agency regulates carcinogens using threshold and nonthreshold approaches depending upon the outcome of a weight-of-evidence determination. More than one-half of all pesticides with some evidence of carcinogenic potential are regulated by the nonthreshold approach. The limitations on product use imposed by this approach have restricted the number of products available to growers and to the public. This restriction has had a direct impact on industry with respect to commercial success and financial returns on investment as well as an indirect impact on the industry's ability to fund the discovery and development of new compounds. This paper explores the question of how well regulation by the nonthreshold approach has achieved the goal of protecting public health, whether it does this better than the alternative use of the threshold approach, and whether the incremental protection it affords is a meaningful public benefit that justifies the aforementioned impacts on industry.

This paper provides an interpretative history of the early genesis of biotechnology in Cambridge and attempts to reconcile how the 1976 adoption of the most restrictive biosafety ordinance in the US created an unexpected business friendly environment that subsequently anchored the industry. The regulation was motivated by community concerns about the environmental effects of recombinant DNA and ignited a lively debate, characterized by an open process with activities to inform and involve citizens in decision-making. [ABSTRACT FROM AUTHOR]

This paper compares the regulation of biotechnology in Britain, Germany and the United States and shows that systematic differences have developed around four issues: abortion, assisted reproduction, stem cells, and genetically modified crops and foods. Policy choices with respect to these issues reflect the capacity of each nation's regulatory institutions to deal with the scientific, social and ethical uncertainties around biotechnology. National regulatory frameworks constitute an apparatus of collective sense-making through which governments and publics interpret biotechnology's risks and promises. Specifically, regulatory choices position the novel ontologies created by biotechnology either on the side of the familiar and manageable or on the side of the unknown and insupportably risky. The comparison shows that public responses to biotechnology are embedded within robust and coherent political cultures and are not ad hoc expressions of concern that vary unpredictably from issue to issue. [ABSTRACT FROM AUTHOR]

Experts presenting statistical DNA evidence are often challenged about their ability to use databases of only a few hundred people to claim probabilities in the billions. This challenge is countered with the inclusion of a sampling error calculation in the case report. Sampling error is present in every DNA calculation because the statistics rely on a sample (database) of individuals to estimate population frequencies of alleles and this error must be quantified. This paper explains in simple terms how Bayesian estimation theory is used to produce Bayesian credible intervals for sampling error calculations in DNA profiles. [ABSTRACT FROM AUTHOR]

This paper reviews judicial opinions that have discussed the April 1992 recommendations of a committee of the U.S. National Research Council concerning the statistics of forensic DNA profiles obtained with single-locus VNTR probes. It observes that a few courts have held 'ceiling frequencies' (as opposed to less 'conservative' estimates) admissible, but that the implications of the scientific criticisms of the ceiling procedures have yet to be addressed adequately in court opinions. It urges courts to distinguish between policy judgments and scientific assessments in both the NRC report and the scientific literature, and to defer less to the former than to the latter.

In healthcare one size does not fit all. If one was ill, wouldn't it be great for them to receive medicines made precisely for them? It is the aim of the All of Us campaign to do just that. Overtime, All of Us hopes to collect one million DNA samples and other valuable health information from a diverse group of people in the United States by about 2024. Studying these samples will reveal to researchers likenesses and differences across the samples to improve health by creating precise personal remedies and treatments. This column introduces the All of Us campaign, illustrates the research efforts using the All of Us data and closes with where one can contribute to this monumental effort. [ABSTRACT FROM AUTHOR]

While writing a book on the history of postpartum depression in the United States, I became interested in an ongoing study about possible genetic markers of postpartum mental illness. I participated in the first step, an online survey. When I qualified for the next step, saliva collection, I was torn over whether or not to continue. Making this decision required reflecting on some overlapping issues: gender, medicalization, genetic research, and the political functions of DNA donation. In this perspectives essay, I explore tensions around situating myself in my historical research project. [ABSTRACT FROM AUTHOR]

Next generation sequencing raises new questions within the context of an existing and still evolving regulatory landscape for device manufacturers and clinical laboratories. FDA cleared the first NGS sequencing platform in November 2013, but it is unclear what lies ahead for this technology. NGS will require new types of training and expertise to interpret the vast quantities of genetic data so as to provide meaningful clinical information to physicians and patients. This paper will describe the current regulatory landscape for NGS technologies, identify the regulatory challenges they present, and consider whether new regulatory paradigms are needed to accommodate NGS technologies and services. [ABSTRACT FROM AUTHOR]

The article focuses on the DNA sequence variants that influence gene expression and disease risk in the U.S. It is pointed out that the effects of variations in DNA sequence are often subtle, such as altered levels of gene expression. Moreover, it is said that identifying those DNA sequences that determine levels of expression across individuals could have great medical potential. It also discusses one paper that illustrates the identification of DNA sequences which looks at the two major contractile proteins of the human heart.

Genomic biobanks present ethical challenges that are qualitatively unique and quantitatively unprecedented. Many critics have questioned whether the current system of informed consent can be meaningfully applied to genomic biobanking. Proposals for reform have come from many directions, but have tended to involve incremental change in current informed consent practice. This paper reports on our efforts to seek new ideas and approaches from those whom informed consent is designed to protect: research subjects. Our model emerged from semi-structured interviews with healthy volunteers who had been recruited to join either of two biobanks (some joined, some did not), and whom we encouraged to explain their concerns and how they understood the relationship between specimen contributors and biobanks. These subjects spoke about their DNA and the information it contains in ways that were strikingly evocative of the legal concept of the trade secret. They then described the terms and conditions under which they might let others study their DNA, and there was a compelling analogy to the commonplace practice of trade secret licensing. We propose a novel biobanking model based on this trade secret concept, and argue that it would be a practical, legal, and ethical improvement on the status quo. [ABSTRACT FROM AUTHOR]

Summary: Background: We aimed to accurately estimate the frequency of a hexanucleotide repeat expansion in C9orf72 that has been associated with a large proportion of cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Methods: We screened 4448 patients diagnosed with ALS (El Escorial criteria) and 1425 patients with FTD (Lund-Manchester criteria) from 17 regions worldwide for the GGGGCC hexanucleotide expansion using a repeat-primed PCR assay. We assessed familial disease status on the basis of self-reported family history of similar neurodegenerative diseases at the time of sample collection. We compared haplotype data for 262 patients carrying the expansion with the known Finnish founder risk haplotype across the chromosomal locus. We calculated age-related penetrance using the Kaplan-Meier method with data for 603 individuals with the expansion. Findings: In patients with sporadic ALS, we identified the repeat expansion in 236 (7·0%) of 3377 white individuals from the USA, Europe, and Australia, two (4·1%) of 49 black individuals from the USA, and six (8·3%) of 72 Hispanic individuals from the USA. The mutation was present in 217 (39·3%) of 552 white individuals with familial ALS from Europe and the USA. 59 (6·0%) of 981 white Europeans with sporadic FTD had the mutation, as did 99 (24·8%) of 400 white Europeans with familial FTD. Data for other ethnic groups were sparse, but we identified one Asian patient with familial ALS (from 20 assessed) and two with familial FTD (from three assessed) who carried the mutation. The mutation was not carried by the three Native Americans or 360 patients from Asia or the Pacific Islands with sporadic ALS who were tested, or by 41 Asian patients with sporadic FTD. All patients with the repeat expansion had (partly or fully) the founder haplotype, suggesting a one-off expansion occurring about 1500 years ago. The pathogenic expansion was non-penetrant in individuals younger than 35 years, 50% penetrant by 58 years, and almost fully penetrant by 80 years. Interpretation: A common Mendelian genetic lesion in C9orf72 is implicated in many cases of sporadic and familial ALS and FTD. Testing for this pathogenic expansion should be considered in the management and genetic counselling of patients with these fatal neurodegenerative diseases. Funding: Full funding sources listed at end of paper (see Acknowledgments). [ABSTRACT FROM AUTHOR]

Abstract: Background: CDC''s Newborn Screening Quality Assurance Program collaborated with several U.S. Cystic Fibrosis Care Centers to collect specimens for development of a molecular CFTR proficiency testing program using dried-blood spots for newborn screening laboratories. Methods: Adult and adolescent patients or carriers donated whole blood that was aliquoted onto filter paper cards. Five blind-coded specimens were sent to participating newborn screening laboratories quarterly. Proficiency testing results were evaluated based on presumptive clinical assessment. Individual evaluations and summary reports were sent to each participating laboratory and technical consultations were offered if incorrect assessments were reported. Results: The current CDC repository contains specimens with 39 different CFTR mutations. Up to 45 laboratories have participated in the program. Three years of data showed that correct assessments were reported 97.7% of the time overall when both mutations could be determined. Incorrect assessments that could have lead to a missed case occurred 0.9% of the time, and no information was reported 1.1% of the time due to sample failure. Conclusions: Results show that laboratories using molecular assays to detect CFTR mutations are performing satisfactorily. The programmatic results presented demonstrate the importance and complexity of providing proficiency testing for DNA-based assays. [Copyright &y& Elsevier]

Abstract: Hypoallergenic novel foods may have benefits for food-allergic consumers. However, other novel foods may exacerbate the problems associated with food allergy. This paper reviews the existing legislation associated with the introduction of novel foods and specifically considers its coverage of allergy risks and benefits. Various regulations are in place to protect consumer health. These regulations require novel food safety to be assessed before they can enter the market, but do not specify how this assessment, which includes allergenicity, should be performed. It is concluded that including a benefit assessment in the novel food legislation, may be beneficial. [ABSTRACT FROM AUTHOR]

DNA technology revolutionized criminal law, family law and trust and estates practice. It is now revolutionizing immigration law. Currently the Department of Homeland Security does not require DNA tests, but it recommends these tests when primary documentation, such as marriage licenses, birth certificates and adoption papers are not available to prove the relationship between the U.S. citizen petitioner and the beneficiary who is seeking permanent resident status in the United States. DNA tests are attractive to the government as a result of administrative convenience and as a means of countering fraud, but adoption of a wholesale policy of DNA testing poses a host of potential problems. In an area of law where family reunification is described as the primary goal, an increase in the use of DNA sometimes results in separating families and other unintended consequences. By promoting the use of DNA evidence, the social interests that are paramount in a family relationship could become subservient to genetic interests. The beneficiaries could become mere genetic entities, whose biological relationship through their genes is paramount. This promotes the view that shared genes are the principal means of identifying human relationships and that one should be entitled to legal benefits solely on this basis. Quality control in the collection, storage and testing of samples, access of individuals to testing facilities, especially in developing countries, privacy interests and the potential for misuse of the results of these tests, particularly in preventing the admission of aliens on health grounds are among the potential problems identified in this article. Using examples from disciplines where DNA evidence has been adopted-criminal, family and estates and trusts law-this article will present a workable policy for the use of this technology in immigration law. [ABSTRACT FROM AUTHOR]

Abstract: The rice super cultivar ‘Koshihikari’, grown on 37% of the total rice area in Japan, has been a leading cultivar since 1979. It is also grown in the USA and Australia. However, its tendency to lodge makes harvest difficult and reduces grain quality, and the regularity of large-scale typhoons compromises its production nationally. The genetic improvement of Koshihikari against lodging has been an extremely important theme for the past 30 years in Japan. This paper describes the development of a semidwarf form of Koshihikari by the fixing of an allele of the Green Revolution semidwarf gene sd1 via eight recurrent backcrosses. The cultivar, with excellent flavor and high yield, was named ‘Hikarishinseiki’, which means “Bright New Century” (rice cultivar No. 12273; Ministry of Agriculture, Forestry and Fisheries of Japan: MAFF). Hikarishinseiki, with ≥99.8% of the Koshihikari genome, is about 20cm shorter than Koshihikari. DNA monitoring of Hikarishinseiki confirmed its genomic substitution into Koshihikari except for sd1 and a marker-based method to distinguish Koshihikari from Hikarishinseiki was developed. Its flavor (upper medium grade) and quality were the same as those of Koshihikari grown at 10 sites across Japan, but its yield was on average 3% higher (maximum 29% higher at Hyogo) than that of Koshihikari and it was highly resistant to lodging. Hikarishinseiki is the first semidwarf form of Koshihikari registered by MAFF. Some economical impact has been achieved by introducing Hikarishinseiki and it is already notified as a brand rice description in the rice-producing districts of Niigata, Shiga, Tottori, Okayama, Tokushima, and Kochi prefectures. [Copyright &y& Elsevier]

This essay examines the current state of knowledge of molecular biology, and how well this science has been conveyed into the public understanding. The article starts by providing a primer on the key concepts of molecular genetics. What this shows is that DNA is not the sole governing component of biological inheritance and cellular reproduction. Rather, the nature of life is the outcome of a complex interaction among DNA, RNA, and proteins. The limitations of genetic theory are evident from the findings of the National Institutes of Health's Encyclopedia of DNA Elements Project (ENCODE). Summarizing a large number of scientific reports created by this project, it is argued that the ENCODE study has replaced the original pattern of colinear transfer of genetic information from simple genes to specific proteins and their engendered inherited traits with a vastly more complex network of overlapping and interlaced relationships. Thus, the ENCODE project has undermined the notion of genetics that underlies much the practices of genetic engineering of crop plants or genetic screening for diseases. Yet there virtually been no press coverage of this fundamental challenge to the core genetic theory and the public remains uninformed about this issue. This unacknowledged issue in molecular genetics creates a crisis in biology. Because the responsible scientific community has not sought to inform the public, there is a serious problem of public information regarding the status of genetic theory and the nature of the risks engendered in genomic research. [ABSTRACT FROM AUTHOR]

While the number of published marine studies using environmental DNA (eDNA) has increased substantially in recent years, marine fish surveys are still scarce. To examine the potential for eDNA to support marine fisheries monitoring surveys, we optimized an eDNA isolation method, developed a multispecies assay and tested it on eDNA samples collected along the Pacific coast of the United States. Four commercial DNA extraction kits that exploit the capability of the nucleic acids binding a solid phase (two using a silica matrix and two magnetic beads) as well an organic separation method were tested. A species-specific multiplex qPCR assay was developed and tested to simultaneously target Pacific hake (Merluccius productus), Pacific lamprey (Entosphenus tridentatus) and eulachon (Thaleichthys pacificus). The specificity of the assay was tested in silico, in vitro and in natura. Environmental DNA isolation using phenol:chloroform:isoamyl purification with a phase lock was optimized and yielded the highest amount of total and target DNA and was used to extract 46 marine water samples for the detection of the three species of interest. The multiplex qPCR assay used in the quantification process was also optimized to provide convenience and accuracy. Pacific hake was present in 44% of the eDNA samples while the other two species were absent. Here, we present a complete workflow for the simultaneous detection and quantification of multiple marine fish species using eDNA. This workflow supports large-scale at-sea sampling efforts with preservation at ambient temperatures and has demonstrated DNA extraction efficiency and reliability. The multiplex qPCR assay is shown to be sensitive and specific for the purposes of simultaneously monitoring the relative abundance of multiple targeted fish species. [ABSTRACT FROM AUTHOR]

A scalable approach for quantifying intact HIV-1 proviruses is critical for basic research and clinical trials directed at HIV-1 cure. The intact proviral DNA assay (IPDA) is a novel approach to characterizing the HIV-1 reservoir, focusing on the genetic integrity of individual proviruses independent of transcriptional status. It uses multiplex digital droplet PCR to distinguish and separately quantify intact proviruses, defined by a lack of overt fatal defects such as large deletions and APOBEC3G-mediated hypermutation, from the majority of proviruses that have such defects. This distinction is important because only intact proviruses cause viral rebound on ART interruption. To evaluate IPDA performance and provide benchmark data to support its implementation, we analyzed peripheral blood samples from 400 HIV-1+ adults on ART from several diverse cohorts, representing a robust sample of treated HIV-1 infection in the United States. We provide direct quantitative evidence that defective proviruses greatly outnumber intact proviruses (by >12.5 fold). However, intact proviruses are present at substantially higher frequencies (median, 54/106 CD4+ T cells) than proviruses detected by the quantitative viral outgrowth assay, which requires induction and in vitro growth (~1/106 CD4+ T cells). IPDA amplicon signal issues resulting from sequence polymorphisms were observed in only 6.3% of individuals and were readily apparent and easily distinguished from low proviral frequency, an advantage of the IPDA over standard PCR assays which generate false-negative results in such situations. The large IPDA dataset provided here gives the clearest quantitative picture to date of HIV-1 proviral persistence on ART. [ABSTRACT FROM AUTHOR]

The Lean Six Sigma (LSS) process continue to be used throughout the public and private sectors to map processes seeking to make them lean and, thereby, more efficient and effective. We make the argument that the LSS process (i.e. Define, Measure, Analyze, Improve, and Control (DMAIC)) is inherently scientific. In Ronald N. Giere's (1979) book entitled Scientific Reasoning, he develops a scientific reasoning methodology and then applies the methodology to describe the process used to discover deoxyribonucleic acid (DNA). The article will overlay real-world LSS project conducted by an element of the United States Office of the Secretary of Defense (OSD) between 2006 and 2008 and its DMAIC process atop Giere's Scientific Reasoning Methodology. Ultimately, this article uses the scientific reasoning methodology to bound the evidence necessary to form the scientific explanation that the DMAIC process is indeed - scientific and the key to Lean Six Sigma's success. [ABSTRACT FROM AUTHOR]

Background: This article describes the research trends in sperm DNA fragmentation (SDF) over the past 20 years (1999–2018) using a scientometric approach. Methods: A stepwise approach was adopted to retrieve scientometric data (articles per year, authors, affiliations, journals, countries) from Scopus and analyze the publication pattern of SDF with reference to key areas of research in the field of Andrology. Results: A total of 2121 articles were retrieved related to SDF. Our data revealed an increasing research trend in SDF (n = 33 to n = 173) over the past 20 years (R2 = 0.894). Most productive country in publications was the USA (n = 450), while Agarwal A. (n = 129) being the most productive author. Most of the articles in SDF were primarily focused on lifestyle (n = 157), asthenozoospermia (n = 135) and varicocele (130). Mechanistic studies on SDF were published twice as much as prognostic/diagnostic studies, with significant emphasis on oxidative stress. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) was the most widely used technique to evaluate SDF. Publications on SDF related to assisted reproductive techniques also showed a linear increasing trend (R2 = 0.933). Conclusions: Our analysis revealed an increasing trend in SDF publications predominantly investigating lifestyle, asthenozoospermia and varicocele conditions with TUNEL being the most widely used technique. A substantial increase in research is warranted to establish SDF as prognostic/diagnostic parameter to evaluate clinical scenarios and ART outcomes. [ABSTRACT FROM AUTHOR]

In April 2018, the U.S. implemented a "zero-tolerance" immigration policy that would lead to the separation of more than 2,000 migrant families over the following months. By that summer, the policy and resultant family separations had generated a media storm that swept up the public. In early June, the government announced its consideration of DNA testing to aid in the detection of human trafficking in immigration contexts. Later that month, as the government retracted the child separation policy, the public began questioning how children and adults would be reunited and discussing the potential usefulness of DNA testing for those reunifications. Then in early July, the government announced that DNA testing was indeed being used, and by mid-month the public's outrage over the use of DNA was strong. We set out to examine the public dialogue on DNA testing—including misunderstandings and miscommunications—both in newspaper coverage and on Twitter in the 2-month summer period of 2018, at the height of public discussion of migrant family separations and then reunifications. We performed database searches identifying 263 newspaper articles and used Twitter's advanced search function identifying 153 Tweets containing discussion of the use of DNA for migrant family reunification. Upon the resulting sources, we performed content analysis, analyzing for slant on the immigration policy and the use of DNA tests using a combination of open and closed codes. Our analysis showed that perspectives on the use of DNA diverged in connection with perspectives on the immigration policy, and that there was a contrast among the cohorts in the stated utility of DNA testing. These findings offer insight into a) how DNA testing in a highly politicized immigration context was represented in media coverage and b) the public's understanding of the role that DNA testing could or should play in immigration. By detailing the role that comments from experts, stakeholders, and the public played in these discussions, we hope to provide lessons for communications with the public about future non-medical applications of genetic technologies. [ABSTRACT FROM AUTHOR]

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