Public Access to Genome-Wide Data: Five Views on Balancing Research with Privacy and Protection

Introductory paragraph: Just over twelve months ago, PLoS Genetics published a paper [1] demonstrating that, given genome-wide genotype data from an individual, it is, in principle, possible to ascertain whether that individual is a member of a larger group defined solely by aggregate genotype frequencies, such as a forensic sample or a cohort of participants in a genome-wide association study (GWAS). As a consequence, the National Institutes of Health (NIH) and Wellcome Trust agreed to shut down public access not just to individual genotype data but even to aggregate genotype frequency data from each study published using their funding. Reactions to this decision span the full breadth of opinion, from ‘‘too little, too late—the public trust has been breached’’ to ‘‘a heavy-handed bureaucratic response to a practically minimal risk that will unnecessarily inhibit scientific research.’’ Scientific concerns have also been raised over the conditions under which individual identity can truly be accurately determined from GWAS data. These concerns are addressed in two papers published in this month’s issue of PLoS Genetics [2,3]. We received several submissions on this topic and decided to assemble these viewpoints as a contribution to the debate and ask readers to contribute their thoughts through the PLoS online commentary features. Five viewpoints are included. The Public Population Project in Genomics (P3G) is calling for a universal researcher ID with an access permit mechanism for bona fide researchers. The contribution by Catherine Heeney, Naomi Hawkins, Jantina de Vries, Paula Boddington, and Jane Kaye of the University of Oxford Ethox Centre outlines some of the concerns over possible misuse of individual identification in conjunction with medical and family history data, and points out that if geneticists mishandle public trust, it will backfire on their ability to conduct further research. George Church posits that actions directed toward restricting data access are likely to exclude researchers who might provide the most novel insights into the data and instead makes the argument that full disclosure and consent to the release of genomic information should be sought from study participants, rather than making difficult-to-guarantee promises of anonymity. Martin Bobrow weighs the risks and benefits and proposes four steps that represent a middle ground: Retain restricted access for now, make malicious de-identification practices illegal, increase public awareness of the issues, and encourage recognition that scientists have a special professional relationship of trust with study participants. Finally, Bruce Weir provides a commentary on the contribution of the two research articles from Braun et al. [2] and Visscher and Hill [3]

European Code against Cancer 4th Edition:Breastfeeding and cancer

Breast cancer is the most frequent cancer in women, and incidence rates have been rising in European Union (EU) countries over recent decades due in part to a sharp decline in breastfeeding practices. Evidence for a protective association between breastfeeding and the risk of breast cancer at all ages is convincing, and modest protective relationships between breastfeeding and the risk of endometrial and ovarian cancers have been suggested. The reduction in breast cancer risk is estimated at 2% for an increase of 5 months of lifetime breastfeeding. The longer women breastfeed, the more they are protected against breast cancer. In addition, breastfeeding is associated with several health benefits for both the mother and the breastfed child. Taking all this evidence into account, the 4th edition of the European Code against Cancer recommends: ‘‘Breastfeeding reduces the mother’s cancer risk. If you can, breastfeed your baby’’

Conceptual dependency and its descendants

This paper surveys representation and processing theories arising out of conceptual dependency theory. One of the primary characteristics of conceptual dependency was the notion of a canonical form, built out of a small number of primitive representations. Although the notion of primitives has largely been lost in subsequent work, many other of the basic notions of CD have remained. In particular, the idea of building representations around inferential capabilities has prevailed in this family of research. The result is a set of representational structures, all of which are highly knowledge-intensive. The use of these structures in various processing theories has led to knowledge-based theories of language understanding, planning, reasoning and other tasks, which have contrasted sharply with the traditional search-oriented approaches used in other systems.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30278/1/0000679.pd

Sexually Antagonistic Selection in Human Male Homosexuality

Several lines of evidence indicate the existence of genetic factors influencing male homosexuality and bisexuality. In spite of its relatively low frequency, the stable permanence in all human populations of this apparently detrimental trait constitutes a puzzling ‘Darwinian paradox’. Furthermore, several studies have pointed out relevant asymmetries in the distribution of both male homosexuality and of female fecundity in the parental lines of homosexual vs. heterosexual males. A number of hypotheses have attempted to give an evolutionary explanation for the long-standing persistence of this trait, and for its asymmetric distribution in family lines; however a satisfactory understanding of the population genetics of male homosexuality is lacking at present. We perform a systematic mathematical analysis of the propagation and equilibrium of the putative genetic factors for male homosexuality in the population, based on the selection equation for one or two diallelic loci and Bayesian statistics for pedigree investigation. We show that only the two-locus genetic model with at least one locus on the X chromosome, and in which gene expression is sexually antagonistic (increasing female fitness but decreasing male fitness), accounts for all known empirical data. Our results help clarify the basic evolutionary dynamics of male homosexuality, establishing this as a clearly ascertained sexually antagonistic human trait

European Code against Cancer 4th Edition:Obesity, body fatness and cancer

AbstractIt is estimated that over half the population of the European Union (EU) is overweight or obese due to an imbalance between energy expenditure and energy intake; this is related to an obesogenic environment of sociocultural, economic and marketing challenges to the control of body weight. Excess body fat is associated with nine cancer sites – oesophagus, colorectum, gall bladder, pancreas, postmenopausal breast, endometrium, ovary, kidney and prostate (advanced) – and 4–38% of these cancers (depending on site and gender) can be attributed to overweight/obesity status. Metabolic alterations which accompany excess body weight are accompanied by increased levels of inflammation, insulin, oestrogens and other hormonal factors. There are some indications that intentional weight loss is associated with reduced cancer incidence (notably in postmenopausal breast and endometrial cancers). Excess body weight is also a risk factor for several other diseases, including diabetes and heart disease, and is related to higher risk of premature death.In reviewing the current evidence related to excess body fat and cancer, the European Code against Cancer Nutrition Working Group has developed the following recommendation: ‘Take action to be a healthy body weight’

Managing clinically significant findings in research:the UK10K example

Recent advances in sequencing technology allow data on the human genome to be generated more quickly and in greater detail than ever before. Such detail includes findings that may be of significance to the health of the research participant involved. Although research studies generally do not feed back information on clinically significant findings (CSFs) to participants, this stance is increasingly being questioned. There may be difficulties and risks in feeding clinically significant information back to research participants, however, the UK10K consortium sought to address these by creating a detailed management pathway. This was not intended to create any obligation upon the researchers to feed back any CSFs they discovered. Instead, it provides a mechanism to ensure that any such findings can be passed on to the participant where appropriate. This paper describes this mechanism and the specific criteria, which must be fulfilled in order for a finding and participant to qualify for feedback. This mechanism could be used by future research consortia, and may also assist in the development of sound principles for dealing with CSFs

Do automated real-time feedback devices improve CPR quality? A systematic review of literature.

Aim: Automated real-time feedback devices have been considered a potential tool to improve the quality of cardiopulmonary resuscitation (CPR). Despite previous studies supporting the usefulness of such devices during training, others have conflicting conclusions regarding its efficacy during real-life CPR. This systematic review aimed to assess the effectiveness of automated real-time feedback devices for improving CPR performance during training, simulation and real-life resuscitation attempts in the adult and paediatric population. Methods: Articles published between January 2010 and November 2020 were searched from BVS, Cinahl, Cochrane, PubMed and Web of Science, and reviewed according to a pre-defined set of eligibility criteria which included healthcare providers and randomised controlled trial studies. CPR quality was assessed based on guideline compliance for chest compression rate, chest compression depth and residual leaning. Results: The selection strategy led to 19 eligible studies, 16 in training/simulation and three in real-life CPR. Feedback devices during training and/or simulation resulted in improved acquisition of skills and enhanced performance in 15 studies. One study resulted in no significant improvement. During real resuscitation attempts, three studies demonstrated significant improvement with the use of feedback devices in comparison with standard CPR (without feedback device). Conclusion: The use of automated real-time feedback devices enhances skill acquisition and CPR performance during training of healthcare professionals. Further research is needed to better understand the role of feedback devices in clinical setting

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants