Germline-focussed analysis of tumour-only sequencing: recommendations from the ESMO Precision Medicine Working Group

It is increasingly common in oncology practice to perform tumour sequencing using large cancer panels. For pathogenic sequence variants in cancer susceptibility genes identified on tumour-only sequencing, it is often unclear whether they are of somatic or constitutional (germline) origin. There is wide-spread disparity regarding both the extent to which systematic 'germline-focussed analysis' is carried out upon tumour sequencing data and for which variants follow-up analysis of a germline sample is carried out. Here we present analyses of paired sequencing data from 17 152 cancer samples, in which 1494 pathogenic sequence variants were identified across 65 cancer susceptibility genes. From these analyses, the European Society of Medical Oncology Precision Medicine Working Group Germline Subgroup has generated (i) recommendations regarding germline-focussed analyses of tumour-only sequencing data, (ii) indications for germline follow-up testing and (iii) guidance on patient information-giving and consent.

United Kingdom: transfers of genomic data to third countries

In the United Kingdom (UK), transfer of genomic data to third countries is regulated by data protection legislation. This is a composite of domestic and European Union (EU) law, with EU law to be adopted as domestic law when Brexit takes place. In this paper we consider the content of data protection legislation and the likely impact of Brexit on transfers of genomic data from the UK to other countries. We examine the advice by regulators not to rely upon consent as a lawful basis for processing under data protection law, at least not when personal data are used for research purposes, and consider some of the other ways in which the research context can qualify an individual's ability to exercise control over processing operations. We explain how the process of pseudonymization is to be understood in the context of transfer of genomic data to third parties, as well as how adequacy of data protection in a third country is to be determined in general terms. We conclude with reflections on the future direction of UK data protection law post Brexit with the reclassification of the UK itself as a third country.

Incidental findings from clinical sequencing in Greece: reporting experts' attitudes

Unprecedented progress in sequencing technologies and decreasing cost have brought genomic testing into the clinical setting. At the same time, the debate in the literature concerning the return of incidental findings (IFs) has made this an important issue internationally. These developments reflect a shift in genetics that will also affect smaller countries, such as Greece, that are just starting to implement these technologies and may look to other countries for examples of good practice. Ten in-depth interviews were conducted with Greek experts in clinical sequencing. Previous experiences and attitudes toward IFs and clinical sequencing were investigated as well as views on the existing policy regarding managing genetic information generated through testing. . Interviews were analysed using thematic analysis. All participants reported the lack of any legal or other supportive mechanism. IFs are currently managed at a “local” level, i.e. within the clinic or the laboratory in an ad hoc way. All participants thought that clinically valid and actionable IFs should be returned, but always with caution and in respect to patients’ wishes, although several experts reported returning IFs according to their clinical discretion. Experts reported that most patients ask for all tests available but they felt that more counselling is needed to understand and manage genetic information. Due to the lack of any supporting mechanisms, professionals in Greece, even those with established experience in the field of genetic and genomic testing, have difficulties dealing with IFs. All experts agreed that it is now time, before the full integration of genomic testing into everyday clinical practice, for guidance to help Greek physicians work with patients and their families when IFs are discovered.

Securing the data economy: translating privacy and enacting security in the development of DataSHIELD

Contemporary bioscience is seeing the emergence of a new data economy: with data as its fundamental unit of exchange. While sharing data within this new 'economy' provides many potential advantages, the sharing of individual data raises important social and ethical concerns. We examine ongoing development of one technology, DataSHIELD, which appears to elide privacy concerns about sharing data by enabling shared analysis while not actually sharing any individual-level data. We combine presentation of the development of DataSHIELD with presentation of an ethnographic study of a workshop to test the technology. DataSHIELD produced an application of the norm of privacy that was practical, flexible and operationalizable in researchers' everyday activities, and one which fulfilled the requirements of ethics committees. We demonstrated that an analysis run via DataSHIELD could precisely replicate results produced by a standard analysis where all data are physically pooled and analyzed together. In developing DataSHIELD, the ethical concept of privacy was transformed into an issue of security. Development of DataSHIELD was based on social practices as well as scientific and ethical motivations. Therefore, the 'success' of DataSHIELD would, likewise, be dependent on more than just the mathematics and the security of the technology.

Nosocomial bloodstream infections in United States hospitals: a three-year analysis

Nosocomial bloodstream infections are important causes of morbidity and mortality. In this study, concurrent surveillance for nosocomial bloodstream infections at 49 hospitals over a 3-year period detected >10,000 infections. Gram-positive organisms accounted for 64% of cases, gram-negative organisms accounted for 27%, and 8% were caused by fungi. The most common organisms were coagulase-negative staphylococci (32%), Staphylococcus aureus (16%), and enterococci (11%). Enterobacter, Serratia, coagulase-negative staphylococci, and Candida were more likely to cause infections in patients in critical care units. In patients with neutropenia, viridans streptococci were significantly more common. Coagulase-negative staphylococci were the most common pathogens on all clinical services except obstetrics, where Escherichia coli was most common. Methicillin resistance was detected in 29% of S. aureus isolates and 80% of coagulase-negative staphylococci. Vancomycin resistance in enterococci was species-dependent--3% of Enterococcus faecalis strains and 50% of Enterococcus faecium isolates displayed resistance. These data may allow clinicians to better target empirical therapy for hospital-acquired cases of bacteremia.

Differential air sac pressures in diving tufted ducks Aythya fuligula

The air in the respiratory system of diving birds contains a large proportion of the body oxygen stores, but it must be in the lungs for gas exchange with blood to occur. To test the hypothesis that locomotion induces mixing of air sac air with lung air during dives, we measured differential pressures between the interclavicular and posterior thoracic air sacs in five diving tufted ducks Aythya fuligula. The peak differential pressure between posterior thoracic and interclavicular air sacs, 0.49+/-0.13 kPa (mean +/- s.d.), varied substantially during underwater paddling as indicated by gastrocnemius muscle activity. These data support the hypothesis that locomotion, perhaps through associated abdominal muscle activity, intermittently compresses the posterior air sacs more than the anterior ones. The result is differential pressure fluctuations that might induce the movement of air between air sacs and through the lungs during dives.

A prolonged outbreak of methicillin-resistant Staphylococcus aureus in the burn unit of a tertiary medical center

OBJECTIVE

To report an outbreak of methicillin-resistant Staphylococcus aureus (MRSA) in our burn unit and the steps we used to eradicate the organism.

DESIGN AND SETTING

Outbreak investigation in the burn unit of a 900-bed tertiary-care medical center.

OUTBREAK

Between March and June 1993, MRSA was isolated from 10 patients in our burn unit. All isolates had identical antibiograms and chromosomal DNA patterns.

CONTROL MEASURES

Infection control personnel encouraged healthcare workers to wash their hands after each patients contact. The unit cohorted all infected or colonized patients, placed each affected patient in isolation, and, if possible, transferred the patient to another unit. Despite these measures, new cases occurred. Infection control personnel obtained nares cultures from 56 healthcare workers, 3 of whom carried the epidemic MRSA strain. One healthcare worker cared for six affected patients, and one cared for five patients. We treated the three healthcare workers with mupirocin. Subsequently, no additional patients became colonized or infected with the epidemic MRSA strain.

CONCLUSIONS

The outbreak ended after we treated healthcare workers who carried the epidemic strain with mupirocin. This approach is not appropriate in all settings. However, we felt it was justified in this case because of a persistent problem after less intrusive measures.

Identification of the cleavage site recognized by the turnip yellow mosaic virus protease

The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150-kDa and C-terminal 70-kDa proteins. By introducing two methionine residues near the N-terminus of the 70-kDa protein, we have obtained N-terminal amino acid sequence of that protein produced from [35S]methionine-labeled in vitro translations. The introduction of methionine residues was demonstrated to not interfere with viral replication or proteolysis, as assayed by inoculating mutant RNA transcripts onto whole plants and protoplasts, as well as by translating the RNAs in a rabbit reticulocyte lysate. This has allowed us to determine that the TYMV protease cleaves between alanine1259 and threonine1260 of the precursor protein p206, yielding proteins of calculated Mr 140,618 and 66,037, which will be referred to henceforth as p141 and p66, respectively. The sequence context around the cleavage site is LNGA/TP.

Penicillin V and rifampin for the treatment of group A streptococcal pharyngitis: a randomized trial of 10 days penicillin vs 10 days penicillin with rifampin during the final 4 days of therapy

To improve the bacteriologic and clinical cure rates of streptococcal pharyngitis, 79 children were randomly assigned to receive penicillin V alone for 10 days (39 patients) or penicillin for the same duration and rifampin during the last 4 days of penicillin therapy (40 patients). Eleven patients given penicillin had evidence of bacteriologic failure (including eight with relapse of clinical illness) on repeat cultures done 4 to 7 days after treatment, whereas there were no failures in children given combination therapy (P = 0.0015). All eight symptomatic children improved with penicillin-rifampin therapy and subsequent cultures were negative, whereas three asymptomatic children continued to harbor group A streptococci even after combination therapy. Antibody response by antistreptolysin O or antideoxyribonuclease B assay was seen in 50.6% of patients; the antibody responses in both groups were comparable. These results show that addition of rifampin to the penicillin regimen improves the clinical and bacteriologic cure rates in children with streptococcal pharyngitis.

Evaluation of a Tay-Sachs screening program on a college campus

A screening program for Tay-Sachs disease was done on a predominantly unmarried, university student population and later evaluated. Ten carriers were detected among a population of 390 screened. Voluntarily screened individuals were given a questionnaire at the time of screening and after their carrier status was revealed. In addition, individuals in a target population were queried as to why they did not attend the screening. Results of evaluation indicate that both the screened and unscreened students were able to answer approximately two thirds of a set of questions on Tay-Sachs correctly, but there was widespread lack of knowledge regarding the implications of carrier status and inheritance of the disease. In general, respondents to the questionnaires were not opposed to abortion. However, when asked about the family planning alternatives that they would consider if they were carriers, more subjects preferred adoption, artificial insemination, or avoidance of pregnancy to abortion.