GA4GH: International policies and standards for data sharing across genomic research and healthcare

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

SPHN - The BioMedIT Network: A Secure IT Platform for Research with Sensitive Human Data

The BioMedIT project is funded by the Swiss government as an integral part of the Swiss Personalized Health Network (SPHN), aiming to provide researchers with access to a secure, powerful and versatile IT infrastructure for doing data-driven research on sensitive biomedical data while ensuring data privacy protection. The BioMedIT network gives researchers the ability to securely transfer, store, manage and process sensitive research data. The underlying BioMedIT nodes provide compute and storage capacity that can be used locally or through a federated environment. The network operates under a common Information Security Policy using state-of-the-art security techniques. It utilizes cloud computing, virtualization, compute accelerators (GPUs), big data storage as well as federation technologies to lower computational boundaries for researchers and to guarantee that sensitive data can be processed in a secure and lawful way. Building on existing expertise and research infrastructure at the partnering Swiss institutions, the BioMedIT network establishes a competitive Swiss private-cloud - a secure national infrastructure resource that can be used by researchers of Swiss universities, hospitals and other research institutions.

Archimedes' principle for characterisation of recombinant whole cell biocatalysts

The ability of whole cells to catalyse multistep reactions, often yielding synthetically demanding compounds later used by industrial biotech or pharma, makes them an indispensable tool of synthetic chemistry. The complex reaction network employed by cellular catalysts and the still only moderate predictive power of modelling approaches leaves this tool challenging to engineer. Frequently, large libraries of semi-rationally generated variants are sampled in high-throughput mode in order to then identify improved catalysts. We present a method for space- and time-efficient processing of very large libraries (10⁷) of recombinant cellular catalysts, in which the phenotypic characterisation and the isolation of positive variants for the entire library is done within one minute in a single, highly parallelized operation. Specifically, product formation in nanolitre-sized cultivation vessels is sensed and translated into the formation of catalase as a reporter protein. Exposure to hydrogen peroxide leads to oxygen gas formation and thus to a density shift of the cultivation vessel. Exploiting Archimedes' principle, this density shift and the resulting upward buoyancy force can be used for batch-wise library sampling. We demonstrate the potential of the method for both, screening and selection protocols, and envision a wide applicability of the system for biosensor-based assays.

Sequence-based prediction of permissive stretches for internal protein tagging and knockdown

BACKGROUND

Internal tagging of proteins by inserting small functional peptides into surface accessible permissive sites has proven to be an indispensable tool for basic and applied science. Permissive sites are typically identified by transposon mutagenesis on a case-by-case basis, limiting scalability and their exploitation as a system-wide protein engineering tool.

METHODS

We developed an apporach for predicting permissive stretches (PSs) in proteins based on the identification of length-variable regions (regions containing indels) in homologous proteins.

RESULTS

We verify that a protein's primary structure information alone is sufficient to identify PSs. Identified PSs are predicted to be predominantly surface accessible; hence, the position of inserted peptides is likely suitable for diverse applications. We demonstrate the viability of this approach by inserting a Tobacco etch virus protease recognition site (TEV-tag) into several PSs in a wide range of proteins, from small monomeric enzymes (adenylate kinase) to large multi-subunit molecular machines (ATP synthase) and verify their functionality after insertion. We apply this method to engineer conditional protein knockdowns directly in the Escherichia coli chromosome and generate a cell-free platform with enhanced nucleotide stability.

CONCLUSIONS

Functional internally tagged proteins can be rationally designed and directly chromosomally implemented. Critical for the successful design of protein knockdowns was the incorporation of surface accessibility and secondary structure predictions, as well as the design of an improved TEV-tag that enables efficient hydrolysis when inserted into the middle of a protein. This versatile and portable approach can likely be adapted for other applications, and broadly adopted. We provide guidelines for the design of internally tagged proteins in order to empower scientists with little or no protein engineering expertise to internally tag their target proteins.

Efficient engineering of chromosomal ribosome binding site libraries in mismatch repair proficient Escherichia coli

Multiplexed gene expression optimization via modulation of gene translation efficiency through ribosome binding site (RBS) engineering is a valuable approach for optimizing artificial properties in bacteria, ranging from genetic circuits to production pathways. Established algorithms design smart RBS-libraries based on a single partially-degenerate sequence that efficiently samples the entire space of translation initiation rates. However, the sequence space that is accessible when integrating the library by CRISPR/Cas9-based genome editing is severely restricted by DNA mismatch repair (MMR) systems. MMR efficiency depends on the type and length of the mismatch and thus effectively removes potential library members from the pool. Rather than working in MMR-deficient strains, which accumulate off-target mutations, or depending on temporary MMR inactivation, which requires additional steps, we eliminate this limitation by developing a pre-selection rule of genome-library-optimized-sequences (GLOS) that enables introducing large functional diversity into MMR-proficient strains with sequences that are no longer subject to MMR-processing. We implement several GLOS-libraries in Escherichia coli and show that GLOS-libraries indeed retain diversity during genome editing and that such libraries can be used in complex genome editing operations such as concomitant deletions. We argue that this approach allows for stable and efficient fine tuning of chromosomal functions with minimal effort.

Toward Genome-Based Metabolic Engineering in Bacteria

Prokaryotes modified stably on the genome are of great importance for production of fine and commodity chemicals. Traditional methods for genome engineering have long suffered from imprecision and low efficiencies, making construction of suitable high-producer strains laborious. Here, we review the recent advances in discovery and refinement of molecular precision engineering tools for genome-based metabolic engineering in bacteria for chemical production, with focus on the λ-Red recombineering and the clustered regularly interspaced short palindromic repeats/Cas9 nuclease systems. In conjunction, they enable the integration of in vitro-synthesized DNA segments into specified locations on the chromosome and allow for enrichment of rare mutants by elimination of unmodified wild-type cells. Combination with concurrently developing improvements in important accessory technologies such as DNA synthesis, high-throughput screening methods, regulatory element design, and metabolic pathway optimization tools has resulted in novel efficient microbial producer strains and given access to new metabolic products. These new tools have made and will likely continue to make a big impact on the bioengineering strategies that transform the chemical industry.

Mind-controlled transgene expression by a wireless-powered optogenetic designer cell implant

Synthetic devices for traceless remote control of gene expression may provide new treatment opportunities in future gene- and cell-based therapies. Here we report the design of a synthetic mind-controlled gene switch that enables human brain activities and mental states to wirelessly programme the transgene expression in human cells. An electroencephalography (EEG)-based brain–computer interface (BCI) processing mental state-specific brain waves programs an inductively linked wireless-powered optogenetic implant containing designer cells engineered for near-infrared (NIR) light-adjustable expression of the human glycoprotein SEAP (secreted alkaline phosphatase). The synthetic optogenetic signalling pathway interfacing the BCI with target gene expression consists of an engineered NIR light-activated bacterial diguanylate cyclase (DGCL) producing the orthogonal second messenger cyclic diguanosine monophosphate (c-di-GMP), which triggers the stimulator of interferon genes (STING)-dependent induction of synthetic interferon-β promoters. Humans generating different mental states (biofeedback control, concentration, meditation) can differentially control SEAP production of the designer cells in culture and of subcutaneous wireless-powered optogenetic implants in mice.

Brain–machine interfaces offer the possibility of controlling prosthetic devices using changes in brain activity. Folcher et al. couple such a system wirelessly to an optogenetic implant in mice to control expression of a transgene, demonstrating its potential for mind-controlled drug delivery.

Clinical and angiographic outcome in the laser angioplasty for restenotic stents (LARS) multicenter registry

In-stent restenosis (ISR), when treated with balloon angioplasty (PTCA) alone, has an angiographic recurrence rate of 30%-85%. Ablating the hypertrophic neointimal tissue prior to PTCA is an attractive alternative, yet the late outcomes of such treatment have not been fully determined. This multicenter case control study assessed the angiographic and clinical outcomes of 157 consecutive procedures in 146 patients with ISR at nine institutions treated with either PTCA alone (n = 64) or excimer laser assisted coronary angioplasty (ELCA, n = 93)) for ISR. Demographics were similar except more unstable angina at presentation in ELCA-treated patients (74.5% vs. 63.5%; P = 0.141). Lesions selected for ELCA were longer (16.8 +/- 11.2 mm vs. 11.2 +/- 8.6 mm; P < 0.001), more complex (ACC/AHA type C: 35.1% vs. 13.6%; P < 0.001), and with compromised antegrade flow (TIMI flow < 3: 18.9% vs. 4.5%; P = 0.008) compared to PTCA-treated patients. ELCA-treated patients had similar rate of procedural success [93 (98.9% vs. 62 (98.4%); P = 1.0] and major clinical complications [1 (1.1%) vs. 1 (1.6%); P = 1.0]. At 30 days, repeat target site coronary intervention was lower in ELCA-treated patients (1.1% vs. 6.4% in PTCA-treated patients; P = 0.158), but not significantly so. At 1 year, ELCA-treated patients had similar rate of major cardiac events (39.1% vs. 45.2%; P = 0.456) and target lesion revascularization (30.0% vs. 32.3%; P = 0.646). These data suggest that ELCA in patients with complex in-stent restenosis is as safe and effective as balloon angioplasty alone. Despite higher lesion complexity in ELCA-treated patients, no increase in event rates was observed. Future studies should evaluate the relative benefit of ELCA over PTCA alone for the prevention of symptom recurrence specifically in patients with complex in-stent restenosis.

Retrieval and analysis of particulate debris after saphenous vein graft intervention

OBJECTIVES

This study was designed to evaluate the composition and quantity of particulate debris resulting from vein graft intervention.

BACKGROUND

Distal embolization and "no reflow" are frequent and important complications resulting from angioplasty of diseased saphenous vein grafts. Little is known about the composition and quantity of embolic particulate debris associated with vein graft intervention, and no intervention has been shown to protect against its clinical consequences.

METHODS

A catheter system, designed to contain, retrieve and protect against distal embolization of this material, was evaluated during 27 percutaneous interventional saphenous vein graft procedures. Clinical, angiographic and pathologic analyses were performed.

RESULTS

The duration of distal graft occlusion required to allow intervention and subsequent debris removal was 150 +/- 54 s, decreasing as experience was gained. Thrombolysis in Myocardial Infarction trial (TIMI) flow grade increased from 2.6 +/- 0.8 to 3.0 +/- 0.0. Creatine kinase (CK) rose above normal in three patients (11.1%) exceeding 3x normal in one (3.7%) resulting in the diagnosis of non-Q-myocardial infarction. Particulate material was identified following 21 of 23 procedures suitable for analysis. Particle size was 204 +/- 57 microm in the major axis and 83 +/- 22 microm in the minor axis. Particles consisted predominantly of soft acellular atheromatous material, such as that typically found under a fibrous cap. Semiquantitative analysis suggested that the quantity of particulate material was less following stenting than following balloon dilation.

CONCLUSIONS

Particulate matter is commonly present following routine angioplasty and stenting of saphenous vein grafts. Containment, retrieval and analysis of this particulate debris are all feasible. Comparison to prior clinical experience is limited by small sample size. However, to the extent that these particles may contribute to distal embolization, no-reflow and infarction, such a system may contribute to the reduction of complications following vein graft intervention.

A new method for assessing right-sided heart pressures using encapsulated microbubbles--a preliminary report

A new noncatheter method for measuring pressures of the right side of the heart uses specially manufactured microbubbles of carbon dioxide injected into the peripheral venous system. Sudden expansion of these bubbles in the cardiac chambers causes bubble oscillations at a frequency that is primarily a function of surrounding pressure. The oscillations are recordable by a microphone on the chest wall. The preliminary experience has been in dogs and further development is needed before we can begin clinical testing of the method. In its current form, the potential for measuring higher systolic pressures seems better than that for lower diastolic pressures.

Advances in guidewire technology

Since the introduction in 1979 of a movable guidewire system for PTCA, significant advances have been made in guidewire technology that have improved primary success rates and reduced complications with the use of this system. Coronary stenoses in distal sites or in branch vessels with abrupt angulations can now routinely be reached and crossed with newer-generation guidewires . This report concentrates on the evolution of advances in guidewire technology and outlines changes in guidewire design that have allowed for improved efficacy and safety with the movable wire system. Appropriate cases are presented to illustrate the advantages of available guidewires .