The Clinical Sequencing Evidence-Generating Research Consortium: Integrating Genomic Sequencing in Diverse and Medically Underserved Populations

The Clinical Sequencing Evidence-Generating Research (CSER) consortium, now in its second funding cycle, is investigating the effectiveness of integrating genomic (exome or genome) sequencing into the clinical care of diverse and medically underserved individuals in a variety of healthcare settings and disease states. The consortium comprises a coordinating center, six funded extramural clinical projects, and an ongoing National Human Genome Research Institute (NHGRI) intramural project. Collectively, these projects aim to enroll and sequence over 6,100 participants in four years. At least 60% of participants will be of non-European ancestry or from underserved settings, with the goal of diversifying the populations that are providing an evidence base for genomic medicine. Five of the six clinical projects are enrolling pediatric patients with various phenotypes. One of these five projects is also enrolling couples whose fetus has a structural anomaly, and the sixth project is enrolling adults at risk for hereditary cancer. The ongoing NHGRI intramural project has enrolled primarily healthy adults. Goals of the consortium include assessing the clinical utility of genomic sequencing, exploring medical follow up and cascade testing of relatives, and evaluating patient-provider-laboratory level interactions that influence the use of this technology. The findings from the CSER consortium will offer patients, healthcare systems, and policymakers a clearer understanding of the opportunities and challenges of providing genomic medicine in diverse populations and settings, and contribute evidence toward developing best practices for the delivery of clinically useful and cost-effective genomic sequencing in diverse healthcare settings

Whole-genome sequencing holds the key to the success of gene-targeted therapies COMMENT

Rare genetic disorders affect as many as 3%-5% of all babies born. Approximately 10,000 such disorders have been identified or hypothesized to exist. Treatment is supportive except in a limited number of instances where specific therapies exist. Development of new therapies has been hampered by at least two major factors: difficulty in diagnosing diseases early enough to enable treatment before irreversible damage occurs, and the high cost of developing new drugs and getting them approved by regulatory agencies. Whole-genome sequencing (WGS) techniques have become exponentially less expensive and more rapid since the beginning of the human genome project, such that return of clinical data can now be achieved in days rather than years and at a cost that is comparable to other less expansive genetic testing. Thus, it is likely that WGS will ultimately become a mainstream, first-tier NBS technique at least for those disorders without appropriate high-throughput functional tests. However, there are likely to be several steps in the evolution to this end. The clinical implications of these advances are profound but highlight the bottlenecks in drug development that still limit transition to treatments. This article summarizes discussions arising from a recent National Institute of Health conference on nucleic acid therapy, with a focus on the impact of WGS in the identification of diagnosis and treatment of rare genetic disorders.CASE VIGNETTEIn 2017, Ipek (her name is used with permission), an apparently healthy baby girl, was born, but newborn screening (NBS) returned a result of concern: a low T-cell Receptor Excision Circle (TREC) count, raising the possibility immunodeficiency. Her ensuing medical evaluation disclosed no signs of severe combined immune deficiency, the usual target of this screening, but unexpectedly pointed to a different diagnosis: ataxia telangiectasia (A-T), a rare and progressive neurodegenerative disorder. In A-T, pathogenic variants in the ATM gene impair the cell's ability to respond to DNA damage, causing the cerebellum to begin to shrink starting in early childhood. The usual course of the disease includes development of symptoms by age five with development of clumsiness and incoordination. By their teenage years, the abilities to walk, talk, swallow, and coordinate her eye movements are lost. She would likely die as a young adult.No treatments for A-T exist. One of the challenges is that most children are diagnosed only after neurologic symptoms emerge, after significant degeneration has already occurred. But because Ipek was diagnosed at such a young age, she could be enrolled in an investigational trial before major neuronal loss. At age two, Ipek began receiving a series of intrathecal injections of an antisense oligonucleotide, designed by Boston Children's Hospital to suppress the effects of an abnormal splice site created by one of her pathogenic ATM variants (Yu lab, manuscript in review). This therapy promises her an improved long-term outcome that would otherwise have been impossible.In an age burgeoning with promising research studies for rare genetic diseases, this case underscores the importance of early screening for access to investigational trials. Early screening with whole-genome sequencing (WGS) can unlock opportunities for genetically targeted or other experimental therapies, such as the mutation-specific therapy designed for Ipek. For instance, 10%-15% of individuals with A-T have been shown to have splice mutations that could make them eligible for treatment with a splice-modulating ASO (and two-thirds of these cases are only detectable via WGS because they involve deep intronic variants and/or structural genomic rearrangements). In the future, early WGS may unlock opportunities for additional targeted therapies like nonsense readthrough or RNA or genome editing.Functional Genomics of Muscle, Nerve and Brain Disorder

Accelerated surgery versus standard care in hip fracture (HIP ATTACK) : an international, randomised, controlled trial

Background: Observational studies have suggested that accelerated surgery is associated with improved outcomes in patients with a hip fracture. The HIP ATTACK trial assessed whether accelerated surgery could reduce mortality and major complications. Methods: HIP ATTACK was an international, randomised, controlled trial done at 69 hospitals in 17 countries. Patients with a hip fracture that required surgery and were aged 45 years or older were eligible. Research personnel randomly assigned patients (1:1) through a central computerised randomisation system using randomly varying block sizes to either accelerated surgery (goal of surgery within 6 h of diagnosis) or standard care. The coprimary outcomes were mortality and a composite of major complications (ie, mortality and non-fatal myocardial infarction, stroke, venous thromboembolism, sepsis, pneumonia, life-threatening bleeding, and major bleeding) at 90 days after randomisation. Patients, health-care providers, and study staff were aware of treatment assignment, but outcome adjudicators were masked to treatment allocation. Patients were analysed according to the intention-to-treat principle. This study is registered at ClinicalTrials.gov (NCT02027896). Findings: Between March 14, 2014, and May 24, 2019, 27 701 patients were screened, of whom 7780 were eligible. 2970 of these were enrolled and randomly assigned to receive accelerated surgery (n=1487) or standard care (n=1483). The median time from hip fracture diagnosis to surgery was 6 h (IQR 4\u20139) in the accelerated-surgery group and 24 h (10\u201342) in the standard-care group (p<0\ub70001). 140 (9%) patients assigned to accelerated surgery and 154 (10%) assigned to standard care died, with a hazard ratio (HR) of 0\ub791 (95% CI 0\ub772 to 1\ub714) and absolute risk reduction (ARR) of 1% ( 121 to 3; p=0\ub740). Major complications occurred in 321 (22%) patients assigned to accelerated surgery and 331 (22%) assigned to standard care, with an HR of 0\ub797 (0\ub783 to 1\ub713) and an ARR of 1% ( 122 to 4; p=0\ub771). Interpretation: Among patients with a hip fracture, accelerated surgery did not significantly lower the risk of mortality or a composite of major complications compared with standard care. Funding: Canadian Institutes of Health Research