Genomics England Research Articles

The UK’s 100,000 Genomes Project: manifesting policymakers’ expectations

The UK’s 100,000 Genomes Project has the aim of sequencing 100,000 genomes from UK National Health Service (NHS) patients while concomitantly transforming clinical care such that whole genome sequencing becomes routine clinical practice in the UK. Policymakers claim that the project will revolutionize NHS care. We wished to explore the 100,000 Genomes Project, and in particular, the extent to which policymaker claims have helped or hindered the work of those associated with Genomics England – the company established by the Department of Health to deliver the project. We interviewed 20 individuals linked to, or working for Genomics England. Interviewees had double-edged views about the context within which they were working. On the one hand, policymakers’ expectations attached to the venture were considered vacuous “genohype”; on the other hand, they were considered the impetus needed for those trying to advance genomic research into clinical practice. Findings should be considered for future genomes projects.

Predicting the Pathogenic Impact of Sequence Variation in the Human Genome.

Sequencing data will become widely available in clinical practice within the near future. Uptake of sequence data is currently being stimulated within the UK through the government-funded 100,000 genomes project (Genomics England), with many similar initiatives being planned and supported internationally. The analysis of the large volumes of data derived from sequencing programmes poses a major challenge for data analysis. In this paper we outline progress we have made in the development of predictors for estimating the pathogenic impact of single nucleotide variants, indels and haploinsufficiency in the human genome. The accuracy of these methods is enhanced through the development of disease-specific predictors, trained on appropriate data, and used within a specific disease context. We outline current research on the development of disease-specific predictors, specifically in the context of cancer research.

The 100 000 Genomes Project: What it means for paediatrics

The 100 000 Genomes Project is a unique, national programme combining research and transformation of clinical care, by undertaking whole genome sequencing (WGS) in patients with rare diseases and cancer....

Identifying High-Risk CLL to Predict Early Relapse after FCR Based Treatment Using Whole Genome Sequencing: First Results from the Genomics England CLL Pilot

BackgroundChemo-immunotherapy (CIT) with fludarabine, cyclophosphamide, and rituximab (FCR) is the standard of care in frontline treatment of CLL. With this approach, 25% of patients relapse within 24 months, whereas approximately one third of patients with hypermutated immunoglobulin heavy chains (IgHV) achieve a functional cure (Hallek et al. Lancet. 2010; Tam et al. Blood, 2014, Fischer et al, Blood 2015; Philip A. Thompson et al. Blood 2016). So far, mutations and/or deletions of TP53 remain the only predictive marker screened for in routine clinical practice, accounting for only one third of patients relapsing early after CIT. Recent next-generation sequencing (NGS) studies have revealed novel candidate predictors of early relapse including somatic mutations in RPS15 (Landau et al. Nature, 2015) and SAMHD1 (Clifford et al., submitted). Taken together with TP53disruption, these only occur in a subset of high-risk patients. Here, we present a comprehensive analysis of high-risk patients using Whole Genome Sequencing (WGS).Patients and MethodsUsing WGS we investigated 149 CLL patients from 5 national UK clinical trials: CLEAR (n=8), RIAltO (n=45), CLL 210 (n=22), ARCTIC (n=32) and AdMIRe (n=42). The two first line FCR-based clinical trials (ARCTIC and AdMIRe) were studied in most detail: 56 patients relapsed within 24 months; this group of patients will be referred to as high risk patients. Leukemia samples (peripheral blood) and germline samples (saliva) were collected for each patient. We performed WGS on the HiSeqX (Illumina). After read alignment, we detected somatic variants using Strelka 2.4.7 for small variants detection (SNV and InDels), Manta 0.28.0 for Structural variant (SV) detection, and Canvas 1.3.1 for Copy number variant (CNV) detection (Illumina). Non-coding regions were annotated with information from primary CLL, CLL cell lines and B-cell ENCODE databases. We interrogated the data at a gene scale and global level in order to identify patterns of early relapsing patients. Operative mutational signatures were analysed according to Alexandrov et al. (Nature, 2013). Putative regions of kataegis were calculated based on Lawrence et al. (Nature, 2013) and Alexandrov et al. (Nature, 2013).ResultsThe mean coverage for CLL tumour and germline samples was 105.2X and 33.7X, respectively. The analysis of the whole cohort highlighted 1,723,603 somatic SNVs (mean= 11,570/sample) and 555,179 InDels (mean= 3,726/sample). Somatic SNVs spectrum consisted mainly of C>T/G>A mutations (30% of total SNVs reported) as previously described. The analysis of 13,490 somatic functional SNVs and InDels revealed novel candidate genes as most commonly mutated in the cohort. In high-risk patients, we noticed an enrichment of mutations in known genes such as TP53, genes of the NF-κB pathway and novel candidate genes previously reported in other cancers. A specific analysis of the functional coding mutations of known CLL driver genes revealed ATM, SF3B1 and IGLL5 as most commonly mutated genes in FCR responders compared to TP53, RPS15 and EGR2 in high risk patients. In depth analysis of somatic non-coding regions also identified potential new candidate regions associated with early relapse. Next, we investigated 52,871 CNAs (mean= 380/sample) and 29,080 SVs (mean= 195/sample) and identified as expected del13q, del17p, del11q and tri12 as the most frequent aberrations. In addition, we identified SVs across genes of interest in CLL, for instance TP53, ATM and BIRC3. Finally, we performed global genome analyses with investigation of mutational signatures and kataegis analyses highlighting hypermutated candidate regions, including the previously described IGLL5gene.ConclusionHere we present initial analysis of WGS data on 149 CLL patients from 5 UK clinical trials. Different patterns of mutations between low and high risk clinical groups are suggested. More detailed analysis with greater numbers of samples is ongoing and will determine the true clinical significance of these preliminary findings. The possibility of using WGS to aid clinical decision-making is becoming a realistic goal. DisclosuresBecq:Illumina: Employment. He:Illumina: Employment. Pettitt:Celgene: Speakers Bureau; Gilead: Research Funding, Speakers Bureau; Roche: Research Funding, Speakers Bureau; Infinity: Research Funding. Hillmen:Pharmacyclics: Research Funding; Janssen: Honoraria, Research Funding; Roche: Honoraria, Research Funding; Gilead: Honoraria, Research Funding; Abbvie: Research Funding. Bentley:Illumina: Employment. Schuh:Gilead: Consultancy, Honoraria, Research Funding; Roche, Janssen, Novartis, Celgene, Abbvie: Consultancy, Honoraria.

Genomics England Adds GenomeOncology Platform for Genomic Reporting

Genomics England Adds GenomeOncology Platform for Genomic Reporting

Next-generation sequencing in neuromuscular diseases.

Neuromuscular diseases are clinically and genetically heterogeneous and probably contain the greatest proportion of causative Mendelian defects than any other group of conditions. These disorders affect muscle and/or nerves with neonatal, childhood or adulthood onset, with significant disability and early mortality. Along with heterogeneity, unidentified and often very large genes require complementary and comprehensive methods in routine molecular diagnosis. Inevitably, this leads to increased diagnostic delays and challenges in the interpretation of genetic variants. The application of next-generation sequencing, as a research and diagnostic strategy, has made significant progress into solving many of these problems. The analysis of these data is by no means simple, and the clinical input is essential to interpret results. In this review, we describe using examples the recent advances in the genetic diagnosis of neuromuscular disorders, in research and clinical practice and the latest developments that are underway in next-generation sequencing. We also discuss the latest collaborative initiatives such as the Genomics England (Department of Health, UK) genome sequencing project that combine rare disease clinical phenotyping with genomics, with the aim of defining the vast majority of rare disease genes in patients as well as modifying risks and pharmacogenomics factors.

Sapientia: accelerating rare disease diagnosis and treatment.

Congenica (Cambridge, UK) is a world leading developer of genome-based discovery and diagnostic technologies. The UK company is a spin-out from the Wellcome Trust Sanger Institute (Cambridge, UK) and was founded by scientists and clinicians at the leading edge of genomic analysis. Congenica's Sapientia™ technology platform allows whole-genome sequence analysis to be easily interpreted and presented within a clinically actionable diagnostic report. It is based on pioneering research from Wellcome Trust Sanger Institute, National Health Service clinicians and regional genetic testing laboratories and validated by Genomics England Ltd (London, UK). Sapientia used for medical diagnosis in hospitals including Great Ormond Street Hospital (London, UK), Manchester Centre for Genomic Medicine (Manchester, UK), Birmingham Women's Hospital (Birmingham, UK) and for new drug development by pharmaceutical companies. This profile follows the journey from proof of concept to clinical diagnosis.

The Dawn of Genomic Medicine: The Role of the 100,000 Genomes Project in Breast Care Management

Department of Clinical Genetics, Leicester Royal Infirmary, Leicester, LE1 5WW, UK *Author for correspondence: Tel.: +44 0 116 258 7597; julian.barwell@uhl-tr.nhs.uk On 25 September 2015, University Hospitals of Leicester National Health Service (NHS) Trust recruited its first family to the 100,000 Genomes Project. This project focuses on patients living in England with rare diseases and their families, and patients with cancer. Sequencing 100,000 genomes will enable scientists and doctors to understand more about specific conditions and how we treat them and will greatly enhance the genomic diagnostic capability in the NHS. Genomics England, a company owned by the Department of Health, is coordinating this work, while 11 NHS Genomic Medicine Centers (GMCs) have been established so far across England. The role of the NHS GMCs is to identify, recruit and consent patients, collect and process samples and capture and submit data through to the validation of the results, to enable clinicians to feed back information to patients and manage the treatment of individuals. University Hospitals of Leicester NHS Trust itself is part of the east of England NHS GMC. The primary aims of the project are: to bring benefit to NHS patients; to create an ethical and transparent program based on consent; to enable new scientific discovery and medical insights and to aid development of a UK genomics industry. This project has the potential to transform the future of healthcare, find conclusive diagnoses for rare diseases and revolutionize treatments. This review discusses familial breast cancer susceptibility, the aims, logistics and vision of the 100,000 Genomes Project and how the patients were recruited to the project [1].

Q&A: Mark Caulfield. National genomics.

Mark Caulfield is chief scientist at Genomics England, which was set up in 2013 to deliver the UK 100,000 Genomes Project, initially focusing on cancers, rare diseases and infection. Caulfield, a cardiovascular clinician and researcher, spoke about the UK approach to big data in biomedicine and the role of Genomics England — including how it plans to embed genomic medicine in Britain's National Health Service (NHS).

Robustness of Massively Parallel Sequencing Platforms.

The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications.

Third Annual Open Meeting of the UK Pharmacogenomics and Stratified Medicine Network Conference.

Third Annual Open Meeting of the UK Pharmacogenetics and Stratified Medicine Network 14 January 2015, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK The third Annual Open Meeting of the UK Pharmacogenetics and Stratified Medicine Network was held on 14 January 2015 in association with the Wellcome Trust on the Wellcome Trust Genome Campus at Hinxton, Cambridge, UK. In the morning, speakers from Cancer Research UK, the Medical Research Council, Genomics England, Innovate UK (formerly TSB) and the Department of Health described the current major projects they are funding. In the afternoon, speakers from various universities around the United Kingdom presented data on pharmacogenetics and stratified medicine research covering diverse disease areas including cancers, warfarin dosing, Gaucher disease and rheumatoid arthritis.

Electronic Health Records in the Genomics Era: Impact of Clinical Genomics

The human genome project has created a huge opportunity to move personalized genomic-based healthcare to the clinic [8-10]. This is greatly facilitated by the plummeting cost of DNA sequencing to about $1,000 a genome. Just this February, the US Federal Drug Administration approved a direct-to-consumer (DTC) genetic test for Bloom syndrome carrier status [11] by the company 23 and Me. The 1000 genome project [12] and more recently the 100,000 Genomes (Genomics England Project) have been generating a large amount of data on genetic variations, the Single Nucleotide Polymorphisms (SNPs) from individu-als around the globe. The Genome-Wide Association Studies (GWAS) are beginning to provide valuable clues to risk of disease development and phenotypic association for diverse diseases [13-19]. The clinical significance of the SNPs is incorporated in the Clinical Variations (ClinVar) database [20] from the National Center for Biotechnology Information (NCBI).Basic and translational researchers are well into the post genome era, but the current generations of physicians (with the exception of medical geneticists) are lagging far behind [21,22]. The Medical schools around the globe have been slow to incorporate modules on clinical genomics. Although use of genetic counselors has been the traditional medical approach, the field of genomics is highly complex and its datasets continuously evolving. Thus, a major gap exists between the advances in the genomics field and the physician interface with patients [23]. Furthermore, the EHR systems that are in wide use today offer little support for incorporation of genomics data. In a recent survey, only a small percentage of EHR specialists, primary care clinicians, medical geneticists, and genetic counselors surveyed (9%), felt that the EHR had an impact on genomics medicine [24]. There is a strong need for incorporating the genomics data into the EHR, if the advances in genetics are to help clinicians make the best-informed treatment decisions. In the past, genet-ic information was gathered, and patients counseled about the findings, only in families with a history of a particular disease or disorder. To begin to address this, the Electronic Medical Records and Genomics (eMERGE) Network, a National Human Genome Research Institute (NHGRI)-funded consortium was created. The eMERGE Network was tasked with developing methods and best practices for the utilization of the EHR as a tool for genomic research [25-27]. The network currently incor-porates nine geographically distinct groups around the US. The initial focus of the eMERGE phenotypes included cataract and High Density Lipoprotein (HDL), dementia, electrocardiograph-ic QRS duration, peripheral arterial disease, type 2 diabetes and hypothyroidism [27]. The eMERGE is now in its sixth year and second funding cycle (eMERGE II) and continues to make ad-vances in the field of genomics and health-care informatics. The first cycle of eMERGE had three major aims: (i) use EHR data for electronic phenotyping, (ii) conduct GWAS using the phenotypes and (iii) explore the ethical, legal, and social implications (ELSI) associated with EHR-based GWAS and wide-scale data sharing [25]. A Phenotype KnowledgeBase (PheKB) effort was created to develop phenotypic algorithms across the eMERGE network to facilitate mining the large-scale data.Integration of the genomics data into the EHR system faces considerable hurdles [28-30]. At the present time, no commercial EHR system is available that incorporates genomic data. Furthermore, the pharmacogenetic information, which could have a major impact in reducing adverse drug effects and efficacy, is still rarely used. This is despite strong evidence for clinical validity and utility for the pharmacogenetics use in the clinic [31-33].Other challenges for integration include the amount of the big data the GWAS studies generate (in terabytes), the rapidly expanding SNP variations dataset and the difficulty of establishing meaningful interpretations from these vast amounts of genetic data. The Version 1.0 of the eMERGE data encompassed more than 13 million SNPs from 42,000 samples [26]. In addition, there are a variety of EHR systems becoming available and a standard for handling the vast genomics information is lacking.

A national approach to clinical genomics

Several countries have recognised the need for a national effort to address the challenges and potential value of genomics, but each have adopted different approaches. Genome Canada provides substantial funding to six major centres across the country to drive genomics across a range of endeavours to benefit the whole economy. Recently, the UK government has set up Genomics England, to deliver the 100,000 genomes project that aims to create a lasting legacy for patients, the NHS and the UK economy. The Australian context shares some similarities with these countries: clinical genetics is delivered predominantly in a public health care system and services are dispersed geographically. However, by contrast Australian genetic services are largely embedded in state-funded health systems. An Australian national approach needs to be federated respecting state responsibilities, while addressing areas of national value. I will discuss progress by a coalition of clinical genetic services, diagnostic laboratories and research institutes from all states that are developing a coordinated national approach to the implementation of genomics into the Australian healthcare system.

αIIbβ3 Variants Defined By Next Generation Sequencing: Implications for Predicting Variants Likely to Cause Glanzmann Thrombasthenia and Alloimmune Disorders

# Authors contributed equally to this work.~ Currently at Genomics England Ltd, London, United KingdomNext generation sequencing is transforming our understanding of human genetic variation and is becoming a routine part of human genetic analysis. The identification of millions of new variants, which are mainly rare and assessing their implications for human health presents new challenges to researchers and clinicians. We have analyzed missense variants in the ITGB2A and ITGB3 genes obtained from whole exome and whole genome sequencing (WES & WGS) data from 5 databases: The Human Genome Mutation Database, the 1000 Genomes project, the UK10K Whole Exome Sequencing project, the UK10K Whole Genome Sequencing project, and The National Heart, Lung and Blood Institute Exome Sequencing Project. Together, these encompass variants of the platelet αIIbβ3 integrin receptor from ~32,000 alleles derived from 16,108 individuals. We identified 111 missense variants that have previously been associated with Glanzmann thrombasthenia (GT), 20 variants associated with alloimmune thrombocytopenia, and 5 variants associated with aniso/macrothrombocytopenia. None of the GT variants were found in the last four databases, indicating that they have minor allele frequencies (MAF) less than ~0.01%, attesting to both their rarity and the likelihood that they entered the population within the last ~2,500 years.We also identified 114 novel missense variants in ITGB2A affecting ~11% of the amino acids and 68 novel missense variants in ITGB3 affecting ~9% of the amino acids. 96% of the novel variants had MAF <0.1%, indicating their rarity. Based on sequence conservation, MAF, and/or location of the substituted residue on a complete model of αIIbβ3 that suggested a possible effect on protein folding, we selected three novel variants (αIIb P943A and P176H, and β3 C547G) that affect amino acids previously associated with GT for expression in HEK 293 cells. Both αIIb P176H and β3 C547G severely affected αIIbβ3 expression, whereas αIIb P943A had only a partial effect on expression and no effect on DTT-induced fibrinogen binding. We were not surprised that the latter variant did not have a severe effect on expression or function because it has an MAF (0.46%) that is much higher than the MAFs of the other GT-causing variants.To estimate the percentage of the 114 novel identified variants that are likely to be deleterious we used 3 different algorithms, CADD, Polyphen 2-HDVI, and SIFT. The algorithms showed moderate concordance in their rankings of the likelihood that a variant is deleterious. To compare their predictive powers, we performed receiver operating characteristic (ROC) analysis based on their ability to discriminate confirmed GT missense variants (positive controls) from alloantigens (negative controls); the area under the curve (AUC) values were 0.91, 0.88, and 0.90, respectively. At cutoff values that achieved greater than 95% sensitivity for each algorithm: 1) the specificity values were 75%, 65%, and 60%, and 2) the percentages of novel αIIb+β3 missense variants predicted to be deleterious were 43%, 56%, and 58%. Polyphen 2-HDVI and SIFT identified αIIb P176H and β3 C547G as highly likely to be deleterious and αIIb P943A as much less likely to be deleterious, whereas CADD did not differentiate them in the same way. We conclude that ~1.1% of individuals in the populations studied carry at least one missense variant in αIIb or β3 and that 0.6% carry a variant that might be deleterious and therefore may result in a hemorrhagic GT-like phenotype. The rarity of almost all of the novel missense variants identified indicates that they entered the population recently. Despite having detailed knowledge of the structure and function of αIIbβ3, it is difficult to predict with certainty the impact of any single missense variant. This will pose serious challenges as more individuals undergo WES and WGS; we anticipate that linkage to health record data, as will happen for the UK 100,000 Genomes project, will aid clinical interpretation. Finally, “hypomorphic” gene variants that produce only a partial decrease in expression, such as αIIb P943A, may contribute to the wide variation in αIIbβ3 surface expression observed in the healthy population. DisclosuresNo relevant conflicts of interest to declare.

Translational tidbits

The FDA reviews the status of RNA sequencing; Serono builds on its lupus partnerships; Genomics England receives over £300 million ($500 million) in new investments; a roundup of recent public-private partnerships.

100k Genome Project: sequencing and much more.

Advances in genome-based technologies have led to the rapid generation of new data regarding the genetic etiology of many traits and conditions. In particular, new and cheaper sequencing technologies have enabled the use of whole-genome sequencing (WGS) and wholeexome sequencing (WES) as oft-used research tools, and increasingly as clinical tests for hardto-diagnose cases. Thus, it is anticipated that WGS/WES may eclipse singleand multi-gene tests used today for disease diagnosis and treatment, and potentially be used for health screening. In December 2012, British Prime Minister David Cameron announced an ambitious initiative to sequence the genomes of 100,000 Britons (100,000 Genome Project or 100kGP) affected with cancer or rare diseases, budgeting UK£100 million for this extraordinary effort [101]. In July 2013, the Department of Health announced that this initiative will be coordinated by the newly-established, governmentowned company Genomics England (London, UK). This project will undoubtedly result in new discoveries and demonstrate whether use of WGS can result in improved health outcomes. Clinical implementation of WGS/WES in a clinical setting poses a formidable barrier. Although it may be prudent to wait until evidence of clinical utility has been gathered, given that clinical implementation studies are relatively less costly and can be done concurrently with clinical effectiveness studies, the 100kGP provides a golden opportunity to inform the delivery of WGS if and when the technology is demonstrated beneficial. In particular, there are two major areas of clinical implementation research that could be conducted concurrently with these 100,000 samples of sequenced Britons and vastly contribute to developing strategies for the effective and safe use of WGS: communication and behavioral impact. While

UK Launches 100,000-Genome Initiative

Abstract The UK Department of Health has set up Genomics England to oversee whole-genome sequencing by 2018 for up to 100,000 patients with genetically driven disease and to integrate the data into their care.