P213: Exploring heterogeneity among gene lists proposed for newborn sequencing by Thomas Minten, Sophia Adelson, Laura Amendola, David Bick, François Boemer, Alison Coffey, Nicolas Encina, Bianca Russell, Laurent Servais, Kristen Sund, Ryan Taft, Robert Green, Nina Gold

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Prognosis and oncogenomic profiling of patients with tropomyosin receptor kinase fusion cancer in the 100,000 genomes project by John Bridgewater, Xiaolong Jiao, Mounika Parimi, Clare Flach, Jeran Stratford, Atanas Kamburov, Arndt A. Schmitz, Jihong Zong, John A. Reeves, Karen Keating, Amanda Bruno, Marc Fellous, Mariana Buongermino Pereira, Lyudmila Bazhenova

“…Materials and Methods: This retrospective study included patients enrolled in the Genomics England 100,000 Genomes Project who had linked clinical data from UK databases. …”
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The State of Long Non-Coding RNA Biology by John S. Mattick

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Optimal strategies for learning multi-ancestry polygenic scores vary across traits by Brieuc Lehmann, Maxine Mackintosh, Gil McVean, Chris Holmes

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Robustness of Massively Parallel Sequencing Platforms. by Pınar Kavak, Bayram Yüksel, Soner Aksu, M Oguzhan Kulekci, Tunga Güngör, Faraz Hach, S Cenk Şahinalp, Turkish Human Genome Project, Can Alkan, Mahmut Şamil Sağıroğlu

“…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. …”
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RSDB: A rare skin disease database to link drugs with potential drug targets for rare skin diseases by Tien-Chueh Kuo, Pei-Hua Wang, Yu-Ke Wang, Chia-I. Chang, Ching-Yao Chang, Yufeng Jane Tseng

“…Measurement(s) Relationships between chemicals and genes • Relationships between diseases and genes • Relationships between diseases and phenotypes • Relationships between genes and phenotypes Technology Type(s) The Comparative Toxicogenomics Database (CTD) and DrugBank • DisGeNET, UniProt, The Comparative Toxicogenomics Database (CTD), Orphanet, ClinGen, Genomics England, NCBI ClinVar, The Human Phenotype Ontology (HPO), the GWAS Catalog, GWASdb28, the LHGDN and BeFree system • The Human Phenotype Ontology (HPO) and Genetic and Rare Diseases Information Center (GARD) Sample Characteristic - Organism Homo sapiens…”
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Managing expectations, rights, and duties in large-scale genomics initiatives: a European comparison by Horn, RJ, Merchant, J

“…Our geographic scope of comparative analysis includes initiatives underway in England (Genomics England), France (Plan France Médecine Génomique) and Germany (German Human Genome-Phenome Archive). …”

Evaluating the performance of a clinical genome sequencing program for diagnosis of rare genetic disease, seen through the lens of craniosynostosis by Hyder, Z, Calpena, E, Pei, Y, Tooze, RS, Twigg, SRF, Wilkie, A, Et al.

“…We evaluated the performance of the Genomics England 100,000 Genomes Project (100kGP) panel-based pipelines, using craniosynostosis as a test disease.…”

The ethics of genomic medicine: redefining values and norms in the UK and France by Gaille, M, Horn, R

“…In 2018, the two countries announced enhanced cooperation between their national strategies, Genomics England and Plan France Médecine Génomique 2025, which offers a unique opportunity to study the impact of genomic medicine and relevant policies in different national contexts. …”

Genomic landscape of adult testicular germ cell tumours in the 100,000 Genomes Project by Ní Leathlobhair, M, Frangou, A, Kinnersley, B, Cornish, AJ, Chubb, D, Lakatos, E, Arumugam, P, Gruber, AJ, Law, P, Tapinos, A, Jakobsdottir, GM, Peneva, I, Sahli, A, Smyth, EM, Ball, RY, Sylva, R, Benes, K, Stark, D, Young, RJ, Lee, ATJ, Wolverson, V, Houlston, RS, Sosinsky, A, Protheroe, A, Wedge, DC, Verrill, C

“…Leveraging samples from participants recruited via the UK National Health Service and data from the Genomics England 100,000 Genomes Project, our results provide an extended description of genomic elements underlying TGCT pathogenesis. …”

Efficient reinterpretation of rare disease cases using Exomiser by Letizia Vestito, Julius O. B. Jacobsen, Susan Walker, Valentina Cipriani, Nomi L. Harris, Melissa A. Haendel, Christopher J. Mungall, Peter Robinson, Damian Smedley

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Fostering public trust in national health data platforms: key considerations for public involvement activities for England and Switzerland by Paola Daniore, Katherine-Helen Hurndall, Federica Zavattaro, Melanie Leis, Felix Gille

“…In this commentary, we refer to three national research programs, namely the UK Biobank, Genomics England, and the Swiss Health Study, which implemented effective public involvement activities and achieved high participation rates. …”
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Association between tumour somatic mutations and venous thromboembolism in the 100,000 Genomes Project cancer cohort: a study protocol [version 2; peer review: 2 approved] by Naomi Cornish, Matthew T. Warkentin, Sarah K. Westbury, Andrew D. Mumford, Chrissie Thirlwell, Philip C. Haycock

“…We plan to examine the association between tumour somatic mutations and VTE in an existing cohort of patients with cancer, who were enrolled to the flagship Genomics England 100,000 Genomes Project. Here, we outline an a-priori analysis plan to address this objective, including details on study cohort selection, exposure and outcome definitions, annotation of genetic variants and planned statistical analyses. …”
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Evidence review and considerations for use of first line genome sequencing to diagnose rare genetic disorders by Kristen M. Wigby, Deanna Brockman, Gregory Costain, Caitlin Hale, Stacie L. Taylor, John Belmont, David Bick, David Dimmock, Susan Fernbach, John Greally, Vaidehi Jobanputra, Shashikant Kulkarni, Elizabeth Spiteri, Ryan J. Taft

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Ethical issues raised by new genomic technologies: the case study of newborn genome screening by Rachel Horton, Anneke Lucassen

“…This aims to ensure timely diagnosis, access to treatment pathways, and enable better outcomes and quality of life for babies and their families’ (Genomics England, 2021). This is a laudable aim, but the path from obtaining genome sequences to enabling better outcomes will not be straightforward and illustrates many of the ethical challenges raised by the use of new genomic technologies. …”
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A comparison of structural variant calling from short-read and nanopore-based whole-genome sequencing using optical genome mapping as a benchmark by Pei, Y, Tanguy, M, Giess, A, Dixit, A, Wilson, LC, Gibbons, RJ, Twigg, SRF, Elgar, G, Wilkie, AOM

“…We prepared high-quality DNA from 9 parent–child trios, who had previously undergone short-read whole-genome sequencing (Illumina platform) as part of the Genomics England 100,000 Genomes Project. We reanalysed the genomes using both Bionano optical genome mapping (OGM; 8 probands and one trio) and Nanopore long-read sequencing (Oxford Nanopore Technologies [ONT] platform; all samples). …”

The use of biomedical big data for economic analyses of genome sequencing in rare genetic diseases: a case study from the 100,000 Genomes Project by Fahr, P

“…This thesis explores the use of BBD for economic analyses of genomic diagnostics in rare genetic diseases in the context of the Genomics England 100,000 Genomes Project (100KGP) and the National Health Service (NHS) in England.…”

Newborn Screening by Genomic Sequencing: Opportunities and Challenges by David Bick, Arzoo Ahmed, Dasha Deen, Alessandra Ferlini, Nicolas Garnier, Dalia Kasperaviciute, Mathilde Leblond, Amanda Pichini, Augusto Rendon, Aditi Satija, Alice Tuff-Lacey, Richard H. Scott

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Genome-wide profiling of highly similar paralogous genes using HiFi sequencing by Xiao Chen, Daniel Baker, Egor Dolzhenko, Joseph M. Devaney, Jessica Noya, April S. Berlyoung, Rhonda Brandon, Kathleen S. Hruska, Lucas Lochovsky, Paul Kruszka, Scott Newman, Emily Farrow, Isabelle Thiffault, Tomi Pastinen, Dalia Kasperaviciute, Christian Gilissen, Lisenka Vissers, Alexander Hoischen, Seth Berger, Eric Vilain, Emmanuèle Délot, UCI Genomics Research to Elucidate the Genetics of Rare diseases (UCI GREGoR) Consortium, Michael A. Eberle

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Recurrence of axial spondyloarthritis among first-degree relatives in a prospective 35-year-follow-up family study by Matthew A Brown, Peter M Villiger, Zhixiu Li, MUHAMMAD ASIM KHAN, Sjef M van der Linden, Heinz Baumberger, Hermine van Zandwijk, Mohammad Kazim Khan

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