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2. Cancer Precision-Prevention trial of Metformin in adults with Li Fraumeni syndrome (MILI) undergoing yearly MRI surveillance: a randomised controlled trial protocol

Author

Dixon-Zegeye, Miriam, Shaw, Rachel, Collins, Linda, Perez-Smith, Kendra, Ooms, Alexander, Qiao, Maggie, Pantziarka, Pan, Izatt, Louise, Tischkowitz, Marc, Harrison, Rachel E., George, Angela, Woodward, Emma R., Lord, Simon, Hawkes, Lara, Evans, D. Gareth, Franklin, James, Hanson, Helen, and Blagden, Sarah P.

Published
2024
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5. Population-based germline testing of BRCA1, BRCA2, and PALB2 in breast cancer patients in the United Kingdom: Evidence to support extended testing, and definition of groups who may not require testing

Author

Evans, D. Gareth, Woodward, Emma R., Burghel, George J., Allen, Sophie, Torr, Beth, Hamill, Monica, Kavanaugh, Grace, Hubank, Mike, Bremner, Stephen, Jones, Christopher I., Schlecht, Helene, Astley, Susan, Bowers, Sarah, Gibbons, Sarah, Ruane, Helen, Fosbury, Caroline, Howell, Sacha J., Forde, Claire, Lalloo, Fiona, Newman, William G., Smith, Miriam J., Howell, Anthony, Turnbull, Clare, and Gandhi, Ashu

Published
2024
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8. Genotype-first approach to identify associations between CDH1 germline variants and cancer phenotypes: a multicentre study by the European Reference Network on Genetic Tumour Risk Syndromes

Author

Garcia-Pelaez, José, Barbosa-Matos, Rita, Lobo, Silvana, Dias, Alexandre, Garrido, Luzia, Castedo, Sérgio, Sousa, Sónia, Pinheiro, Hugo, Sousa, Liliana, Monteiro, Rita, Maqueda, Joaquin J, Fernandes, Susana, Carneiro, Fátima, Pinto, Nádia, Lemos, Carolina, Pinto, Carla, Teixeira, Manuel R, Aretz, Stefan, Bajalica-Lagercrantz, Svetlana, Balmaña, Judith, Blatnik, Ana, Benusiglio, Patrick R, Blanluet, Maud, Bours, Vincent, Brems, Hilde, Brunet, Joan, Calistri, Daniele, Capellá, Gabriel, Carrera, Sergio, Colas, Chrystelle, Dahan, Karin, de Putter, Robin, Desseignés, Camille, Domínguez-Garrido, Elena, Egas, Conceição, Evans, D Gareth, Feret, Damien, Fewings, Eleanor, Fitzgerald, Rebecca C, Coulet, Florence, Garcia-Barcina, María, Genuardi, Maurizio, Golmard, Lisa, Hackmann, Karl, Hanson, Helen, Holinski-Feder, Elke, Hüneburg, Robert, Krajc, Mateja, Lagerstedt-Robinson, Kristina, Lázaro, Conxi, Ligtenberg, Marjolijn J L, Martínez-Bouzas, Cristina, Merino, Sonia, Michils, Geneviève, Novaković, Srdjan, Patiño-García, Ana, Ranzani, Guglielmina Nadia, Schröck, Evelin, Silva, Inês, Silveira, Catarina, Soto, José L, Spier, Isabel, Steinke-Lange, Verena, Tedaldi, Gianluca, Tejada, María-Isabel, Woodward, Emma R, Tischkowitz, Marc, Hoogerbrugge, Nicoline, and Oliveira, Carla

Published
2023
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10. Genotype-phenotype associations in a large PTEN Hamartoma Tumor Syndrome (PHTS) patient cohort

Author

Duijkers, Floor, Giltay, Jacques C., van Hest, Liselotte P., Kleefstra, Tjitske, Leter, Edward M., Nielsen, Maartje, Nijmeijer, Sebastiaan W.R., Olderode-Berends, Maran J.W., Hendricks, Linda A.J., Hoogerbrugge, Nicoline, Venselaar, Hanka, Aretz, Stefan, Spier, Isabel, Legius, Eric, Brems, Hilde, de Putter, Robin, Claes, Kathleen B.M., Evans, D. Gareth, Woodward, Emma R., Genuardi, Maurizio, Brugnoletti, Fulvia, van Ierland, Yvette, Dijke, Kim, Tham, Emma, Tesi, Bianca, Schuurs-Hoeijmakers, Janneke H.M., Branchaud, Maud, Salvador, Hector, Jahn, Arne, Schnaiter, Simon, Anastasiadou, Violetta Christophidou, Brunet, Joan, Oliveira, Carla, Roht, Laura, Blatnik, Ana, Irmejs, Arvids, Mensenkamp, Arjen R., and Vos, Janet R.

Published
2022
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12. Extended gene panel testing in lobular breast cancer

Author

van Veen, Elke M., Evans, D. Gareth, Harkness, Elaine F., Byers, Helen J., Ellingford, Jamie M., Woodward, Emma R., Bowers, Naomi L., Wallace, Andrew J., Howell, Sacha J., Howell, Anthony, Lalloo, Fiona, Newman, William G., and Smith, Miriam J.

Published
2022
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19. Mainstreaming germline BRCA1/2 testing in non-mucinous epithelial ovarian cancer in the North West of England

Author

Flaum, Nicola, Morgan, Robert D., Burghel, George J., Bulman, Michael, Clamp, Andrew R., Hasan, Jurjees, Mitchell, Claire L., Badea, Doina, Moon, Sarah, Hogg, Martin, Hadjiyiannakis, Dennis, Clancy, Tara, Schlecht, Helene, Woodward, Emma R., Crosbie, Emma J., Edmondson, Richard J., Wallace, Andrew J., Jayson, Gordon C., Lalloo, Fiona I., Harkness, Elaine F., and Evans, D. Gareth R.

Published
2020
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20. Germline testing of BRCA1, BRCA2, PALB2 and CHEK2 c.1100delC in 1514 triple negative familial and isolated breast cancers from a single centre, with extended testing of ATM, RAD51C and RAD51D in over 400.

Author

Woodward, Emma R., Lalloo, Fiona, Forde, Claire, Pugh, Sarah, Burghel, George J., Schlecht, Helene, Harkness, Elaine F., Howell, Anthony, Howell, Sacha J., Gandhi, Ashu, and Evans, D. Gareth

Abstract

Background The identification of germline pathogenic gene variants (PGVs) in triple negative breast cancer (TNBC) is important to inform further primary cancer risk reduction and TNBC treatment strategies. We therefore investigated the contribution of breast cancer associated PGVs to familial and isolated invasive TNBC. Methods Outcomes of germline BRCA1, BRCA2 and CHEK2_c.1100delC testing were recorded in 1514 women (743--isolated, 771--familial), and for PALB2 in 846 women (541--isolated, 305--familial), with TNBC and smaller numbers for additional genes. Breast cancer free controls were identified from Predicting Risk Of Cancer At Screening and BRIDGES (Breast cancer RIsk after Diagnostic GEne Sequencing) studies. Results BRCA1_PGVs were detected in 52 isolated (7.0%) and 195 (25.3%) familial cases (isolated--OR=58.9, 95% CI: 16.6 to 247.0), BRCA2_PGVs in 21 (2.8%) isolated and 67 (8.7%) familial cases (isolated--OR=5.0, 95% CI: 2.3 to 11.2), PALB2_PGVs in 9 (1.7%) isolated and 12 (3.9%) familial cases (isolated--OR=8.8, 95% CI: 2.5 to 30.4) and CHEK2_c.1100delC in 0 isolated and 3 (0.45%) familial cases (isolated--OR=0.0, 95% CI: 0.00 to 2.11). BRCA1_PGV detection rate was >10% for all familial TNBC age groups and significantly higher for younger diagnoses (familial: <50 years, n=165/538 (30.7%); =50 years, n=30/233 (12.9%); p<0.0001). Women with a G3_TNBC were more likely to have a BRCA1_PGV as compared with a BRCA2 or PALB2_PGV (p<0.0001). 0/743 isolated TNBC had the CHEK2_c.1100delC PGV and 0/305 any ATM_PGV, but 2/240 (0.83%) had a RAD51D_PGV. Conclusion PGVs in BRCA1 are associated with G3_ TNBCs. Familial TNBCs and isolated TNBCs <30 years have a >10% likelihood of a PGV in BRCA1. BRCA1_ PGVs are associated with younger age of familial TNBC. There was no evidence for any increased risk of TNBC with CHEK2 or ATM PGVs. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Population based germline testing of BRCA1, BRCA2 and PALB2 in breast cancer patients in the UK: Evidence to support extended testing and definition of groups who may not require testing

Author

Evans, D. Gareth, primary, Woodward, Emma R., additional, Burghel, George J., additional, Allen, Sophie, additional, Torr, Beth, additional, Hamill, Monica, additional, Kavanaugh, Grace, additional, Hubank, Mike, additional, Bremner, Stephen, additional, Jones, Christopher I., additional, Schlecht, Helene, additional, Astley, Susan, additional, Bowers, Sarah, additional, Gibbons, Sarah, additional, Ruane, Helen, additional, Fosbury, Caroline, additional, Howell, Sacha J., additional, Forde, Claire, additional, Lalloo, Fiona, additional, Newman, William G., additional, Smith, Miriam J., additional, Howell, Anthony, additional, Turnbull, Clare, additional, and Gandhi, Ashu, additional

Published
2023
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22. Real-World Concordance between Germline and Tumour BRCA1/2 Status in Epithelial Ovarian Cancer.

Author

Morgan, Robert D., Burghel, George J., Schlecht, Helene, Clamp, Andrew R., Hasan, Jurjees, Mitchell, Claire L., Salih, Zena, Shaw, Joseph, Desai, Sudha, Jayson, Gordon C., Woodward, Emma R., and Evans, D. Gareth R.

Subjects
GENETIC mutation, SEQUENCE analysis, SPECIALTY hospitals, DNA, BRCA genes, OVARIAN epithelial cancer, AGE distribution, GENETIC testing, MOLECULAR pathology, CANCER patients, CANCER treatment, STEM cells, DESCRIPTIVE statistics, RESEARCH funding, NUCLEIC acid amplification techniques
Abstract

Simple Summary: Approximately 10–15% of patients with epithelial ovarian cancer have an inherited (germline) BRCA1 or BRCA2 mutation. Following a diagnosis of epithelial ovarian cancer, patients are routinely tested for germline and/or somatic (tumour) BRCA1/2 mutations. Our study shows that if germline BRCA1/2 testing is only performed for patients with a positive tumour BRCA1/2 test result, and tumour testing is performed using Myriad's myChoice® companion diagnostic, a proportion of germline BRCA1/2 large rearrangements could be missed. If paired germline-tumour DNA testing is not possible for all patients, our data shows that it would be appropriate to test all patients with epithelial ovarian cancer aged < 79 years old for germline BRCA1/2 mutations, regardless of the tumour BRCA1/2 result, whilst only needing to test patients aged ≥ 80 years old for a germline BRCA1/2 mutation if they have a positive tumour BRCA1/2 result. Patients diagnosed with epithelial ovarian cancer may undergo reflex tumour BRCA1/2 testing followed by germline BRCA1/2 testing in patients with a positive tumour test result. This testing model relies on tumour BRCA1/2 tests being able to detect all types of pathogenic variant. We analysed germline and tumour BRCA1/2 test results from patients treated for epithelial ovarian cancer at our specialist oncological referral centre. Tumour BRCA1/2 testing was performed using the next-generation sequencing (NGS)-based myChoice® companion diagnostic (CDx; Myriad Genetics, Inc.). Germline BRCA1/2 testing was performed in the North West Genomic Laboratory Hub using NGS and multiplex ligation-dependent probe amplification. Between 11 April 2021 and 11 October 2023, 382 patients were successfully tested for tumour BRCA1 and BRCA2 variants. Of these, 367 (96.1%) patients were tested for germline BRCA1/2 variants. In those patients who underwent tumour and germline testing, 15.3% (56/367) had a BRCA1/2 pathogenic variant (36 germline and 20 somatic). All germline BRCA1/2 pathogenic small sequencing variants were detected in tumour DNA. By contrast, 3 out of 8 germline BRCA1/2 pathogenic large rearrangements were not reported in tumour DNA. The overall concordance of germline BRCA1/2 pathogenic variants detected in germline and tumour DNA was clinically acceptable at 91.7% (33/36). The myChoice® CDx was able to detect most germline BRCA1/2 pathogenic variants in tumour DNA, although a proportion of pathogenic large rearrangements were not reported. If Myriad's myChoice® CDx is used for tumour BRCA1/2 testing, our data supports a testing strategy of germline and tumour BRCA1/2 testing in all patients diagnosed with epithelial ovarian cancer aged < 79 years old, with germline BRCA1/2 testing only necessary for patients aged ≥ 80 years old with a tumour BRCA1/2 pathogenic variant. [ABSTRACT FROM AUTHOR]

Published
2024
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24. Clinical practice guidelines for the diagnosis and surveillance of BAP1 tumour predisposition syndrome

Author

Lalloo, Fiona, Kulkarni, Anju, Chau, Cindy, Nielsen, Maartje, Sheaff, Michael, Steele, Jeremy, van Doorn, Remco, Wadt, Karin, Hamill, Monica, Torr, Beth, Tischkowitz, Marc, Ahmed, Munaza, Bajalica-Lagercrantz, Svetlana, Blatnik, Ana, Brunet, Joan, Cleaver, Ruth, Colas, Chrystelle, Dabir, Tabib, Evans, D. Gareth, Feshtali, Shirin, Ghiorzo, Paola, Graversen, Lise, Griewank, Klaus, Helgadottir, Hildur, Jewell, Rosalyn, Kohut, Kelly, Lorentzen, Henrik, Massi, Daniela, Missotten, Guy, Murray, Alex, Murray, Jennie, Nadal, Ernest, Ong, Kai Ren, Piulats, Josep M., Puig, Susana, Rajan, Neil, Ribero, Simone, Salle, Galateau, Teulé, Alexandre, Tham, Emma, van Paassen, Barbara, De Putter, Robin, Verdijk, Robert, Wagner, Anja, Woodward, Emma R., Hanson, Helen, Lalloo, Fiona, Kulkarni, Anju, Chau, Cindy, Nielsen, Maartje, Sheaff, Michael, Steele, Jeremy, van Doorn, Remco, Wadt, Karin, Hamill, Monica, Torr, Beth, Tischkowitz, Marc, Ahmed, Munaza, Bajalica-Lagercrantz, Svetlana, Blatnik, Ana, Brunet, Joan, Cleaver, Ruth, Colas, Chrystelle, Dabir, Tabib, Evans, D. Gareth, Feshtali, Shirin, Ghiorzo, Paola, Graversen, Lise, Griewank, Klaus, Helgadottir, Hildur, Jewell, Rosalyn, Kohut, Kelly, Lorentzen, Henrik, Massi, Daniela, Missotten, Guy, Murray, Alex, Murray, Jennie, Nadal, Ernest, Ong, Kai Ren, Piulats, Josep M., Puig, Susana, Rajan, Neil, Ribero, Simone, Salle, Galateau, Teulé, Alexandre, Tham, Emma, van Paassen, Barbara, De Putter, Robin, Verdijk, Robert, Wagner, Anja, Woodward, Emma R., and Hanson, Helen

Abstract

BRCA1-associated protein-1 (BAP1) is a recognised tumour suppressor gene. Germline BAP1 pathogenic/likely pathogenic variants are associated with predisposition to multiple tumours, including uveal melanoma, malignant pleural and peritoneal mesothelioma, renal cell carcinoma and specific non-malignant neoplasms of the skin, as part of the autosomal dominant BAP1-tumour predisposition syndrome. The overall lifetime risk for BAP1 carriers to develop at least one BAP1-associated tumour is up to 85%, although due to ascertainment bias, current estimates of risk are likely to be overestimated. As for many rare cancer predisposition syndromes, there is limited scientific evidence to support the utility of surveillance and, therefore, management recommendations for BAP1 carriers are based on expert opinion. To date, European recommendations for BAP1 carriers have not been published but are necessary due to the emerging phenotype of this recently described syndrome and increased identification of BAP1 carriers via large gene panels or tumour sequencing. To address this, the Clinical Guideline Working Group of the CanGene-CanVar project in the United Kingdom invited European collaborators to collaborate to develop guidelines to harmonize surveillance programmes within Europe. Recommendations with respect to BAP1 testing and surveillance were achieved following literature review and Delphi survey completed by a core group and an extended expert group of 34 European specialists including Geneticists, Ophthalmologists, Oncologists, Dermatologists and Pathologists. It is recognised that these largely evidence-based but pragmatic recommendations will evolve over time as further data from research collaborations informs the phenotypic spectrum and surveillance outcomes.

Published
2023

25. Cancer risks by sex and variant type in PTEN hamartoma tumor syndrome

Author

Hendricks, Linda A.J., Hoogerbrugge, Nicoline, Mensenkamp, Arjen R., Brunet, Joan, Lleuger-Pujol, Roser, Høberg-Vetti, Hildegunn, Haavind, Marianne Tveit, Innella, Giovanni, Turchetti, Daniela, Aretz, Stefan, Spier, Isabel, Tischkowitz, Marc, Jahn, Arne, Links, Thera P., Olderode-Berends, Maran J.W., Blatnik, Ana, Leter, Edward M., Evans, D. Gareth, Woodward, Emma R., Steinke-Lange, Verena, Anastasiadou, Violetta C., Colas, Chrystelle, Villy, Marie Charlotte, Benusiglio, Patrick R., Gerasimenko, Anna, Barili, Valeria, Branchaud, Maud, Houdayer, Claude, Tesi, Bianca, Yazicioglu, M. Omer, van der Post, Rachel S., Schuurs-Hoeijmakers, Janneke H.M., Vos, Janet R., Duijkers, Floor, van Ierland, Yvette, Hendricks, Linda A.J., Hoogerbrugge, Nicoline, Mensenkamp, Arjen R., Brunet, Joan, Lleuger-Pujol, Roser, Høberg-Vetti, Hildegunn, Haavind, Marianne Tveit, Innella, Giovanni, Turchetti, Daniela, Aretz, Stefan, Spier, Isabel, Tischkowitz, Marc, Jahn, Arne, Links, Thera P., Olderode-Berends, Maran J.W., Blatnik, Ana, Leter, Edward M., Evans, D. Gareth, Woodward, Emma R., Steinke-Lange, Verena, Anastasiadou, Violetta C., Colas, Chrystelle, Villy, Marie Charlotte, Benusiglio, Patrick R., Gerasimenko, Anna, Barili, Valeria, Branchaud, Maud, Houdayer, Claude, Tesi, Bianca, Yazicioglu, M. Omer, van der Post, Rachel S., Schuurs-Hoeijmakers, Janneke H.M., Vos, Janet R., Duijkers, Floor, and van Ierland, Yvette

Abstract

Background: PTEN Hamartoma Tumor Syndrome (PHTS) is a rare syndrome with a broad phenotypic spectrum, including increased risks of breast (BC, 67%-78% at age 60 years), endometrial (EC, 19%-28%), and thyroid cancer (TC, 6%-38%). Current risks are likely overestimated due to ascertainment bias. We aimed to provide more accurate and personalized cancer risks. Methods: This was a European, adult PHTS cohort study with data from medical files, registries, and/or questionnaires. Cancer risks and hazard ratios were assessed with Kaplan-Meier and Cox regression analyses, and standardized incidence ratios were calculated. Bias correction consisted of excluding cancer index cases and incident case analyses. Results: A total of 455 patients were included, including 50.5% index cases, 372 with prospective follow-up (median 6 years, interquartile range ¼ 3-10 years), and 159 of 281 females and 39 of 174 males with cancer. By age 60 years, PHTS-related cancer risk was higher in females (68.4% to 86.3%) than males (16.4% to 20.8%). Female BC risks ranged from 54.3% (95% confidence interval [CI] ¼ 43.0% to 66.4%) to 75.8% (95% CI ¼ 60.7% to 88.4%), with two- to threefold increased risks for PTEN truncating and approximately twofold for phosphatase domain variants. EC risks ranged from 6.4% (95% CI ¼ 2.1% to 18.6%) to 22.1% (95% CI ¼ 11.6% to 39.6%) and TC risks from 8.9% (95% CI ¼ 5.1% to 15.3%) to 20.5% (95% CI ¼ 11.3% to 35.4%). Colorectal cancer, renal cancer, and melanoma risks were each less than 10.0%. Conclusions: Females have a different BC risk depending on their PTEN germline variant. PHTS patients are predominantly at risk of BC (females), EC, and TC. This should be the main focus of surveillance. These lower, more unbiased and personalized risks provide guidance for optimized cancer risk management.

Published
2023

26. Germline testing of BRCA1, BRCA2, PALB2and CHEK2c.1100delC in 1514 triple negative familial and isolated breast cancers from a single centre, with extended testing of ATM, RAD51Cand RAD51Din over 400

Author

Woodward, Emma R, Lalloo, Fiona, Forde, Claire, Pugh, Sarah, Burghel, George J, Schlecht, Helene, Harkness, Elaine F, Howell, Anthony, Howell, Sacha J, Gandhi, Ashu, and Evans, D Gareth

Abstract

BackgroundThe identification of germline pathogenic gene variants (PGVs) in triple negative breast cancer (TNBC) is important to inform further primary cancer risk reduction and TNBC treatment strategies. We therefore investigated the contribution of breast cancer associated PGVs to familial and isolated invasive TNBC.MethodsOutcomes of germline BRCA1, BRCA2and CHEK2_c.1100delC testing were recorded in 1514 women (743—isolated, 771—familial), and for PALB2in 846 women (541—isolated, 305—familial), with TNBC and smaller numbers for additional genes. Breast cancer free controls were identified from Predicting Risk Of Cancer At Screening and BRIDGES (Breast cancer RIsk after Diagnostic GEne Sequencing) studies.ResultsBRCA1_PGVs were detected in 52 isolated (7.0%) and 195 (25.3%) familial cases (isolated—OR=58.9, 95% CI: 16.6 to 247.0), BRCA2_PGVs in 21 (2.8%) isolated and 67 (8.7%) familial cases (isolated—OR=5.0, 95% CI: 2.3 to 11.2), PALB2_PGVs in 9 (1.7%) isolated and 12 (3.9%) familial cases (isolated—OR=8.8, 95% CI: 2.5 to 30.4) and CHEK2_c.1100delC in 0 isolated and 3 (0.45%) familial cases (isolated—OR=0.0, 95% CI: 0.00 to 2.11). BRCA1_PGV detection rate was >10% for all familial TNBC age groups and significantly higher for younger diagnoses (familial: <50 years, n=165/538 (30.7%); ≥50 years, n=30/233 (12.9%); p<0.0001). Women with a G3_TNBC were more likely to have a BRCA1_PGV as compared with a BRCA2or PALB2_PGV (p<0.0001). 0/743 isolated TNBC had the CHEK2_c.1100delC PGV and 0/305 any ATM_PGV, but 2/240 (0.83%) had a RAD51D_PGV.ConclusionPGVs in BRCA1are associated with G3_TNBCs. Familial TNBCs and isolated TNBCs <30 years have a >10% likelihood of a PGV in BRCA1. BRCA1_PGVs are associated with younger age of familial TNBC. There was no evidence for any increased risk of TNBC with CHEK2or ATMPGVs.

Published
2024
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27. ERN GENTURIS clinical practice guidelines for the diagnosis, surveillance and management of people with Birt-Hogg-Dubé syndrome

Author

Geilswijk, Marianne, Genuardi, Maurizio, Woodward, Emma R., Nightingale, Katie, Huber, Jazzmin, Madsen, Mia Gebauer, Liekelema - van der Heij, Dieke, Lisseman, Ian, Marlé-Ballangé, Jenny, McCarthy, Cormac, Menko, Fred H., Moorselaar, R. Jeroen A. van, Radzikowska, Elzbieta, Richard, Stéphane, Rajan, Neil, Sommerlund, Mette, Wetscherek, Maria T. A., Di Donato, Nataliya, Maher, Eamonn R., and Brunet, Joan

Abstract

Birt-Hogg-Dubé syndrome (BHD syndrome) is an autosomal dominant multisystem disorder with variable expression due to pathogenic constitutional variants in the FLCNgene. Patients with BHD syndrome are predisposed to benign cutaneous fibrofolliculomas/trichodischomas, pulmonary cysts with an associated risk of spontaneous pneumothorax, and renal cell carcinoma. A requirement for updated International consensus recommendations for the diagnosis and management of BHD syndrome was identified. Based on a comprehensive literature review and expert consensus within the fields of respiratory medicine, urology, radiology, dermatology, clinical oncology and clinical genetics, updated recommendations for diagnosis, surveillance and management in BHD syndrome were developed. With the widespread availability of FLCNgenetic testing, clinical scenarios in which a diagnosis should be considered and criteria for genetic testing were defined. Following a clinical and/or molecular diagnosis of BHD syndrome, a multidisciplinary approach to disease management is required. Regular renal cancer surveillance is recommended in adulthood and life-long, but the evidence base for additional tumour surveillance is limited and further research warranted. Recommendations for the treatment of cutaneous, pulmonary and renal manifestations are provided. Awareness of BHD syndrome needs to be raised and better knowledge of the clinical settings in which the diagnosis should be considered should enable earlier diagnosis. Further details, including areas for future research topics are available at: https://www.genturis.eu/l=eng/Guidelines-and-pathways/Clinical-practice-guidelines.html.

Published
2024
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28. TP53 c.455C>T p.(Pro152Leu) pathogenic variant is a lower risk allele with attenuated risks of breast cancer and sarcoma.

Author

Evans, D. Gareth, Harkness, Elaine F., and Woodward, Emma R.

Abstract

Germline (likely) pathogenic TP53 variants cause Li-Fraumeni syndrome (LFS), typically associated with sarcoma, brain, breast and adrenal tumours. Although classical LFS is highly penetrant, the p.R337H variant, common in Brazil, is typically associated with childhood adrenal tumours and an older onset age of other LFS tumours. Previously, we reported the finding of p.P152L in 6 children from 5 families with adrenal tumours. We have now assessed cancer risks over the subsequent 23 years, and in one further family with p.P152L. Cancer risks were compared with those in the 11 families known to our service with classical dominant negative mutations affecting neighbouring codons 245 and 248 (codon 245/248). Compared with codon 245/248 families, we found lower age-related risks for all non-adrenal tumours in codon 152 families (p<0.0001) with an absence of breast cancer as compared with 100% penetrance by age 36 years in codon 245/248 families (p<0.0001), and lower rates of sarcoma in non-irradiated individuals (p=0.0001). Although there were more adrenal tumours in codon 152 families (6/26 individuals, 1/27 for codon 245/248), this was not significant (p=0.05). Understanding codon-specific cancer risks in LFS is important for accurate personalised cancer risk assessment, and subsequent prevention and early detection strategies. [ABSTRACT FROM AUTHOR]

Published
2023
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29. Predicting the likelihood of a BRCA1/2 pathogenic variant being somatic by testing only tumour DNA in non-mucinous high-grade epithelial ovarian cancer.

Author

Morgan, Robert D., Burghel, George J., Flaum, Nicola, Bulman, Michael, Smith, Philip, Clamp, Andrew R., Hasan, Jurjees, Mitchell, Claire, Salih, Zena, Woodward, Emma R., Lalloo, Fiona, Shaw, Joseph, Desai, Sudha, Crosbie, Emma J., Edmondson, Richard J., Schlecht, Helene, Wallace, Andrew J., Jayson, Gordon C., and Evans, Gareth R.

Subjects
BREAST, OVARIAN epithelial cancer, TUMORS, NUCLEOTIDE sequencing, CLINICAL trials, DNA
Published
2023
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30. Is Reflex Germline BRCA1/2 Testing Necessary in Women Diagnosed with Non-Mucinous High-Grade Epithelial Ovarian Cancer Aged 80 Years or Older?

Author

Morgan, Robert D., primary, Burghel, George J., additional, Flaum, Nicola, additional, Bulman, Michael, additional, Smith, Philip, additional, Clamp, Andrew R., additional, Hasan, Jurjees, additional, Mitchell, Claire L., additional, Salih, Zena, additional, Woodward, Emma R., additional, Lalloo, Fiona, additional, Crosbie, Emma J., additional, Edmondson, Richard J., additional, Schlecht, Helene, additional, Jayson, Gordon C., additional, and Evans, D. Gareth R., additional

Published
2023
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34. Genotype-phenotype associations in a large PTEN Hamartoma Tumor Syndrome (PHTS) patient cohort

Author

Hendricks, Linda A.J., primary, Hoogerbrugge, Nicoline, additional, Venselaar, Hanka, additional, Aretz, Stefan, additional, Spier, Isabel, additional, Legius, Eric, additional, Brems, Hilde, additional, de Putter, Robin, additional, Claes, Kathleen B.M., additional, Evans, D. Gareth, additional, Woodward, Emma R., additional, Genuardi, Maurizio, additional, Brugnoletti, Fulvia, additional, van Ierland, Yvette, additional, Dijke, Kim, additional, Tham, Emma, additional, Tesi, Bianca, additional, Schuurs-Hoeijmakers, Janneke H.M., additional, Branchaud, Maud, additional, Salvador, Hector, additional, Jahn, Arne, additional, Schnaiter, Simon, additional, Anastasiadou, Violetta Christophidou, additional, Brunet, Joan, additional, Oliveira, Carla, additional, Roht, Laura, additional, Blatnik, Ana, additional, Irmejs, Arvids, additional, Mensenkamp, Arjen R., additional, Vos, Janet R., additional, Duijkers, Floor, additional, Giltay, Jacques C., additional, van Hest, Liselotte P., additional, Kleefstra, Tjitske, additional, Leter, Edward M., additional, Nielsen, Maartje, additional, Nijmeijer, Sebastiaan W.R., additional, and Olderode-Berends, Maran J.W., additional

Published
2022
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35. Cancer risks by sex and variant type in PTEN Hamartoma Tumor Syndrome

Author

Hendricks, Linda A J, Hoogerbrugge, Nicoline, Mensenkamp, Arjen R, Brunet, Joan, Lleuger-Pujol, Roser, Høberg-Vetti, Hildegunn, Haavind, Marianne Tveit, Innella, Giovanni, Turchetti, Daniela, Aretz, Stefan, Spier, Isabel, Tischkowitz, Marc, Jahn, Arne, Links, Thera P, Olderode-Berends, Maran J W, Blatnik, Ana, Leter, Edward M, Evans, D Gareth, Woodward, Emma R, Steinke-Lange, Verena, Anastasiadou, Violetta C, Colas, Chrystelle, Villy, Marie-Charlotte, Benusiglio, Patrick R, Gerasimenko, Anna, Barili, Valeria, Branchaud, Maud, Houdayer, Claude, Tesi, Bianca, Yazicioglu, M Omer, van der Post, Rachel S, Schuurs-Hoeijmakers, Janneke H M, Vos, Janet R, MUMC+: DA KG Polikliniek (9), RS: FHML non-thematic output, Human genetics, CCA - Cancer biology and immunology, and Cancer Center Amsterdam

Subjects
Tumours of the digestive tract Radboud Institute for Health Sciences [Radboudumc 14], Cancer Research, All institutes and research themes of the Radboud University Medical Center, Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], SDG 3 - Good Health and Well-being, Oncology, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14]
Abstract

Background PTEN Hamartoma Tumor Syndrome (PHTS) is a rare syndrome with a broad phenotypic spectrum, including increased risks of breast (BC, 67%-78% at age 60 years), endometrial (EC, 19%-28%), and thyroid cancer (TC, 6%-38%). Current risks are likely overestimated due to ascertainment bias. We aimed to provide more accurate and personalized cancer risks. Methods This was a European, adult PHTS cohort study with data from medical files, registries, and/or questionnaires. Cancer risks and hazard ratios were assessed with Kaplan-Meier and Cox regression analyses, and standardized incidence ratios were calculated. Bias correction consisted of excluding cancer index cases and incident case analyses. Results A total of 455 patients were included, including 50.5% index cases, 372 with prospective follow-up (median 6 years, interquartile range = 3-10 years), and 159 of 281 females and 39 of 174 males with cancer. By age 60 years, PHTS-related cancer risk was higher in females (68.4% to 86.3%) than males (16.4% to 20.8%). Female BC risks ranged from 54.3% (95% confidence interval [CI] = 43.0% to 66.4%) to 75.8% (95% CI = 60.7% to 88.4%), with two- to threefold increased risks for PTEN truncating and approximately twofold for phosphatase domain variants. EC risks ranged from 6.4% (95% CI = 2.1% to 18.6%) to 22.1% (95% CI = 11.6% to 39.6%) and TC risks from 8.9% (95% CI = 5.1% to 15.3%) to 20.5% (95% CI = 11.3% to 35.4%). Colorectal cancer, renal cancer, and melanoma risks were each less than 10.0%. Conclusions Females have a different BC risk depending on their PTEN germline variant. PHTS patients are predominantly at risk of BC (females), EC, and TC. This should be the main focus of surveillance. These lower, more unbiased and personalized risks provide guidance for optimized cancer risk management.

Published
2022
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36. Cancer risks by sex and variant type in PTEN hamartoma tumor syndrome

Author

Hendricks, Linda AJ, Hoogerbrugge, Nicoline, Mensenkamp, Arjen R, Brunet, Joan, Lleuger-Pujol, Roser, Høberg-Vetti, Hildegunn, Tveit Haavind, Marianne, Innella, Giovanni, Turchetti, Daniela, Aretz, Stefan, Spier, Isabel, Tischkowitz, Marc, Jahn, Arne, Links, Thera P, Olderode-Berends, Maran JW, Blatnik, Ana, Leter, Edward M, Evans, D Gareth, Woodward, Emma R, Steinke-Lange, Verena, Anastasiadou, Violetta C, Colas, Chrystelle, Villy, Marie-Charlotte, Benusiglio, Patrick R, Gerasimenko, Anna, Barili, Valeria, Branchaud, Maud, Houdayer, Claude, Tesi, Bianca, Yazicioglu, M Omer, Van Der Post, Rachel S, Schuurs-Hoeijmakers, Janneke HM, PTEN Study Group, Vos, Janet R, Hendricks, Linda AJ [0000-0002-1008-0265], Hoogerbrugge, Nicoline [0000-0003-2393-8141], Mensenkamp, Arjen R [0000-0003-3805-877X], Brunet, Joan [0000-0003-1945-3512], Tischkowitz, Marc [0000-0002-7880-0628], Links, Thera P [0000-0001-5327-1718], Vos, Janet R [0000-0001-8802-7002], and Apollo - University of Cambridge Repository

Subjects
Adult, Male, Cohort Studies, PTEN Phosphohydrolase, Humans, Female, Prospective Studies, Thyroid Neoplasms, Middle Aged, Hamartoma Syndrome, Multiple, Kidney Neoplasms, Germ-Line Mutation
Abstract

BACKGROUND: PTEN Hamartoma Tumor Syndrome (PHTS) is a rare syndrome with a broad phenotypic spectrum, including increased risks of breast (BC, 67%-78% at age 60 years), endometrial (EC, 19%-28%), and thyroid cancer (TC, 6%-38%). Current risks are likely overestimated due to ascertainment bias. We aimed to provide more accurate and personalized cancer risks. METHODS: This was a European, adult PHTS cohort study with data from medical files, registries, and/or questionnaires. Cancer risks and hazard ratios were assessed with Kaplan-Meier and Cox regression analyses, and standardized incidence ratios were calculated. Bias correction consisted of excluding cancer index cases and incident case analyses. RESULTS: A total of 455 patients were included, including 50.5% index cases, 372 with prospective follow-up (median 6 years, interquartile range = 3-10 years), and 159 of 281 females and 39 of 174 males with cancer. By age 60 years, PHTS-related cancer risk was higher in females (68.4% to 86.3%) than males (16.4% to 20.8%). Female BC risks ranged from 54.3% (95% confidence interval [CI] = 43.0% to 66.4%) to 75.8% (95% CI = 60.7% to 88.4%), with two- to threefold increased risks for PTEN truncating and approximately twofold for phosphatase domain variants. EC risks ranged from 6.4% (95% CI = 2.1% to 18.6%) to 22.1% (95% CI = 11.6% to 39.6%) and TC risks from 8.9% (95% CI = 5.1% to 15.3%) to 20.5% (95% CI = 11.3% to 35.4%). Colorectal cancer, renal cancer, and melanoma risks were each less than 10.0%. CONCLUSIONS: Females have a different BC risk depending on their PTEN germline variant. PHTS patients are predominantly at risk of BC (females), EC, and TC. This should be the main focus of surveillance. These lower, more unbiased and personalized risks provide guidance for optimized cancer risk management.

Published
2022
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38. Reclassification of clinically-detected sequence variants: Framework for genetic clinicians and clinical scientists by CanVIG-UK (Cancer Variant Interpretation Group UK)

Author

Loong, Lucy, primary, Garrett, Alice, additional, Allen, Sophie, additional, Choi, Subin, additional, Durkie, Miranda, additional, Callaway, Alison, additional, Drummond, James, additional, Burghel, George J., additional, Robinson, Rachel, additional, Torr, Beth, additional, Berry, Ian R., additional, Wallace, Andrew J., additional, Eccles, Diana M., additional, Ellard, Sian, additional, Baple, Emma, additional, Evans, D. Gareth, additional, Woodward, Emma R., additional, Kulkarni, Anjana, additional, Lalloo, Fiona, additional, Tischkowitz, Marc, additional, Lucassen, Anneke, additional, Hanson, Helen, additional, and Turnbull, Clare, additional

Published
2022
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40. Breast cancer risk stratification in women of screening age: Incremental effects of adding mammographic density, polygenic risk, and a gene panel

Author

Evans, D. Gareth R., primary, van Veen, Elke M., additional, Harkness, Elaine F., additional, Brentnall, Adam R., additional, Astley, Susan M., additional, Byers, Helen, additional, Woodward, Emma R., additional, Sampson, Sarah, additional, Southworth, Jake, additional, Howell, Sacha J., additional, Maxwell, Anthony J., additional, Newman, William G., additional, Cuzick, Jack, additional, and Howell, Anthony, additional

Published
2022
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41. Predicting the likelihood of a BRCA1/2 pathogenic variant being somatic by testing only tumour DNA in non-mucinous high-grade epithelial ovarian cancer

Author

Morgan, Robert D, primary, Burghel, George J, additional, Flaum, Nicola, additional, Bulman, Michael, additional, Smith, Philip, additional, Clamp, Andrew R, additional, Hasan, Jurjees, additional, Mitchell, Claire, additional, Salih, Zena, additional, Woodward, Emma R, additional, Lalloo, Fiona, additional, Shaw, Joseph, additional, Desai, Sudha, additional, Crosbie, Emma J, additional, Edmondson, Richard J, additional, Schlecht, Helene, additional, Wallace, Andrew J, additional, Jayson, Gordon C, additional, and Evans, D Gareth R, additional

Published
2022
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42. Genotype-phenotype associations in a large PTEN Hamartoma Tumor Syndrome (PHTS) patient cohort

Author

Hendricks, Linda A.J., Hoogerbrugge, Nicoline, Venselaar, Hanka, Aretz, Stefan, Spier, Isabel, Legius, Eric, Brems, Hilde, de Putter, Robin, Claes, Kathleen B.M., Evans, D. Gareth, Woodward, Emma R., Genuardi, Maurizio, Brugnoletti, Fulvia, van Ierland, Yvette, Dijke, Kim, Tham, Emma, Tesi, Bianca, Schuurs-Hoeijmakers, Janneke H.M., Branchaud, Maud, Salvador, Hector, Jahn, Arne, Schnaiter, Simon, Anastasiadou, Violetta Christophidou, Brunet, Joan, Oliveira, Carla, Roht, Laura, Blatnik, Ana, Irmejs, Arvids, Mensenkamp, Arjen R., Vos, Janet R., Hendricks, Linda A.J., Hoogerbrugge, Nicoline, Venselaar, Hanka, Aretz, Stefan, Spier, Isabel, Legius, Eric, Brems, Hilde, de Putter, Robin, Claes, Kathleen B.M., Evans, D. Gareth, Woodward, Emma R., Genuardi, Maurizio, Brugnoletti, Fulvia, van Ierland, Yvette, Dijke, Kim, Tham, Emma, Tesi, Bianca, Schuurs-Hoeijmakers, Janneke H.M., Branchaud, Maud, Salvador, Hector, Jahn, Arne, Schnaiter, Simon, Anastasiadou, Violetta Christophidou, Brunet, Joan, Oliveira, Carla, Roht, Laura, Blatnik, Ana, Irmejs, Arvids, Mensenkamp, Arjen R., and Vos, Janet R.

Abstract

Background: Pathogenic PTEN germline variants cause PTEN Hamartoma Tumor Syndrome (PHTS), a rare disease with a variable genotype and phenotype. Knowledge about these spectra and genotype-phenotype associations could help diagnostics and potentially lead to personalized care. Therefore, we assessed the PHTS genotype and phenotype spectrum in a large cohort study. Methods: Information was collected of 510 index patients with pathogenic or likely pathogenic (LP/P) PTEN variants (n = 467) or variants of uncertain significance. Genotype-phenotype associations were assessed using logistic regression analyses adjusted for sex and age. Results: At time of genetic testing, the majority of children (n = 229) had macrocephaly (81%) or developmental delay (DD, 61%), and about half of the adults (n = 238) had cancer (51%), macrocephaly (61%), or cutaneous pathology (49%). Across PTEN, 268 LP/P variants were identified, with exon 5 as hotspot. Missense variants (n = 161) were mainly located in the phosphatase domain (PD, 90%) and truncating variants (n = 306) across all domains. A trend towards 2 times more often truncating variants was observed in adults (OR = 2.3, 95%CI = 1.5–3.4) and patients with cutaneous pathology (OR = 1.6, 95%CI = 1.1–2.5) or benign thyroid pathology (OR = 2.0, 95%CI = 1.1–3.5), with trends up to 2–4 times more variants in PD. Whereas patients with DD (OR = 0.5, 95%CI = 0.3–0.9) or macrocephaly (OR = 0.6, 95%CI = 0.4–0.9) had about 2 times less often truncating variants compared to missense variants. In DD patients these missense variants were often located in domain C2. Conclusion: The PHTS phenotypic diversity may partly be explained by the PTEN variant coding effect and the combination of coding effect and domain. PHTS patients with early-onset disease often had missense variants, and those with later-onset disease often truncating variants.

Published
2022

43. Clinical and Molecular Features of Renal and Pheochromocytoma/Paraganglioma Tumor Association Syndrome (RAPTAS): Case Series and Literature Review

Author

Casey, Ruth T, Warren, Anne Y, Martin, Jose Ezequiel, Challis, Benjamin G, Rattenberry, Eleanor, Whitworth, James, Andrews, Katrina A, Roberts, Thomas, Clark, Graeme R, West, Hannah, Smith, Philip S, Docquier, France M, Rodger, Fay, Murray, Vicki, Simpson, Helen L, Wallis, Yvonne, Giger, Olivier, Tran, Maxine, Tomkins, Susan, Stewart, Grant D, Park, Soo-Mi, Woodward, Emma R, and Maher, Eamonn R

Published
2017

46. Quantifying evidence toward pathogenicity for rare phenotypes: The case of succinate dehydrogenase genes, SDHB and SDHD

Author

Garrett, Alice, primary, Loveday, Chey, additional, King, Laura, additional, Butler, Samantha, additional, Robinson, Rachel, additional, Horton, Carrie, additional, Yussuf, Amal, additional, Choi, Subin, additional, Torr, Beth, additional, Durkie, Miranda, additional, Burghel, George J., additional, Drummond, James, additional, Berry, Ian, additional, Wallace, Andrew, additional, Callaway, Alison, additional, Eccles, Diana, additional, Tischkowitz, Marc, additional, Tatton-Brown, Katrina, additional, Snape, Katie, additional, McVeigh, Terri, additional, Izatt, Louise, additional, Woodward, Emma R., additional, Burnichon, Nelly, additional, Gimenez-Roqueplo, Anne-Paule, additional, Mazzarotto, Francesco, additional, Whiffin, Nicola, additional, Ware, James, additional, Hanson, Helen, additional, Pesaran, Tina, additional, LaDuca, Holly, additional, Buffet, Alexandre, additional, Maher, Eamonn R., additional, and Turnbull, Clare, additional

Published
2022
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48. Uptake of bilateral-risk-reducing-mastectomy: Prospective analysis of 7195 women at high-risk of breast cancer

Author

Evans, D.Gareth, primary, Gandhi, Ashu, additional, Wisely, Julie, additional, Clancy, Tara, additional, Woodward, Emma R., additional, Harvey, James, additional, Highton, Lyndsey, additional, Murphy, John, additional, Barr, Lester, additional, Howell, Sacha J., additional, Lalloo, Fiona, additional, Harkness, Elaine F., additional, and Howell, Anthony, additional

Published
2021
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49. Whole-genome sequencing of patients with rare diseases in a national health system

Author

Turro, Ernest, Astle, William J., Megy, Karyn, Gräf, Stefan, Greene, Daniel, Shamardina, Olga, Allen, Hana Lango, Sanchis-Juan, Alba, Frontini, Mattia, Thys, Chantal, Stephens, Jonathan, Mapeta, Rutendo, Burren, Oliver S., Downes, Kate, Haimel, Matthias, Tuna, Salih, Deevi, Sri V.V., Aitman, Timothy J., Bennett, David L., Calleja, Paul, Carss, Keren, Caulfield, Mark J., Chinnery, Patrick F., Dixon, Peter H., Gale, Daniel P., James, Roger, Koziell, Ania, Laffan, Michael A., Levine, Adam P., Maher, Eamonn R., Markus, Hugh S., Morales, Joannella, Morrell, Nicholas W., Mumford, Andrew D., Ormondroyd, Elizabeth, Rankin, Stuart, Rendon, Augusto, Richardson, Sylvia, Roberts, Irene, Roy, Noemi B.A., Saleem, Moin A., Smith, Kenneth G.C., Stark, Hannah, Tan, Rhea Y.Y., Themistocleous, Andreas C., Thrasher, Adrian J., Watkins, Hugh, Webster, Andrew R., Wilkins, Martin R., Williamson, Catherine, Whitworth, James, Humphray, Sean, Bentley, David R., Abbs, Stephen, Abulhoul, Lara, Adlard, Julian, Ahmed, Munaza, Alachkar, Hana, Allsup, David J., Almeida-King, Jeff, Ancliff, Philip, Antrobus, Richard, Armstrong, Ruth, Arno, Gavin, Ashford, Sofie, Attwood, Anthony, Aurora, Paul, Babbs, Christian, Bacchelli, Chiara, Bakchoul, Tamam, Banka, Siddharth, Bariana, Tadbir, Barwell, Julian, Batista, Joana, Baxendale, Helen E., Beales, Phil L., Bierzynska, Agnieszka, Biss, Tina, Bitner-Glindzicz, Maria A.K., Black, Graeme C., Bleda, Marta, Blesneac, Iulia, Bockenhauer, Detlef, Bogaard, Harm, Bourne, Christian J., Boyce, Sara, Bradley, John R., Bragin, Eugene, Breen, Gerome, Brennan, Paul, Brewer, Carole, Brown, Matthew, Browning, Andrew C., Browning, Michael J., Buchan, Rachel J., Buckland, Matthew S., Bueser, Teofila, Diz, Carmen Bugarin, Burn, John, Burns, Siobhan O., Burrows, Nigel, Campbell, Carolyn, Carr-White, Gerald, Casey, Ruth, Chambers, Jenny, Chambers, John, Chan, Melanie M.Y., Cheah, Calvin, Cheng, Floria, Chitre, Manali, Christian, Martin T., Church, Colin, Clayton-Smith, Jill, Cleary, Maureen, Brod, Naomi Clements, Coghlan, Gerry, Colby, Elizabeth, Cole, Trevor R.P., Collins, Janine, Collins, Peter W., Colombo, Camilla, Compton, Cecilia J., Condliffe, Robin, Cook, Stuart, Cook, H. Terence, Cooper, Nichola, Corris, Paul A A., Furnell, Abigail, Cunningham, Fiona, Curry, Nicola S., Cutler, Antony J., Daniels, Matthew J., Dattani, Mehul, Daugherty, Louise C., Davis, John, De Soyza, Anthony, Dent, Timothy, Deshpande, Charu, Dewhurst, Eleanor F., Douzgou, Sofia, Drazyk, Anna M., Drewe, Elizabeth, Duarte, Daniel, Dutt, Tina, Edgar, J. David M., Edwards, Karen, Egner, William, Ekani, Melanie N., Elliott, Perry, Erber, Wendy N., Erwood, Marie, Estiu, Maria C., Evans, Dafydd Gareth, Evans, Gillian, Everington, Tamara, Eyries, Mélanie, Fassihi, Hiva, Favier, Remi, Findhammer, Jack, Fletcher, Debra, Flinter, Frances A., Floto, R. Andres, Fowler, Tom, Fox, James, Frary, Amy J., French, Courtney E., Freson, Kathleen, Gall, Henning, Ganesan, Vijeya, Gattens, Michael, Geoghegan, Claire, Gerighty, Terence S.A., Gharavi, Ali G., Ghio, Stefano, Ghofrani, Hossein Ardeschir, Gibbs, J. Simon R., Gibson, Kate, Gilmour, Kimberly C., Girerd, Barbara, Gleadall, Nicholas S., Goddard, Sarah, Goldstein, David B., Gomez, Keith, Gordins, Pavels, Gosal, David, Graham, Jodie, Grassi, Luigi, Greenhalgh, Lynn, Greinacher, Andreas, Gresele, Paolo, Griffiths, Philip, Grigoriadou, Sofia, Grocock, Russell J., Grozeva, Detelina, Gurnell, Mark, Hackett, Scott, Hadinnapola, Charaka, Hague, William M., Hague, Rosie, Hall, Matthew, Hanson, Helen L., Haque, Eshika, Harkness, Kirsty, Harper, Andrew R., Harris, Claire L L., Hart, Daniel, Hassan, Ahamad, Hayman, Grant, Henderson, Alex, Herwadkar, Archana, Hoffman, Jonathan, Holden, Simon, Horvath, Rita, Houlden, Henry, Houweling, Arjan C C., Howard, Luke S., Hu, Fengyuan, Hudson, Gavin, Hughes, Joseph, Huissoon, Aarnoud P., Humbert, Marc, Hunter, Sarah, Hurles, Matthew, Irving, Melita, Izatt, Louise, Johnson, Sally A., Jolles, Stephen, Jolley, Jennifer, Josifova, Dragana, Jurkute, Neringa, Karten, Tim, Karten, Johannes, Kasanicki, Mary A., Kazkaz, Hanadi, Kazmi, Rashid, Kelleher, Peter, Kelly, Anne M., Kelsall, Wilf, Kempster, Carly, Kiely, David G., Kingston, Nathalie, Klima, Robert, Koelling, Nils, Kostadima, Myrto, Kovacs, Gabor, Kreuzhuber, Roman, Kuijpers, Taco W., Kumar, Ajith, Kumararatne, Dinakantha, Kurian, Manju A., Lalloo, Fiona, Lambert, Michele, Lawrie, Allan, Layton, D. Mark, Lench, Nick, Lentaigne, Claire, Lester, Tracy, Linger, Rachel, Longhurst, Hilary, Lorenzo, Lorena E., Louka, Eleni, Lyons, Paul A., Machado, Rajiv D., MacKenzie Ross, Robert V., Madan, Bella, Maimaris, Jesmeen, Malka, Samantha, Mangles, Sarah, Marchbank, Kevin J., Marks, Stephen, Marschall, Hanns Ulrich, Marshall, Andrew, Martin, Jennifer, Mathias, Mary, Matthews, Emma, Maxwell, Heather, McAlinden, Paul, McCarthy, Mark I., McKinney, Harriet, McMahon, Aoife, Meacham, Stuart, Mead, Adam J., Castello, Ignacio Medina, Mehta, Sarju G G., Michaelides, Michel, Millar, Carolyn, Mohammed, Shehla N., Moledina, Shahin, Montani, David, Moore, Anthony T., Mozere, Monika, Muir, Keith W., Nemeth, Andrea H., Newman, William G., Newnham, Michael, Noorani, Sadia, Nurden, Paquita, O’Sullivan, Jennifer, Obaji, Samya, Odhams, Chris, Okoli, Steven, Olschewski, Andrea, Olschewski, Horst, Ong, Kai Ren, Oram, S. Helen, Ouwehand, Willem H., Palles, Claire, Papadia, Sofia, Park, Soo Mi, Parry, David, Patel, Smita, Paterson, Joan, Peacock, Andrew, Pearce, Simon H H., Peden, John, Peerlinck, Kathelijne, Penkett, Christopher J., Pepke-Zaba, Joanna, Petersen, Romina, Pilkington, Clarissa, Poole, Kenneth E.S., Prathalingam, Radhika, Psaila, Bethan, Pyle, Angela, Quinton, Richard, Rahman, Shamima, Rao, Anupama, Raymond, F. Lucy, Rayner-Matthews, Paula J., Rees, Christine, Renton, Tara, Rhodes, Christopher J., Rice, Andrew S.C., Richter, Alex, Robert, Leema, Rogers, Anthony, Rose, Sarah J., Ross-Russell, Robert, Roughley, Catherine, Roy, Noemi B. A, Ruddy, Deborah M., Sadeghi-Alavijeh, Omid, Samani, Nilesh, Samarghitean, Crina, Sargur, Ravishankar B., Sarkany, Robert N., Satchell, Simon, Savic, Sinisa, Sayer, John A., Sayer, Genevieve, Scelsi, Laura, Schaefer, Andrew M., Schulman, Sol, Scott, Richard, Scully, Marie, Searle, Claire, Seeger, Werner, Sen, Arjune, Sewell, W. A.Carrock, Seyres, Denis, Shah, Neil, Shapiro, Susan E., Shaw, Adam C., Short, Patrick J., Sibson, Keith, Side, Lucy, Simeoni, Ilenia, Simpson, Michael A A., Sims, Matthew C., Sivapalaratnam, Suthesh, Smedley, Damian, Smith, Katherine R., Snape, Katie, Soranzo, Nicole, Soubrier, Florent, Southgate, Laura, Spasic-Boskovic, Olivera, Staines, Simon, Staples, Emily, Steward, Charles, Stirrups, Kathleen E., Stuckey, Alex, Suntharalingam, Jay, Swietlik, Emilia M., Syrris, Petros, Tait, R. Campbell, Talks, Kate, Tate, Katie, Taylor, John M., Taylor, Jenny C., Thaventhiran, James E., Thomas, Ellen, Thomas, David, Thomas, Moira J., Thomas, Patrick, Thomson, Kate, Threadgold, Glen, Tilly, Tobias, Tischkowitz, Marc, Titterton, Catherine, Todd, John A., Toh, Cheng Hock, Tolhuis, Bas, Tomlinson, Ian P., Toshner, Mark, Traylor, Matthew, Treacy, Carmen, Treadaway, Paul, Trembath, Richard, Turek, Wojciech, Twiss, Philip, Vale, Tom, Geet, Chris Van, Zuydam, Natalie van, Vandekuilen, Maarten, Vandersteen, Anthony M., Vazquez-Lopez, Marta, von Ziegenweidt, Julie, Vonk Noordegraaf, Anton, Wagner, Annette, Waisfisz, Quinten, Walker, Suellen M., Walker, Neil, Walter, Klaudia, Ware, James S., Watt, Christopher, Wedderburn, Lucy, Wei, Wei, Welch, Steven B., Wessels, Julie, Westbury, Sarah K., Westwood, John Paul, Wharton, John, Whitehorn, Deborah, Wilkie, Andrew O. M, Wilson, Brian T., Wong, Edwin K.S., Wood, Nicholas, Wood, Yvette, Woods, Christopher Geoffrey, Woodward, Emma R R., Wort, Stephen J., Worth, Austen, Wright, Michael, Yates, Katherine, Yong, Patrick F.K., Young, Timothy, Yu, Ping, Yu-Wai-Man, Patrick, Zlamalova, Eliska, University of Cambridge [UK] (CAM), John Wyeth & Brother Limited, Medical Research Council (MRC), Wellcome Trust, Pulmonary medicine, ACS - Pulmonary hypertension & thrombosis, Human genetics, ACS - Atherosclerosis & ischemic syndromes, Landsteiner Laboratory, Paediatric Infectious Diseases / Rheumatology / Immunology, ARD - Amsterdam Reproduction and Development, and Project, NIHR BioResource for the 100,000 Genomes

Subjects
0301 basic medicine, Erythrocytes, Internationality, Databases, Factual, National Health Programs, [SDV]Life Sciences [q-bio], Disease, VARIANTS, Genome, State Medicine, NIHR BioResource for the 100,000 Genomes Project, 0302 clinical medicine, Medicine, GATA1 Transcription Factor, Genetics, Multidisciplinary, Translational bioinformatics, ASSOCIATION, 3. Good health, Multidisciplinary Sciences, Phenotype, 030220 oncology & carcinogenesis, disease genetics, Medical genetics, Science & Technology - Other Topics, Receptors, Thrombopoietin, medicine.medical_specialty, General Science & Technology, Quantitative Trait Loci, Genomics, Computational biology, Biology, DIAGNOSIS, computational biology and bioinformatics, Actin-Related Protein 2-3 Complex, Article, LRBA, LINKS, 03 medical and health sciences, Rare Diseases, Humans, Alleles, Adaptor Proteins, Signal Transducing, Whole genome sequencing, National health, Science & Technology, Whole Genome Sequencing, MUTATIONS, business.industry, THROMBOCYTOPENIA, United Kingdom, MACROTHROMBOCYTOPENIA, genetics research, 030104 developmental biology, business, Rare disease
Abstract

Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and causative genes for more than half such disorders remain to be discovered1. Here we used whole-genome sequencing (WGS) in a national health system to streamline diagnosis and to discover unknown aetiological variants in the coding and non-coding regions of the genome. We generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,138 of the 7,065 extensively phenotyped participants. We identified 95 Mendelian associations between genes and rare diseases, of which 11 have been discovered since 2015 and at least 79 are confirmed to be aetiological. By generating WGS data of UK Biobank participants2, we found that rare alleles can explain the presence of some individuals in the tails of a quantitative trait for red blood cells. Finally, we identified four novel non-coding variants that cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.

Published
2021
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