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3. Second Primary Cancer Risks After Breast Cancer in BRCA1 and BRCA2 Pathogenic Variant Carriers

Author

Allen, Isaac, Hassan, Hend, Walburga, Yvonne, Huntley, Catherine, Loong, Lucy, Rahman, Tameera, Allen, Sophie, Garrett, Alice, Torr, Bethany, Bacon, Andrew, Knott, Craig, Jose, Sophie, Vernon, Sally, Lüchtenborg, Margreet, Pethick, Joanna, Santaniello, Francesco, Goel, Shilpi, Wang, Ying-Wen, Lavelle, Katrina, McRonald, Fiona, Eccles, Diana, Morris, Eva, Hardy, Steven, Turnbull, Clare, Tischkowitz, Marc, Pharoah, Paul, and Antoniou, Antonis C.

Published
2024
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4. Risks of second primary cancers among 584,965 female and male breast cancer survivors in England: a 25-year retrospective cohort study

Author

Allen, Isaac, Hassan, Hend, Joko-Fru, Walburga Yvonne, Huntley, Catherine, Loong, Lucy, Rahman, Tameera, Torr, Bethany, Bacon, Andrew, Knott, Craig, Jose, Sophie, Vernon, Sally, Lüchtenborg, Margreet, Pethick, Joanna, Lavelle, Katrina, McRonald, Fiona, Eccles, Diana, Morris, Eva J.A, Hardy, Steven, Turnbull, Clare, Tischkowitz, Marc, Pharoah, Paul, and Antoniou, Antonis C.

Published
2024
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5. The comprehensive English National Lynch Syndrome Registry: development and description of a new genomics data resource

Author

Cook, Jacqueline, Armstrong, Ruth, Ahmed, Munaza, McVeigh, Terri, DeSouza, Bianca, Kulkarni, Anjana, Bezuidenhout, Heirdre, Martin, Richard, Holliday, Debbie, Hart, Rachel, Lalloo, Fiona, Donaldson, Alan, Cleaver, Ruth, Willis, Catherine, Kiesel, Victoria, O'Reilly, Marie-Anne, Halliday, Dorothy, Solomons, Joyce, Ong, Kai Ren, Huntley, Catherine, Loong, Lucy, Mallinson, Corinne, Bethell, Rachel, Rahman, Tameera, Alhaddad, Neelam, Tulloch, Oliver, Zhou, Xue, Lee, Jason, Eves, Paul, McRonald, Fiona, Torr, Bethany, Burn, John, Shaw, Adam, Morris, Eva J.A., Monahan, Kevin, Hardy, Steven, and Turnbull, Clare

Published
2024
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8. Lung adenocarcinoma promotion by air pollutants

Author

Hill, William, Lim, Emilia L., Weeden, Clare E., Lee, Claudia, Augustine, Marcellus, Chen, Kezhong, Kuan, Feng-Che, Marongiu, Fabio, Evans, Jr, Edward J., Moore, David A., Rodrigues, Felipe S., Pich, Oriol, Bakker, Bjorn, Cha, Hongui, Myers, Renelle, van Maldegem, Febe, Boumelha, Jesse, Veeriah, Selvaraju, Rowan, Andrew, Naceur-Lombardelli, Cristina, Karasaki, Takahiro, Sivakumar, Monica, De, Swapnanil, Caswell, Deborah R., Nagano, Ai, Black, James R. M., Martínez-Ruiz, Carlos, Ryu, Min Hyung, Huff, Ryan D., Li, Shijia, Favé, Marie-Julie, Magness, Alastair, Suárez-Bonnet, Alejandro, Priestnall, Simon L., Lüchtenborg, Margreet, Lavelle, Katrina, Pethick, Joanna, Hardy, Steven, McRonald, Fiona E., Lin, Meng-Hung, Troccoli, Clara I., Ghosh, Moumita, Miller, York E., Merrick, Daniel T., Keith, Robert L., Al Bakir, Maise, Bailey, Chris, Hill, Mark S., Saal, Lao H., Chen, Yilun, George, Anthony M., Abbosh, Christopher, Kanu, Nnennaya, Lee, Se-Hoon, McGranahan, Nicholas, Berg, Christine D., Sasieni, Peter, Houlston, Richard, Turnbull, Clare, Lam, Stephen, Awadalla, Philip, Grönroos, Eva, Downward, Julian, Jacks, Tyler, Carlsten, Christopher, Malanchi, Ilaria, Hackshaw, Allan, Litchfield, Kevin, DeGregori, James, Jamal-Hanjani, Mariam, and Swanton, Charles

Published
2023
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10. Implementation of a national rapid prenatal exome sequencing service in England: evaluation of service outcomes and factors associated with regional variation.

Author

Ramakrishnan, Rema, Mallinson, Corinne, Hardy, Steven, Broughan, Jennifer, Blyth, Maisie, Melis, Gabriella, Franklin, Catherine, Hill, Melissa, Mellis, Rhiannon, Wu, Wing Han, Allen, Stephanie, Chitty, Lyn S., Knight, Marian, Armstrong, Ruth, Ashraf, Tazeen, Beleza-Meireles, Ana, Bertoli, Marta, Bownass, Lucy, Campbell, Jennifer, and Canham, Natalie

Subjects
ABORTION, FETAL abnormalities, GENETIC disorder diagnosis, REPORTING of diseases, TURNAROUND time, PREGNANCY
Abstract

Introduction: Prenatal exome sequencing (pES) can enhance genetic diagnosis of fetuses with structural anomalies and has recently been introduced as a national service in England. We aimed to examine service outcomes such as diagnostic yield (definite final diagnosis), referral rate, and sources of referral, and explore variation in outcomes of pES by individual or service level factors between 01 October 2021 and 30 June 2022. Methods: pES testing results from the National Health Service laboratories performing testing were linked to National Congenital Anomaly and Rare Disease Registration Service data and the Maternity Services Data Set and descriptive statistics computed. Results: There were 475,089 women who gave birth in England during the study period. The referral rate for pES was 8.6 (95% CI 7.8, 9.4) per 10,000 maternities. About 59% of those referred proceeded with pES testing and 35% of women who proceeded received a definite final diagnosis with a median turnaround time of 15 days. Of those who had pES testing, 64.6% had a live birth, 25.3% underwent termination of pregnancy (median gestational age at termination: 26 weeks), and 9.3% had a stillbirth. Among the 85 women who had a definite final diagnosis, 40% had a termination of pregnancy, 18% had a stillbirth, and 42% had a live birth. The corresponding figures among women without a definite final diagnosis were 18%, 5%, and 78%, respectively. Among women who had a termination of pregnancy, the median gestational age at final report was 24.9 weeks and 26.2 weeks at termination. Variation observed in some of the characteristics and outcomes between regional services were limited by small sample size. Conclusion: This study showed that of those referred, pES testing provided a diagnosis for one in three pregnancies with a fetal anomaly across England during the study period when other tests had been non-informative. Women who opted for a termination of pregnancy underwent the procedure at relatively late gestations. Earlier referral for pES, streamlining pathways, and faster turnaround times may help results to be available at an earlier gestation to allow families more time to make decisions around continuing or terminating their pregnancy. The variation in service outcomes between regional services needs to be investigated further to understand the reasons for these differences. [ABSTRACT FROM AUTHOR]

Published
2024
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13. The comprehensive English National Lynch Syndrome Registry: development and description of a new genomics data resource

Author

Huntley, Catherine, primary, Loong, Lucy, additional, Mallinson, Corinne, additional, Bethell, Rachel, additional, Rahman, Tameera, additional, Alhaddad, Neelam, additional, Tulloch, Oliver, additional, Zhou, Xue, additional, Lee, Jason, additional, Eves, Paul, additional, McRonald, Fiona, additional, Torr, Bethany, additional, Burn, John, additional, Shaw, Adam, additional, Morris, Eva J.A., additional, Monahan, Kevin, additional, Hardy, Steven, additional, Turnbull, Clare, additional, Cook, Jacqueline, additional, Armstrong, Ruth, additional, Ahmed, Munaza, additional, McVeigh, Terri, additional, DeSouza, Bianca, additional, Kulkarni, Anjana, additional, Bezuidenhout, Heirdre, additional, Martin, Richard, additional, Holliday, Debbie, additional, Hart, Rachel, additional, Lalloo, Fiona, additional, Donaldson, Alan, additional, Cleaver, Ruth, additional, Willis, Catherine, additional, Kiesel, Victoria, additional, O'Reilly, Marie-Anne, additional, Halliday, Dorothy, additional, Solomons, Joyce, additional, and Ong, Kai Ren, additional

Published
2024
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14. Pathogenic mtDNA mutations causing mitochondrial myopathy

Author

Hardy, Steven A, Blakely, Emma L, Purvis, Andrew I, Rocha, Mariana C, Ahmed, Syeda, Falkous, Gavin, Poulton, Joanna, Rose, Michael R, O'Mahony, Olivia, Bermingham, Niamh, Dougan, Charlotte F, Ng, Yi Shiau, Horvath, Rita, Turnbull, Doug M, Gorman, Grainne S, and Taylor, Robert W

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Aetiology, 2.1 Biological and endogenous factors, Neurosciences, Clinical sciences
Abstract

Pathogenic mitochondrial tRNA (mt-tRNA) gene mutations represent a prominent cause of primary mitochondrial DNA (mtDNA)-related disease despite accounting for only 5%-10% of the mitochondrial genome.(1,2) Although some common mt-tRNA mutations, such as the m.3243A>G mutation, exist, the majority are rare and have been reported in only a small number of cases.(3) The MT-TP gene, encoding mt-tRNA(Pro), is one of the less polymorphic mt-tRNA genes, and only 5 MT-TP mutations have been reported as a cause of mitochondrial muscle disease to date (table e-1 at Neurology.org/ng, P6-10). We report 5 patients with myopathic phenotypes, each harboring different pathogenic mutations in the MT-TP gene, highlighting the importance of MT-TP mutations as a cause of mitochondrial muscle disease and the requirement to study clinically relevant tissue.

Published
2016

15. Study of hyperpolarised 3He MRI diffusion on asthma and cystic fibrosis, and development of hyperpolarised 129Xe MRI lung imaging

Author

Hardy, Steven M.

Subjects
616.07, QC501 Electricity and magnetism, RC Internal medicine
Abstract

Hyperpolarised gas Magnetic Resonance Imaging (MRI) is a non-invasive method developed to provide images of the void spaces of the lungs, and evaluate the distal airways via diffusion weighted techniques. The work in this thesis covers the use of both hyperpolarised 3He and hyperpolarised 129Xe gas MRI, for both diffusion measurement studies and ventilation imaging, on healthy, asthmatic and cystic fibrosis volunteers. The first study covered in this thesis aimed to determine the nature of the acinar airway involvement in asthma sufferers via the use of Computed Tomography densitometry and hyperpolarised 3He diffusion MRI at multiple timescales alongside standard lung function tests such as spirometry and multiple breath washout (MBW). It was hypothesised that Asthma patients with an elevated MBW parameter 'Sacin' would manifest altered long-range diffusion, as suggestive of intra-acinar airway disease. It was found that there appeared to be an association between the MBW 'Sacin' parameter and subtle alterations in diffusion within the acinar airways for participants with asthma, suggesting a structural abnormality in the pulmonary acinus. However, further longitudinal studies are required before the long-term prognostic significance of acinar airway disease in asthma can be determined. The second study aimed to determine if a relationship exists between measurements from standard lung function test, spirometry and body plethysmography, and the measurements of hyperpolarised 3He diffusion MRI. 18 Cystic Fibrosis patients were recruited, alongside 27 age-matched healthy subjects. It was found that the short timescale diffusion values were lower in patients with Cystic Fibrosis, although not substantial enough to use an indicator to distinguish between a healthy volunteer and a Cystic Fibrosis patient. No strong correlations were found between the lung function measurements and the hyperpolarised 3He diffusion MRI measurements. The final section of this thesis looks at the preliminary results of a pilot study to develop scan sequences, protocols and gas delivery of hyperpolarised 129Xe MRI, in preparation for future clinical studies at the University of Nottingham. The main focus was on the development of in vivo ventilation images of the human lungs, to a high standard of quality and repeatability. Good progress was demonstrated, with lung images achieved down to 2.5 cm thick slices, with initial images of both dynamic ventilation and dissolved-phase 129Xe lung images. However the pilot study was not yet complete, and more development on the techniques discussed was still required.

Published
2016

16. Massive-Scale Models of Urban Infrastructure and Populations

Author

Baeder, Daniel, Christensen, Eric, Doanvo, Anhvinh, Han, Andrew, Intoy, Ben F. M., Hardy, Steven, Humayun, Zachary, Kain, Melissa, Liberman, Kevin, Myers, Adrian, Patel, Meera, Porter, William J., III, Ramos, Lenny, Shen, Michelle, Sparks, Lance, Toriel, Allan, Wu, Benjamin, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Thomson, Robert, editor, Bisgin, Halil, editor, Dancy, Christopher, editor, and Hyder, Ayaz, editor

Published
2019
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18. Recommendations for laboratory workflow that better support centralised amalgamation of genomic variant data: findings from CanVIG-UK national molecular laboratory survey

Author

Allen, Sophie, primary, Loong, Lucy, additional, Garrett, Alice, additional, Torr, Bethany, additional, Durkie, Miranda, additional, Drummond, James, additional, Callaway, Alison, additional, Robinson, Rachel, additional, Burghel, George J, additional, Hanson, Helen, additional, Field, Joanne, additional, McDevitt, Trudi, additional, McVeigh, Terri P, additional, Bedenham, Tina, additional, Bowles, Christopher, additional, Bradshaw, Kirsty, additional, Brooks, Claire, additional, Butler, Samantha, additional, Del Rey Jimenez, Juan Carlos, additional, Hawkes, Lorraine, additional, Stinton, Victoria, additional, MacMahon, Suzanne, additional, Owens, Martina, additional, Palmer-Smith, Sheila, additional, Smith, Kenneth, additional, Tellez, James, additional, Valganon-Petrizan, Mikel, additional, Waskiewicz, Erik, additional, Yau, Michael, additional, Eccles, Diana M, additional, Tischkowitz, Marc, additional, Goel, Shilpi, additional, McRonald, Fiona, additional, Antoniou, Antonis C, additional, Morris, Eva, additional, Hardy, Steven, additional, and Turnbull, Clare, additional

Published
2023
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19. 25 Role of Kndy and Arcuate Kiss1r-Containing Neurons in the Preovulatory Luteinizing Hormone Surge and Puberty Onset of Female sheep

Author

Griesgraber, Max J, primary, Onslow, Kayla M, additional, Shuping, Sydney, additional, Bowdridge, Elizabeth, additional, Hardy, Steven, additional, Aerts, Eliana, additional, Coolen, Lique, additional, Nestor, Casey, additional, Hileman, Stanley, additional, Lehman, Michael, additional, and Goodman, Robert, additional

Published
2023
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21. Disclosing the functional changes of two genetic alterations in a patient with Chronic Progressive External Ophthalmoplegia: Report of the novel mtDNA m.7486G>A variant

Author

Bacalhau, Mafalda, Simões, Marta, Rocha, Mariana C., Hardy, Steven A., Vincent, Amy E., Durães, João, Macário, Maria C., Santos, Maria João, Rebelo, Olinda, Lopes, Carla, Pratas, João, Mendes, Cândida, Zuzarte, Mónica, Rego, A. Cristina, Girão, Henrique, Wong, Lee-Jun C., Taylor, Robert W., and Grazina, Manuela

Published
2018
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22. Mesenchymal stem cells as trophic mediators of neural differentiation

Author

Hardy, Steven Allan

Subjects
571.6
Abstract

Intense excitement and optimism surrounds the rapidly-expanding field of stem cell research, owing to their high capacity for self-renewal and intrinsic ability to differentiate into mature cell lineages. Although it may be envisioned that embryonic stem cells will be of significantly greater therapeutic value than their adult stem cell counterparts, the use of embryonic stem cells is fraught with both technical and ethical challenges and, as such, significant impetus has been placed on adult stem cell-based research. In particular, mesenchymal stem cells (MSCs) present as exciting candidates for potential use in cellular therapies and tissue engineering strategies. MSCs are defined at the functional level in terms of their ability to differentiate into mesodermal derivatives such as bone and fat. However, this functional definition is evolving, and there is considerable evidence to suggest that MSCs have a key role within their niche involving the release and/or uptake of soluble factors and cytokines, significantly influencing the behaviour of other cell types within the niche. Both facets of MSC behaviour are valuable from a clinical perspective, and have been examined in the present thesis. The most obvious and realistically-achievable clinical application of MSCs at present is in the treatment of osseous and adipose tissue defects. However, before the use of MSCs in the clinic becomes more commonplace, it is crucial to gain a more comprehensive understanding of the complex molecular and cellular mechanism(s) by which MSCs commit to a given fate and undergo differentiation to produce mature, fully-functional derivatives. Much of our present knowledge is derived from studies performed on the highly unnatural, 2D environment of tissue culture plastic. The present study assessed the behaviour of MSCs cultured on AlvetexTM, a novel, 3D scaffold manufactured by ReInnervate, with particular emphasis on the ability of MSCs to undergo osteogenic and adipogenic differentiation. Results obtained suggest that AlvetexTM may provide a more realistic and physiologically-relevant system in which to study osteogenesis and adipogenesis, in a manner more pertinent to that which occurs in vivo. Furthermore, the ability of MSCs to influence the behaviour of other cell types via the release of trophic factors and cytokines was examined, with particular emphasis on the nervous system. An in vitro conditioned media model was developed in order to investigate the influence(s) of MSC-derived soluble factors/cytokines on neural development and plasticity, using the adult rat hippocampal progenitor cell (AHPC) line as a model system. Results obtained suggest that, under defined conditions, MSCs secreted a complement of soluble factors/cytokines that induce AHPCs to commit to and undergo astrogenesis. This effect was characterised at both the cellular and molecular level. The specific complement of bioactive factors secreted by MSCs has been investigated using a combination of targeted transcriptional profiling and shotgun proteomics, and several putative candidate factors have been identified for further investigation.

Published
2010

24. The English National Lynch Syndrome transformation project: an NHS Genomic Medicine Service Alliance (GMSA) programme

Author

Monahan, Kevin J, primary, Ryan, Neil, additional, Monje-Garcia, Laura, additional, Armstrong, Ruth, additional, Church, David N, additional, Cook, Jackie, additional, Elghobashy, Alaa, additional, Lalloo, Fiona, additional, Lane, Sally, additional, McDermott, Frank D, additional, Miles, Tracie, additional, Hardy, Steven A, additional, Tyson, Adele, additional, Wang, Valerie Ya Wen, additional, Kim, Anna, additional, Gelinas, Simone, additional, Faravelli, Francesca, additional, Elmslie, Frances, additional, and Shaw, Adam C, additional

Published
2023
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26. Pointers for Young Lawyers Considering or Beginning In-House Counsel Roles.

Author

Hardy, Steven K.

Subjects
Career changes -- Methods, Corporate counsel -- Social aspects -- Customer relations -- Evaluation -- Practice
Abstract

Transitioning from private practice to an in-house counsel role is a major career move and one that I made 12 months ago. If you are contemplating such a move yourself [...]

Published
2023

33. Massive-Scale Models of Urban Infrastructure and Populations

Author

Baeder, Daniel, primary, Christensen, Eric, additional, Doanvo, Anhvinh, additional, Han, Andrew, additional, Intoy, Ben F. M., additional, Hardy, Steven, additional, Humayun, Zachary, additional, Kain, Melissa, additional, Liberman, Kevin, additional, Myers, Adrian, additional, Patel, Meera, additional, Porter, William J., additional, Ramos, Lenny, additional, Shen, Michelle, additional, Sparks, Lance, additional, Toriel, Allan, additional, and Wu, Benjamin, additional

Published
2019
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34. The effect of NK3-Saporin injection within the arcuate nucleus on puberty, the LH surge, and the response to Senktide in female sheep†

Author

Aerts, Eliana G, Griesgraber, Max J, Shuping, Sydney L, Bowdridge, Elizabeth C, Hardy, Steven L, Goodman, Robert L, Nestor, Casey C, and Hileman, Stanley M

Abstract

The timing of puberty onset is reliant on increased gonadotropin-releasing hormone (GnRH). This elicits a corresponding increase in luteinizing hormone (LH) due to a lessening of sensitivity to the inhibitory actions of estradiol (E2). The mechanisms underlying the increase in GnRH release likely involve a subset of neurons within the arcuate (ARC) nucleus of the hypothalamus that contain kisspeptin, neurokinin B (NKB), and dynorphin (KNDy neurons). We aimed to determine if KNDy neurons in female sheep are critical for: timely puberty onset; the LH surge; and the response to an intravenous injection of the neurokinin-3 receptor (NK3R) agonist, senktide. Prepubertal ewes received injections aimed at the ARC containing blank-saporin (control, n = 5) or NK3-saporin (NK3-SAP, n = 6) to ablate neurons expressing NK3R. Blood samples taken 3/week for 65 days following surgery were assessed for progesterone to determine onset of puberty. Control ewes exhibited onset of puberty at 33.2 ± 3.9 days post sampling initiation, whereas 5/6 NK3-SAP treated ewes didn’t display an increase in progesterone. After an artificial LH surge protocol, surge amplitude was lower in NK3-SAP ewes. Finally, ewes were treated with senktide to determine if an LH response was elicited. LH pulses were evident in both groups in the absence of injections, but the response to senktide vs saline was similar between groups. These results show that KNDy cells are necessary for timely puberty onset and for full expresson of the LH surge. The occurrence of LH pulses in NK3-SAP treated ewes may indicate a recovery from an apulsatile state.Ablation of NK3R-containing neurons in the arcuate delays puberty onset in female sheep.

Published
2024
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35. Novel compound mutations in the mitochondrial translation elongation factor (TSFM) gene cause severe cardiomyopathy with myocardial fibro-adipose replacement

Author

Perli, Elena, Pisano, Annalinda, Glasgow, Ruth I. C., Carbo, Miriam, Hardy, Steven A., Falkous, Gavin, He, Langping, Cerbelli, Bruna, Pignataro, Maria Gemma, Zacara, Elisabetta, Re, Federica, Della Monica, Paola Lilla, Morea, Veronica, Bonnen, Penelope E., Taylor, Robert W., d’Amati, Giulia, and Giordano, Carla

Published
2019
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38. Abstract 988: Long-term health outcomes of bilateral salpingo-oophorectomy in women with personal history of breast cancer

Author

Hassan, Hend, primary, Rahman, Tameera, additional, Bacon, Andrew, additional, Knott, Craig, additional, Allen, Isaac, additional, Huntley, Catherine, additional, Loong, Lucy, additional, Walburga, Yvonne, additional, Lavelle, Katrina, additional, Morris, Eva, additional, Hardy, Steven, additional, Torr, Bethany, additional, Eccles, Diana M, additional, Turnbull, Clare, additional, Tischkowitz, Marc, additional, Pharoah, Paul, additional, and Antoniou, Antonis C., additional

Published
2023
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39. Abstract 3057: Second primary cancer risks for female and male breast cancer survivors

Author

Allen, Isaac, primary, Rahman, Tameera, additional, Bacon, Andrew, additional, Knott, Craig, additional, Jose, Sophie, additional, Vernon, Sally, additional, Hassan, Hend, additional, Huntley, Catherine, additional, Loong, Lucy, additional, Walburga, Yvonne, additional, Lavelle, Katrina, additional, Morris, Eva, additional, Hardy, Steven, additional, Torr, Beth, additional, Eccles, Diana, additional, Turnbull, Clare, additional, Tischkowitz, Marc, additional, Pharoah, Paul, additional, and Antoniou, Antonis C., additional

Published
2023
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40. Germline mismatch repair (MMR) gene analyses from English NHS regional molecular genomics laboratories 1996–2020: development of a national resource of patient-level genomics laboratory records

Author

Loong, Lucy, primary, Huntley, Catherine, additional, McRonald, Fiona, additional, Santaniello, Francesco, additional, Pethick, Joanna, additional, Torr, Bethany, additional, Allen, Sophie, additional, Tulloch, Oliver, additional, Goel, Shilpi, additional, Shand, Brian, additional, Rahman, Tameera, additional, Luchtenborg, Margreet, additional, Garrett, Alice, additional, Barber, Richard, additional, Bedenham, Tina, additional, Bourn, David, additional, Bradshaw, Kirsty, additional, Brooks, Claire, additional, Bruty, Jonathan, additional, Burghel, George J, additional, Butler, Samantha, additional, Buxton, Chris, additional, Callaway, Alison, additional, Callaway, Jonathan, additional, Drummond, James, additional, Durkie, Miranda, additional, Field, Joanne, additional, Jenkins, Lucy, additional, McVeigh, Terri P, additional, Mountford, Roger, additional, Nyanhete, Rodney, additional, Petrides, Evgenia, additional, Robinson, Rachel, additional, Scott, Tracy, additional, Stinton, Victoria, additional, Tellez, James, additional, Wallace, Andrew J, additional, Yarram-Smith, Laura, additional, Sahan, Kate, additional, Hallowell, Nina, additional, Eccles, Diana M, additional, Pharoah, Paul, additional, Tischkowitz, Marc, additional, Antoniou, Antonis C, additional, Evans, D Gareth, additional, Lalloo, Fiona, additional, Norbury, Gail, additional, Morris, Eva, additional, Burn, John, additional, Hardy, Steven, additional, and Turnbull, Clare, additional

Published
2022
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43. A New Phen X Collection: Sickle Cell Disease Psychosocial and Social Determinants of Health Protocols

Author

Crosby, Lori E., primary, King, Allison A., additional, Porter, Jerlym S., additional, Badawy, Sherif M., additional, Bulgin, Dominique, additional, Hardy, Steven J., additional, Arnold, Staci D., additional, Williford, Desiree, additional, Treadwell, Marsha, additional, Huggins, Wayne, additional, Ives, Cataia, additional, Sullivan, Marian, additional, and Hamilton, Carol, additional

Published
2022
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47. OXA1L mutations cause mitochondrial encephalopathy and a combined oxidative phosphorylation defect

Author

Thompson, Kyle, Mai, Nicole, Oláhová, Monika, Scialó, Filippo, Formosa, Luke E, Stroud, David A, Garrett, Madeleine, Lax, Nichola Z, Robertson, Fiona M, Jou, Cristina, Nascimento, Andres, Ortez, Carlos, Jimenez‐Mallebrera, Cecilia, Hardy, Steven A, He, Langping, Brown, Garry K, Marttinen, Paula, McFarland, Robert, Sanz, Alberto, Battersby, Brendan J, Bonnen, Penelope E, Ryan, Michael T, Chrzanowska‐Lightowlers, Zofia MA, Lightowlers, Robert N, and Taylor, Robert W

Published
2018
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49. Recommendations for laboratory workflow that better support centralised amalgamation of genomic variant data: findings from CanVIG-UK national molecular laboratory survey

Author

Allen, Sophie, Loong, Lucy, Garrett, Alice, Torr, Bethany, Durkie, Miranda, Drummond, James, Callaway, Alison, Robinson, Rachel, Burghel, George J, Hanson, Helen, Field, Joanne, McDevitt, Trudi, McVeigh, Terri P, Bedenham, Tina, Bowles, Christopher, Bradshaw, Kirsty, Brooks, Claire, Butler, Samantha, Del Rey Jimenez, Juan Carlos, Hawkes, Lorraine, Stinton, Victoria, MacMahon, Suzanne, Owens, Martina, Palmer-Smith, Sheila, Smith, Kenneth, Tellez, James, Valganon-Petrizan, Mikel, Waskiewicz, Erik, Yau, Michael, Eccles, Diana M, Tischkowitz, Marc, Goel, Shilpi, McRonald, Fiona, Antoniou, Antonis C, Morris, Eva, Hardy, Steven, and Turnbull, Clare

Abstract

BackgroundNational and international amalgamation of genomic data offers opportunity for research and audit, including analyses enabling improved classification of variants of uncertain significance. Review of individual-level data from National Health Service (NHS) testing of cancer susceptibility genes (2002–2023) submitted to the National Disease Registration Service revealed heterogeneity across participating laboratories regarding (1) the structure, quality and completeness of submitted data, and (2) the ease with which that data could be assembled locally for submission.MethodsIn May 2023, we undertook a closed online survey of 51 clinical scientists who provided consensus responses representing all 17 of 17 NHS molecular genetic laboratories in England and Wales which undertake NHS diagnostic analyses of cancer susceptibility genes. The survey included 18 questions relating to ‘next-generation sequencing workflow’ (11), ‘variant classification’ (3) and ‘phenotypical context’ (4).ResultsWidely differing processes were reported for transfer of variant data into their local LIMS (Laboratory Information Management System), for the formatting in which the variants are stored in the LIMS and which classes of variants are retained in the local LIMS. Differing local provisions and workflow for variant classifications were also reported, including the resources provided and the mechanisms by which classifications are stored.ConclusionThe survey responses illustrate heterogeneous laboratory workflow for preparation of genomic variant data from local LIMS for centralised submission. Workflow is often labour-intensive and inefficient, involving multiple manual steps which introduce opportunities for error. These survey findings and adoption of the concomitant recommendations may support improvement in laboratory dataflows, better facilitating submission of data for central amalgamation.

Published
2024
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