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Detecting oncogenic selection through biased allele retention in The Cancer Genome Atlas [article]

Juliet Luft, Robert S Young, Alison M Meynert, Martin S Taylor
2020 bioRxiv   pre-print
M. BEDTools: a flexible suite of utilities for comparing 801 genomic features. Bioinformatics 26, 841-842 (2010). 802 38. Van der Auwera, G. A. et al.  ... 
doi:10.1101/2020.07.03.186593 fatcat:c7m7jn5uo5gwpbfpkwbyq2qfiy

Variant detection sensitivity and biases in whole genome and exome sequencing

Alison M Meynert, Morad Ansari, David R FitzPatrick, Martin S Taylor
2014 BMC Bioinformatics  
© 2014 Meynert et al.; licensee BioMed Central Ltd.  ... 
doi:10.1186/1471-2105-15-247 pmid:25038816 pmcid:PMC4122774 fatcat:43yv3xlctfh65nz5nclfbltxeu

Quantifying single nucleotide variant detection sensitivity in exome sequencing

Alison M Meynert, Louise S Bicknell, Matthew E Hurles, Andrew P Jackson, Martin S Taylor
2013 BMC Bioinformatics  
Meynert et al. BMC Bioinformatics 2013, 14:195 http://www.biomedcentral.com/1471-2105/14/195 © 2013 Meynert et al.; licensee BioMed Central Ltd.  ...  Quantifying single nucleotide variant detection sensitivity in exome sequencing Meynert et al.  ... 
doi:10.1186/1471-2105-14-195 pmid:23773188 pmcid:PMC3695811 fatcat:qdiq4zc2ovemlnbpxtikszlzwi

Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence repair outcome [article]

Eirini M Kallimasioti-Pazi, Keerthi Thelakkad Chathoth, Gillian C Taylor, Alison Meynert, Tracy Ballinger, Martijn J Kelder, Sebastien Lalevee, Ildem Sanli, Robert Feil, Andrew J Wood
2018 bioRxiv   pre-print
the "protospacer"), and a tracrRNA, which acts as Mouse embryonic stem cell (mESC) lines were derived from male F1 hybrid blastocysts of 97 inter-subspecies crosses between (C57BL6/J (B6) and the Mus m.  ...  Digestions were carried out at 37 383 °C with 0-60 units of DNaseI (Sigma) per 100µL nuclei, for five minutes before the reaction 384 was stopped by the addition of an equal volume of stop buffer (0.1 M  ... 
doi:10.1101/267690 fatcat:62i4rt7qxzbsbip45kad5xnjza

Molecular stratification of endometrioid ovarian carcinoma predicts clinical outcome

Robert L. Hollis, John P. Thomson, Barbara Stanley, Michael Churchman, Alison M. Meynert, Tzyvia Rye, Clare Bartos, Yasushi Iida, Ian Croy, Melanie Mackean, Fiona Nussey, Aikou Okamoto (+3 others)
2020 Nature Communications  
Comparisons were made using the two-sided Mann-Whitney U-test without adjustment for multiple testing (P < 0.0001 and P = 0.0353). m mutant, wt wild-type.  ...  TP53wt/CTNNB1wt = 0.31, 95% CI 0.11-0.88. b Summary of the PRISTINE algorithm for molecular subtyping in endometrioid ovarian carcinoma. m mutant, wt wild-type, RD residual disease, WES whole exome sequencing  ... 
doi:10.1038/s41467-020-18819-5 pmid:33020491 fatcat:jjvgfrrfgfdgvk7jpnhisexfv4

CAG-encoded polyglutamine length polymorphism in the human genome

Stefanie L Butland, Rebecca S Devon, Yong Huang, Carri-Lyn Mead, Alison M Meynert, Scott J Neal, Soo Lee, Anna Wilkinson, George S Yang, Macaire MS Yuen, Michael R Hayden, Robert A Holt (+2 others)
2007 BMC Genomics  
Expansion of polyglutamine-encoding CAG trinucleotide repeats has been identified as the pathogenic mutation in nine different genes associated with neurodegenerative disorders. The majority of individuals clinically diagnosed with spinocerebellar ataxia do not have mutations within known disease genes, and it is likely that additional ataxias or Huntington disease-like disorders will be found to be caused by this common mutational mechanism. We set out to determine the length distributions of
more » ... AG-polyglutamine tracts for the entire human genome in a set of healthy individuals in order to characterize the nature of polyglutamine repeat length variation across the human genome, to establish the background against which pathogenic repeat expansions can be detected, and to prioritize candidate genes for repeat expansion disorders. Results: We found that repeats, including those in known disease genes, have unique distributions of glutamine tract lengths, as measured by fragment analysis of PCR-amplified repeat regions. This emphasizes the need to characterize each distribution and avoid making generalizations between loci. The best predictors of known disease genes were occurrence of a long CAG-tract uninterrupted by CAA codons in their reference genome sequence, and high glutamine tract length variance in the normal population. We used these parameters to identify eight priority candidate genes for polyglutamine expansion disorders. Twelve CAG-polyglutamine repeats were invariant and these can likely be excluded as candidates. We outline some confusion in the literature about this type of data, difficulties in comparing such data between publications, and its application to studies of disease prevalence in different populations.
doi:10.1186/1471-2164-8-126 pmid:17519034 pmcid:PMC1896166 fatcat:2huq7twa6zdevjkc4jgoaafvti

Integrated molecular characterisation of endometrioid ovarian carcinoma identifies opportunities for stratification

Robert L. Hollis, Barbara Stanley, John P. Thomson, Michael Churchman, Ian Croy, Tzyvia Rye, Clare Bartos, Fiona Nussey, Melanie Mackean, Alison M. Meynert, Colin A. Semple, Charlie Gourley (+1 others)
2021 npj Precision Oncology  
PR, progesterone receptor; m, mutant; wt, wildtype.  ...  PR, progesterone receptor; ER, oestrogen receptor; m, mutant; wt, wild-type.RL Hollis et al.  ... 
doi:10.1038/s41698-021-00187-y pmid:34079052 fatcat:pwgxdjdpofbrpfr3jgtuuley4e

Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair

Eirini M. Kallimasioti-Pazi, Keerthi Thelakkad Chathoth, Gillian C. Taylor, Alison Meynert, Tracy Ballinger, Martijn J. E. Kelder, Sébastien Lalevée, Ildem Sanli, Robert Feil, Andrew J. Wood, Tom Misteli
2018 PLoS Biology  
Cell culture and transfection Hybrid mESCs were derived in serum-free (2i) medium with LIF, Mek inhibitor PD0325901 (1 μM), and Gsk3 inhibitor CHIR99021 (3 μM) as described previously [53] and were maintained  ...  Cells were crosslinked in 1% formaldehyde at a density of 2 × 10 6 per mL for 10 minutes, and then glycine (0.125 M final concentration) was added for an additional 10 minutes.  ... 
doi:10.1371/journal.pbio.2005595 pmid:30540740 pmcid:PMC6306241 fatcat:3bkhsdmokna45oaaalfdja2k4i

Clinical and molecular characterization of ovarian carcinoma displaying isolated lymph node relapse

Robert L. Hollis, Juliet Carmichael, Alison M. Meynert, Michael Churchman, Amelia Hallas-Potts, Tzyvia Rye, Melanie Mackean, Fiona Nussey, Colin A. Semple, C. Simon Herrington, Charlie Gourley
2019 American Journal of Obstetrics and Gynecology  
This is the first report demonstrating significantly improved clinical outcome in ILNR ovarian tumor-containing 500µm by 500µm fields per sample.  ...  Gynecologic oncology. 363 2007;104:41-5. 364 [12] Legge F, Petrillo M, Adamo V, Pisconti S, Scambia G, Ferrandina G.  ... 
doi:10.1016/j.ajog.2019.04.035 pmid:31055034 pmcid:PMC6857430 fatcat:bc2hjljrkng7jltfoc7nycxere

An actionable KCNH2 Long QT Syndrome variant detected by sequence and haplotype analysis in a population research cohort

Shona M. Kerr, Lucija Klaric, Mihail Halachev, Caroline Hayward, Thibaud S. Boutin, Alison M. Meynert, Colin A. Semple, Annukka M. Tuiskula, Heikki Swan, Javier Santoyo-Lopez, Veronique Vitart, Chris Haley (+4 others)
2019 Scientific Reports  
of pedigree of ID1 Yes ID3 F 21-25 448 Sanger sequencing of pedigree of ID1 Yes ID4 F 36-40 504 Haplotype, confirmed by Sanger sequencing Yes ID5 M 66-70 431 Haplotype, confirmed by  ...  Participant Gender Age Range at Clinic (years) QTc (ms) rs199473428 Identification Method Letter to GP ID1 M 46-50 442 WGS, confirmed by Sanger sequencing Yes ID2 F 46-50 467 Sanger sequencing  ... 
doi:10.1038/s41598-019-47436-6 pmid:31358886 pmcid:PMC6662790 fatcat:hbdjuip5drcttdu2khxlucszce

Whole genome sequencing of mutation-negative individuals with Cornelia de Lange Syndrome [article]

Morad Ansari, Mihail Halachev, David Parry, Jose Campos, Elston D Souza, Christopher Barnett, Andrew O. M. Wilkie, Angela Barnicoat, Chirag V. Patel, Elena Sukarova-Angelovska, Katta M. Girisha, Helen V. Firth (+14 others)
2022 medRxiv   pre-print
Aims This study assesses the diagnostic utility of whole genome sequence analysis in a well-characterised research cohort of individuals referred with a clinical suspicion of Cornelia de Lange syndrome (CdLS) in whom prior genetic testing had not identified a causative variant. Methods Short read, whole genome sequencing was performed in 195 individuals from 105 families, 108 of whom were affected. 100/108 of the affected individuals had prior relevant genetic testing with no pathogenic variant
more » ... being identified. The study group comprised 42 trios (affected individuals with both unaffected parents), 61 singletons (unrelated affected individuals) and two families with more than one affected individual. Results 32/105 (30.5%) unrelated probands had likely causative coding region disrupting variants. 4 loci were identified in >1 proband; NIPBL (10), ANKRD11 (6), EP300 (3), EHMT1 (2). Single alleles were detected in the remaining genes (EBF3, KMT2A, MED13L, NLGN3, NR2F1, PHIP, PUF60, SET, SETD5, SMC1A, TBL1XR1). Possibly causative variants in non-coding regions of NIPBL were identified in four individuals. Single de novo variants were identified in five genes not previously reported to be associated with any developmental disorder: ARID3A, PIK3C3, MCM7, MIS18BP1 and WDR18. Conclusions Clustering of de novo non-coding variants implicate a single uORF and a small region in intron 21 in NIPBL regulation. Causative variants in genes encoding chromatin-associated proteins, with no defined influence on cohesin function, appear to result in CdLS-like clinical features.
doi:10.1101/2022.09.18.22277970 fatcat:z4zqcffaabcwhddcww4vkhck5m

Toll-like receptor 2 orchestrates a potent anti-tumor response in non-small cell lung cancer [article]

Fraser R Millar, Adam Pennycuick, Morwenna Muir, Andrea Quintanilla, Priya Hari, Elisabeth Freyer, Philippe Gautier, Alison Meynert, Vitor H. Teixeira, John Connelly, William AH Wallace, Andrew H Sims (+5 others)
2021 bioRxiv   pre-print
Co-immunofluorescence staining was performed on 3µm FFPE 494 samples that were dewaxed and rehydrated as above.  ...  Finch, M. 594 Christophorou, A. von Kriegheim, N. Gammoh and the ECAT fellowship directors for helpful 595 criticism, discussion and encouragement.  ... 
doi:10.1101/2021.06.04.446876 fatcat:h4r3tfzzqzbxlamskash4eu5ti

Enhanced response rate to pegylated liposomal doxorubicin in high grade serous ovarian carcinomas harbouring BRCA1 and BRCA2 aberrations

Robert L. Hollis, Alison M. Meynert, Michael Churchman, Tzyvia Rye, Melanie Mackean, Fiona Nussey, Mark J. Arends, Andrew H. Sims, Colin A. Semple, C. Simon Herrington, Charlie Gourley
2018 BMC Cancer  
Of these, tumour material was available for translational research use in 119 cases. 10 μm sections were taken from archival tissue blocks alongside a 5 μm section to be stained with haemotoxylin and eosin  ...  DNA extraction H&E stained slides were used to guide macrodissection of four 10 μm FFPE tissue sections per specimen.  ... 
doi:10.1186/s12885-017-3981-2 pmid:29298688 pmcid:PMC5753521 fatcat:2yyrqesfnvgufhlyrbwzvvv674

Novel PEX11B Mutations Extend the Peroxisome Biogenesis Disorder 14B Phenotypic Spectrum and Underscore Congenital Cataract as an Early Feature

Rachel L. Taylor, Mark T. Handley, Sarah Waller, Christopher Campbell, Jill Urquhart, Alison M. Meynert, Jamie M. Ellingford, Deirdre Donnelly, Gisela Wilcox, I. Chris Lloyd, Helen Mundy, David R. FitzPatrick (+3 others)
2017 Investigative Ophthalmology and Visual Science  
TABLE 1 . 1 Overview of Phenotypic and Genetic Findings in PEX11B Cases Family (Ebberink et al. 10 ) I II III Patient (age [sex]) 1 (26 y [M]) I.1 (23 y [F]) I.2 (6 y 6 mo [M]) II.1  ...  (6 y 3 mo [F]) III.1 (2 y 11 mo [M]) III.2 Ethnicity (consanguinity) Dutch (No) South Asian (Yes) South Asian (Yes) Caucasian (No) Pregnancy (birth weight) Normal (3.5 kg) Normal  ... 
doi:10.1167/iovs.16-21026 pmid:28129423 pmcid:PMC5841568 fatcat:asqpunuojzeztobndetegw4nsy

Integrated genomic and histopathological analysis of low grade serous ovarian carcinoma identifies clinically distinct disease subtypes [article]

John P Thomson, Robert L Hollis, Juliette van Baal, Narthana Ilenkovan, Michael Churchman, Koen van de Vijver, Frederike Dijk, Alison M Meynert, Clare Bartos, Tzyvia Rye, Ian Croy, Patricia Diana (+7 others)
2022 medRxiv   pre-print
AbstractBackgroundLow-grade serous ovarian carcinoma (LGSOC) is a distinct, under-investigated and relatively chemotherapy-resistant ovarian cancer type. Understanding the molecular landscape is crucial to maximise the impact of molecularly-targeted therapy.MethodsWhole exome sequencing and copy number data were integrated with histopathological patterns, ER/PR expression, and detailed clinical annotation, including survival, in a carefully curated LGSOC cohort.Results63 tumours were analysed
more » ... the largest comprehensive genomic LGSOC study to date. Three genomic subgroups were identified: canonical MAPK mutant (cMAPKm: 52%, KRAS/BRAF/NRAS), MAPK-associated mutation (27%, 14 MAPK-associated genes) and MAPK wild-type (MAPKwt: 21%). MAPKwt patients were younger at diagnosis (median 47 versus 62 years in the cMAPKm subgroup) and demonstrated shorter survival [multivariable HR (mHR) 4.17]. The inferior survival in the MAPKwt subgroup was due to shorter post-relapse survival (mHR 5.22) rather than shorter time to first progression (mHR 1.15). Patients in the MAPK-associated mutation subgroup had similar survival to cMAPKm cases. The cMAPKm subgroup more frequently demonstrated macropapillary invasion. Desmoplasia and micropapillary invasion were independently associated with poor survival. NOTCH pathway activation occurred independently of MAPK subgroup.ConclusionsLGSOC comprises multiple genomic subgroups with distinct clinical, molecular and histopathological features. True MAPKwt cases represent around a fifth of patients: they are younger but have poorer survival. New therapeutic strategies with activity in this subgroup are urgently required. NOTCH inhibitors represent a therapeutic strategy worthy of exploration.
doi:10.1101/2022.02.01.22270258 fatcat:s3uva57qzzcdlk2rbplarosl2m
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