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  1. Article ; Online: A Novel Transcriptome Approach to the Investigation of the Molecular Pathology of Vitreous and Retinal Detachment.

    Maranian, Mel / Snead, Martin

    Genes

    2022  Volume 13, Issue 10

    Abstract: Retinal detachment (RD) is one of the most common, sight-threatening ocular conditions requiring emergency intervention. Posterior vitreous detachment (PVD) occurs in the majority of an aging population whereby the vitreous body separates from the retina. ...

    Abstract Retinal detachment (RD) is one of the most common, sight-threatening ocular conditions requiring emergency intervention. Posterior vitreous detachment (PVD) occurs in the majority of an aging population whereby the vitreous body separates from the retina. It is well established that PVD is the common precursor to the most common forms of RD; however, it remains unknown why in most individuals PVD will cause no/few complications (physiological PVD) but in a small percentage will cause retinal tears and detachment (pathological PVD). Despite over 100 years of scientific research, the anatomical definitions of PVD and its pathogenesis remain controversial. Recent research has identified a novel cell population (laminocyte), present at significantly higher numbers in pathological PVD when compared to physiological PVD. We review and summarise the seven distinct clinical sub-groups of retinal breaks and focus on the role of the laminocyte in those secondary to PVD and the transcriptomic profile of this unique cell. Provisional whole transcriptome analysis using bulk RNA-Seq shows marked differentially expressed genes when comparing physiological PVD with PVD associated with RD. The limitations of bulk RNA-Seq are considered and the potential to address these using spatial transcriptomics are discussed. Understanding the pathogenesis of PVD-related retinal tears will provide a baseline for the development of novel therapeutic targets and prophylactic treatments.
    MeSH term(s) Humans ; Aged ; Retinal Detachment/genetics ; Retinal Perforations/complications ; Transcriptome/genetics ; Pathology, Molecular ; Vitreous Detachment
    Language English
    Publishing date 2022-10-18
    Publishing country Switzerland
    Document type Review ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes13101885
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Posterior vitreous detachment in absentia.

    Maranian, Mel J / Snead, Martin P

    Eye (London, England)

    2022  Volume 37, Issue 3, Page(s) 388–390

    MeSH term(s) Humans ; Vitreous Detachment ; Vitreous Body ; Retinal Detachment
    Language English
    Publishing date 2022-09-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 91001-6
    ISSN 1476-5454 ; 0950-222X
    ISSN (online) 1476-5454
    ISSN 0950-222X
    DOI 10.1038/s41433-022-02248-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: SDHC epi-mutation testing in gastrointestinal stromal tumours and related tumours in clinical practice.

    Casey, Ruth T / Ten Hoopen, Rogier / Ochoa, Eguzkine / Challis, Benjamin G / Whitworth, James / Smith, Philip S / Martin, Jose Ezequiel / Clark, Graeme R / Rodger, Fay / Maranian, Mel / Allinson, Kieren / Madhu, Basetti / Roberts, Thomas / Campos, Luis / Anstee, Joanne / Park, Soo-Mi / Marker, Alison / Watts, Colin / Bulusu, Venkata R /
    Giger, Olivier T / Maher, Eamonn R

    Scientific reports

    2019  Volume 9, Issue 1, Page(s) 10244

    Abstract: The enzyme succinate dehydrogenase (SDH) functions in the citric acid cycle and loss of function predisposes to the development of phaeochromocytoma/paraganglioma (PPGL), wild type gastrointestinal stromal tumour (wtGIST) and renal cell carcinoma. SDH- ... ...

    Abstract The enzyme succinate dehydrogenase (SDH) functions in the citric acid cycle and loss of function predisposes to the development of phaeochromocytoma/paraganglioma (PPGL), wild type gastrointestinal stromal tumour (wtGIST) and renal cell carcinoma. SDH-deficient tumours are most commonly associated with a germline SDH subunit gene (SDHA/B/C/D) mutation but can also be associated with epigenetic silencing of the SDHC gene. However, clinical diagnostic testing for an SDHC epimutation is not widely available. The objective of this study was to investigate the indications for and the optimum diagnostic pathways for the detection of SDHC epimutations in clinical practice. SDHC promoter methylation analysis of 32 paraffin embedded tumours (including 15 GIST and 17 PPGL) was performed using a pyrosequencing technique and correlated with SDHC gene expression. SDHC promoter methylation was identified in 6 (18.7%) tumours. All 6 SDHC epimutation cases presented with SDH deficient wtGIST and 3/6 cases had multiple primary tumours. No case of constitutional SDHC promoter hypermethylation was detected. Whole genome sequencing of germline DNA from three wtGIST cases with an SDHC epimutation, did not reveal any causative sequence anomalies. Herein, we recommend a diagnostic workflow for the detection of an SDHC epimutation in a service setting.
    MeSH term(s) Adolescent ; Adrenal Gland Neoplasms/genetics ; Adult ; Aged ; DNA Methylation/genetics ; Epigenesis, Genetic/genetics ; Epigenomics/methods ; Female ; Gastrointestinal Stromal Tumors/genetics ; Gastrointestinal Stromal Tumors/metabolism ; Genes, Regulator/genetics ; Germ-Line Mutation ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Middle Aged ; Mutation ; Paraganglioma/genetics ; Pheochromocytoma/genetics ; Promoter Regions, Genetic/genetics ; Succinate Dehydrogenase/genetics ; Succinate Dehydrogenase/metabolism ; Transcriptome/genetics
    Chemical Substances Membrane Proteins ; SDHC protein, human ; Succinate Dehydrogenase (EC 1.3.99.1)
    Language English
    Publishing date 2019-07-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-019-46124-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Saliva samples are a viable alternative to blood samples as a source of DNA for high throughput genotyping

    Abraham Jean E / Maranian Mel J / Spiteri Inmaculada / Russell Roslin / Ingle Susan / Luccarini Craig / Earl Helena M / Pharoah Paul PD / Dunning Alison M / Caldas Carlos

    BMC Medical Genomics, Vol 5, Iss 1, p

    2012  Volume 19

    Abstract: Abstract Background The increasing trend for incorporation of biological sample collection within clinical trials requires sample collection procedures which are convenient and acceptable for both patients and clinicians. This study investigated the ... ...

    Abstract Abstract Background The increasing trend for incorporation of biological sample collection within clinical trials requires sample collection procedures which are convenient and acceptable for both patients and clinicians. This study investigated the feasibility of using saliva-extracted DNA in comparison to blood-derived DNA, across two genotyping platforms: Applied Biosystems Taqman TM and Illumina Beadchip TM genome-wide arrays. Method Patients were recruited from the Pharmacogenetics of Breast Cancer Chemotherapy (PGSNPS) study. Paired blood and saliva samples were collected from 79 study participants. The Oragene DNA Self-Collection kit (DNAgenotek®) was used to collect and extract DNA from saliva. DNA from EDTA blood samples (median volume 8 ml) was extracted by Gen-Probe, Livingstone, UK. DNA yields, standard measures of DNA quality, genotype call rates and genotype concordance between paired, duplicated samples were assessed. Results Total DNA yields were lower from saliva (mean 24 μg, range 0.2–52 μg) than from blood (mean 210 μg, range 58–577 μg) and a 2-fold difference remained after adjusting for the volume of biological material collected. Protein contamination and DNA fragmentation measures were greater in saliva DNA. 78/79 saliva samples yielded sufficient DNA for use on Illumina Beadchip arrays and using Taqman assays. Four samples were randomly selected for genotyping in duplicate on the Illumina Beadchip arrays. All samples were genotyped using Taqman assays. DNA quality, as assessed by genotype call rates and genotype concordance between matched pairs of DNA was high (>97%) for each measure in both blood and saliva-derived DNA. Conclusion We conclude that DNA from saliva and blood samples is comparable when genotyping using either Taqman assays or genome-wide chip arrays. Saliva sampling has the potential to increase participant recruitment within clinical trials, as well as reducing the resources and organisation required for multicentre sample collection.
    Keywords Internal medicine ; RC31-1245 ; Genetics ; QH426-470
    Subject code 612
    Language English
    Publishing date 2012-05-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: No evidence for association of the protein kinase C alpha gene with multiple sclerosis.

    Ban, Maria / Maranian, Mel / Yeo, Tai Wai / Gray, Julia / Compston, Alastair / Sawcer, Stephen

    Journal of neurology

    2005  Volume 252, Issue 5, Page(s) 619–620

    MeSH term(s) Alleles ; Humans ; Multiple Sclerosis/genetics ; Polymorphism, Single Nucleotide/genetics
    Language English
    Publishing date 2005-03-04
    Publishing country Germany
    Document type Letter ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 187050-6
    ISSN 1432-1459 ; 0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
    ISSN (online) 1432-1459
    ISSN 0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
    DOI 10.1007/s00415-005-0706-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Ultraconserved regions in multiple sclerosis.

    Ban, Maria / Maranian, Mel / Yeo, Tai Wai / Gray, Julia / Compston, Alastair / Sawcer, Stephen

    European journal of human genetics : EJHG

    2005  Volume 13, Issue 9, Page(s) 998–999

    MeSH term(s) Conserved Sequence ; Genetic Variation ; Genotype ; Humans ; Multiple Sclerosis/genetics ; Polymorphism, Single Nucleotide ; Sequence Homology, Nucleic Acid
    Language English
    Publishing date 2005-06-28
    Publishing country England
    Document type Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 1141470-4
    ISSN 1476-5438 ; 1018-4813
    ISSN (online) 1476-5438
    ISSN 1018-4813
    DOI 10.1038/sj.ejhg.5201457
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Cis acting expression loci in multiple sclerosis.

    Ban, Maria / Maranian, Mel / Wai Yeo, Tai / Gray, Julia / Compston, Alastair / Sawcer, Stephen

    Journal of neuroimmunology

    2005  Volume 162, Issue 1-2, Page(s) 3–4

    MeSH term(s) Gene Expression Regulation ; Genes, Regulator ; Humans ; Multiple Sclerosis/genetics
    Language English
    Publishing date 2005-03-15
    Publishing country Netherlands
    Document type Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 8335-5
    ISSN 1872-8421 ; 0165-5728
    ISSN (online) 1872-8421
    ISSN 0165-5728
    DOI 10.1016/j.jneuroim.2005.02.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Four single nucleotide polymorphisms from the vitamin D receptor gene in UK multiple sclerosis.

    Yeo, Tai Wai / Maranian, Mel / Singlehurst, Sara / Gray, Julia / Compston, Alastair / Sawcer, Stephen

    Journal of neurology

    2004  Volume 251, Issue 6, Page(s) 753–754

    MeSH term(s) Chi-Square Distribution ; Humans ; Multiple Sclerosis/epidemiology ; Multiple Sclerosis/genetics ; Polymorphism, Single Nucleotide ; Receptors, Calcitriol/genetics ; United Kingdom/epidemiology
    Chemical Substances Receptors, Calcitriol
    Language English
    Publishing date 2004-06
    Publishing country Germany
    Document type Comparative Study ; Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 187050-6
    ISSN 1432-1459 ; 0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
    ISSN (online) 1432-1459
    ISSN 0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
    DOI 10.1007/s00415-004-0425-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Saliva samples are a viable alternative to blood samples as a source of DNA for high throughput genotyping.

    Abraham, Jean E / Maranian, Mel J / Spiteri, Inmaculada / Russell, Roslin / Ingle, Susan / Luccarini, Craig / Earl, Helena M / Pharoah, Paul P D / Dunning, Alison M / Caldas, Carlos

    BMC medical genomics

    2012  Volume 5, Page(s) 19

    Abstract: Background: The increasing trend for incorporation of biological sample collection within clinical trials requires sample collection procedures which are convenient and acceptable for both patients and clinicians. This study investigated the feasibility ...

    Abstract Background: The increasing trend for incorporation of biological sample collection within clinical trials requires sample collection procedures which are convenient and acceptable for both patients and clinicians. This study investigated the feasibility of using saliva-extracted DNA in comparison to blood-derived DNA, across two genotyping platforms: Applied Biosystems Taqman™ and Illumina Beadchip™ genome-wide arrays.
    Method: Patients were recruited from the Pharmacogenetics of Breast Cancer Chemotherapy (PGSNPS) study. Paired blood and saliva samples were collected from 79 study participants. The Oragene DNA Self-Collection kit (DNAgenotek®) was used to collect and extract DNA from saliva. DNA from EDTA blood samples (median volume 8 ml) was extracted by Gen-Probe, Livingstone, UK. DNA yields, standard measures of DNA quality, genotype call rates and genotype concordance between paired, duplicated samples were assessed.
    Results: Total DNA yields were lower from saliva (mean 24 μg, range 0.2-52 μg) than from blood (mean 210 μg, range 58-577 μg) and a 2-fold difference remained after adjusting for the volume of biological material collected. Protein contamination and DNA fragmentation measures were greater in saliva DNA. 78/79 saliva samples yielded sufficient DNA for use on Illumina Beadchip arrays and using Taqman assays. Four samples were randomly selected for genotyping in duplicate on the Illumina Beadchip arrays. All samples were genotyped using Taqman assays. DNA quality, as assessed by genotype call rates and genotype concordance between matched pairs of DNA was high (>97%) for each measure in both blood and saliva-derived DNA.
    Conclusion: We conclude that DNA from saliva and blood samples is comparable when genotyping using either Taqman assays or genome-wide chip arrays. Saliva sampling has the potential to increase participant recruitment within clinical trials, as well as reducing the resources and organisation required for multicentre sample collection.
    MeSH term(s) Alleles ; DNA/blood ; Female ; Genotype ; Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Polymorphism, Single Nucleotide/genetics ; Saliva/metabolism
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2012-05-30
    Publishing country England
    Document type Journal Article
    ISSN 1755-8794
    ISSN (online) 1755-8794
    DOI 10.1186/1755-8794-5-19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: CYP2D6 gene variants and their association with breast cancer susceptibility.

    Abraham, Jean E / Maranian, Mel J / Driver, Kristy E / Platte, Radka / Kalmyrzaev, Bolot / Baynes, Caroline / Luccarini, Craig / Earl, Helena M / Dunning, Alison M / Pharoah, Paul D P / Caldas, Carlos

    Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

    2011  Volume 20, Issue 6, Page(s) 1255–1258

    Abstract: Background: The gene encoding the phase I enzyme cytochrome P4502D6 (CYP2D6) has been previously investigated for its potential predictive role in the efficacy of breast cancer treatments such as tamoxifen, but its role in breast cancer susceptibility ... ...

    Abstract Background: The gene encoding the phase I enzyme cytochrome P4502D6 (CYP2D6) has been previously investigated for its potential predictive role in the efficacy of breast cancer treatments such as tamoxifen, but its role in breast cancer susceptibility is unclear. This study aims to evaluate the association between germ line variations in CYP2D6 and breast cancer susceptibility.
    Methods: DNA samples from 13,472 cases and controls were genotyped for seven known functional variants [minor allele frequency (MAF) ≥ 0.01] and five single nucleotide polymorphisms (SNP) that tag common genetic variation (MAF > 0.05) in CYP2D6.
    Results: One relatively rare functional variant, CYP2D6*6, (MAF = 0.01) showed a modest increased association with breast cancer susceptibility (P(trend) = 0.02; OR = 1.32; 95% CI = 1.04-1.68). All other functional and tagSNPs showed no association with breast cancer susceptibility.
    Conclusions: Common variants of CYP2D6 do not play a significant role in breast cancer susceptibility. However, this study raises questions regarding the role of rare variants, such as CYP2D6*6, in breast cancer susceptibility which merit further investigation.
    Impact: This large case-control study, involving 13,472 women, found no evidence of any association between common CYP2D6 gene variants and breast cancer susceptibility. However, one relatively rare functional variant CYP2D6*6 showed a modest association with breast cancer susceptibility, indicating that the role of rare CYP2D6 variants in breast cancer risk is unclear and requires further investigation in an adequately powered study.
    MeSH term(s) Breast/metabolism ; Breast/pathology ; Breast Neoplasms/genetics ; Case-Control Studies ; Cytochrome P-450 CYP2D6/genetics ; DNA, Neoplasm/genetics ; Female ; Genetic Predisposition to Disease ; Genotype ; Humans ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/genetics ; Prognosis ; Risk Factors
    Chemical Substances DNA, Neoplasm ; Cytochrome P-450 CYP2D6 (EC 1.14.14.1)
    Language English
    Publishing date 2011-04-28
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1153420-5
    ISSN 1538-7755 ; 1055-9965
    ISSN (online) 1538-7755
    ISSN 1055-9965
    DOI 10.1158/1055-9965.EPI-11-0321
    Database MEDical Literature Analysis and Retrieval System OnLINE

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