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Addition of Broad Bean Hull to Wheat Flour for the Development of High-Fiber Bread : Effects on Physical and Nutritional Properties
Author Contributions: Conceptualization, V. Ranawana and V. Raikos.; methodology, Q.Q. Ni, H.E. Hayes, N.J. Hayward. and D. Stead.; formal analysis, Q.Q. Ni; writing—original draft preparation, Q.Q. Ni and V. Raikos; writing—review and editing, all authors; visualization, Q.Q. Ni.; supervision, V. Raikos; project administration, Q.Q. Ni. All authors have read and agreed to the published version of the manuscript. Funding: This work is part of the Strategic Research Programme 2016-2021 and is funded by the Scottish Government's Rural and Environment Science and Analytical Services Division (RESAS). Acknowledgments: Microscopy was performed in the Microscopy and Histology Core Facility at the University of Aberdeen. Conflicts of Interest: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. ; Peer reviewed ; Publisher PDF
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Polymorphisms in Nevus-Associated Genes MTAP, PLA2G6, and IRF4 and the Risk of Invasive Cutaneous Melanoma
In: Twin research and human genetics: the official journal of the International Society for Twin Studies (ISTS) and the Human Genetics Society of Australasia, Band 14, Heft 5, S. 422-432
ISSN: 1839-2628
An evolving hypothesis postulates that melanomas may arise through 'nevus-associated' and 'chronic sun exposure' pathways. We explored this hypothesis by examining associations between nevus-associated loci and melanoma risk across strata of body site and histological subtype. We genotyped 1028 invasive case patients and 1469 controls for variants in methylthioadenosine phosphorylase (MTAP), phospholipase A2, group VI (PLA2G6), and Interferon regulatory factor 4 (IRF4), and compared allelic frequencies globally and by anatomical site and histological subtype of melanoma. Odds-ratios (ORs) and 95% confidence intervals (CIs) were calculated using classical and multinomial logistic regression models. Among controls, MTAP rs10757257, PLA2G6 rs132985 and IRF4 rs12203592 were the variants most significantly associated with number of nevi. In adjusted models, a significant association was found between MTAP rs10757257 and overall melanoma risk (OR = 1.32, 95% CI = 1.14–1.53), with no evidence of heterogeneity across sites (Phomogeneity =.52). In contrast, MTAP rs10757257 was associated with superficial spreading/nodular melanoma (OR = 1.34, 95% CI = 1.15– 1.57), but not with lentigo maligna melanoma (OR = 0.79, 95% CI = 0.46–1.35) (Phomogeneity =.06), the subtype associated with chronic sun exposure. Melanoma was significantly inversely associated with rs12203592 in children (OR = 0.35, 95% CI = 0.16–0.77) and adolescents (OR = 0.61, 95% CI = 0.42–0.91), but not in adults (Phomogeneity =.0008). Our results suggest that the relationship between MTAP and melanoma is subtype-specific, and that the association between IRF4 and melanoma is more evident for cases with a younger age at onset. These findings lend some support to the 'divergent pathways' hypothesis and may provide at least one candidate gene underlying this model. Further studies are warranted to confirm these findings and improve our understanding of these relationships.
Prevalence of GermlineBAP1, CDKN2A, andCDK4Mutations in an Australian Population-Based Sample of Cutaneous Melanoma Cases
In: Twin research and human genetics: the official journal of the International Society for Twin Studies (ISTS) and the Human Genetics Society of Australasia, Band 18, Heft 2, S. 126-133
ISSN: 1839-2628
Mutations in Cyclin-Dependent Kinase Inhibitor 2A (CDKN2A)and Cyclin-Dependent Kinase 4 (CDK4) contribute to susceptibility in approximately 40% of high-density cutaneous melanoma (CMM) families and about 2% of unselected CMM cases. BRCA-1 associated protein-1 (BAP1)has been more recently shown to predispose to CMM and uveal melanoma (UMM) in some families; however, its contribution to CMM development in the general population is unreported. We sought to determine the contribution of these genes to CMM susceptibility in a population-based sample of cases from Australia. We genotyped 1,109 probands from Queensland families and found that approximately 1.31% harbored mutations inCDKN2A, including some with novel missense mutations (p.R22W, p.G35R and p.I49F).BAP1missense variants occurred in 0.63% of cases but noCDK4variants were observed in the sample. This is the first estimate of the contribution ofBAP1andCDK4to a population-based sample of CMM and supports the previously reported estimate ofCDKN2Agermline mutation prevalence.
The Queensland Study of Melanoma: Environmental and Genetic Associations (Q-MEGA); Study Design, Baseline Characteristics, and Repeatability of Phenotype and Sun Exposure Measures
In: Twin research and human genetics: the official journal of the International Society for Twin Studies (ISTS) and the Human Genetics Society of Australasia, Band 11, Heft 2, S. 183-196
ISSN: 1839-2628
AbstractCutaneous malignant melanoma (CMM) is a major health issue in Queensland, Australia, which has the world's highest incidence. Recent molecular and epidemiologic studies suggest that CMM arises through multiple etiological pathways involving gene–environment interactions. Understanding the potential mechanisms leading to CMM requires larger studies than those previously conducted. This article describes the design and baseline characteristics of Q-MEGA, the Queensland Study of Melanoma: Environmental and Genetic Associations, which followed up 4 population-based samples of CMM patients in Queensland, including children, adolescents, men aged over 50, and a large sample of adult cases and their families, including twins. Q-MEGA aims to investigate the roles of genetic and environmental factors, and their interaction, in the etiology of melanoma. Three thousand, four hundred and seventy-one participants took part in the follow-up study and were administered a computer-assisted telephone interview in 2002–2005. Updated data on environmental and phenotypic risk factors, and 2777 blood samples were collected from interviewed participants as well as a subset of relatives. This study provides a large and well-described population-based sample of CMM cases with follow-up data. Characteristics of the cases and repeatability of sun exposure and phenotype measures between the baseline and the follow-up surveys, from 6 to 17 years later, are also described.
Association Study of the Dystrobrevin-Binding Gene With Schizophrenia in Australian and Indian Samples
In: Twin research and human genetics: the official journal of the International Society for Twin Studies (ISTS) and the Human Genetics Society of Australasia, Band 9, Heft 4, S. 531-539
ISSN: 1839-2628
A Genome Scan for Eye Color in 502 Twin Families: Most Variation is due to a QTL on Chromosome 15q
In: Twin research, Band 7, Heft 2, S. 197-210
ISSN: 2053-6003
Germline Variation at CDKN2A and Associations with Nevus Phenotypes among Members of Melanoma Families
Germline mutations in CDKN2A are frequently identified among melanoma kindreds and are associated with increased atypical nevus counts. However, a clear relationship between pathogenic CDKN2A mutation carriage and other nevus phenotypes including counts of common acquired nevi has not yet been established. Using data from GenoMEL, we investigated the relationships between CDKN2A mutation carriage and 2-mm, 5-mm, and atypical nevus counts among blood-related members of melanoma families. Compared with individuals without a pathogenic mutation, those who carried one had an overall higher prevalence of atypical (odds ratio = 1.64; 95% confidence interval = 1.18-2.28) nevi but not 2-mm nevi (odds ratio = 1.06; 95% confidence interval = 0.92-1.21) or 5-mm nevi (odds ratio = 1.26; 95% confidence interval = 0.94-1.70). Stratification by case status showed more pronounced positive associations among non-case family members, who were nearly three times (odds ratio = 2.91; 95% confidence interval = 1.75-4.82) as likely to exhibit nevus counts at or above the median in all three nevus categories simultaneously when harboring a pathogenic mutation (vs. not harboring one). Our results support the hypothesis that unidentified nevogenic genes are co-inherited with CDKN2A and may influence carcinogenesis. ; European Commission under the 6th and 7th Framework Programme ; Cancer Research UK Programme ; Cancer Research UK ; US National Institutes of Health ; NIH, National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics ; National Health and Medical Research Council of Australia ; Cancer Council New South Wales ; Cancer Institute New South Wales ; Cancer Council Victoria ; Cancer Council Queensland ; CAPES (Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior) ; FAPESP (Fundacao para o Amparo da Pesquisa do Estado de Sao Paulo)-SP, Brazil ; National Health and Medical Research Council of Australia ; NCI ; Cancer Research Foundations of Radiumhemmet ; Swedish Cancer Society ; Paulsson Trust ; Lund University ; European Research Council ; Fondo de Investigaciones Sanitarias, Spain ; CIBER de Enfermedades Raras of the Instituto de Salud Carlos III, Spain ; Fondo Europeo de Desarrollo Regional (FEDER), Union Europea, Una manera de hacer Europa ; Catalan Government, Spain ; Fundacio La Marato de TV3, Catalonia, Spain ; Italian Association for Cancer research (AIRC) ; Italian Ministry of Health ; Programme Hospitalier de Recherche Clinique ; Institut National du Cancer (INCA) ; Comision Honoraria de Lucha Contra el Cancer, Montevideo, Uruguay ; Dutch Cancer Society ; CONACYT, Mexico ; NHMRC ; Cancer Institute NSW ; National Institutes of Health ; Texas A&M Hlth Sci Ctr, Dept Epidemiol & Biostat, College Stn, TX USA ; Univ Penn, Dept Biostat & Epidemiol, Philadelphia, PA USA ; Natl Canc Inst, Div Canc Epidemiol & Genet, Human Genet Program, Bethesda, MD USA ; Hop Cochin, AP HP, Paris, France ; Univ Paris 05, Paris, France ; Tel Aviv Univ, Sackler Fac Med, Sheba Med Ctr, Dept Dermatol, Tel Aviv, Israel ; Leiden Univ, Med Ctr, Dept Dermatol, Leiden, Netherlands ; St James Univ Hosp, Canc Res UK Clin Ctr Leeds, Leeds Inst Canc & Pathol, Sect Epidemiol & Biostat, Leeds, W Yorkshire, England ; Univ Paris Saclay, Gustave Roussy, Dept Biol & Pathol Med, INSERM,U1186, Villejuif, France ; Univ Genoa, Dept Internal Med & Med Specialties, Genoa, Italy ; IRCCS, AOU San Martino IST, Genoa, Italy ; Maurizio Bufalini Hosp, Dermatol Unit, Cesena, Italy ; Univ Utah, Dept Genet Epidemiol, Salt Lake City, UT USA ; Univ Utah, Dept Biomed Informat, Salt Lake City, UT USA ; Hosp Clin Barcelona, IDIBAPS, Dermatol Dept, Melanoma Unit, Barcelona, Spain ; CIBER Enfermedades Raras, Barcelona, Spain ; Univ Sydney, Sydney Sch Publ Hlth, Sydney, NSW, Australia ; Melanoma Inst Australia, Westmead, NSW, Australia ; Univ Paris Diderot, Univ Sorbonne Paris Cite, INSERM, Genet Variat & Human Dis Unit,UMR 946, Paris, France ; Univ Penn, Sch Med, Dept Pathol & Lab Med, Philadelphia, PA USA ; Univ Copenhagen Hosp, Dept Clin Genet, Copenhagen, Denmark ; Univ Fed Ciencias Sau Porto Alegre, Porto Alegre, RS, Brazil ; Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden ; QIMR Berghofer Med Res Inst, Herston, Qld, Australia ; Inst Oncol Ljubljana, Ljubljana, Slovenia ; Lund Univ, Dept Clin Sci, Lund, Sweden ; Lund Univ, Dept Surg, Lund, Sweden ; Univ Fed Sao Paulo, Escola Paulista Med, Dept Pathol, Sao Paulo, Brazil ; Univ Republica, Hosp Clin, Unidad Lesiones Pigmentadas Catedra Dermatol, Montevideo, Uruguay ; Oregon Hlth & Sci Univ, Dept Dermatol, Portland, OR 97201 USA ; Univ Sydney, Westmead Millennium Inst, Westmead Inst Canc Res, Sydney, NSW, Australia ; Inst Valenciano Oncol, Dept Dermatol, Valencia, Spain ; Latvian Biomed Res & Study Ctr, Riga, Latvia ; H Lee Moffitt Canc Ctr & Res Inst, Dept Canc Epidemiol, Tampa, FL USA ; Univ Fed Sao Paulo, Escola Paulista Med, Dept Pathol, Sao Paulo, Brazil ; European Commission under the 6th and 7th Framework Programme: LSH-CT-2006-018702 ; Cancer Research UK Programme: C588/A4994 ; Cancer Research UK Programme: C588/ A10589 ; Cancer Research UK: C8216/A6129 ; US National Institutes of Health: R01-CA83115 ; US National Institutes of Health: R01CA5558-01A2 ; US National Institutes of Health: 5R25-CA147832-04 ; National Health and Medical Research Council of Australia: NHMRC 107359 ; National Health and Medical Research Council of Australia: 402761 ; National Health and Medical Research Council of Australia: 633004 ; National Health and Medical Research Council of Australia: 566946 ; National Health and Medical Research Council of Australia: 211172 ; Cancer Council New South Wales: 77/00 ; Cancer Council New South Wales: 06/10 ; Cancer Institute New South Wales: CINSW 05/TPG/1-01 ; |Cancer Institute New South Wales: 10/TPG/1-02 ; Cancer Council Queensland: 371 ; FAPESP: 2007/04313-2 ; NCI: CA88363 ; European Research Council: ERC-2011-294576 ; Fondo de Investigaciones Sanitarias, Spain: P.I. 09/01393 ; Fondo de Investigaciones Sanitarias, Spain: P.I. 12/ 00840 ; Catalan Government, Spain: AGAUR 2009 SGR 1337 ; Catalan Government, Spain: AGAUR 2014_SGR_603 ; Fundacio La Marato de TV3, Catalonia, Spain: 201331-30 ; Italian Association for Cancer research (AIRC): 15460 ; Programme Hospitalier de Recherche Clinique: PHRC-AOM-07-195 ; Dutch Cancer Society: UL 2012-5489 ; CONACYT, Mexico: 152256/158706 ; NHMRC: 1063593 ; Cancer Institute NSW: 15/CDF/1-14 ; National Institutes of Health: P30CA042014 ; Web of Science
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An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale.
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An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types.
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