Genomes and Genes
M C Southey
Affiliation: University of Melbourne
- Common variants at 12p11, 12q24, 9p21, 9q31.2 and in ZNF365 are associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriersAntonis C Antoniou
Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
Breast Cancer Res 14:R33. 2012..2)...
- FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasetsBernard J Pope
Victorian Life Sciences Computation Initiative, The University of Melbourne, 187 Grattan Street Carlton, Melbourne, Victoria 3010, Australia
BMC Bioinformatics 14:65. 2013..Great challenges remain in resolving genetic variants that are genuine from the millions of artefactual signals...
- The use of DNA from archival dried blood spots with the Infinium HumanMethylation450 arrayJihoon E Joo
Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Victoria, 3010, Australia
BMC Biotechnol 13:23. 2013....
- A genome-wide linkage study of mammographic density, a risk factor for breast cancerCelia M T Greenwood
Program in Genetics and Genome Biology, The Hospital for Sick Children, 101 College Street, East Tower, Toronto, ON M5G 1L7, Canada
Breast Cancer Res 13:R132. 2011..Mammographic breast density is a highly heritable (h2 > 0.6) and strong risk factor for breast cancer. We conducted a genome-wide linkage study to identify loci influencing mammographic breast density (MD)...
- Common breast cancer susceptibility alleles are associated with tumour subtypes in BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2Anna Marie Mulligan
Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, 2 Worts Causeway, Cambridge, CB1 8RN, UK
Breast Cancer Res 13:R110. 2011..It is currently unknown how these alleles are associated with different breast cancer subtypes in BRCA1 and BRCA2 mutation carriers defined by estrogen (ER) or progesterone receptor (PR) status of the tumour...
- Rare variants in the ATM gene and risk of breast cancerDavid E Goldgar
Department of Dermatology, University of Utah School of Medicine, 30 N 1900 E, Salt Lake City, UT 84132 2101, USA
Breast Cancer Res 13:R73. 2011..However, the magnitude of risk and the subset of variants that are pathogenic for breast cancer remain unresolved...
- Exploring the link between MORF4L1 and risk of breast cancerGriselda Martrat
Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research IDIBELL, Gran Via 199, L Hospitalet del Llobregat 08908, Spain
Breast Cancer Res 13:R40. 2011..To gain deeper insight into this pathway and its influence on cancer risk, we searched for novel components through protein physical interaction screens...
- Rare, evolutionarily unlikely missense substitutions in CHEK2 contribute to breast cancer susceptibility: results from a breast cancer family registry case-control mutation-screening studyFlorence Le Calvez-Kelm
International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon Cedex 08, F 69372, France
Breast Cancer Res 13:R6. 2011..This absence has been due in part to a lack of validated statistical methods for summarizing risk attributable to large numbers of individually rare missense substitutions...
- Assessing interactions between the associations of common genetic susceptibility variants, reproductive history and body mass index with breast cancer risk in the breast cancer association consortium: a combined case-control studyRoger L Milne
Genetic and Molecular Epidemiology Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre CNIO, Madrid, 28029, Spain
Breast Cancer Res 12:R110. 2010....
- Are the so-called low penetrance breast cancer genes, ATM, BRIP1, PALB2 and CHEK2, high risk for women with strong family histories?Graham B Byrnes
Epidemiology Methods and Support Group, International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon, France
Breast Cancer Res 10:208. 2008..Therefore, mutation testing of these genes for women with a strong family history, especially if it is of early onset, may be as clinically relevant as it is for BRCA1 and BRCA2...
- The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriersAmanda B Spurdle
Queensland Institute of Medical Research, Brisbane, Australia
Breast Cancer Res 7:R176-83. 2005..Women with germline BRCA1 mutations who carry at least one AR allele with 28 or more repeats have been reported to have an earlier age at onset of breast cancer...
- The Breast Cancer Family Registry: an infrastructure for cooperative multinational, interdisciplinary and translational studies of the genetic epidemiology of breast cancerEsther M John
Clinical and Genetic Epidemiology Research Branch, Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland, USA
Breast Cancer Res 6:R375-89. 2004....
- Genomewide high-density SNP linkage analysis of non-BRCA1/2 breast cancer families identifies various candidate regions and has greater power than microsatellite studiesAnna Gonzalez-Neira
Genotyping Unit, CeGen, Human Cancer Genetics Programme, Spanish National Cancer Centre, Spain
BMC Genomics 8:299. 2007....
- Comparing the frequency of common genetic variants and haplotypes between carriers and non-carriers of BRCA1 and BRCA2 deleterious mutations in Australian women diagnosed with breast cancer before 40 years of ageLidija Turkovic
Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, The University of Melbourne, Victoria 3010, Australia
BMC Cancer 10:466. 2010....
- The 4q27 locus and prostate cancer riskElizabeth A Tindall
Cancer Genetics Group, Children s Cancer Institute Australia for Medical Research, Sydney Children s Hospital, High St, Randwick, NSW, Australia
BMC Cancer 10:69. 2010..This region harbors two cytokine genes IL-2 and the recently described IL-21...
- A specific GFP expression assay, penetrance estimate, and histological assessment for a putative splice site mutation in BRCA1M C Southey
Department of Pathology, Peter MacCallum Cancer Institute, Melbourne, Australia
Hum Mutat 22:86-91. 2003....
- A PALB2 mutation associated with high risk of breast cancerMelissa C Southey
Department of Pathology, The University of Melbourne, Victoria 3010, Australia
Breast Cancer Res 12:R109. 2010..Little is known about by how much or whether risk differs by mutation or family history, owing to the paucity of studies of cases unselected for family history...
- Contribution of large genomic BRCA1 alterations to early-onset breast cancer selected for family history and tumour morphology: a report from The Breast Cancer Family RegistryLetitia D Smith
Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
Breast Cancer Res 13:R14. 2011..We sought to test the value of selecting women for BRCA1 mutation testing on the basis of family history and/or breast tumour morphology criteria as well as the value of testing for large genomic alterations in BRCA1...
- CFTR deltaF508 carrier status, risk of breast cancer before the age of 40 and histological grading in a population-based case-control studyM C Southey
Department of Pathology, Peter MacCallum Cancer Institute, Melbourne, Australia
Int J Cancer 79:487-9. 1998..A combination of our data with other large population-based samples of cases and controls is required to resolve this issue...
- Morphological predictors of BRCA1 germline mutations in young women with breast cancerM C Southey
Department of Pathology, Genetic Epidemiology Laboratory, Victoria, Carlton, Australia
Br J Cancer 104:903-9. 2011..We sought an optimal strategy for identifying carriers using family history, breast cancer morphology and hormone receptor status data...
- Increased cancer risks for relatives of very early-onset breast cancer cases with and without BRCA1 and BRCA2 mutationsG S Dite
Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Level 1, 723 Swanston Street, Melbourne, Carlton VIC 3053, Australia
Br J Cancer 103:1103-8. 2010..Little is known regarding cancer risks for relatives of women with very early-onset breast cancer...
- Population-based estimate of the average age-specific cumulative risk of breast cancer for a defined set of protein-truncating mutations in BRCA1 and BRCA2. Australian Breast Cancer Family StudyJ L Hopper
The University of Melbourne, Centre for Genetic Epidemiology, Carlton, Victoria, Australia
Cancer Epidemiol Biomarkers Prev 8:741-7. 1999..Breast cancer risk in BRCA1 or BRCA2 mutation carriers may be modified by other genetic or environmental factors. Genetic counselors may need to take into account the family history of the consultand...
- Estrogen receptor polymorphism at codon 325 and risk of breast cancer in women before age fortyM C Southey
Department of Pathology and Research, Peter MacCallum Cancer Institute, Melbourne, Australia
J Natl Cancer Inst 90:532-6. 1998..28+/-0.05 versus 0.11+/-0.02; P<.001). To determine whether this polymorphism is a risk factor for early-onset breast cancer, we conducted a population-based, case-control-family study in Australia...
- Using tumour pathology to identify people at high genetic risk of breast and colorectal cancersJ L Hopper
The University of Melbourne, School of Population Health, Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, Carlton, Australia
Pathology 44:89-98. 2012..We propose how this new approach could be undertaken by having genetic testing and counselling prioritised to those with the greatest probability of carrying a germline mutation in these known cancer predisposition genes...
- The role of SMAD4 in early-onset colorectal cancerS G Royce
Department of Pathology, University of Melbourne, Victoria, Australia
Colorectal Dis 12:213-9. 2010..Chromosomal loss within the region of 18q and loss of SMAD4 expression have been reported to be frequent somatic events during colorectal cancer tumour progression; however, their associations with age at onset have not been widely studied...
- BRCA1 promoter deletions in young women with breast cancer and a strong family history: a population-based studyL D Smith
Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Vic, Australia
Eur J Cancer 43:823-7. 2007..Our data support the inclusion of testing for large genomic alterations in the BRCA1 promoter region in routine clinical mutation detection within BRCA1...
- BRCA1 mutations and other sequence variants in a population-based sample of Australian women with breast cancerM C Southey
Department of Pathology and Research, Peter MacCallum Cancer Institute, Melbourne, Victoria, Australia
Br J Cancer 79:34-9. 1999..6%). Seven rare variants were also detected, but for none was there evidence of a strong effect on breast cancer susceptibility. Therefore, on a population basis, rare variants are likely to contribute little to breast cancer incidence...
- Rare mutations in XRCC2 increase the risk of breast cancerD J Park
Genetic Epidemiology Laboratory, The University of Melbourne, Victoria, Australia
Am J Hum Genet 90:734-9. 2012..This study demonstrates the power of massively parallel sequencing for discovering susceptibility genes for common, complex diseases...
- Plasma concentration of Propionibacterium acnes antibodies and prostate cancer risk: results from an Australian population-based case-control studyG Severi
Cancer Epidemiology Centre, The Cancer Council of Victoria, Melbourne, Victoria 3053, Australia
Br J Cancer 103:411-5. 2010..The aim of our study was to test whether circulating levels of P. acnes antibodies are associated with prostate cancer risk and tumour characteristics using plasma samples from a population-based case-control study...
- Molecular characterization and cancer risk associated with BRCA1 and BRCA2 splice site variants identified in multiple-case breast cancer familiesA A Tesoriero
Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Victoria, Australia
Hum Mutat 26:495. 2005..0001). Therefore five of these seven consensus splice site variants of BRCA1 and BRCA2 produce a transcript similar to that of other previously described deleterious exonic variants and are associated with similar high lifetime risks...
- Validation study of the LAMBDA model for predicting the BRCA1 or BRCA2 mutation carrier status of North American Ashkenazi Jewish womenC Apicella
Centre for Molecular, Environmental, Analytic and Genetic Epidemiology, The University of Melbourne, Victoria, Australia
Clin Genet 72:87-97. 2007..Therefore, LAMBDA is comparable to BRCAPRO for ranking AJ women according to their probability of being a BRCA1 or BRCA2 mutation carrier and is more accurate than brcapro which substantially overpredicts carriers in this population...
- Sibship analysis of associations between SNP haplotypes and a continuous trait with application to mammographic densityJ Stone
Centre for Molecular, Environmental, Genetic, and Analytic MEGA Epidemiology, University of Melbourne, Melbourne, Australia
Genet Epidemiol 34:309-18. 2010..We found evidence of association between MD and a 4-SNP VDR haplotype. In conclusion, our proposed method retains the benefits of the between- and within-pair analysis for pairs of siblings and can be implemented in standard software...
- Molecular pathologic analysis enhances the diagnosis and management of Muir-Torre syndrome and gives insight into its underlying molecular pathogenesisM C Southey
Department of Pathology, Victorian Breast Cancer Research Consortium, Peter MacCallum Cancer Institute, and the Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
Am J Surg Pathol 25:936-41. 2001..The profile of microsatellite instability and the genes rendered dysfunctional differed between tumor samples, suggesting that the molecular pathogenesis varied between lesions, despite a common germline mutation...
- Chromosomal localization of the human P2y6 purinoceptor gene and phylogenetic analysis of the P2y purinoceptor familyG R Somers
Department of Pathology, Peter MacCallum Cancer Institute, East Melbourne, Victoria, Australia
Genomics 44:127-30. 1997..Phylogenetic analysis of the P2Y purinoceptor family demonstrated the presence of five evolutionary branches and suggests the occurrence of an ancient gene duplication event...
- Prospective validation of the breast cancer risk prediction model BOADICEA and a batch-mode version BOADICEACentreR J MacInnis
1 Cancer Epidemiology Centre, Cancer Council Victoria, Victoria, Melbourne, Australia 2 Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Victoria, Melbourne, Australia
Br J Cancer 109:1296-301. 2013..70 (95% CI 0.66-0.75) and there was no evidence of systematic under- or over-dispersion (P=0.2).Conclusion:BOADICEA is well calibrated for Australian women, and had good discrimination and accuracy at the individual level. ..
- Overexpression of the steroid receptor coactivator AIB1 in breast cancer correlates with the absence of estrogen and progesterone receptors and positivity for p53 and HER2/neuT Bouras
Department to Pathology, Peter MacCallum Cancer Institute, Melbourne, Victoria, Australia
Cancer Res 61:903-7. 2001....
- Tumour morphology predicts PALB2 germline mutation statusZ L Teo
Genetic Epidemiology Laboratory, The University of Melbourne, Melbourne, Victoria 3010, Australia
Br J Cancer 109:154-63. 2013..We sought to determine whether morphological features of breast tumours can predict PALB2 germline mutation status...
- Spatiotemporally exact cDNA libraries from quail embryos: a resource for studying neural crest development and neurocristopathiesS G Bevan
Embryology Laboratory, Murdoch Institute, Parkville, Victoria, Australia
Genomics 38:206-14. 1996....
- High and low mammographic density human breast tissues maintain histological differential in murine tissue engineering chambersG L Chew
Department of Surgery, St Vincent s Hospital, The University of Melbourne, Fitzroy, Melbourne, VIC 3065, Australia
Breast Cancer Res Treat 135:177-87. 2012..Our study provides a murine model for future studies into the biomolecular basis of MD as a risk factor for breast cancer...
- SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosisClare C Constantine
The Centre for Molecular, Environmental, Genetic and Analytic MEGA Epidemiology, School of Population Health, The University of Melbourne, Melbourne, Australia
BMC Med Genet 9:18. 2008..We report our experience of selecting tag SNPs in 35 genes involved in iron metabolism in a cohort study seeking to discover genetic modifiers of hereditary hemochromatosis...
- The steroid 5alpha-reductase type II TA repeat polymorphism is not associated with risk of breast or ovarian cancer in Australian womenA B Spurdle
Oncology Division, Joint Experimental Oncology Programme, The Queensland Institute of Medical Research, and The University of Queensland, Brisbane, QLD 4029 Australia
Cancer Epidemiol Biomarkers Prev 10:1287-93. 2001..4- to 1.7-fold, our results suggest that the SRD5A2 (TA)(9) allele is unlikely to be associated with moderate alterations in breast or ovarian cancer risk...
- The BOADICEA model of genetic susceptibility to breast and ovarian cancers: updates and extensionsA C Antoniou
Cancer Research UK, Genetic Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
Br J Cancer 98:1457-66. 2008..BOADICEA can be used to predict carrier probabilities and cancer risks to individuals with any family history, and has been implemented in a user-friendly Web-based program (http://www.srl.cam.ac.uk/genepi/boadicea/boadicea_home.html)...
- An ancestral Ashkenazi haplotype at the HMPS/CRAC1 locus on 15q13-q14 is associated with hereditary mixed polyposis syndromeE E M Jaeger
Molecular and Population Genetics Laboratory, Cancer Research UK, London, United Kingdom
Am J Hum Genet 72:1261-7. 2003..Although there are probably multiple causes of the multiple colorectal adenoma and cancer phenotype in Ashkenazim, an important one is the HMPS/CRAC1 locus on 15q13-q14...
- Risk factors for breast cancer in young women by oestrogen receptor and progesterone receptor statusM R E McCredie
Department of Preventive and Social Medicine, University of Otago, Dunedin, New Zealand
Br J Cancer 89:1661-3. 2003..As hypothesised, no significant differences were found...
- Cytomegalovirus, Epstein-Barr virus and risk of breast cancer before age 40 years: a case-control studyA K Richardson
Department of Public Health and General Practice, Christchurch School of Medicine and Health Sciences, University of Otago, PO Box 4345, Christchurch, New Zealand
Br J Cancer 90:2149-52. 2004..11 (0.93-1.33) for EBV IgG. The higher mean CMV IgG levels found in women with breast cancer could be the result of a more recent infection with CMV, and may mean that late exposure to CMV is a risk factor for breast cancer...
- Large genomic alterations in hMSH2 and hMLH1 in early-onset colorectal cancer: identification of a large complex de novo hMLH1 alterationL Smith
Clin Genet 70:250-2. 2006
- CYP17 promoter polymorphism and breast cancer in Australian women under age forty yearsA B Spurdle
Cancer Unit, Joint Experimental Oncology Programme, The Queensland Institute of Medical Research, and The University of Queensland, Brisbane, Australia
J Natl Cancer Inst 92:1674-81. 2000..Because steroid hormone exposure is known to influence breast cancer risk, we conducted a population-based, case-control-family study to assess the relationship between the CYP17 promoter polymorphism and early-onset breast cancer...
- Population-based estimates of breast cancer risks associated with ATM gene variants c.7271T>G and c.1066-6T>G (IVS10-6T>G) from the Breast Cancer Family RegistryJ L Bernstein
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
Hum Mutat 27:1122-8. 2006....