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5 results on '"Bui, Quang M."'

1. Detection of skewed X-chromosome inactivation in Fragile X syndrome and X chromosome aneuploidy using quantitative melt analysis.

Author

Godler, David E, Inaba, Yoshimi, Schwartz, Charles E, Bui, Quang M, Shi, Elva Z, Li, Xin, Herlihy, Amy S, Skinner, Cindy, Hagerman, Randi J, Francis, David, Amor, David J, Metcalfe, Sylvia A, Hopper, John L, and Slater, Howard R

Subjects
Chromosomes, Human, X, Saliva, Humans, Fragile X Syndrome, Aneuploidy, DNA, DNA Methylation, Gene Expression, CpG Islands, Nucleic Acid Denaturation, Introns, Exons, Adolescent, Adult, Aged, Aged, 80 and over, Middle Aged, Child, Child, Preschool, Infant, Infant, Newborn, Female, Male, X Chromosome Inactivation, Fragile X Mental Retardation Protein, and over, Preschool, Chromosomes, Human, X, Newborn, Biochemistry and Cell Biology, Immunology
Abstract

Methylation of the fragile X mental retardation 1 (FMR1) exon 1/intron 1 boundary positioned fragile X related epigenetic element 2 (FREE2), reveals skewed X-chromosome inactivation (XCI) in fragile X syndrome full mutation (FM: CGG > 200) females. XCI skewing has been also linked to abnormal X-linked gene expression with the broader clinical impact for sex chromosome aneuploidies (SCAs). In this study, 10 FREE2 CpG sites were targeted using methylation specific quantitative melt analysis (MS-QMA), including 3 sites that could not be analysed with previously used EpiTYPER system. The method was applied for detection of skewed XCI in FM females and in different types of SCA. We tested venous blood and saliva DNA collected from 107 controls (CGG

Published
2015

2. A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11

Author

Siddiq, Afshan, Couch, Fergus J, Chen, Gary K, Lindström, Sara, Eccles, Diana, Millikan, Robert C, Michailidou, Kyriaki, Stram, Daniel O, Beckmann, Lars, Rhie, Suhn Kyong, Ambrosone, Christine B, Aittomäki, Kristiina, Amiano, Pilar, Apicella, Carmel, Investigators, Australian Breast Cancer Tissue Bank, Baglietto, Laura, Bandera, Elisa V, Beckmann, Matthias W, Berg, Christine D, Bernstein, Leslie, Blomqvist, Carl, Brauch, Hiltrud, Brinton, Louise, Bui, Quang M, Buring, Julie E, Buys, Saundra S, Campa, Daniele, Carpenter, Jane E, Chasman, Daniel I, Chang-Claude, Jenny, Chen, Constance, Clavel-Chapelon, Françoise, Cox, Angela, Cross, Simon S, Czene, Kamila, Deming, Sandra L, Diasio, Robert B, Diver, W Ryan, Dunning, Alison M, Durcan, Lorraine, Ekici, Arif B, Fasching, Peter A, Study, Familial Breast Cancer, Feigelson, Heather Spencer, Fejerman, Laura, Figueroa, Jonine D, Fletcher, Olivia, Flesch-Janys, Dieter, Gaudet, Mia M, Consortium, The GENICA, Gerty, Susan M, Rodriguez-Gil, Jorge L, Giles, Graham G, van Gils, Carla H, Godwin, Andrew K, Graham, Nikki, Greco, Dario, Hall, Per, Hankinson, Susan E, Hartmann, Arndt, Hein, Rebecca, Heinz, Judith, Hoover, Robert N, Hopper, John L, Hu, Jennifer J, Huntsman, Scott, Ingles, Sue A, Irwanto, Astrid, Isaacs, Claudine, Jacobs, Kevin B, John, Esther M, Justenhoven, Christina, Kaaks, Rudolf, Kolonel, Laurence N, Coetzee, Gerhard A, Lathrop, Mark, Le Marchand, Loic, Lee, Adam M, Lee, I-Min, Lesnick, Timothy, Lichtner, Peter, Liu, Jianjun, Lund, Eiliv, Makalic, Enes, Martin, Nicholas G, McLean, Catriona A, Meijers-Heijboer, Hanne, Meindl, Alfons, Miron, Penelope, Monroe, Kristine R, Montgomery, Grant W, Müller-Myhsok, Bertram, Nickels, Stefan, Nyante, Sarah J, Olswold, Curtis, Overvad, Kim, Palli, Domenico, Park, Daniel J, Palmer, Julie R, and Pathak, Harsh

Subjects
Biological Sciences, Genetics, Clinical Research, Aging, Human Genome, Breast Cancer, Cancer, Aetiology, 2.1 Biological and endogenous factors, Breast Neoplasms, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Receptors, Estrogen, Australian Breast Cancer Tissue Bank Investigators, Familial Breast Cancer Study, GENICA Consortium, Medical and Health Sciences, Genetics & Heredity
Abstract

Genome-wide association studies (GWAS) of breast cancer defined by hormone receptor status have revealed loci contributing to susceptibility of estrogen receptor (ER)-negative subtypes. To identify additional genetic variants for ER-negative breast cancer, we conducted the largest meta-analysis of ER-negative disease to date, comprising 4754 ER-negative cases and 31 663 controls from three GWAS: NCI Breast and Prostate Cancer Cohort Consortium (BPC3) (2188 ER-negative cases; 25 519 controls of European ancestry), Triple Negative Breast Cancer Consortium (TNBCC) (1562 triple negative cases; 3399 controls of European ancestry) and African American Breast Cancer Consortium (AABC) (1004 ER-negative cases; 2745 controls). We performed in silico replication of 86 SNPs at P ≤ 1 × 10(-5) in an additional 11 209 breast cancer cases (946 with ER-negative disease) and 16 057 controls of Japanese, Latino and European ancestry. We identified two novel loci for breast cancer at 20q11 and 6q14. SNP rs2284378 at 20q11 was associated with ER-negative breast cancer (combined two-stage OR = 1.16; P = 1.1 × 10(-8)) but showed a weaker association with overall breast cancer (OR = 1.08, P = 1.3 × 10(-6)) based on 17 869 cases and 43 745 controls and no association with ER-positive disease (OR = 1.01, P = 0.67) based on 9965 cases and 22 902 controls. Similarly, rs17530068 at 6q14 was associated with breast cancer (OR = 1.12; P = 1.1 × 10(-9)), and with both ER-positive (OR = 1.09; P = 1.5 × 10(-5)) and ER-negative (OR = 1.16, P = 2.5 × 10(-7)) disease. We also confirmed three known loci associated with ER-negative (19p13) and both ER-negative and ER-positive breast cancer (6q25 and 12p11). Our results highlight the value of large-scale collaborative studies to identify novel breast cancer risk loci.

Published
2012

3. Use of a Novel Nonparametric Version of DEPTH to Identify Genomic Regions Associated with Prostate Cancer Risk

Author

MacInnis, Robert J, Schmidt, Daniel F, Makalic, Enes, Severi, Gianluca, FitzGerald, Liesel M, Reumann, Matthias, Kapuscinski, Miroslaw K, Kowalczyk, Adam, Zhou, Zeyu, Goudey, Benjamin, Qian, Guoqi, Bui, Quang M, Park, Daniel J, Freeman, Adam, Southey, Melissa C, Al Olama, Ali Amin, Kote-Jarai, Zsofia, Eeles, Rosalind A, Hopper, John L, Giles, Graham G, UK Genetic Prostate Cancer Study Collaborators, Amin Al Olama, Ali [0000-0002-7178-3431], and Apollo - University of Cambridge Repository

Subjects
Machine Learning, Male, Australia, Humans, Prostatic Neoplasms, Genetic Predisposition to Disease, Middle Aged, Polymorphism, Single Nucleotide, United Kingdom, Genome-Wide Association Study
Abstract

BACKGROUND: We have developed a genome-wide association study analysis method called DEPTH (DEPendency of association on the number of Top Hits) to identify genomic regions potentially associated with disease by considering overlapping groups of contiguous markers (e.g., SNPs) across the genome. DEPTH is a machine learning algorithm for feature ranking of ultra-high dimensional datasets, built from well-established statistical tools such as bootstrapping, penalized regression, and decision trees. Unlike marginal regression, which considers each SNP individually, the key idea behind DEPTH is to rank groups of SNPs in terms of their joint strength of association with the outcome. Our aim was to compare the performance of DEPTH with that of standard logistic regression analysis. METHODS: We selected 1,854 prostate cancer cases and 1,894 controls from the UK for whom 541,129 SNPs were measured using the Illumina Infinium HumanHap550 array. Confirmation was sought using 4,152 cases and 2,874 controls, ascertained from the UK and Australia, for whom 211,155 SNPs were measured using the iCOGS Illumina Infinium array. RESULTS: From the DEPTH analysis, we identified 14 regions associated with prostate cancer risk that had been reported previously, five of which would not have been identified by conventional logistic regression. We also identified 112 novel putative susceptibility regions. CONCLUSIONS: DEPTH can reveal new risk-associated regions that would not have been identified using a conventional logistic regression analysis of individual SNPs. IMPACT: This study demonstrates that the DEPTH algorithm could identify additional genetic susceptibility regions that merit further investigation. Cancer Epidemiol Biomarkers Prev; 25(12); 1619-24. ©2016 AACR.

Published
2016
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4. FMR1 Intron 1 Methylation Predicts FMRP Expression in Blood of Female Carriers of Expanded FMR1 Alleles

Author

Randi J Hagerman, Quang M. Bui, Danuta Z. Loesch, Michele Ono, Freya Gehling, David J. Amor, John L. Hopper, David Francis, David E. Godler, Howard R. Slater, Godler, David E, Slater, Howard R, Bui, Quang M, Ono, Michele, Gehling, Freya, Francis, David, Amor, David J, Hopper, John L, Hagerman, Randi, and Loesch, Danuta Z

Subjects
Adult, Heterozygote, congenital, hereditary, and neonatal diseases and abnormalities, Adolescent, Biology, Pathology and Forensic Medicine, Fragile X Mental Retardation Protein, fragile X mental retardation gene protein product (FMRP), medicine, Humans, Epigenetics, fragile X syndrome, Allele, Child, FMR 1 gene, Alleles, X chromosome, Genetics, Reproducibility of Results, Regular Article, Methylation, DNA Methylation, Middle Aged, medicine.disease, FMR1, Molecular biology, Introns, Fragile X syndrome, Blotting, Southern, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, DNA methylation, Linear Models, Molecular Medicine, CpG Islands, Female, Trinucleotide Repeat Expansion, Trinucleotide repeat expansion
Abstract

Fragile X syndrome (FXS) is caused by loss of the fragile X mental retardation gene protein product (FMRP) through promoter hypermethylation, which is usually associated with CGG expansion to full mutation size (>200 CGG repeats). Methylation-sensitive Southern blotting is the current gold standard for the molecular diagnosis of FXS. For females, Southern blotting provides the activation ratio (AR), which is the proportion of unmethylated alleles on the active X chromosome. Herein, we examine the relationship of FMRP expression with methylation patterns of two fragile X-related epigenetic elements (FREE) analyzed using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry and the AR. We showed that the differential methylation of the FREE2 sequence within fragile X mental retardation gene intron 1 was related to depletion of FMRP expression. We also show that, using the combined cohort of 12 females with premutation (55 to 200 CGG repeats) and 22 females with full mutation alleles, FREE2 methylation analysis was superior to the AR as a predictor of the proportion of FMRP-positive cells in blood. Because matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry is amenable to high-throughput processing and requires minimal DNA, these findings have implications for routine FXS testing and population screening. Refereed/Peer-reviewed

Published
2011

5. Evidence for the toxicity of bidirectional transcripts and mitochondrial dysfunction in blood associated with small CGG expansions in the FMR1 gene in patients with parkinsonism

Author

Quang M. Bui, Elsdon Storey, Glynda J. Kinsella, Nicholas Trost, David E. Godler, Freya Gehling, Alison Venn, Katya Kotschet, David R. Thorburn, Howard R. Slater, Andrew Evans, David Francis, Paige Stimpson, Danuta Z. Loesch, Malcolm K. Horne, Loesch, Danuta Z, Godler, David E, Evans, Andrew, Bui, Quang M, Gehling, Freya, Kotschet, Katya E, Trost, Nicholas, Storey, Elsdon, Stimpson, Paige, Kinsella, Glynda, Francis, David, Thorburn, David R, Venn, Alison, Slater, Howard R, and Horne, Malcolm

Subjects
Male, medicine.medical_specialty, Pathology, Transcription, Genetic, Population, Disease, Motor Activity, Biology, DNA, Mitochondrial, Article, Pathogenesis, Fragile X Mental Retardation Protein, Parkinsonian Disorders, gray zone, Internal medicine, mitochondrial dysfunction, medicine, Humans, RNA, Messenger, Allele, Cognitive decline, education, Alleles, Genetic Association Studies, parkinsonism, Genetics (clinical), Aged, Aged, 80 and over, education.field_of_study, Parkinsonism, Middle Aged, medicine.disease, FMR1, nervous system diseases, premutation, Endocrinology, Trinucleotide Repeat Expansion, Trinucleotide repeat expansion
Abstract

Purpose: Our previous results showed that both gray zone and lower end premutation range (40-85 repeats) fragile X mental retardation 1(FMR1) alleles were more common among males with parkinsonism than in the general population. This study aimed to determine whether these alleles have a significant role in the manifestations and pathogenesis of parkinsonian disorders. Methods: Detailed clinical assessment and genetic testing were performed in 14 male carriers of premutation and gray zone FMR1 alleles and in 24 non carriers identified in a sample of males with parkinsonism. Results: The premutation gray zone carriers presented with more severe symptoms than disease controls matched for age, diagnosis, disease duration, and treatment. The Parkinson disease (Unified Parkinson's Disease Rating Scale) motor score and the measures of cognitive decline (Mini-Mental State Examination and/or Addenbrooke's Cognitive Examination Final Revised Version Ascores) were significantly correlated with the size of the CGG repeat and the (elevated) levels of antisense FMR1 and Cytochrome C1 mRNAs in blood leukocytes. In addition, the carriers showed a significant depletion of the nicotinamide adenine dinucleotide, reduced dehydrogenase sub unit 1 mitochondrial gene in whole blood. Conclusion: Small CGG expansion FMR1 alleles (gray zone and lower end premutation) play a significant role in the development of the parkinsonian phenotype,possibly through the cytotoxic effect of elevated sense and/or antisense FMR1 transcripts involving mitochondrial dysfunction and leading to progressive neurodegeneration. Refereed/Peer-reviewed

Published
2011

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