Daniel Park

Rare germline genetic variants and risk of aggressive prostate cancer

Tu Nguyen-Dumont, Robert J MacInnis, Jason A Steen, Derrick Theys, Helen Tsimiklis, Fleur Hammet, Maryam Mahmoodi, Bernard J Pope, Daniel J Park, Khalid Mahmood, Gianluca Severi, Damien Bolton, Roger L Milne, Graham G Giles, Melissa C Southey

Journal article  |  2020  |  International Journal of Cancer

Few genetic risk factors have been demonstrated to be specifically associated with aggressive prostate cancer (PrCa). Here, we rep..

Mismatch repair gene pathogenic germline variants in a population-based cohort of breast cancer

Tu Nguyen-Dumont, Jason A Steen, Ingrid Winship, Daniel J Park, Bernard J Pope, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Derrick Theys, Mark Clendenning, Graham G Giles, John L Hopper, Melissa C Southey

Journal article  |  2020  |  Familial Cancer

The advent of gene panel testing is challenging the previous practice of using clinically defined cancer family syndromes to infor..

Hi-Plex2: a simple and robust approach to targeted sequencing-based genetic screening

Fleur Hammet, Khalid Mahmood, Thomas R Green, Nguyen-Dumont Tu, Melissa C Southey, Daniel D Buchanan, Andrew Lonie, Katherine L Nathanson, Fergus J Couch, Bernard J Pope, Daniel J Park

Journal article  |  2019  |  BioTechniques

We have previously reported Hi-Plex, a multiplex PCR methodology for building targeted DNA sequencing libraries that offers a low-..

sEst: Accurate Sex-Estimation and Abnormality Detection in Methylation Microarray Data

Chol-Hee Jung, Daniel J Park, Peter Georgeson, Khalid Mahmood, Roger L Milne, Melissa C Southey, Bernard J Pope

Journal article  |  2018  |  International Journal of Molecular Sciences

Targeted massively parallel sequencing characterises the mutation spectrum of PALB2 in breast and ovarian cancer cases from Poland and Ukraine

Aleksander Myszka, Nguyen-Dumont Tu, Pawel Karpinski, Maria M Sasiadek, Hayane Akopyan, Fleur Hammet, Helen Tsimiklis, Daniel J Park, Bernard J Pope, Ryszard Slezak, Nataliya Kitsera, Aleksandra Siekierzynska, Melissa C Southey

Journal article  |  2018  |  FAMILIAL CANCER

Is RNASEL:p.Glu265*a modifier of early-onset breast cancer risk for carriers of high-risk mutations?

Tu Nguyen-Dumont, Zhi L Teo, Fleur Hammet, Alexis Roberge, Maryam Mahmoodi, Helen Tsimiklis, Daniel J Park, Bernard J Pope, Andrew Lonie, Miroslav K Kapuscinski, Khalid Mahmood, David E Goldgar, Graham G Giles, Ingrid Winship, John L Hopper, Melissa C Southey

Journal article  |  2018  |  BMC Cancer

FANCM and RECQL genetic variants and breast cancer susceptibility: relevance to South Poland and West Ukraine

Nguyen-Dumont Tu, Aleksander Myszka, Pawel Karpinski, Maria M Sasiadek, Hayane Akopyan, Fleur Hammet, Helen Tsimiklis, Daniel J Park, Bernard J Pope, Ryszard Slezak, Nataliya Kitsera, Aleksandra Siekierzynska, Melissa C Southey

Journal article  |  2018  |  BMC Medical Genetics

Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing.

Bernard J Pope, Fleur Hammet, Tu Nguyen-Dumont, Daniel J Park

Book Chapter  |  2018  |  Methods in Molecular Biology

Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguye..

A novel Drosophila injury model reveals severed axons are cleared through a Draper/MMP-1 signaling cascade

Maria D Purice, Arpita Ray, Eva Jolanda Munzel, Bernard J Pope, Daniel J Park, Sean D Speese, Mary A Logan

Journal article  |  2017  |  eLife

Mutation screening of ACKR3 and COPS8 in kidney cancer cases from the CONFIRM study

Maryam Mahmoodi, Nguyen-Dumont Tu, Fleur Hammet, Bernard J Pope, Daniel J Park, Melissa C Southey, John M Darlow, Fiona Bruinsma, Ingrid Winship

Journal article  |  2017  |  FAMILIAL CANCER

Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics

Khalid Mahmood, Chol-hee Jung, Gayle Philip, Peter Georgeson, Jessica Chung, Bernard J Pope, Daniel J Park

Journal article  |  2017  |  Human Genomics

Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells

Bernard J Pope, Khalid Mahmood, Chol-hee Jung, Peter Georgeson, Daniel J Park

Journal article  |  2017  |  Genomics Data

Fine resolution mapping of double-strand break sites for human ribosomal DNA units

Bernard J Pope, Khalid Mahmood, Chol-hee Jung, Daniel J Park

Journal article  |  2016  |  GENOMICS DATA

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

Robert J MacInnis, Daniel F Schmidt, Enes Makalic, Gianluca Severi, Liesel M FitzGerald, Matthias Reumann, Miroslaw K Kapuscinski, Adam Kowalczyk, Zeyu Zhou, Benjamin Goudey, Guoqi Qian, Quang M Bui, Daniel J Park, Adam Freeman, Melissa C Southey, Ali Amin Al Olama, Zsofia Kote-Jarai, Rosalind A Eeles, John L Hopper, Graham G Giles

Journal article  |  2016  |  Cancer Epidemiology Biomarkers & Prevention

Genome-wide measures of DNA methylation in peripheral blood and the risk of urothelial cell carcinoma: a prospective nested case-control study

Pierre-Antoine Dugue, Maree T Brinkman, Roger L Milne, Ee Ming Wong, Liesel M FitzGerald, Julie K Bassett, Jihoon E Joo, Chol-Hee Jung, Enes Makalic, Daniel F Schmidt, Daniel J Park, Jessica Chung, Anthony D Ta, Damien M Bolton, Andrew Lonie, Anthony Longano, John L Hopper, Gianluca Severi, Richard Saffery, Dallas R English, et al.

Journal article  |  2016  |  British Journal of Cancer

Evaluation of germline BRCA1 and BRCA2 mutations in a multi-ethnic Asian cohort of ovarian cancer patients

Hanis Nazihah Hasmad, Kah Nyin Lai, Wei Xiong Wen, Daniel Jonathan Park, Tu Nguyen-Dumont, Peter Choon Eng Kang, Eswary Thirthagiri, Mahirah Ma'som, Boon Kiong Lim, Melissa Southey, Yin Ling Woo, Soo-Hwang Teo

Journal article  |  2016  |  Gynecologic Oncology

UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing

Daniel J Park, Roger Li, Edmund Lau, Peter Georgeson, Nguyen-Dumont Tu, Bernard J Pope

Journal article  |  2016  |  BMC BIOINFORMATICS

Global measures of peripheral blood-derived DNA methylation as a risk factor in the development of mature B-cell neoplasms

Nicole Wong Doo, Enes Makalic, JiHoon E Joo, Claire M Vajdic, Daniel F Schmidt, Ee Ming Wong, Chol-Hee Jung, Gianluca Severi, Daniel J Park, Jessica Chung, Laura Baglietto, Henry Miles Prince, John F Seymour, Constantine Tam, John L Hopper, Dallas R English, Roger L Milne, Simon J Harrison, Melissa C Southey, Graham G Giles

Journal article  |  2016  |  Epigenomics

Hi-Plex targeted sequencing is effective using DNA derived from archival dried blood spots

T Nguyen-Dumont, M Mahmoodi, F Hammet, T Tran, H Tsimiklis, GG Giles, JL Hopper, MC Southey, DJ Park

Journal article  |  2015  |  Analytical Biochemistry

Abridged adapter primers increase the target scope of Hi-Plex

Nguyen-Dumont Tu, Fleur Hammet, Maryam Mahmoodi, Bernard J Pope, Graham G Giles, Graham G Hopper, Melissa C Southey, Daniel J Park

Journal article  |  2015  |  BioTechniques

Mutation screening of PALB2 in clinically ascertained families from the Breast Cancer Family Registry

Nguyen-Dumont Tu, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Zhi L Teo, Roger Li, Bernard J Pope, Mary Beth Terry, Saundra S Buys, Mary Daly, John L Hopper, Ingrid Winship, David E Goldgar, Daniel J Park, Melissa C Southey

Journal article  |  2015  |  Breast Cancer Research and Treatment

Rare Mutations in RINT1 Predispose Carriers to Breast and Lynch Syndrome-Spectrum Cancers

Daniel J Park, Kayoko Tao, Florence Le Calvez-Kelm, Nguyen-Dumont Tu, Nivonirina Robinot, Fleur Hammet, Fabrice Odefrey, Helen Tsimiklis, Zhi L Teo, Louise B Thingholm, Erin L Young, Catherine Voegele, Andrew Lonie, Bernard J Pope, Terrell C Roane, Russell Bell, Hao Hu, undefined Shankaracharya, Chad D Huff, Jonathan Ellis, et al.

Journal article  |  2014  |  Cancer Discovery

A Genome-wide Association Study of Early-Onset Breast Cancer Identifies PFKM as a Novel Breast Cancer Gene and Supports a Common Genetic Spectrum for Breast Cancer at Any Age

Habibul Ahsan, Jerry Halpern, Muhammad G Kibriya, Brandon L Pierce, Lin Tong, Eric Gamazon, Valerie McGuire, Anna Felberg, Jianxin Shi, Farzana Jasmine, Shantanu Roy, Rachelle Brutus, Maria Argos, Stephanie Melkonian, Jenny Chang-Claude, Irene Andrulis, John L Hopper, Esther M John, Kathi Malone, Giske Ursin, et al.

Journal article  |  2014  |  CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets.

Bernard J Pope, Tú Nguyen-Dumont, Fleur Hammet, Daniel J Park

Journal article  |  2014  |  Source Code for Biology and Medicine

BACKGROUND: We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequenci..

Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database.

Daniel J Park, Tú Nguyen-Dumont, Sori Kang, Karin Verspoor, Bernard J Pope

Journal article  |  2014  |  Source Code for Biology and Medicine

BackgroundThe NCBI Entrez Gene and PubMed databases contain a wealth of high-quality information about genes for many different or..

Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing

Nguyen-Dumont Tu, Bernard J Pope, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Melissa C Southey, Daniel J Park

Journal article  |  2013  |  ANALYTICAL BIOCHEMISTRY

Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2

Nguyen-Dumont Tu, Zhi L Teo, Bernard J Pope, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Nelly Sabbaghian, Marc Tischkowitz, William D Foulkes, Graham G Giles, John L Hopper, Melissa C Southey, Daniel J Park

Journal article  |  2013  |  BMC MEDICAL GENOMICS

A high-plex PCR approach for massively parallel sequencing

Nguyen-Dumont Tu, Bernard J Pope, Fleur Hammet, Melissa C Southey, Daniel J Park

Journal article  |  2013  |  BIOTECHNIQUES

Tumour morphology predicts PALB2 germline mutation status

ZL Teo, E Provenzano, GS Dite, DJ Park, C Apicella, SD Sawyer, PA James, G Mitchell, AH Trainer, GJ Lindeman, K Shackleton, L Cicciarelli, SS Buys, IL Andrulis, AM Mulligan, G Glendon, EM John, MB Terry, M Daly, FA Odefrey, et al.

Journal article  |  2013  |  BRITISH JOURNAL OF CANCER

Genome-wide association studies identify four ER negative-specific breast cancer risk loci

Montserrat Garcia-Closas, Fergus J Couch, Sara Lindstrom, Kyriaki Michailidouo, Marjanka K Schmidt, Mark N Brook, Nick Orr, Suhn Kyong Rhie, Elio Riboli, Heather S Feigelson, Loic Le Marchand, Julie E Buring, Diana Eccles, Penelope Miron, Peter A Fasching, Hiltrud Brauch, Jenny Chang-Claude, Jane Carpenter, Andrew K Godwin, Heli Nevanlinna, et al.

Journal article  |  2013  |  Nature Genetics

The use of DNA from archival dried blood spots with the Infinium HumanMethylation450 array

JiHoon E Joo, Ee Ming Wong, Laura Baglietto, Chol-Hee Jung, Helen Tsimiklis, Daniel J Park, Nicholas C Wong, Dallas R English, John L Hopper, Gianluca Severi, Graham G Giles, Melissa C Southey

Journal article  |  2013  |  BMC BIOTECHNOLOGY

FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets

Bernard J Pope, Nguyen-Dumont Tu, Fabrice Odefrey, Fleur Hammet, Russell Bell, Kayoko Tao, Sean V Tavtigian, David E Goldgar, Andrew Lonie, Melissa C Southey, Daniel J Park

Journal article  |  2013  |  BMC BIOINFORMATICS

Prevalence of PALB2 mutations in Australasian multiple-case breast cancer families

Zhi L Teo, Daniel J Park, Elena Provenzano, Catherine A Chatfield, Fabrice A Odefrey, Nguyen-Dumont Tu, James G Dowty, John L Hopper, Ingrid Winship, David E Goldgar, Melissa C Southey

Journal article  |  2013  |  Breast Cancer Research

Prevalence of PALB2 mutations in Australasian multiple-case breast cancer families

ZL Teo, DJ Park, E Provenzano, undefined Chatfield, FA Odefrey, undefined Nguyen-Dumont, undefined KConFab, JG Dowty, JL Hopper, IM Winship, E Goldgar, MC Southey

Journal article  |  2013  |  Breast Cancer Research

COMPLEXO: identifying the missing heritability of breast cancer via next generation collaboration

Melissa C Southey, Daniel J Park, Tu Nguyen-Dumont, Ian Campbell, Ella Thompson, Alison H Trainer, Georgia Chenevix-Trench, Jacques Simard, Martine Dumont, Penny Soucy, Mads Thomassen, Lars Jonson, Inge S Pedersen, Thomas VO Hansen, Heli Nevanlinna, Sofia Khan, Olga Sinilnikova, Sylvie Mazoyer, Fabienne Lesueur, Francesca Damiola, et al.

Journal article  |  2013  |  Breast Cancer Research

Prevalence of PALB2 mutations in Australasian multiple-case breast cancer families

Z Teo, DJ Park, E Provenzano, CA Chatfield, FA Odefrey, T Nguyen-Dumont, JG Dowty, J HOPPER, I Winship, D Goldgar, MC Southey

Journal article  |  2013  |  Breast Cancer Research

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

Afshan Siddiq, Fergus J Couch, Gary K Chen, Sara Lindstrom, Diana Eccles, Robert C Millikan, Kyriaki Michailidou, Daniel O Stram, Lars Beckmann, Suhn Kyong Rhie, Christine B Ambrosone, Kristiina Aittomaki, Pilar Amiano, Carmel Apicella, Laura Baglietto, Elisa V Bandera, Matthias W Beckmann, Christine D Berg, Leslie Bernstein, Carl Blomqvist, et al.

Journal article  |  2012  |  Human Molecular Genetics

Supercomputing enabling exhaustive statistical analysis of genome wide association study data: Preliminary results

M Reumann, E Makalic, BW Goudey, M Inouye, A Bickerstaffe, M Bui, DJ Park, MK Kapuscinski, DF Schmidt, Z Zhou, G Qian, J Zobel, J Wagner, JL Hopper

Conference Proceedings  |  2012  |  Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS

Comparison of 6q25 Breast Cancer Hits from Asian and European Genome Wide Association Studies in the Breast Cancer Association Consortium (BCAC)

Rebecca Hein, Melanie Maranian, John L Hopper, Miroslaw K Kapuscinski, Melissa C Southey, Daniel J Park, Marjanka K Schmidt, Annegien Broeks, Frans BL Hogervorst, H Bas Bueno-de-Mesquit, Kenneth R Muir, Artitaya Lophatananon, Suthee Rattanamongkongul, Puttisak Puttawibul, Peter A Fasching, Alexander Hein, Arif B Ekici, Matthias W Beckmann, Olivia Fletcher, Nichola Johnson, et al.

Journal article  |  2012  |  PLoS One

Rare Mutations in XRCC2 Increase the Risk of Breast Cancer

DJ Park, F Lesueur, T Nguyen-Dumont, M Pertesi, F Odefrey, F Hammet, SL Neuhausen, EM John, IL Andrulis, MB Terry, M Daly, S Buys, F Le Calvez-Kelm, A Lonie, BJ Pope, H Tsimiklis, C Voegele, FM Hilbers, N Hoogerbrugge, A Barroso, et al.

Journal article  |  2012  |  American Journal of Human Genetics

19p13.1 Is a Triple-Negative-Specific Breast Cancer Susceptibility Locus

Kristen N Stevens, Zachary Fredericksen, Celine M Vachon, Xianshu Wang, Sara Margolin, Annika Lindblom, Heli Nevanlinna, Dario Greco, Kristiina Aittomaki, Carl Blomqvist, Jenny Chang-Claude, Alina Vrieling, Dieter Flesch-Janys, Hans-Peter Sinn, Shan Wang-Gohrke, Stefan Nickels, Hiltrud Brauch, Yon-Dschun Ko, Hans-Peter Fischer, Rita K Schmutzler, et al.

Journal article  |  2012  |  Cancer Research

Genome-wide association analysis identifies three new breast cancer susceptibility loci

Maya Ghoussaini, Olivia Fletcher, Kyriaki Michailidou, Clare Turnbull, Marjanka K Schmidt, Ed Dicks, Joe Dennis, Qin Wang, Manjeet K Humphreys, Craig Luccarini, Caroline Baynes, Don Conroy, Melanie Maranian, Shahana Ahmed, Kristy Driver, Nichola Johnson, Nicholas Orr, Isabel dos Santos Silva, Quinten Waisfisz, Hanne Meijers-Heijboer, et al.

Journal article  |  2012  |  Nature Genetics

Supercomputing Enabling Exhaustive Statistical Analysis of Genome Wide Association Study Data: Preliminary Results

Matthias Reumann, Enes Makalic, Benjamin W Goudey, Michael Inouye, Adrian Bickerstaffe, Minh Bui, Daniel J Park, Miroslaw K Kapuscinski, Daniel F Schmidt, Zeyu Zhou, Guoqi Qian, Justin Zobel, John Wagner, John L Hopper

Conference Proceedings  |  2012  |  Proceedings of the 34th Annual International Conference of the IEEE Engineering in Medicine and Biology Society

FAN1 variants identified in multiple-case early-onset breast cancer families via exome sequencing: no evidence for association with risk for breast cancer

Daniel J Park, Fabrice A Odefrey, Fleur Hammet, Graham G Giles, Laura Baglietto, John L Hopper, Daniel F Schmidt, Enes Makalic, Olga M Sinilnikova, David E Goldgar, Melissa C Southey

Journal article  |  2011  |  Breast Cancer Research and Treatment

Presence of MMTV-like env gene sequences in human breast cancer

DJ Park, M SOUTHEY, G GILES, J HOPPER

Journal article  |  2011  |  Breast Cancer Research and Treatment

Response 'Presence of MMTV-like env gene sequences in human breast cancer'

Daniel J Park, Melissa C Southey, Graham G Giles, John L Hopper

Journal article  |  2011  |  Breast Cancer Research and Treatment

No evidence of MMTV-like env sequences in specimens from the Australian Breast Cancer Family Study

Daniel J Park, Melissa C Southey, Graham G Giles, John L Hopper

Journal article  |  2011  |  Breast Cancer Research and Treatment

Lariat-Dependent Nested PCR for Flanking Sequence Determination

Daniel J Park

Book Chapter  |  2011  |  Methods in Molecular Biology

Enhanced Solid Phase PCR for Increased Loading of Amplicon onto Solid Support

Daniel J Park

Journal article  |  2011  |  Methods in molecular biology (Clifton, N.J.)

Null findings with respect to MMTV-like env sequences in human breast cancer

Daniel J Park, Melissa C Southey, Graham G Giles, John L Hopper

Journal article  |  2010  |  Breast Cancer Research and Treatment

Are PALB2 mutations associated with increased risk of male breast cancer?

A Sauty de Chalon, Z Teo, DJ Park, FA Odefrey, JL Hopper, MC Southey

Journal article  |  2010  |  Breast Cancer Research and Treatment

Null findings with respect to MMTV-like env sequences in human breast cancer

DJ Park, M SOUTHEY, G GILES, J HOPPER

Journal article  |  2010  |  Breast Cancer Research and Treatment

A PALB2 mutation associated with high risk of breast cancer

Melissa C Southey, Zhi L Teo, James G Dowty, Fabrice A Odefrey, Daniel J Park, Marc Tischkowitz, Nelly Sabbaghian, Carmel Apicella, Graham B Byrnes, Ingrid Winship, Laura Baglietto, Graham G Giles, David E Goldgar, William D Foulkes, John L Hopper

Journal article  |  2010  |  Breast Cancer Research

Enhanced solid phase PCR: mechanisms to increase priming by solid support primers

Zaheer Khan, Karl Poetter, Daniel J Park

Journal article  |  2008  |  Analytical Biochemistry

Characterisation of the marsupial-specific ATRY gene: Implications for the evolution of male-specific function

DJ Park, AJ Pask, K Huynh, VR Harley, MB Renfree, JAM Graves

Journal article  |  2005  |  Gene

LaNe RAGE: a new tool for genomic DNA flanking sequence determination

DJ Park

Journal article  |  2005  |  Journal of Biotechnology

A new 5 ' terminal murine GAPDH exon identified using 5(') RACE LaNe

DJ Park

Journal article  |  2005  |  Molecular Biotechnology

Comparative analysis of ATRX, a chromatin remodeling protein

DJ Park, AJ Pask, K Huynh, MB Renfree, VR Harley, JAM Graves

Journal article  |  2004  |  Gene

ATRX and sex differentiation

PS Tang, DJ Park, JAM Graves, VR Harley

Journal article  |  2004  |  Trends in Endocrinology and Metabolism

3 ' RACE LaNe: a simple and rapid fully nested PCR method to determine 3 '-terminal cDNA sequence

DJ Park

Journal article  |  2004  |  Biotechniques

Universal fast walking applied to cDNA

DJ Park, MB Renfree, JAM Graves

Journal article  |  2004  |  Preparative Biochemistry & Biotechnology

3 ' RACE walking along a large cDNA employing tiered suppression PCR

DJ Park, AJ Pask, MB Renfree, JAM Graves

Journal article  |  2003  |  Biotechniques

Use of a phage-based assay for phenotypic detection of mycobacteria directly from sputum

DJ Park, FA Drobniewski, A Meyer, SM Wilson

Journal article  |  2003  |  Journal of Clinical Microbiology

The phage amplified biologically assay is a new method for rapid and low-cost phenotypic determination of the drug sensitivities o..

Activities of Bacillus thuringiensis insecticidal crystal proteins Cyt1Aa and Cyt2Aa against three species of sheep blowfly

CN Chilcott, PJ Wigley, AH Broadwell, DJ Park, DJ Ellar

Journal article  |  1998  |  Applied and environmental microbiology

The toxicity of Bacillus thuringiensis Cyt1Aa protein to sheep blowfly larvae depends on its solubilization and proteolytic activa..