Serveur d'exploration sur les relations entre la France et l'Australie

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Confirmation of Childhood Acute Lymphoblastic Leukemia Variants, ARID5B and IKZF1, and Interaction with Parental Environmental Exposures

Identifieur interne : 000365 ( Pmc/Curation ); précédent : 000364; suivant : 000366

Confirmation of Childhood Acute Lymphoblastic Leukemia Variants, ARID5B and IKZF1, and Interaction with Parental Environmental Exposures

Auteurs : Tiffany-Jane Evans [Australie] ; Elizabeth Milne [Australie] ; Denise Anderson [Australie] ; Nicholas H. De Klerk [Australie] ; Sarra E. Jamieson [Australie] ; Bente A. Talseth-Palmer [Australie] ; Nikola A. Bowden [Australie] ; Elizabeth G. Holliday [Australie] ; Jérémie Rudant [France] ; Laurent Orsi [France] ; Ebony Richardson [Australie] ; Laura Lavis [Australie] ; Daniel Catchpoole [Australie] ; John R. Attia [Australie] ; Bruce K. Armstrong [Australie] ; Jacqueline Clavel [France] ; Rodney J. Scott [Australie]

Source :

RBID : PMC:4195717

Abstract

Genome wide association studies (GWAS) have established association of ARID5B and IKZF1 variants with childhood acute lymphoblastic leukemia (ALL). Epidemiological studies suggest that environmental factors alone appear to make a relatively minor contribution to disease risk. The polygenic nature of childhood ALL predisposition together with the timing of environmental triggers may hold vital clues for disease etiology. This study presents results from an Australian GWAS of childhood ALL cases (n = 358) and population controls (n = 1192). Furthermore, we utilised family trio (n = 204) genotypes to extend our investigation to gene-environment interaction of significant loci with parental exposures before conception, and child’s sex and age. Thirteen SNPs achieved genome wide significance in the population based case/control analysis; ten annotated to ARID5B and three to IKZF1. The most significant SNPs in these regions were ARID5B rs4245595 (OR 1.63, CI 1.38–1.93, P = 2.13×10−9), and IKZF1 rs1110701 (OR 1.69, CI 1.42–2.02, p = 7.26×10−9). There was evidence of gene-environment interaction for risk genotype at IKZF1, whereby an apparently stronger genetic effect was observed if the mother took folic acid or if the father did not smoke prior to pregnancy (respective interaction P-values: 0.04, 0.05). There were no interactions of risk genotypes with age or sex (P-values >0.2). Our results evidence that interaction of genetic variants and environmental exposures may further alter risk of childhood ALL however, investigation in a larger population is required. If interaction of folic acid supplementation and IKZF1 variants holds, it may be useful to quantify folate levels prior to initiating use of folic acid supplements.


Url:
DOI: 10.1371/journal.pone.0110255
PubMed: 25310577
PubMed Central: 4195717

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PMC:4195717

Le document en format XML

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<title xml:lang="en">Confirmation of Childhood Acute Lymphoblastic Leukemia Variants,
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and
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, and Interaction with Parental Environmental Exposures</title>
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<name sortKey="Evans, Tiffany Jane" sort="Evans, Tiffany Jane" uniqKey="Evans T" first="Tiffany-Jane" last="Evans">Tiffany-Jane Evans</name>
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<addr-line>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia</addr-line>
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<country xml:lang="fr">Australie</country>
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<addr-line>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
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<name sortKey="Milne, Elizabeth" sort="Milne, Elizabeth" uniqKey="Milne E" first="Elizabeth" last="Milne">Elizabeth Milne</name>
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<name sortKey="Anderson, Denise" sort="Anderson, Denise" uniqKey="Anderson D" first="Denise" last="Anderson">Denise Anderson</name>
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<name sortKey="De Klerk, Nicholas H" sort="De Klerk, Nicholas H" uniqKey="De Klerk N" first="Nicholas H." last="De Klerk">Nicholas H. De Klerk</name>
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<name sortKey="Jamieson, Sarra E" sort="Jamieson, Sarra E" uniqKey="Jamieson S" first="Sarra E." last="Jamieson">Sarra E. Jamieson</name>
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<name sortKey="Talseth Palmer, Bente A" sort="Talseth Palmer, Bente A" uniqKey="Talseth Palmer B" first="Bente A." last="Talseth-Palmer">Bente A. Talseth-Palmer</name>
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<name sortKey="Bowden, Nikola A" sort="Bowden, Nikola A" uniqKey="Bowden N" first="Nikola A." last="Bowden">Nikola A. Bowden</name>
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<name sortKey="Holliday, Elizabeth G" sort="Holliday, Elizabeth G" uniqKey="Holliday E" first="Elizabeth G." last="Holliday">Elizabeth G. Holliday</name>
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<addr-line>Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
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<wicri:regionArea>Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales</wicri:regionArea>
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<name sortKey="Rudant, Jeremie" sort="Rudant, Jeremie" uniqKey="Rudant J" first="Jérémie" last="Rudant">Jérémie Rudant</name>
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<addr-line>INSERM, U1018, Department of Environmental Epidemiology of Cancers, Villejuif, France</addr-line>
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<addr-line>Paris-Sud University, UMR-S1018, Department of Environmental Epidemiology of Cancers, Research Center in Epidemiology and Population Health, Villejuif, France</addr-line>
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<name sortKey="Orsi, Laurent" sort="Orsi, Laurent" uniqKey="Orsi L" first="Laurent" last="Orsi">Laurent Orsi</name>
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<addr-line>French National Registry of Childhood Blood Malignancies (RNHE), Villejuif, France</addr-line>
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<name sortKey="Richardson, Ebony" sort="Richardson, Ebony" uniqKey="Richardson E" first="Ebony" last="Richardson">Ebony Richardson</name>
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<name sortKey="Lavis, Laura" sort="Lavis, Laura" uniqKey="Lavis L" first="Laura" last="Lavis">Laura Lavis</name>
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<addr-line>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
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<name sortKey="Catchpoole, Daniel" sort="Catchpoole, Daniel" uniqKey="Catchpoole D" first="Daniel" last="Catchpoole">Daniel Catchpoole</name>
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<addr-line>The Tumour Bank, The Children’s Cancer Research Unit, The Children’s Hospital Westmead, Westmead, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>The Tumour Bank, The Children’s Cancer Research Unit, The Children’s Hospital Westmead, Westmead, New South Wales</wicri:regionArea>
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<name sortKey="Attia, John R" sort="Attia, John R" uniqKey="Attia J" first="John R." last="Attia">John R. Attia</name>
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<addr-line>Department of Medicine, John Hunter Hospital and Hunter Medical Research Institute, New Lambton, New South Wales, Australia</addr-line>
</nlm:aff>
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<wicri:regionArea>Department of Medicine, John Hunter Hospital and Hunter Medical Research Institute, New Lambton, New South Wales</wicri:regionArea>
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<name sortKey="Armstrong, Bruce K" sort="Armstrong, Bruce K" uniqKey="Armstrong B" first="Bruce K." last="Armstrong">Bruce K. Armstrong</name>
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<addr-line>School of Public Health, The University of Sydney and Sax Institute, Sydney, New South Wales, Australia</addr-line>
</nlm:aff>
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<name sortKey="Clavel, Jacqueline" sort="Clavel, Jacqueline" uniqKey="Clavel J" first="Jacqueline" last="Clavel">Jacqueline Clavel</name>
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<addr-line>INSERM, U1018, Department of Environmental Epidemiology of Cancers, Villejuif, France</addr-line>
</nlm:aff>
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<addr-line>Paris-Sud University, UMR-S1018, Department of Environmental Epidemiology of Cancers, Research Center in Epidemiology and Population Health, Villejuif, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Paris-Sud University, UMR-S1018, Department of Environmental Epidemiology of Cancers, Research Center in Epidemiology and Population Health, Villejuif</wicri:regionArea>
</affiliation>
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<addr-line>French National Registry of Childhood Blood Malignancies (RNHE), Villejuif, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>French National Registry of Childhood Blood Malignancies (RNHE), Villejuif</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Scott, Rodney J" sort="Scott, Rodney J" uniqKey="Scott R" first="Rodney J." last="Scott">Rodney J. Scott</name>
<affiliation wicri:level="1">
<nlm:aff id="aff1">
<addr-line>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<addr-line>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff11">
<addr-line>Molecular Genetics, Hunter Area Pathology Service, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Molecular Genetics, Hunter Area Pathology Service, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
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<title xml:lang="en" level="a" type="main">Confirmation of Childhood Acute Lymphoblastic Leukemia Variants,
<italic>ARID5B</italic>
and
<italic>IKZF1</italic>
, and Interaction with Parental Environmental Exposures</title>
<author>
<name sortKey="Evans, Tiffany Jane" sort="Evans, Tiffany Jane" uniqKey="Evans T" first="Tiffany-Jane" last="Evans">Tiffany-Jane Evans</name>
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<addr-line>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<addr-line>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Milne, Elizabeth" sort="Milne, Elizabeth" uniqKey="Milne E" first="Elizabeth" last="Milne">Elizabeth Milne</name>
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<nlm:aff id="aff3">
<addr-line>Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Telethon Kids Institute, The University of Western Australia, Perth, Western Australia</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Anderson, Denise" sort="Anderson, Denise" uniqKey="Anderson D" first="Denise" last="Anderson">Denise Anderson</name>
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</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Telethon Kids Institute, The University of Western Australia, Perth, Western Australia</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="De Klerk, Nicholas H" sort="De Klerk, Nicholas H" uniqKey="De Klerk N" first="Nicholas H." last="De Klerk">Nicholas H. De Klerk</name>
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<addr-line>Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia</addr-line>
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<country xml:lang="fr">Australie</country>
<wicri:regionArea>Telethon Kids Institute, The University of Western Australia, Perth, Western Australia</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Jamieson, Sarra E" sort="Jamieson, Sarra E" uniqKey="Jamieson S" first="Sarra E." last="Jamieson">Sarra E. Jamieson</name>
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<nlm:aff id="aff3">
<addr-line>Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Telethon Kids Institute, The University of Western Australia, Perth, Western Australia</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Talseth Palmer, Bente A" sort="Talseth Palmer, Bente A" uniqKey="Talseth Palmer B" first="Bente A." last="Talseth-Palmer">Bente A. Talseth-Palmer</name>
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<nlm:aff id="aff1">
<addr-line>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<addr-line>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Bowden, Nikola A" sort="Bowden, Nikola A" uniqKey="Bowden N" first="Nikola A." last="Bowden">Nikola A. Bowden</name>
<affiliation wicri:level="1">
<nlm:aff id="aff1">
<addr-line>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<addr-line>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Holliday, Elizabeth G" sort="Holliday, Elizabeth G" uniqKey="Holliday E" first="Elizabeth G." last="Holliday">Elizabeth G. Holliday</name>
<affiliation wicri:level="1">
<nlm:aff id="aff1">
<addr-line>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff4">
<addr-line>Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Rudant, Jeremie" sort="Rudant, Jeremie" uniqKey="Rudant J" first="Jérémie" last="Rudant">Jérémie Rudant</name>
<affiliation wicri:level="1">
<nlm:aff id="aff5">
<addr-line>INSERM, U1018, Department of Environmental Epidemiology of Cancers, Villejuif, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>INSERM, U1018, Department of Environmental Epidemiology of Cancers, Villejuif</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff6">
<addr-line>Paris-Sud University, UMR-S1018, Department of Environmental Epidemiology of Cancers, Research Center in Epidemiology and Population Health, Villejuif, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Paris-Sud University, UMR-S1018, Department of Environmental Epidemiology of Cancers, Research Center in Epidemiology and Population Health, Villejuif</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Orsi, Laurent" sort="Orsi, Laurent" uniqKey="Orsi L" first="Laurent" last="Orsi">Laurent Orsi</name>
<affiliation wicri:level="1">
<nlm:aff id="aff5">
<addr-line>INSERM, U1018, Department of Environmental Epidemiology of Cancers, Villejuif, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>INSERM, U1018, Department of Environmental Epidemiology of Cancers, Villejuif</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff6">
<addr-line>Paris-Sud University, UMR-S1018, Department of Environmental Epidemiology of Cancers, Research Center in Epidemiology and Population Health, Villejuif, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Paris-Sud University, UMR-S1018, Department of Environmental Epidemiology of Cancers, Research Center in Epidemiology and Population Health, Villejuif</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff7">
<addr-line>French National Registry of Childhood Blood Malignancies (RNHE), Villejuif, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>French National Registry of Childhood Blood Malignancies (RNHE), Villejuif</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Richardson, Ebony" sort="Richardson, Ebony" uniqKey="Richardson E" first="Ebony" last="Richardson">Ebony Richardson</name>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<addr-line>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Lavis, Laura" sort="Lavis, Laura" uniqKey="Lavis L" first="Laura" last="Lavis">Laura Lavis</name>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<addr-line>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Catchpoole, Daniel" sort="Catchpoole, Daniel" uniqKey="Catchpoole D" first="Daniel" last="Catchpoole">Daniel Catchpoole</name>
<affiliation wicri:level="1">
<nlm:aff id="aff8">
<addr-line>The Tumour Bank, The Children’s Cancer Research Unit, The Children’s Hospital Westmead, Westmead, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>The Tumour Bank, The Children’s Cancer Research Unit, The Children’s Hospital Westmead, Westmead, New South Wales</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Attia, John R" sort="Attia, John R" uniqKey="Attia J" first="John R." last="Attia">John R. Attia</name>
<affiliation wicri:level="1">
<nlm:aff id="aff1">
<addr-line>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff4">
<addr-line>Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff9">
<addr-line>Department of Medicine, John Hunter Hospital and Hunter Medical Research Institute, New Lambton, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Department of Medicine, John Hunter Hospital and Hunter Medical Research Institute, New Lambton, New South Wales</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Armstrong, Bruce K" sort="Armstrong, Bruce K" uniqKey="Armstrong B" first="Bruce K." last="Armstrong">Bruce K. Armstrong</name>
<affiliation wicri:level="1">
<nlm:aff id="aff10">
<addr-line>School of Public Health, The University of Sydney and Sax Institute, Sydney, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Public Health, The University of Sydney and Sax Institute, Sydney, New South Wales</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Clavel, Jacqueline" sort="Clavel, Jacqueline" uniqKey="Clavel J" first="Jacqueline" last="Clavel">Jacqueline Clavel</name>
<affiliation wicri:level="1">
<nlm:aff id="aff5">
<addr-line>INSERM, U1018, Department of Environmental Epidemiology of Cancers, Villejuif, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>INSERM, U1018, Department of Environmental Epidemiology of Cancers, Villejuif</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff6">
<addr-line>Paris-Sud University, UMR-S1018, Department of Environmental Epidemiology of Cancers, Research Center in Epidemiology and Population Health, Villejuif, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Paris-Sud University, UMR-S1018, Department of Environmental Epidemiology of Cancers, Research Center in Epidemiology and Population Health, Villejuif</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff7">
<addr-line>French National Registry of Childhood Blood Malignancies (RNHE), Villejuif, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>French National Registry of Childhood Blood Malignancies (RNHE), Villejuif</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Scott, Rodney J" sort="Scott, Rodney J" uniqKey="Scott R" first="Rodney J." last="Scott">Rodney J. Scott</name>
<affiliation wicri:level="1">
<nlm:aff id="aff1">
<addr-line>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<addr-line>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff11">
<addr-line>Molecular Genetics, Hunter Area Pathology Service, Newcastle, New South Wales, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Molecular Genetics, Hunter Area Pathology Service, Newcastle, New South Wales</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series>
<title level="j">PLoS ONE</title>
<idno type="eISSN">1932-6203</idno>
<imprint>
<date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass></textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<p>Genome wide association studies (GWAS) have established association of
<italic>ARID5B</italic>
and
<italic>IKZF1</italic>
variants with childhood acute lymphoblastic leukemia (ALL). Epidemiological studies suggest that environmental factors alone appear to make a relatively minor contribution to disease risk. The polygenic nature of childhood ALL predisposition together with the timing of environmental triggers may hold vital clues for disease etiology. This study presents results from an Australian GWAS of childhood ALL cases (n = 358) and population controls (n = 1192). Furthermore, we utilised family trio (n = 204) genotypes to extend our investigation to gene-environment interaction of significant loci with parental exposures before conception, and child’s sex and age. Thirteen SNPs achieved genome wide significance in the population based case/control analysis; ten annotated to
<italic>ARID5B</italic>
and three to
<italic>IKZF1</italic>
. The most significant SNPs in these regions were
<italic>ARID5B</italic>
rs4245595 (OR 1.63, CI 1.38–1.93,
<italic>P</italic>
 = 2.13×10
<sup>−9</sup>
), and
<italic>IKZF1</italic>
rs1110701 (OR 1.69, CI 1.42–2.02, p = 7.26×10
<sup>−9</sup>
). There was evidence of gene-environment interaction for risk genotype at
<italic>IKZF1</italic>
, whereby an apparently stronger genetic effect was observed if the mother took folic acid or if the father did not smoke prior to pregnancy (respective interaction P-values: 0.04, 0.05). There were no interactions of risk genotypes with age or sex (P-values >0.2). Our results evidence that interaction of genetic variants and environmental exposures may further alter risk of childhood ALL however, investigation in a larger population is required. If interaction of folic acid supplementation and
<italic>IKZF1</italic>
variants holds, it may be useful to quantify folate levels prior to initiating use of folic acid supplements.</p>
</div>
</front>
<back>
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<name sortKey="Krivtsov, A" uniqKey="Krivtsov A">A Krivtsov</name>
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<name sortKey="Flatley, Rm" uniqKey="Flatley R">RM Flatley</name>
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<name sortKey="Imai, K" uniqKey="Imai K">K Imai</name>
</author>
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<name sortKey="Matsuyama, S" uniqKey="Matsuyama S">S Matsuyama</name>
</author>
<author>
<name sortKey="Miyake, S" uniqKey="Miyake S">S Miyake</name>
</author>
<author>
<name sortKey="Suga, K" uniqKey="Suga K">K Suga</name>
</author>
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<name sortKey="Troen, Am" uniqKey="Troen A">AM Troen</name>
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<name sortKey="Mitchell, B" uniqKey="Mitchell B">B Mitchell</name>
</author>
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<name sortKey="Sorensen, B" uniqKey="Sorensen B">B Sorensen</name>
</author>
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<name sortKey="Wener, Mh" uniqKey="Wener M">MH Wener</name>
</author>
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<name sortKey="Johnston, A" uniqKey="Johnston A">A Johnston</name>
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</TEI>
<pmc article-type="research-article">
<pmc-dir>properties open_access</pmc-dir>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group>
<journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher>
<publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">25310577</article-id>
<article-id pub-id-type="pmc">4195717</article-id>
<article-id pub-id-type="publisher-id">PONE-D-14-28304</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0110255</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2">
<subject>Medicine and Health Sciences</subject>
<subj-group>
<subject>Oncology</subject>
<subj-group>
<subject>Cancer Risk Factors</subject>
<subj-group>
<subject>Cancer Predisposing Conditions and Syndromes</subject>
<subject>Environmental Causes of Cancer</subject>
<subject>Genetic Causes of Cancer</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Confirmation of Childhood Acute Lymphoblastic Leukemia Variants,
<italic>ARID5B</italic>
and
<italic>IKZF1</italic>
, and Interaction with Parental Environmental Exposures</article-title>
<alt-title alt-title-type="running-head">Gene Environment Interactions Act on
<italic>ARID5B</italic>
and
<italic>IKZF1</italic>
</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Evans</surname>
<given-names>Tiffany-Jane</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Milne</surname>
<given-names>Elizabeth</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Anderson</surname>
<given-names>Denise</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>de Klerk</surname>
<given-names>Nicholas H.</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Jamieson</surname>
<given-names>Sarra E.</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Talseth-Palmer</surname>
<given-names>Bente A.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Bowden</surname>
<given-names>Nikola A.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Holliday</surname>
<given-names>Elizabeth G.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Rudant</surname>
<given-names>Jérémie</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
<xref ref-type="aff" rid="aff6">
<sup>6</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Orsi</surname>
<given-names>Laurent</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
<xref ref-type="aff" rid="aff6">
<sup>6</sup>
</xref>
<xref ref-type="aff" rid="aff7">
<sup>7</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Richardson</surname>
<given-names>Ebony</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Lavis</surname>
<given-names>Laura</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Catchpoole</surname>
<given-names>Daniel</given-names>
</name>
<xref ref-type="aff" rid="aff8">
<sup>8</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Attia</surname>
<given-names>John R.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<xref ref-type="aff" rid="aff9">
<sup>9</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Armstrong</surname>
<given-names>Bruce K.</given-names>
</name>
<xref ref-type="aff" rid="aff10">
<sup>10</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Clavel</surname>
<given-names>Jacqueline</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
<xref ref-type="aff" rid="aff6">
<sup>6</sup>
</xref>
<xref ref-type="aff" rid="aff7">
<sup>7</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Scott</surname>
<given-names>Rodney J.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff11">
<sup>11</sup>
</xref>
<xref ref-type="corresp" rid="cor1">
<sup>*</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1">
<label>1</label>
<addr-line>Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia</addr-line>
</aff>
<aff id="aff2">
<label>2</label>
<addr-line>School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</aff>
<aff id="aff3">
<label>3</label>
<addr-line>Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia</addr-line>
</aff>
<aff id="aff4">
<label>4</label>
<addr-line>Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia</addr-line>
</aff>
<aff id="aff5">
<label>5</label>
<addr-line>INSERM, U1018, Department of Environmental Epidemiology of Cancers, Villejuif, France</addr-line>
</aff>
<aff id="aff6">
<label>6</label>
<addr-line>Paris-Sud University, UMR-S1018, Department of Environmental Epidemiology of Cancers, Research Center in Epidemiology and Population Health, Villejuif, France</addr-line>
</aff>
<aff id="aff7">
<label>7</label>
<addr-line>French National Registry of Childhood Blood Malignancies (RNHE), Villejuif, France</addr-line>
</aff>
<aff id="aff8">
<label>8</label>
<addr-line>The Tumour Bank, The Children’s Cancer Research Unit, The Children’s Hospital Westmead, Westmead, New South Wales, Australia</addr-line>
</aff>
<aff id="aff9">
<label>9</label>
<addr-line>Department of Medicine, John Hunter Hospital and Hunter Medical Research Institute, New Lambton, New South Wales, Australia</addr-line>
</aff>
<aff id="aff10">
<label>10</label>
<addr-line>School of Public Health, The University of Sydney and Sax Institute, Sydney, New South Wales, Australia</addr-line>
</aff>
<aff id="aff11">
<label>11</label>
<addr-line>Molecular Genetics, Hunter Area Pathology Service, Newcastle, New South Wales, Australia</addr-line>
</aff>
<contrib-group>
<contrib contrib-type="editor">
<name>
<surname>Chang</surname>
<given-names>Jeffrey S.</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">
<addr-line>National Health Research Institutes, Taiwan</addr-line>
</aff>
<author-notes>
<corresp id="cor1">* E-mail:
<email>rodney.scott@newcastle.edu.au</email>
</corresp>
<fn fn-type="conflict">
<p>
<bold>Competing Interests: </bold>
RJS is a PLOS ONE Editorial Board member. This does not alter our adherence to PLOS ONE Editorial policies and criteria.</p>
</fn>
<fn fn-type="con">
<p>Conceived and designed the experiments: RJS JRA EM BKA DC. Performed the experiments: T-JE DA SJ JR LO ER LL. Analyzed the data: T-JE NdK SJ EGH JC EM JRA. Contributed reagents/materials/analysis tools: BAT-P NAB LO JR DA EM NdK RJS. Contributed to the writing of the manuscript: T-JE EM NdK BAT-P NAB EGH DC JRA BKA JC RJS.</p>
</fn>
</author-notes>
<pub-date pub-type="collection">
<year>2014</year>
</pub-date>
<pub-date pub-type="epub">
<day>13</day>
<month>10</month>
<year>2014</year>
</pub-date>
<volume>9</volume>
<issue>10</issue>
<elocation-id>e110255</elocation-id>
<history>
<date date-type="received">
<day>25</day>
<month>6</month>
<year>2014</year>
</date>
<date date-type="accepted">
<day>8</day>
<month>9</month>
<year>2014</year>
</date>
</history>
<permissions>
<copyright-year>2014</copyright-year>
<copyright-holder>Evans et al</copyright-holder>
<license>
<license-p>This is an open-access article distributed under the terms of the
<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>
, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
</license>
</permissions>
<abstract>
<p>Genome wide association studies (GWAS) have established association of
<italic>ARID5B</italic>
and
<italic>IKZF1</italic>
variants with childhood acute lymphoblastic leukemia (ALL). Epidemiological studies suggest that environmental factors alone appear to make a relatively minor contribution to disease risk. The polygenic nature of childhood ALL predisposition together with the timing of environmental triggers may hold vital clues for disease etiology. This study presents results from an Australian GWAS of childhood ALL cases (n = 358) and population controls (n = 1192). Furthermore, we utilised family trio (n = 204) genotypes to extend our investigation to gene-environment interaction of significant loci with parental exposures before conception, and child’s sex and age. Thirteen SNPs achieved genome wide significance in the population based case/control analysis; ten annotated to
<italic>ARID5B</italic>
and three to
<italic>IKZF1</italic>
. The most significant SNPs in these regions were
<italic>ARID5B</italic>
rs4245595 (OR 1.63, CI 1.38–1.93,
<italic>P</italic>
 = 2.13×10
<sup>−9</sup>
), and
<italic>IKZF1</italic>
rs1110701 (OR 1.69, CI 1.42–2.02, p = 7.26×10
<sup>−9</sup>
). There was evidence of gene-environment interaction for risk genotype at
<italic>IKZF1</italic>
, whereby an apparently stronger genetic effect was observed if the mother took folic acid or if the father did not smoke prior to pregnancy (respective interaction P-values: 0.04, 0.05). There were no interactions of risk genotypes with age or sex (P-values >0.2). Our results evidence that interaction of genetic variants and environmental exposures may further alter risk of childhood ALL however, investigation in a larger population is required. If interaction of folic acid supplementation and
<italic>IKZF1</italic>
variants holds, it may be useful to quantify folate levels prior to initiating use of folic acid supplements.</p>
</abstract>
<funding-group>
<funding-statement>The collection of samples and data from the patients with childhood ALL was funded by the National Health and Medical Research Council of Australia (
<ext-link ext-link-type="uri" xlink:href="https://www.rgms.nhmrc.gov.au">https://www.rgms.nhmrc.gov.au</ext-link>
) Grant number APP254534. Genotyping was funded by the Hunter Medical Research Institute - the Lawrie Bequest Paediatric Oncology Grant, and the Hunter Children’s Research Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts>
<page-count count="7"></page-count>
</counts>
<custom-meta-group>
<custom-meta id="data-availability">
<meta-name>Data Availability</meta-name>
<meta-value>The authors confirm that, for approved reasons, some access restrictions apply to the data underlying the findings. Data are available from the AUS-ALL Institutional Data Access/Ethics Committee for researchers who meet the criteria for access to confidential data. We will provide data but due to restrictions from our ethics committees we are unable to freely provide all data unless an agreement between all parties has been made. Data are from the AusALL study whose authors may be contacted at
<email>rodney.scott@newcastle.edu.au</email>
,
<email>t.evans@newcastle.edu.au</email>
or
<email>lizm@ichr.uwa.edu.au</email>
.</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
<notes>
<title>Data Availability</title>
<p>The authors confirm that, for approved reasons, some access restrictions apply to the data underlying the findings. Data are available from the AUS-ALL Institutional Data Access/Ethics Committee for researchers who meet the criteria for access to confidential data. We will provide data but due to restrictions from our ethics committees we are unable to freely provide all data unless an agreement between all parties has been made. Data are from the AusALL study whose authors may be contacted at
<email>rodney.scott@newcastle.edu.au</email>
,
<email>t.evans@newcastle.edu.au</email>
or
<email>lizm@ichr.uwa.edu.au</email>
.</p>
</notes>
</front>
</pmc>
</record>

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