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Use of a novel non-parametric version of DEPTH to identify genomic regions associated with prostate cancer risk

Identifieur interne : 001478 ( Main/Exploration ); précédent : 001477; suivant : 001479

Use of a novel non-parametric version of DEPTH to identify genomic regions associated with prostate cancer risk

Auteurs : Robert J. Macinnis [Australie] ; Daniel F. Schmidt [Australie] ; Enes Makalic [Australie] ; Gianluca Severi [France] ; Liesel M. Fitzgerald ; Matthias Reumann [Suisse, Pays-Bas] ; Miroslaw K. Kapuscinski [Australie] ; Adam Kowalczyk [Pologne, Australie] ; Zeyu Zhou [Australie] ; Benjamin W. Goudey [Australie] ; Guoqi Qian [Australie] ; Quang M. Bui [Australie] ; Daniel J. Park [Australie] ; Adam Freeman [Australie] ; Melissa C. Southey [Australie] ; Ali Amin Al Olama [Royaume-Uni] ; Zsofia Kote-Jarai [Royaume-Uni] ; Rosalind A. Eeles [Royaume-Uni] ; John L. Hopper [Australie, Corée du Sud] ; Graham G. Giles [Australie]

Source :

RBID : PMC:5232414

Abstract

Background

We have developed a GWAS 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. single nucleotide polymorphisms, 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, penalised 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.


Url:
DOI: 10.1158/1055-9965.EPI-16-0301
PubMed: 27539266
PubMed Central: 5232414


Affiliations:


Links toward previous steps (curation, corpus...)


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<nlm:aff id="A4">Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania</nlm:aff>
<wicri:noCountry code="subfield">Tasmania</wicri:noCountry>
</affiliation>
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<name sortKey="Reumann, Matthias" sort="Reumann, Matthias" uniqKey="Reumann M" first="Matthias" last="Reumann">Matthias Reumann</name>
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</affiliation>
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<author>
<name sortKey="Kapuscinski, Miroslaw K" sort="Kapuscinski, Miroslaw K" uniqKey="Kapuscinski M" first="Miroslaw K." last="Kapuscinski">Miroslaw K. Kapuscinski</name>
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<nlm:aff id="A2">Centre For Epidemiology and Biostatistics, University of Melbourne, Melbourne, Australia</nlm:aff>
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<wicri:regionArea>Centre For Epidemiology and Biostatistics, University of Melbourne, Melbourne</wicri:regionArea>
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<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
<settlement type="city">Melbourne</settlement>
</placeName>
<orgName type="university">Université de Melbourne</orgName>
</affiliation>
</author>
<author>
<name sortKey="Kowalczyk, Adam" sort="Kowalczyk, Adam" uniqKey="Kowalczyk A" first="Adam" last="Kowalczyk">Adam Kowalczyk</name>
<affiliation wicri:level="1">
<nlm:aff id="A7">Warsaw University of Technology, Warsaw, Poland</nlm:aff>
<country xml:lang="fr">Pologne</country>
<wicri:regionArea>Warsaw University of Technology, Warsaw</wicri:regionArea>
<wicri:noRegion>Warsaw</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4">
<nlm:aff id="A8">School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
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<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Zhou, Zeyu" sort="Zhou, Zeyu" uniqKey="Zhou Z" first="Zeyu" last="Zhou">Zeyu Zhou</name>
<affiliation wicri:level="1">
<nlm:aff id="A9">IBM Research – Australia, Carlton, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>IBM Research – Australia, Carlton</wicri:regionArea>
<wicri:noRegion>Carlton</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Goudey, Benjamin W" sort="Goudey, Benjamin W" uniqKey="Goudey B" first="Benjamin W." last="Goudey">Benjamin W. Goudey</name>
<affiliation wicri:level="1">
<nlm:aff id="A9">IBM Research – Australia, Carlton, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>IBM Research – Australia, Carlton</wicri:regionArea>
<wicri:noRegion>Carlton</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Qian, Guoqi" sort="Qian, Guoqi" uniqKey="Qian G" first="Guoqi" last="Qian">Guoqi Qian</name>
<affiliation wicri:level="4">
<nlm:aff id="A8">School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName>
<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Bui, Quang M" sort="Bui, Quang M" uniqKey="Bui Q" first="Quang M." last="Bui">Quang M. Bui</name>
<affiliation wicri:level="4">
<nlm:aff id="A2">Centre For Epidemiology and Biostatistics, University of Melbourne, Melbourne, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre For Epidemiology and Biostatistics, University of Melbourne, Melbourne</wicri:regionArea>
<placeName>
<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
<settlement type="city">Melbourne</settlement>
</placeName>
<orgName type="university">Université de Melbourne</orgName>
</affiliation>
</author>
<author>
<name sortKey="Park, Daniel J" sort="Park, Daniel J" uniqKey="Park D" first="Daniel J." last="Park">Daniel J. Park</name>
<affiliation wicri:level="4">
<nlm:aff id="A10">Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, VIC, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, VIC</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
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<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
<affiliation wicri:level="4">
<nlm:aff id="A11">Melbourne Bioinformatics Platform, Victorian Life Sciences Computation Initiative, University of Melbourne, VIC, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Melbourne Bioinformatics Platform, Victorian Life Sciences Computation Initiative, University of Melbourne, VIC</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName>
<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Freeman, Adam" sort="Freeman, Adam" uniqKey="Freeman A" first="Adam" last="Freeman">Adam Freeman</name>
<affiliation wicri:level="4">
<nlm:aff id="A2">Centre For Epidemiology and Biostatistics, University of Melbourne, Melbourne, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre For Epidemiology and Biostatistics, University of Melbourne, Melbourne</wicri:regionArea>
<placeName>
<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
<settlement type="city">Melbourne</settlement>
</placeName>
<orgName type="university">Université de Melbourne</orgName>
</affiliation>
</author>
<author>
<name sortKey="Southey, Melissa C" sort="Southey, Melissa C" uniqKey="Southey M" first="Melissa C." last="Southey">Melissa C. Southey</name>
<affiliation wicri:level="4">
<nlm:aff id="A10">Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, VIC, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, VIC</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName>
<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Al Olama, Ali Amin" sort="Al Olama, Ali Amin" uniqKey="Al Olama A" first="Ali Amin" last="Al Olama">Ali Amin Al Olama</name>
<affiliation wicri:level="4">
<nlm:aff id="A12">Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge</wicri:regionArea>
<placeName>
<settlement type="city">Cambridge</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Angleterre de l'Est</region>
</placeName>
<orgName type="university">Université de Cambridge</orgName>
</affiliation>
</author>
<author>
<name sortKey="Kote Jarai, Zsofia" sort="Kote Jarai, Zsofia" uniqKey="Kote Jarai Z" first="Zsofia" last="Kote-Jarai">Zsofia Kote-Jarai</name>
<affiliation wicri:level="3">
<nlm:aff id="A13">The Institute of Cancer Research, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>The Institute of Cancer Research, London</wicri:regionArea>
<placeName>
<settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Eeles, Rosalind A" sort="Eeles, Rosalind A" uniqKey="Eeles R" first="Rosalind A" last="Eeles">Rosalind A. Eeles</name>
<affiliation wicri:level="3">
<nlm:aff id="A13">The Institute of Cancer Research, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>The Institute of Cancer Research, London</wicri:regionArea>
<placeName>
<settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="A14">The Royal Marsden NHS Foundation Trust, Surrey, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>The Royal Marsden NHS Foundation Trust, Surrey</wicri:regionArea>
<wicri:noRegion>Surrey</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Hopper, John L" sort="Hopper, John L" uniqKey="Hopper J" first="John L." last="Hopper">John L. Hopper</name>
<affiliation wicri:level="4">
<nlm:aff id="A2">Centre For Epidemiology and Biostatistics, University of Melbourne, Melbourne, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre For Epidemiology and Biostatistics, University of Melbourne, Melbourne</wicri:regionArea>
<placeName>
<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
<settlement type="city">Melbourne</settlement>
</placeName>
<orgName type="university">Université de Melbourne</orgName>
</affiliation>
<affiliation wicri:level="4">
<nlm:aff id="A15">Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea</nlm:aff>
<country xml:lang="fr">Corée du Sud</country>
<wicri:regionArea>Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul</wicri:regionArea>
<placeName>
<settlement type="city">Séoul</settlement>
<region type="capital">Région capitale de Séoul</region>
<settlement type="city">Séoul</settlement>
</placeName>
<orgName type="university">Université nationale de Séoul</orgName>
</affiliation>
</author>
<author>
<name sortKey="Giles, Graham G" sort="Giles, Graham G" uniqKey="Giles G" first="Graham G." last="Giles">Graham G. Giles</name>
<affiliation wicri:level="3">
<nlm:aff id="A1">Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne</wicri:regionArea>
<placeName>
<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
<affiliation wicri:level="4">
<nlm:aff id="A2">Centre For Epidemiology and Biostatistics, University of Melbourne, Melbourne, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Centre For Epidemiology and Biostatistics, University of Melbourne, Melbourne</wicri:regionArea>
<placeName>
<settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
<settlement type="city">Melbourne</settlement>
</placeName>
<orgName type="university">Université de Melbourne</orgName>
</affiliation>
</author>
</analytic>
<series>
<title level="j">Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology</title>
<idno type="ISSN">1055-9965</idno>
<idno type="eISSN">1538-7755</idno>
<imprint>
<date when="2016">2016</date>
</imprint>
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<textClass></textClass>
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<front>
<div type="abstract" xml:lang="en">
<sec id="S1">
<title>Background</title>
<p id="P1">We have developed a GWAS 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. single nucleotide polymorphisms, 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, penalised 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.</p>
</sec>
<sec id="S2">
<title>Methods</title>
<p id="P2">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.</p>
</sec>
<sec id="S3">
<title>Results</title>
<p id="P3">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.</p>
</sec>
<sec id="S4">
<title>Conclusions</title>
<p id="P4">DEPTH can reveal new risk-associated regions that would not have been identified using a conventional logistic regression analysis of individual SNPs.</p>
</sec>
<sec id="S5">
<title>Impact</title>
<p id="P5">This study demonstrates that the DEPTH algorithm could identify additional genetic susceptibility regions that merit further investigation.</p>
</sec>
</div>
</front>
</TEI>
<affiliations>
<list>
<country>
<li>Australie</li>
<li>Corée du Sud</li>
<li>France</li>
<li>Pays-Bas</li>
<li>Pologne</li>
<li>Royaume-Uni</li>
<li>Suisse</li>
</country>
<region>
<li>Angleterre</li>
<li>Angleterre de l'Est</li>
<li>Grand Londres</li>
<li>Région capitale de Séoul</li>
<li>Victoria (État)</li>
</region>
<settlement>
<li>Cambridge</li>
<li>Londres</li>
<li>Melbourne</li>
<li>Séoul</li>
</settlement>
<orgName>
<li>Université de Cambridge</li>
<li>Université de Melbourne</li>
<li>Université nationale de Séoul</li>
</orgName>
</list>
<tree>
<noCountry>
<name sortKey="Fitzgerald, Liesel M" sort="Fitzgerald, Liesel M" uniqKey="Fitzgerald L" first="Liesel M." last="Fitzgerald">Liesel M. Fitzgerald</name>
</noCountry>
<country name="Australie">
<region name="Victoria (État)">
<name sortKey="Macinnis, Robert J" sort="Macinnis, Robert J" uniqKey="Macinnis R" first="Robert J." last="Macinnis">Robert J. Macinnis</name>
</region>
<name sortKey="Bui, Quang M" sort="Bui, Quang M" uniqKey="Bui Q" first="Quang M." last="Bui">Quang M. Bui</name>
<name sortKey="Freeman, Adam" sort="Freeman, Adam" uniqKey="Freeman A" first="Adam" last="Freeman">Adam Freeman</name>
<name sortKey="Giles, Graham G" sort="Giles, Graham G" uniqKey="Giles G" first="Graham G." last="Giles">Graham G. Giles</name>
<name sortKey="Giles, Graham G" sort="Giles, Graham G" uniqKey="Giles G" first="Graham G." last="Giles">Graham G. Giles</name>
<name sortKey="Goudey, Benjamin W" sort="Goudey, Benjamin W" uniqKey="Goudey B" first="Benjamin W." last="Goudey">Benjamin W. Goudey</name>
<name sortKey="Hopper, John L" sort="Hopper, John L" uniqKey="Hopper J" first="John L." last="Hopper">John L. Hopper</name>
<name sortKey="Kapuscinski, Miroslaw K" sort="Kapuscinski, Miroslaw K" uniqKey="Kapuscinski M" first="Miroslaw K." last="Kapuscinski">Miroslaw K. Kapuscinski</name>
<name sortKey="Kowalczyk, Adam" sort="Kowalczyk, Adam" uniqKey="Kowalczyk A" first="Adam" last="Kowalczyk">Adam Kowalczyk</name>
<name sortKey="Macinnis, Robert J" sort="Macinnis, Robert J" uniqKey="Macinnis R" first="Robert J." last="Macinnis">Robert J. Macinnis</name>
<name sortKey="Makalic, Enes" sort="Makalic, Enes" uniqKey="Makalic E" first="Enes" last="Makalic">Enes Makalic</name>
<name sortKey="Park, Daniel J" sort="Park, Daniel J" uniqKey="Park D" first="Daniel J." last="Park">Daniel J. Park</name>
<name sortKey="Park, Daniel J" sort="Park, Daniel J" uniqKey="Park D" first="Daniel J." last="Park">Daniel J. Park</name>
<name sortKey="Qian, Guoqi" sort="Qian, Guoqi" uniqKey="Qian G" first="Guoqi" last="Qian">Guoqi Qian</name>
<name sortKey="Schmidt, Daniel F" sort="Schmidt, Daniel F" uniqKey="Schmidt D" first="Daniel F." last="Schmidt">Daniel F. Schmidt</name>
<name sortKey="Southey, Melissa C" sort="Southey, Melissa C" uniqKey="Southey M" first="Melissa C." last="Southey">Melissa C. Southey</name>
<name sortKey="Zhou, Zeyu" sort="Zhou, Zeyu" uniqKey="Zhou Z" first="Zeyu" last="Zhou">Zeyu Zhou</name>
</country>
<country name="France">
<noRegion>
<name sortKey="Severi, Gianluca" sort="Severi, Gianluca" uniqKey="Severi G" first="Gianluca" last="Severi">Gianluca Severi</name>
</noRegion>
</country>
<country name="Suisse">
<noRegion>
<name sortKey="Reumann, Matthias" sort="Reumann, Matthias" uniqKey="Reumann M" first="Matthias" last="Reumann">Matthias Reumann</name>
</noRegion>
</country>
<country name="Pays-Bas">
<noRegion>
<name sortKey="Reumann, Matthias" sort="Reumann, Matthias" uniqKey="Reumann M" first="Matthias" last="Reumann">Matthias Reumann</name>
</noRegion>
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<country name="Pologne">
<noRegion>
<name sortKey="Kowalczyk, Adam" sort="Kowalczyk, Adam" uniqKey="Kowalczyk A" first="Adam" last="Kowalczyk">Adam Kowalczyk</name>
</noRegion>
</country>
<country name="Royaume-Uni">
<region name="Angleterre">
<name sortKey="Al Olama, Ali Amin" sort="Al Olama, Ali Amin" uniqKey="Al Olama A" first="Ali Amin" last="Al Olama">Ali Amin Al Olama</name>
</region>
<name sortKey="Eeles, Rosalind A" sort="Eeles, Rosalind A" uniqKey="Eeles R" first="Rosalind A" last="Eeles">Rosalind A. Eeles</name>
<name sortKey="Eeles, Rosalind A" sort="Eeles, Rosalind A" uniqKey="Eeles R" first="Rosalind A" last="Eeles">Rosalind A. Eeles</name>
<name sortKey="Kote Jarai, Zsofia" sort="Kote Jarai, Zsofia" uniqKey="Kote Jarai Z" first="Zsofia" last="Kote-Jarai">Zsofia Kote-Jarai</name>
</country>
<country name="Corée du Sud">
<region name="Région capitale de Séoul">
<name sortKey="Hopper, John L" sort="Hopper, John L" uniqKey="Hopper J" first="John L." last="Hopper">John L. Hopper</name>
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</record>

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