PLoS genetics
We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) gene...
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| creator | Stacey Simon N Sulem Patrick Zanon Carlo Gudjonsson Sigurjon A Thorleifsson Gudmar Helgason Agnar Jonasdottir Aslaug Besenbacher Soren Kostic Jelena P Fackenthal James D Huo Dezheng Adebamowo Clement Ogundiran Temidayo Olson Janet E Fredericksen Zachary S Wang Xianshu Look Maxime P Sieuwerts Anieta M Martens John W M Pajares Isabel Garcia-Prats Maria D Ramon-Cajal Jose M de Juan Ana Panadero Angeles Ortega Eugenia Aben Katja K H Vermeulen Sita H Asadzadeh Fatemeh van Engelenburg K C Anton Margolin Sara Shen Chen-Yang Wu Pei-Ei Försti Asta Lenner Per , Umeå universitet, Onkologi Henriksson Roger , Umeå universitet, Onkologi Johansson Robert , Umeå universitet, Onkologi Enquist Kerstin , Umeå universitet, Näringsforskning Hallmans Göran , Umeå universitet, Näringsforskning Jonsson Thorvaldur Sigurdsson Helgi Alexiusdottir Kristin Gudmundsson Julius Sigurdsson Asgeir Frigge Michael L Gudmundsson Larus Kristjansson Kristleifur Halldorsson Bjarni V Styrkarsdottir Unnur Gulcher Jeffrey R Hemminki Kari Lindblom Annika Kiemeney Lambertus A Mayordomo Jose I Foekens John A Couch Fergus J Olopade Olufunmilayo I Gudbjartsson Daniel F Thorsteinsdottir Unnur Rafnar Thorunn Johannsson Oskar T Stefansson Kari |
| description | We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case:control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2 x 10(-3)), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9 x 10(-4)) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9 x 10(-7)), was without significant heterogeneity between ancestries (P(het) = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping.
Published
We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case:control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of |
| format | Article |
| fullrecord | <record><control><sourceid>europeana_1GC</sourceid><recordid>TN_cdi_europeana_collections_9200111_BibliographicResource_1000085992805</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>9200111_BibliographicResource_1000085992805</sourcerecordid><originalsourceid>FETCH-europeana_collections_9200111_BibliographicResource_10000859928053</originalsourceid><addsrcrecordid>eNrjZOAN8MkPVkhPzUstyUwu5mFgTUvMKU7lhdLcDB5uriHOHrqppUX5BamJeYnxyfk5OanJJZn5ecXxlkYGBoaGhvFOmUk5mfnpRYkFGZnJQanF-aVFyanxhgZAYGFqaWlkYWBqTEWjAIVBOfg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype></control><display><type>article</type><title>PLoS genetics</title><source>Europeana Collections</source><creator>Stacey Simon N ; Sulem Patrick ; Zanon Carlo ; Gudjonsson Sigurjon A ; Thorleifsson Gudmar ; Helgason Agnar ; Jonasdottir Aslaug ; Besenbacher Soren ; Kostic Jelena P ; Fackenthal James D ; Huo Dezheng ; Adebamowo Clement ; Ogundiran Temidayo ; Olson Janet E ; Fredericksen Zachary S ; Wang Xianshu ; Look Maxime P ; Sieuwerts Anieta M ; Martens John W M ; Pajares Isabel ; Garcia-Prats Maria D ; Ramon-Cajal Jose M ; de Juan Ana ; Panadero Angeles ; Ortega Eugenia ; Aben Katja K H ; Vermeulen Sita H ; Asadzadeh Fatemeh ; van Engelenburg K C Anton ; Margolin Sara ; Shen Chen-Yang ; Wu Pei-Ei ; Försti Asta ; Lenner Per , Umeå universitet, Onkologi ; Henriksson Roger , Umeå universitet, Onkologi ; Johansson Robert , Umeå universitet, Onkologi ; Enquist Kerstin , Umeå universitet, Näringsforskning ; Hallmans Göran , Umeå universitet, Näringsforskning ; Jonsson Thorvaldur ; Sigurdsson Helgi ; Alexiusdottir Kristin ; Gudmundsson Julius ; Sigurdsson Asgeir ; Frigge Michael L ; Gudmundsson Larus ; Kristjansson Kristleifur ; Halldorsson Bjarni V ; Styrkarsdottir Unnur ; Gulcher Jeffrey R ; Hemminki Kari ; Lindblom Annika ; Kiemeney Lambertus A ; Mayordomo Jose I ; Foekens John A ; Couch Fergus J ; Olopade Olufunmilayo I ; Gudbjartsson Daniel F ; Thorsteinsdottir Unnur ; Rafnar Thorunn ; Johannsson Oskar T ; Stefansson Kari</creator><creatorcontrib>Stacey Simon N ; Sulem Patrick ; Zanon Carlo ; Gudjonsson Sigurjon A ; Thorleifsson Gudmar ; Helgason Agnar ; Jonasdottir Aslaug ; Besenbacher Soren ; Kostic Jelena P ; Fackenthal James D ; Huo Dezheng ; Adebamowo Clement ; Ogundiran Temidayo ; Olson Janet E ; Fredericksen Zachary S ; Wang Xianshu ; Look Maxime P ; Sieuwerts Anieta M ; Martens John W M ; Pajares Isabel ; Garcia-Prats Maria D ; Ramon-Cajal Jose M ; de Juan Ana ; Panadero Angeles ; Ortega Eugenia ; Aben Katja K H ; Vermeulen Sita H ; Asadzadeh Fatemeh ; van Engelenburg K C Anton ; Margolin Sara ; Shen Chen-Yang ; Wu Pei-Ei ; Försti Asta ; Lenner Per , Umeå universitet, Onkologi ; Henriksson Roger , Umeå universitet, Onkologi ; Johansson Robert , Umeå universitet, Onkologi ; Enquist Kerstin , Umeå universitet, Näringsforskning ; Hallmans Göran , Umeå universitet, Näringsforskning ; Jonsson Thorvaldur ; Sigurdsson Helgi ; Alexiusdottir Kristin ; Gudmundsson Julius ; Sigurdsson Asgeir ; Frigge Michael L ; Gudmundsson Larus ; Kristjansson Kristleifur ; Halldorsson Bjarni V ; Styrkarsdottir Unnur ; Gulcher Jeffrey R ; Hemminki Kari ; Lindblom Annika ; Kiemeney Lambertus A ; Mayordomo Jose I ; Foekens John A ; Couch Fergus J ; Olopade Olufunmilayo I ; Gudbjartsson Daniel F ; Thorsteinsdottir Unnur ; Rafnar Thorunn ; Johannsson Oskar T ; Stefansson Kari</creatorcontrib><description>We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case:control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2 x 10(-3)), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9 x 10(-4)) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9 x 10(-7)), was without significant heterogeneity between ancestries (P(het) = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping.
Published
We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case:control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2 x 10(-3)), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9 x 10(-4)) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9 x 10(-7)), was without significant heterogeneity between ancestries (P(het) = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping.
Published</description><language>eng ; swe</language><publisher>Public Library of Science</publisher><creationdate>2010</creationdate><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://data.europeana.eu/item/9200111/BibliographicResource_1000085992805$$EHTML$$P50$$Geuropeana$$Hfree_for_read</linktohtml><link.rule.ids>781,38519,76178</link.rule.ids><linktorsrc>$$Uhttps://data.europeana.eu/item/9200111/BibliographicResource_1000085992805$$EView_record_in_Europeana$$FView_record_in_$$GEuropeana$$Hfree_for_read</linktorsrc></links><search><creatorcontrib>Stacey Simon N</creatorcontrib><creatorcontrib>Sulem Patrick</creatorcontrib><creatorcontrib>Zanon Carlo</creatorcontrib><creatorcontrib>Gudjonsson Sigurjon A</creatorcontrib><creatorcontrib>Thorleifsson Gudmar</creatorcontrib><creatorcontrib>Helgason Agnar</creatorcontrib><creatorcontrib>Jonasdottir Aslaug</creatorcontrib><creatorcontrib>Besenbacher Soren</creatorcontrib><creatorcontrib>Kostic Jelena P</creatorcontrib><creatorcontrib>Fackenthal James D</creatorcontrib><creatorcontrib>Huo Dezheng</creatorcontrib><creatorcontrib>Adebamowo Clement</creatorcontrib><creatorcontrib>Ogundiran Temidayo</creatorcontrib><creatorcontrib>Olson Janet E</creatorcontrib><creatorcontrib>Fredericksen Zachary S</creatorcontrib><creatorcontrib>Wang Xianshu</creatorcontrib><creatorcontrib>Look Maxime P</creatorcontrib><creatorcontrib>Sieuwerts Anieta M</creatorcontrib><creatorcontrib>Martens John W M</creatorcontrib><creatorcontrib>Pajares Isabel</creatorcontrib><creatorcontrib>Garcia-Prats Maria D</creatorcontrib><creatorcontrib>Ramon-Cajal Jose M</creatorcontrib><creatorcontrib>de Juan Ana</creatorcontrib><creatorcontrib>Panadero Angeles</creatorcontrib><creatorcontrib>Ortega Eugenia</creatorcontrib><creatorcontrib>Aben Katja K H</creatorcontrib><creatorcontrib>Vermeulen Sita H</creatorcontrib><creatorcontrib>Asadzadeh Fatemeh</creatorcontrib><creatorcontrib>van Engelenburg K C Anton</creatorcontrib><creatorcontrib>Margolin Sara</creatorcontrib><creatorcontrib>Shen Chen-Yang</creatorcontrib><creatorcontrib>Wu Pei-Ei</creatorcontrib><creatorcontrib>Försti Asta</creatorcontrib><creatorcontrib>Lenner Per , Umeå universitet, Onkologi</creatorcontrib><creatorcontrib>Henriksson Roger , Umeå universitet, Onkologi</creatorcontrib><creatorcontrib>Johansson Robert , Umeå universitet, Onkologi</creatorcontrib><creatorcontrib>Enquist Kerstin , Umeå universitet, Näringsforskning</creatorcontrib><creatorcontrib>Hallmans Göran , Umeå universitet, Näringsforskning</creatorcontrib><creatorcontrib>Jonsson Thorvaldur</creatorcontrib><creatorcontrib>Sigurdsson Helgi</creatorcontrib><creatorcontrib>Alexiusdottir Kristin</creatorcontrib><creatorcontrib>Gudmundsson Julius</creatorcontrib><creatorcontrib>Sigurdsson Asgeir</creatorcontrib><creatorcontrib>Frigge Michael L</creatorcontrib><creatorcontrib>Gudmundsson Larus</creatorcontrib><creatorcontrib>Kristjansson Kristleifur</creatorcontrib><creatorcontrib>Halldorsson Bjarni V</creatorcontrib><creatorcontrib>Styrkarsdottir Unnur</creatorcontrib><creatorcontrib>Gulcher Jeffrey R</creatorcontrib><creatorcontrib>Hemminki Kari</creatorcontrib><creatorcontrib>Lindblom Annika</creatorcontrib><creatorcontrib>Kiemeney Lambertus A</creatorcontrib><creatorcontrib>Mayordomo Jose I</creatorcontrib><creatorcontrib>Foekens John A</creatorcontrib><creatorcontrib>Couch Fergus J</creatorcontrib><creatorcontrib>Olopade Olufunmilayo I</creatorcontrib><creatorcontrib>Gudbjartsson Daniel F</creatorcontrib><creatorcontrib>Thorsteinsdottir Unnur</creatorcontrib><creatorcontrib>Rafnar Thorunn</creatorcontrib><creatorcontrib>Johannsson Oskar T</creatorcontrib><creatorcontrib>Stefansson Kari</creatorcontrib><title>PLoS genetics</title><description>We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case:control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2 x 10(-3)), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9 x 10(-4)) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9 x 10(-7)), was without significant heterogeneity between ancestries (P(het) = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping.
Published
We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case:control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2 x 10(-3)), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9 x 10(-4)) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9 x 10(-7)), was without significant heterogeneity between ancestries (P(het) = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping.
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V</creatorcontrib><creatorcontrib>Styrkarsdottir Unnur</creatorcontrib><creatorcontrib>Gulcher Jeffrey R</creatorcontrib><creatorcontrib>Hemminki Kari</creatorcontrib><creatorcontrib>Lindblom Annika</creatorcontrib><creatorcontrib>Kiemeney Lambertus A</creatorcontrib><creatorcontrib>Mayordomo Jose I</creatorcontrib><creatorcontrib>Foekens John A</creatorcontrib><creatorcontrib>Couch Fergus J</creatorcontrib><creatorcontrib>Olopade Olufunmilayo I</creatorcontrib><creatorcontrib>Gudbjartsson Daniel F</creatorcontrib><creatorcontrib>Thorsteinsdottir Unnur</creatorcontrib><creatorcontrib>Rafnar Thorunn</creatorcontrib><creatorcontrib>Johannsson Oskar T</creatorcontrib><creatorcontrib>Stefansson Kari</creatorcontrib><collection>Europeana Collections</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Stacey Simon N</au><au>Sulem Patrick</au><au>Zanon Carlo</au><au>Gudjonsson Sigurjon A</au><au>Thorleifsson Gudmar</au><au>Helgason Agnar</au><au>Jonasdottir Aslaug</au><au>Besenbacher Soren</au><au>Kostic Jelena P</au><au>Fackenthal James D</au><au>Huo Dezheng</au><au>Adebamowo Clement</au><au>Ogundiran Temidayo</au><au>Olson Janet E</au><au>Fredericksen Zachary S</au><au>Wang Xianshu</au><au>Look Maxime P</au><au>Sieuwerts Anieta M</au><au>Martens John W M</au><au>Pajares Isabel</au><au>Garcia-Prats Maria D</au><au>Ramon-Cajal Jose M</au><au>de Juan Ana</au><au>Panadero Angeles</au><au>Ortega Eugenia</au><au>Aben Katja K H</au><au>Vermeulen Sita H</au><au>Asadzadeh Fatemeh</au><au>van Engelenburg K C Anton</au><au>Margolin Sara</au><au>Shen Chen-Yang</au><au>Wu Pei-Ei</au><au>Försti Asta</au><au>Lenner Per , Umeå universitet, Onkologi</au><au>Henriksson Roger , Umeå universitet, Onkologi</au><au>Johansson Robert , Umeå universitet, Onkologi</au><au>Enquist Kerstin , Umeå universitet, Näringsforskning</au><au>Hallmans Göran , Umeå universitet, Näringsforskning</au><au>Jonsson Thorvaldur</au><au>Sigurdsson Helgi</au><au>Alexiusdottir Kristin</au><au>Gudmundsson Julius</au><au>Sigurdsson Asgeir</au><au>Frigge Michael L</au><au>Gudmundsson Larus</au><au>Kristjansson Kristleifur</au><au>Halldorsson Bjarni V</au><au>Styrkarsdottir Unnur</au><au>Gulcher Jeffrey R</au><au>Hemminki Kari</au><au>Lindblom Annika</au><au>Kiemeney Lambertus A</au><au>Mayordomo Jose I</au><au>Foekens John A</au><au>Couch Fergus J</au><au>Olopade Olufunmilayo I</au><au>Gudbjartsson Daniel F</au><au>Thorsteinsdottir Unnur</au><au>Rafnar Thorunn</au><au>Johannsson Oskar T</au><au>Stefansson Kari</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>PLoS genetics</atitle><date>2010</date><risdate>2010</risdate><abstract>We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case:control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2 x 10(-3)), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9 x 10(-4)) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9 x 10(-7)), was without significant heterogeneity between ancestries (P(het) = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping.
Published
We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case:control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2 x 10(-3)), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9 x 10(-4)) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9 x 10(-7)), was without significant heterogeneity between ancestries (P(het) = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping.
Published</abstract><pub>Public Library of Science</pub><oa>free_for_read</oa></addata></record> |
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| source | Europeana Collections |
| title | PLoS genetics |
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