Prediction of years of life after diagnosis of breast cancer using omics and omic-by-treatment interactions
Identifieur interne : 000284 ( Main/Exploration ); précédent : 000283; suivant : 000285Prediction of years of life after diagnosis of breast cancer using omics and omic-by-treatment interactions
Auteurs : Agustín González-Reymúndez [États-Unis] ; Gustavo De Los Campos [États-Unis] ; Lucía Gutiérrez [États-Unis] ; Sophia Y. Lunt [États-Unis] ; Ana I. Vazquez [États-Unis]Source :
- European Journal of Human Genetics [ 1018-4813 ] ; 2017.
Abstract
Breast cancer (BC) is the second most common type of cancer and a major cause of death for women. Commonly, BC patients are assigned to risk groups based on the combination of prognostic and prediction factors (eg, patient age, tumor size, tumor grade, hormone receptor status, etc). Although this approach is able to identify risk groups with different prognosis, patients are highly heterogeneous in their response to treatments. To improve the prediction of BC patients, we extended clinical models (including prognostic and prediction factors with whole-omic data) to integrate omics profiles for gene expression and copy number variants (CNVs). We describe a modeling framework that is able to incorporate clinical risk factors, high-dimensional omics profiles, and interactions between omics and non-omic factors (eg, treatment). We used the proposed modeling framework and data from METABRIC (Molecular Taxonomy of Breast Cancer Consortium) to assess the impact on the accuracy of BC patient survival predictions when omics and omic-by-treatment interactions are being considered. Our analysis shows that omics and omic-by-treatment interactions explain a sizable fraction of the variance on survival time that is not explained by commonly used clinical covariates. The sizable interaction effects observed, together with the increase in prediction accuracy, suggest that whole-omic profiles could be used to improve prognosis prediction among BC patients.
Url:
DOI: 10.1038/ejhg.2017.12
PubMed: 28272536
PubMed Central: 5437894
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000921
- to stream Pmc, to step Curation: 000921
- to stream Pmc, to step Checkpoint: 000135
- to stream Ncbi, to step Merge: 008E25
- to stream Ncbi, to step Curation: 008E25
- to stream Ncbi, to step Checkpoint: 008E25
- to stream Main, to step Merge: 000284
- to stream Main, to step Curation: 000284
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Prediction of years of life after diagnosis of breast cancer using omics and omic-by-treatment interactions</title>
<author><name sortKey="Gonzalez Reymundez, Agustin" sort="Gonzalez Reymundez, Agustin" uniqKey="Gonzalez Reymundez A" first="Agustín" last="González-Reymúndez">Agustín González-Reymúndez</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>QuantGen Group, Department of Epidemiology and Biostatistics, Michigan State University</institution>
, East Lansing, MI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="De Los Campos, Gustavo" sort="De Los Campos, Gustavo" uniqKey="De Los Campos G" first="Gustavo" last="De Los Campos">Gustavo De Los Campos</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>QuantGen Group, Department of Epidemiology and Biostatistics, Michigan State University</institution>
, East Lansing, MI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Statistics and Probability, Michigan State University</institution>
, East Lansing, MI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Gutierrez, Lucia" sort="Gutierrez, Lucia" uniqKey="Gutierrez L" first="Lucía" last="Gutiérrez">Lucía Gutiérrez</name>
<affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Department of Agronomy, University of Wisconsin-Madison</institution>
, Madison, WI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lunt, Sophia Y" sort="Lunt, Sophia Y" uniqKey="Lunt S" first="Sophia Y" last="Lunt">Sophia Y. Lunt</name>
<affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Department of Biochemistry and Molecular Biology, Michigan State University</institution>
, East Lansing, MI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Vazquez, Ana I" sort="Vazquez, Ana I" uniqKey="Vazquez A" first="Ana I" last="Vazquez">Ana I. Vazquez</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>QuantGen Group, Department of Epidemiology and Biostatistics, Michigan State University</institution>
, East Lansing, MI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">28272536</idno>
<idno type="pmc">5437894</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437894</idno>
<idno type="RBID">PMC:5437894</idno>
<idno type="doi">10.1038/ejhg.2017.12</idno>
<date when="2017">2017</date>
<idno type="wicri:Area/Pmc/Corpus">000921</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000921</idno>
<idno type="wicri:Area/Pmc/Curation">000921</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000921</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000135</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000135</idno>
<idno type="wicri:Area/Ncbi/Merge">008E25</idno>
<idno type="wicri:Area/Ncbi/Curation">008E25</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">008E25</idno>
<idno type="wicri:doubleKey">1018-4813:2017:Gonzalez Reymundez A:prediction:of:years</idno>
<idno type="wicri:Area/Main/Merge">000284</idno>
<idno type="wicri:Area/Main/Curation">000284</idno>
<idno type="wicri:Area/Main/Exploration">000284</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Prediction of years of life after diagnosis of breast cancer using omics and omic-by-treatment interactions</title>
<author><name sortKey="Gonzalez Reymundez, Agustin" sort="Gonzalez Reymundez, Agustin" uniqKey="Gonzalez Reymundez A" first="Agustín" last="González-Reymúndez">Agustín González-Reymúndez</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>QuantGen Group, Department of Epidemiology and Biostatistics, Michigan State University</institution>
, East Lansing, MI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="De Los Campos, Gustavo" sort="De Los Campos, Gustavo" uniqKey="De Los Campos G" first="Gustavo" last="De Los Campos">Gustavo De Los Campos</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>QuantGen Group, Department of Epidemiology and Biostatistics, Michigan State University</institution>
, East Lansing, MI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Statistics and Probability, Michigan State University</institution>
, East Lansing, MI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Gutierrez, Lucia" sort="Gutierrez, Lucia" uniqKey="Gutierrez L" first="Lucía" last="Gutiérrez">Lucía Gutiérrez</name>
<affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Department of Agronomy, University of Wisconsin-Madison</institution>
, Madison, WI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lunt, Sophia Y" sort="Lunt, Sophia Y" uniqKey="Lunt S" first="Sophia Y" last="Lunt">Sophia Y. Lunt</name>
<affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Department of Biochemistry and Molecular Biology, Michigan State University</institution>
, East Lansing, MI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Vazquez, Ana I" sort="Vazquez, Ana I" uniqKey="Vazquez A" first="Ana I" last="Vazquez">Ana I. Vazquez</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>QuantGen Group, Department of Epidemiology and Biostatistics, Michigan State University</institution>
, East Lansing, MI,<country>USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">European Journal of Human Genetics</title>
<idno type="ISSN">1018-4813</idno>
<idno type="eISSN">1476-5438</idno>
<imprint><date when="2017">2017</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Breast cancer (BC) is the second most common type of cancer and a major cause of death for women. Commonly, BC patients are assigned to risk groups based on the combination of prognostic and prediction factors (eg, patient age, tumor size, tumor grade, hormone receptor status, etc). Although this approach is able to identify risk groups with different prognosis, patients are highly heterogeneous in their response to treatments. To improve the prediction of BC patients, we extended clinical models (including prognostic and prediction factors with whole-omic data) to integrate omics profiles for gene expression and copy number variants (CNVs). We describe a modeling framework that is able to incorporate clinical risk factors, high-dimensional omics profiles, and interactions between omics and non-omic factors (eg, treatment). We used the proposed modeling framework and data from METABRIC (Molecular Taxonomy of Breast Cancer Consortium) to assess the impact on the accuracy of BC patient survival predictions when omics and omic-by-treatment interactions are being considered. Our analysis shows that omics and omic-by-treatment interactions explain a sizable fraction of the variance on survival time that is not explained by commonly used clinical covariates. The sizable interaction effects observed, together with the increase in prediction accuracy, suggest that whole-omic profiles could be used to improve prognosis prediction among BC patients.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<affiliations><list><country><li>États-Unis</li>
</country>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Gonzalez Reymundez, Agustin" sort="Gonzalez Reymundez, Agustin" uniqKey="Gonzalez Reymundez A" first="Agustín" last="González-Reymúndez">Agustín González-Reymúndez</name>
</noRegion>
<name sortKey="De Los Campos, Gustavo" sort="De Los Campos, Gustavo" uniqKey="De Los Campos G" first="Gustavo" last="De Los Campos">Gustavo De Los Campos</name>
<name sortKey="De Los Campos, Gustavo" sort="De Los Campos, Gustavo" uniqKey="De Los Campos G" first="Gustavo" last="De Los Campos">Gustavo De Los Campos</name>
<name sortKey="Gutierrez, Lucia" sort="Gutierrez, Lucia" uniqKey="Gutierrez L" first="Lucía" last="Gutiérrez">Lucía Gutiérrez</name>
<name sortKey="Lunt, Sophia Y" sort="Lunt, Sophia Y" uniqKey="Lunt S" first="Sophia Y" last="Lunt">Sophia Y. Lunt</name>
<name sortKey="Vazquez, Ana I" sort="Vazquez, Ana I" uniqKey="Vazquez A" first="Ana I" last="Vazquez">Ana I. Vazquez</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/LymphedemaV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000284 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000284 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Sante |area= LymphedemaV1 |flux= Main |étape= Exploration |type= RBID |clé= PMC:5437894 |texte= Prediction of years of life after diagnosis of breast cancer using omics and omic-by-treatment interactions }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:28272536" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \ | NlmPubMed2Wicri -a LymphedemaV1
This area was generated with Dilib version V0.6.31. |