High resolution non-invasive detection of a fetal microdeletion using the GCREM algorithm.
Identifieur interne : 003062 ( PubMed/Corpus ); précédent : 003061; suivant : 003063High resolution non-invasive detection of a fetal microdeletion using the GCREM algorithm.
Auteurs : Tianjiao Chu ; Suveyda Yeniterzi ; Aleksandar Rajkovic ; W Allen Hogge ; Mary Dunkel ; Patricia Shaw ; Kimberly Bunce ; David G. PetersSource :
- Prenatal diagnosis [ 1097-0223 ] ; 2014.
English descriptors
- KwdEn :
- MESH :
- chemical , blood : DNA.
- methods : Karyotyping, Sequence Analysis, DNA.
- Algorithms, Aneuploidy, Female, Fetus, Gene Duplication, Humans, Pregnancy, Prenatal Diagnosis.
Abstract
The non-invasive prenatal detection of fetal microdeletions becomes increasingly challenging as the size of the mutation decreases, with current practical lower limits in the range of a few megabases. Our goals were to explore the lower limits of microdeletion size detection via non-invasive prenatal tests using Minimally Invasive Karyotyping (MINK) and introduce/evaluate a novel statistical approach we recently developed called the GC Content Random Effect Model (GCREM).
DOI: 10.1002/pd.4331
PubMed: 24452987
Links to Exploration step
pubmed:24452987Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">High resolution non-invasive detection of a fetal microdeletion using the GCREM algorithm.</title><author><name sortKey="Chu, Tianjiao" sort="Chu, Tianjiao" uniqKey="Chu T" first="Tianjiao" last="Chu">Tianjiao Chu</name><affiliation><nlm:affiliation>Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA; Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, PA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Yeniterzi, Suveyda" sort="Yeniterzi, Suveyda" uniqKey="Yeniterzi S" first="Suveyda" last="Yeniterzi">Suveyda Yeniterzi</name></author><author><name sortKey="Rajkovic, Aleksandar" sort="Rajkovic, Aleksandar" uniqKey="Rajkovic A" first="Aleksandar" last="Rajkovic">Aleksandar Rajkovic</name></author><author><name sortKey="Hogge, W Allen" sort="Hogge, W Allen" uniqKey="Hogge W" first="W Allen" last="Hogge">W Allen Hogge</name></author><author><name sortKey="Dunkel, Mary" sort="Dunkel, Mary" uniqKey="Dunkel M" first="Mary" last="Dunkel">Mary Dunkel</name></author><author><name sortKey="Shaw, Patricia" sort="Shaw, Patricia" uniqKey="Shaw P" first="Patricia" last="Shaw">Patricia Shaw</name></author><author><name sortKey="Bunce, Kimberly" sort="Bunce, Kimberly" uniqKey="Bunce K" first="Kimberly" last="Bunce">Kimberly Bunce</name></author><author><name sortKey="Peters, David G" sort="Peters, David G" uniqKey="Peters D" first="David G" last="Peters">David G. Peters</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24452987</idno><idno type="pmid">24452987</idno><idno type="doi">10.1002/pd.4331</idno><idno type="wicri:Area/PubMed/Corpus">003062</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003062</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">High resolution non-invasive detection of a fetal microdeletion using the GCREM algorithm.</title><author><name sortKey="Chu, Tianjiao" sort="Chu, Tianjiao" uniqKey="Chu T" first="Tianjiao" last="Chu">Tianjiao Chu</name><affiliation><nlm:affiliation>Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA; Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, PA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Yeniterzi, Suveyda" sort="Yeniterzi, Suveyda" uniqKey="Yeniterzi S" first="Suveyda" last="Yeniterzi">Suveyda Yeniterzi</name></author><author><name sortKey="Rajkovic, Aleksandar" sort="Rajkovic, Aleksandar" uniqKey="Rajkovic A" first="Aleksandar" last="Rajkovic">Aleksandar Rajkovic</name></author><author><name sortKey="Hogge, W Allen" sort="Hogge, W Allen" uniqKey="Hogge W" first="W Allen" last="Hogge">W Allen Hogge</name></author><author><name sortKey="Dunkel, Mary" sort="Dunkel, Mary" uniqKey="Dunkel M" first="Mary" last="Dunkel">Mary Dunkel</name></author><author><name sortKey="Shaw, Patricia" sort="Shaw, Patricia" uniqKey="Shaw P" first="Patricia" last="Shaw">Patricia Shaw</name></author><author><name sortKey="Bunce, Kimberly" sort="Bunce, Kimberly" uniqKey="Bunce K" first="Kimberly" last="Bunce">Kimberly Bunce</name></author><author><name sortKey="Peters, David G" sort="Peters, David G" uniqKey="Peters D" first="David G" last="Peters">David G. Peters</name></author></analytic><series><title level="j">Prenatal diagnosis</title><idno type="eISSN">1097-0223</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Aneuploidy</term><term>DNA (blood)</term><term>Female</term><term>Fetus</term><term>Gene Duplication</term><term>Humans</term><term>Karyotyping (methods)</term><term>Pregnancy</term><term>Prenatal Diagnosis</term><term>Sequence Analysis, DNA (methods)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="blood" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Karyotyping</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Aneuploidy</term><term>Female</term><term>Fetus</term><term>Gene Duplication</term><term>Humans</term><term>Pregnancy</term><term>Prenatal Diagnosis</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The non-invasive prenatal detection of fetal microdeletions becomes increasingly challenging as the size of the mutation decreases, with current practical lower limits in the range of a few megabases. Our goals were to explore the lower limits of microdeletion size detection via non-invasive prenatal tests using Minimally Invasive Karyotyping (MINK) and introduce/evaluate a novel statistical approach we recently developed called the GC Content Random Effect Model (GCREM).</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24452987</PMID><DateCreated><Year>2014</Year><Month>04</Month><Day>22</Day></DateCreated><DateCompleted><Year>2015</Year><Month>01</Month><Day>09</Day></DateCompleted><DateRevised><Year>2016</Year><Month>10</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1097-0223</ISSN><JournalIssue CitedMedium="Internet"><Volume>34</Volume><Issue>5</Issue><PubDate><Year>2014</Year><Month>May</Month></PubDate></JournalIssue><Title>Prenatal diagnosis</Title><ISOAbbreviation>Prenat. Diagn.</ISOAbbreviation></Journal><ArticleTitle>High resolution non-invasive detection of a fetal microdeletion using the GCREM algorithm.</ArticleTitle><Pagination><MedlinePgn>469-77</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/pd.4331</ELocationID><Abstract><AbstractText Label="BACKGROUND/OBJECTIVE" NlmCategory="OBJECTIVE">The non-invasive prenatal detection of fetal microdeletions becomes increasingly challenging as the size of the mutation decreases, with current practical lower limits in the range of a few megabases. Our goals were to explore the lower limits of microdeletion size detection via non-invasive prenatal tests using Minimally Invasive Karyotyping (MINK) and introduce/evaluate a novel statistical approach we recently developed called the GC Content Random Effect Model (GCREM).</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">Maternal plasma was obtained from a pregnancy affected by a 4.2-Mb fetal microdeletion and three normal controls. Plasma DNA was subjected to capture an 8-Mb sequence spanning the breakpoint region and sequence. Data were analyzed with our published method, MINK, and a new method called GCREM.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The 8-Mb capture segment was divided into either 38 or 76 non-overlapping regions of 200 and 100 Kb, respectively. At 200 Kb resolution, using GCREM (but not MINK), we obtained significant adjusted p-values for all 20 regions overlapping the deleted sequence, and non-significant p-values for all 18 reference regions. At 100 Kb resolution, GCREM identified significant adjusted p-values for all but one 100-Kb region located inside the deleted region.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Targeted sequencing and GCREM analysis may enable cost effective detection of fetal microdeletions and microduplications at high resolution.</AbstractText><CopyrightInformation>© 2014 John Wiley & Sons, Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chu</LastName><ForeName>Tianjiao</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA; Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, PA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yeniterzi</LastName><ForeName>Suveyda</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Rajkovic</LastName><ForeName>Aleksandar</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Hogge</LastName><ForeName>W Allen</ForeName><Initials>WA</Initials></Author><Author ValidYN="Y"><LastName>Dunkel</LastName><ForeName>Mary</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Shaw</LastName><ForeName>Patricia</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Bunce</LastName><ForeName>Kimberly</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Peters</LastName><ForeName>David G</ForeName><Initials>DG</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 HD068578</GrantID><Acronym>HD</Acronym><Agency>NICHD NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>02</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Prenat Diagn</MedlineTA><NlmUniqueID>8106540</NlmUniqueID><ISSNLinking>0197-3851</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Am J Obstet Gynecol. 2011 Mar;204(3):205.e1-11</RefSource><PMID Version="1">21310373</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Ultrasound Obstet Gynecol. 2011 Jan;37(1):6-14</RefSource><PMID Version="1">20658510</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>N Engl J Med. 2011 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