PittsburghV1, Pmc, Corpus, bibRecord, 001485

High Resolution Non-Invasive Detection of a Fetal Microdeletion Using the GCREM Algorithm

Identifieur interne : 001485 ( Pmc/Corpus ); précédent : 001484; suivant : 001486

High 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. Peters

Source :

Prenatal diagnosis [ 0197-3851 ] ; 2014.

RBID : PMC:4266320

Abstract

Background/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 Mb. Our goals were to explore the lower limits of microdeletion size detection via NIPT using MINK and introduce/evaluate a novel statistical approach we recently developed called the GC Content Random Effect Model (GCREM).

Methods:

Maternal plasma was obtained from a pregnancy affected by a 4.2Mb fetal microdeletion and three normal controls. Plasma DNA was subjected to capture of an 8Mb sequence spanning the breakpoint region and sequenced. Data were analyzed with our published method, Minimally Invasive Karyotyping (MINK) and a new method called GCREM.

Results:

The 8Mb capture segment was divided into either 38 or 76 non-overlapping regions of 200Kb and 100Kb respectively. At 200Kb 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 100Kb resolution, GCREM identified significant adjusted p values for all but one 100Kb region located inside the deleted region.

Conclusion:

Targeted sequencing and GCREM analysis may enable cost effective detection of fetal microdeletions and microduplications at high resolution.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266320

DOI: 10.1002/pd.4331
PubMed: 24452987
PubMed Central: 4266320

Links to Exploration step

PMC:4266320

Le 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:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="A2">Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yeniterzi, Suveyda" sort="Yeniterzi, Suveyda" uniqKey="Yeniterzi S" first="Suveyda" last="Yeniterzi">Suveyda Yeniterzi</name>
<affiliation><nlm:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="A2">Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Rajkovic, Aleksandar" sort="Rajkovic, Aleksandar" uniqKey="Rajkovic A" first="Aleksandar" last="Rajkovic">Aleksandar Rajkovic</name>
<affiliation><nlm:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Hogge, W Allen" sort="Hogge, W Allen" uniqKey="Hogge W" first="W. Allen" last="Hogge">W. Allen Hogge</name>
<affiliation><nlm:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Dunkel, Mary" sort="Dunkel, Mary" uniqKey="Dunkel M" first="Mary" last="Dunkel">Mary Dunkel</name>
<affiliation><nlm:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Shaw, Patricia" sort="Shaw, Patricia" uniqKey="Shaw P" first="Patricia" last="Shaw">Patricia Shaw</name>
<affiliation><nlm:aff id="A2">Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bunce, Kimberly" sort="Bunce, Kimberly" uniqKey="Bunce K" first="Kimberly" last="Bunce">Kimberly Bunce</name>
<affiliation><nlm:aff id="A2">Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Peters, David G" sort="Peters, David G" uniqKey="Peters D" first="David G." last="Peters">David G. Peters</name>
<affiliation><nlm:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="A2">Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania</nlm:aff>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">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:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="A2">Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania</nlm:aff>
</affiliation>
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<author><name sortKey="Yeniterzi, Suveyda" sort="Yeniterzi, Suveyda" uniqKey="Yeniterzi S" first="Suveyda" last="Yeniterzi">Suveyda Yeniterzi</name>
<affiliation><nlm:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="A2">Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Rajkovic, Aleksandar" sort="Rajkovic, Aleksandar" uniqKey="Rajkovic A" first="Aleksandar" last="Rajkovic">Aleksandar Rajkovic</name>
<affiliation><nlm:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Hogge, W Allen" sort="Hogge, W Allen" uniqKey="Hogge W" first="W. Allen" last="Hogge">W. Allen Hogge</name>
<affiliation><nlm:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Dunkel, Mary" sort="Dunkel, Mary" uniqKey="Dunkel M" first="Mary" last="Dunkel">Mary Dunkel</name>
<affiliation><nlm:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Shaw, Patricia" sort="Shaw, Patricia" uniqKey="Shaw P" first="Patricia" last="Shaw">Patricia Shaw</name>
<affiliation><nlm:aff id="A2">Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bunce, Kimberly" sort="Bunce, Kimberly" uniqKey="Bunce K" first="Kimberly" last="Bunce">Kimberly Bunce</name>
<affiliation><nlm:aff id="A2">Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Peters, David G" sort="Peters, David G" uniqKey="Peters D" first="David G." last="Peters">David G. Peters</name>
<affiliation><nlm:aff id="A1">Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="A2">Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Prenatal diagnosis</title>
<idno type="ISSN">0197-3851</idno>
<idno type="eISSN">1097-0223</idno>
<imprint><date when="2014">2014</date>
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<front><div type="abstract" xml:lang="en"><sec id="S1"><title>Background/Objective:</title>
<p id="P1">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 Mb. Our goals were to explore the lower limits of microdeletion size detection via NIPT using MINK and introduce/evaluate a novel statistical approach we recently developed called the GC Content Random Effect Model (GCREM).</p>
</sec>
<sec id="S2"><title>Methods:</title>
<p id="P2">Maternal plasma was obtained from a pregnancy affected by a 4.2Mb fetal microdeletion and three normal controls. Plasma DNA was subjected to capture of an 8Mb sequence spanning the breakpoint region and sequenced. Data were analyzed with our published method, Minimally Invasive Karyotyping (MINK) and a new method called GCREM.</p>
</sec>
<sec id="S3"><title>Results:</title>
<p id="P3">The 8Mb capture segment was divided into either 38 or 76 non-overlapping regions of 200Kb and 100Kb respectively. At 200Kb 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 100Kb resolution, GCREM identified significant adjusted p values for all but one 100Kb region located inside the deleted region.</p>
</sec>
<sec id="S4"><title>Conclusion:</title>
<p id="P4">Targeted sequencing and GCREM analysis may enable cost effective detection of fetal microdeletions and microduplications at high resolution.</p>
</sec>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
  <pmc-dir>properties manuscript</pmc-dir>
  <front><journal-meta><journal-id journal-id-type="nlm-journal-id">8106540</journal-id>
<journal-id journal-id-type="pubmed-jr-id">6583</journal-id>
<journal-id journal-id-type="nlm-ta">Prenat Diagn</journal-id>
<journal-id journal-id-type="iso-abbrev">Prenat. Diagn.</journal-id>
<journal-title-group><journal-title>Prenatal diagnosis</journal-title>
</journal-title-group>
<issn pub-type="ppub">0197-3851</issn>
<issn pub-type="epub">1097-0223</issn>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24452987</article-id>
<article-id pub-id-type="pmc">4266320</article-id>
<article-id pub-id-type="doi">10.1002/pd.4331</article-id>
<article-id pub-id-type="manuscript">NIHMS568786</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>High Resolution Non-Invasive Detection of a Fetal Microdeletion Using the GCREM Algorithm</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Chu</surname>
<given-names>Tianjiao</given-names>
</name>
<degrees>PhD</degrees>
<xref ref-type="aff" rid="A1">1</xref>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yeniterzi</surname>
<given-names>Suveyda</given-names>
</name>
<degrees>MS</degrees>
<xref ref-type="aff" rid="A1">1</xref>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rajkovic</surname>
<given-names>Aleksandar</given-names>
</name>
<degrees>MD, PhD</degrees>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hogge</surname>
<given-names>W. Allen</given-names>
</name>
<degrees>MD</degrees>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Dunkel</surname>
<given-names>Mary</given-names>
</name>
<degrees>MS</degrees>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Shaw</surname>
<given-names>Patricia</given-names>
</name>
<degrees>BS</degrees>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bunce</surname>
<given-names>Kimberly</given-names>
</name>
<degrees>PhD</degrees>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Peters</surname>
<given-names>David G.</given-names>
</name>
<degrees>PhD</degrees>
<xref ref-type="aff" rid="A1">1</xref>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="corresp" rid="CR1">3</xref>
</contrib>
</contrib-group>
<aff id="A1"><label>1</label>
Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, USA</aff>
<aff id="A2"><label>2</label>
Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania</aff>
<author-notes><corresp id="CR1"><label>3</label>
<bold><underline>Correspondence to:</underline>
</bold>
 David G. Peters, Ph.D. University of Pittsburgh Magee-Womens Research Institute Department of Obstetrics, Gynecology and Reproductive Sciences 204 Craft Avenue, Pittsburgh, PA 15213 Office: 412 641 2979, Fax: 412 641 6156 <email>david.peters@mail.hgen.pitt.edu</email>
</corresp>
</author-notes>
<pub-date pub-type="nihms-submitted"><day>1</day>
<month>4</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>27</day>
<month>2</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="ppub"><month>5</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>01</day>
<month>5</month>
<year>2015</year>
</pub-date>
<volume>34</volume>
<issue>5</issue>
<fpage>469</fpage>
<lpage>477</lpage>
<pmc-comment>elocation-id from pubmed: 10.1002/pd.4331</pmc-comment>
      <abstract><sec id="S1"><title>Background/Objective:</title>
<p id="P1">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 Mb. Our goals were to explore the lower limits of microdeletion size detection via NIPT using MINK and introduce/evaluate a novel statistical approach we recently developed called the GC Content Random Effect Model (GCREM).</p>
</sec>
<sec id="S2"><title>Methods:</title>
<p id="P2">Maternal plasma was obtained from a pregnancy affected by a 4.2Mb fetal microdeletion and three normal controls. Plasma DNA was subjected to capture of an 8Mb sequence spanning the breakpoint region and sequenced. Data were analyzed with our published method, Minimally Invasive Karyotyping (MINK) and a new method called GCREM.</p>
</sec>
<sec id="S3"><title>Results:</title>
<p id="P3">The 8Mb capture segment was divided into either 38 or 76 non-overlapping regions of 200Kb and 100Kb respectively. At 200Kb 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 100Kb resolution, GCREM identified significant adjusted p values for all but one 100Kb region located inside the deleted region.</p>
</sec>
<sec id="S4"><title>Conclusion:</title>
<p id="P4">Targeted sequencing and GCREM analysis may enable cost effective detection of fetal microdeletions and microduplications at high resolution.</p>
</sec>
</abstract>
<kwd-group><kwd>DNA Sequencing</kwd>
<kwd>Deletion</kwd>
<kwd>Prenatal</kwd>
<kwd>Genetics</kwd>
<kwd>Fetus</kwd>
<kwd>Plasma</kwd>
<kwd>Region Capture</kwd>
<kwd>Hybridization</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>

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High Resolution Non-Invasive Detection of a Fetal Microdeletion Using the GCREM Algorithm

High Resolution Non-Invasive Detection of a Fetal Microdeletion Using the GCREM Algorithm

Source :

Abstract

Links to Exploration step

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