Implementing prenatal diagnosis based on cell-free fetal DNA: accurate identification of factors affecting fetal DNA yield
Cell-free fetal DNA is a source of fetal genetic material that can be used for non-invasive prenatal diagnosis. Usually constituting less than 10% of the total cell free DNA in maternal plasma, the majority is maternal in origin. Optimizing conditions for maximizing yield of cell-free fetal DNA will...
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| description | Cell-free fetal DNA is a source of fetal genetic material that can be used for non-invasive prenatal diagnosis. Usually constituting less than 10% of the total cell free DNA in maternal plasma, the majority is maternal in origin. Optimizing conditions for maximizing yield of cell-free fetal DNA will be crucial for effective implementation of testing. We explore factors influencing yield of fetal DNA from maternal blood samples, including assessment of collection tubes containing cell-stabilizing agents, storage temperature, interval to sample processing and DNA extraction method used.
Microfluidic digital PCR was performed to precisely quantify male (fetal) DNA, total DNA and long DNA fragments (indicative of maternal cellular DNA). Real-time qPCR was used to assay for the presence of male SRY signal in samples.
Total cell-free DNA quantity increased significantly with time in samples stored in K(3)EDTA tubes, but only minimally in cell stabilizing tubes. This increase was solely due to the presence of additional long fragment DNA, with no change in quantity of fetal or short DNA, resulting in a significant decrease in proportion of cell-free fetal DNA over time. Storage at 4 °C did not prevent these changes.
When samples can be processed within eight hours of blood draw, K(3)EDTA tubes can be used. Prolonged transfer times in K(3)EDTA tubes should be avoided as the proportion of fetal DNA present decreases significantly; in these situations the use of cell stabilising tubes is preferable. The DNA extraction kit used may influence success rate of diagnostic tests. |
| doi_str_mv | 10.1371/journal.pone.0025202 |
| format | Article |
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Microfluidic digital PCR was performed to precisely quantify male (fetal) DNA, total DNA and long DNA fragments (indicative of maternal cellular DNA). Real-time qPCR was used to assay for the presence of male SRY signal in samples.
Total cell-free DNA quantity increased significantly with time in samples stored in K(3)EDTA tubes, but only minimally in cell stabilizing tubes. This increase was solely due to the presence of additional long fragment DNA, with no change in quantity of fetal or short DNA, resulting in a significant decrease in proportion of cell-free fetal DNA over time. Storage at 4 °C did not prevent these changes.
When samples can be processed within eight hours of blood draw, K(3)EDTA tubes can be used. Prolonged transfer times in K(3)EDTA tubes should be avoided as the proportion of fetal DNA present decreases significantly; in these situations the use of cell stabilising tubes is preferable. The DNA extraction kit used may influence success rate of diagnostic tests.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0025202</identifier><identifier>PMID: 21998643</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Aldehydes ; Biology ; Blood ; Cell-Free System ; Chemistry ; Deoxyribonucleic acid ; Diagnosis ; Diagnostic systems ; DNA ; DNA - blood ; DNA - chemistry ; DNA - genetics ; Female ; Fetus ; Fetuses ; Humans ; Laboratories ; Male ; Medical diagnosis ; Medicine ; Microfluidics ; Mothers ; Optimization ; Polymerase Chain Reaction ; Pregnancy ; Pregnant women ; Prenatal development ; Prenatal diagnosis ; Prenatal Diagnosis - methods ; Storage ; Storage temperature ; Tubes ; Womens health ; Yield</subject><ispartof>PloS one, 2011-10, Vol.6 (10), p.e25202-e25202</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Barrett et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Barrett et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c691t-8823117c7f046cbd1184585fc7897cfbd930b212ddc7b6ad73e2c8afcca758a63</citedby><cites>FETCH-LOGICAL-c691t-8823117c7f046cbd1184585fc7897cfbd930b212ddc7b6ad73e2c8afcca758a63</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187716/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187716/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21998643$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Novelli, Giuseppe</contributor><creatorcontrib>Barrett, Angela N</creatorcontrib><creatorcontrib>Zimmermann, Bernhard G</creatorcontrib><creatorcontrib>Wang, Darrell</creatorcontrib><creatorcontrib>Holloway, Andrew</creatorcontrib><creatorcontrib>Chitty, Lyn S</creatorcontrib><title>Implementing prenatal diagnosis based on cell-free fetal DNA: accurate identification of factors affecting fetal DNA yield</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Cell-free fetal DNA is a source of fetal genetic material that can be used for non-invasive prenatal diagnosis. Usually constituting less than 10% of the total cell free DNA in maternal plasma, the majority is maternal in origin. Optimizing conditions for maximizing yield of cell-free fetal DNA will be crucial for effective implementation of testing. We explore factors influencing yield of fetal DNA from maternal blood samples, including assessment of collection tubes containing cell-stabilizing agents, storage temperature, interval to sample processing and DNA extraction method used.
Microfluidic digital PCR was performed to precisely quantify male (fetal) DNA, total DNA and long DNA fragments (indicative of maternal cellular DNA). Real-time qPCR was used to assay for the presence of male SRY signal in samples.
Total cell-free DNA quantity increased significantly with time in samples stored in K(3)EDTA tubes, but only minimally in cell stabilizing tubes. This increase was solely due to the presence of additional long fragment DNA, with no change in quantity of fetal or short DNA, resulting in a significant decrease in proportion of cell-free fetal DNA over time. Storage at 4 °C did not prevent these changes.
When samples can be processed within eight hours of blood draw, K(3)EDTA tubes can be used. Prolonged transfer times in K(3)EDTA tubes should be avoided as the proportion of fetal DNA present decreases significantly; in these situations the use of cell stabilising tubes is preferable. The DNA extraction kit used may influence success rate of diagnostic tests.</description><subject>Aldehydes</subject><subject>Biology</subject><subject>Blood</subject><subject>Cell-Free System</subject><subject>Chemistry</subject><subject>Deoxyribonucleic acid</subject><subject>Diagnosis</subject><subject>Diagnostic systems</subject><subject>DNA</subject><subject>DNA - blood</subject><subject>DNA - chemistry</subject><subject>DNA - genetics</subject><subject>Female</subject><subject>Fetus</subject><subject>Fetuses</subject><subject>Humans</subject><subject>Laboratories</subject><subject>Male</subject><subject>Medical diagnosis</subject><subject>Medicine</subject><subject>Microfluidics</subject><subject>Mothers</subject><subject>Optimization</subject><subject>Polymerase Chain Reaction</subject><subject>Pregnancy</subject><subject>Pregnant women</subject><subject>Prenatal development</subject><subject>Prenatal diagnosis</subject><subject>Prenatal Diagnosis - methods</subject><subject>Storage</subject><subject>Storage temperature</subject><subject>Tubes</subject><subject>Womens health</subject><subject>Yield</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk1uL1DAYhoso7jr6D0QLguLFjDm0TeqFMKyngcUFT7fhaw6dLG0zm7Ti-utNd7rDVPZCctHw9XnfJG_yJclTjFaYMvzm0g2-g2a1c51eIURygsi95BSXlCwLguj9o_lJ8iiES4RyyoviYXJCcFnyIqOnyZ9Nu2t0q7vednW687qDHppUWag7F2xIKwhapa5LpW6apfFap0aPyPsv67cpSDl46HVq1WhhrITeRtiZ1IDsnQ8pGKPljftBl15b3ajHyQMDTdBPpu8i-fHxw_ezz8vzi0-bs_X5UhYl7pecE4oxk8ygrJCVwphnOc-NZLxk0lSqpKgimCglWVWAYlQTycFICSznUNBF8nzvu2tcEFNsQWCKSowwivaLZLMnlINLsfO2BX8tHFhxU3C-FuB7KxstlM6JIibPgJpMEsxzyCiSmuVUZbESvd5Nqw1Vq5WMsXhoZqbzP53ditr9EhRzxvC43VeTgXdXgw69aG0Yw4dOuyEIXvIcFePtLZIX_5B3H26iaoj7t51xcVk5eop1xqJRSUoeqdUdVBxKt1bGJ2ZsrM8Er2eCyPT6d1_DEILYfPv6_-zFzzn78ojdamj6bXDNMD6rMAezPSi9C8Frc8gYIzF2yG0aYuwQMXVIlD07vp-D6LYl6F9NgQyJ</recordid><startdate>20111004</startdate><enddate>20111004</enddate><creator>Barrett, Angela N</creator><creator>Zimmermann, Bernhard G</creator><creator>Wang, Darrell</creator><creator>Holloway, Andrew</creator><creator>Chitty, Lyn S</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20111004</creationdate><title>Implementing prenatal diagnosis based on cell-free fetal DNA: accurate identification of factors affecting fetal DNA yield</title><author>Barrett, Angela N ; Zimmermann, Bernhard G ; Wang, Darrell ; Holloway, Andrew ; Chitty, Lyn S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c691t-8823117c7f046cbd1184585fc7897cfbd930b212ddc7b6ad73e2c8afcca758a63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Aldehydes</topic><topic>Biology</topic><topic>Blood</topic><topic>Cell-Free System</topic><topic>Chemistry</topic><topic>Deoxyribonucleic acid</topic><topic>Diagnosis</topic><topic>Diagnostic systems</topic><topic>DNA</topic><topic>DNA - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Barrett, Angela N</au><au>Zimmermann, Bernhard G</au><au>Wang, Darrell</au><au>Holloway, Andrew</au><au>Chitty, Lyn S</au><au>Novelli, Giuseppe</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Implementing prenatal diagnosis based on cell-free fetal DNA: accurate identification of factors affecting fetal DNA yield</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2011-10-04</date><risdate>2011</risdate><volume>6</volume><issue>10</issue><spage>e25202</spage><epage>e25202</epage><pages>e25202-e25202</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Cell-free fetal DNA is a source of fetal genetic material that can be used for non-invasive prenatal diagnosis. Usually constituting less than 10% of the total cell free DNA in maternal plasma, the majority is maternal in origin. Optimizing conditions for maximizing yield of cell-free fetal DNA will be crucial for effective implementation of testing. We explore factors influencing yield of fetal DNA from maternal blood samples, including assessment of collection tubes containing cell-stabilizing agents, storage temperature, interval to sample processing and DNA extraction method used.
Microfluidic digital PCR was performed to precisely quantify male (fetal) DNA, total DNA and long DNA fragments (indicative of maternal cellular DNA). Real-time qPCR was used to assay for the presence of male SRY signal in samples.
Total cell-free DNA quantity increased significantly with time in samples stored in K(3)EDTA tubes, but only minimally in cell stabilizing tubes. This increase was solely due to the presence of additional long fragment DNA, with no change in quantity of fetal or short DNA, resulting in a significant decrease in proportion of cell-free fetal DNA over time. Storage at 4 °C did not prevent these changes.
When samples can be processed within eight hours of blood draw, K(3)EDTA tubes can be used. Prolonged transfer times in K(3)EDTA tubes should be avoided as the proportion of fetal DNA present decreases significantly; in these situations the use of cell stabilising tubes is preferable. The DNA extraction kit used may influence success rate of diagnostic tests.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>21998643</pmid><doi>10.1371/journal.pone.0025202</doi><tpages>e25202</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS) Journals Open Access; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Aldehydes Biology Blood Cell-Free System Chemistry Deoxyribonucleic acid Diagnosis Diagnostic systems DNA DNA - blood DNA - chemistry DNA - genetics Female Fetus Fetuses Humans Laboratories Male Medical diagnosis Medicine Microfluidics Mothers Optimization Polymerase Chain Reaction Pregnancy Pregnant women Prenatal development Prenatal diagnosis Prenatal Diagnosis - methods Storage Storage temperature Tubes Womens health Yield |
| title | Implementing prenatal diagnosis based on cell-free fetal DNA: accurate identification of factors affecting fetal DNA yield |
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