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Article ; Online: Bio-inspired vision mimetics toward next-generation collision-avoidance automation.

Xu, Gary J W / Guo, Kun / Park, Seop Hyeong / Sun, Poly Z H / Song, Aiguo

Innovation (Cambridge (Mass.))

2022 Volume 4, Issue 1, Page(s) 100368

Language	English
Publishing date	2022-12-29
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2666-6758
ISSN (online)	2666-6758
DOI	10.1016/j.xinn.2022.100368
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Non-invasive prenatal testing using cell-free fetal DNA in maternal circulation.

Liao, Gary J W / Gronowski, Ann M / Zhao, Zhen

Clinica chimica acta; international journal of clinical chemistry

2014 Volume 428, Page(s) 44–50

Abstract: The identification of cell-free fetal DNA (cffDNA) in maternal circulation has made non-invasive prenatal testing (NIPT) possible. Maternal plasma cell free DNA is a mixture of maternal and fetal DNA, of which, fetal DNA represents a minor population in ... ...

Abstract	The identification of cell-free fetal DNA (cffDNA) in maternal circulation has made non-invasive prenatal testing (NIPT) possible. Maternal plasma cell free DNA is a mixture of maternal and fetal DNA, of which, fetal DNA represents a minor population in maternal plasma. Therefore, methods with high sensitivity and precision are required to detect and differentiate fetal DNA from the large background of maternal DNA. In recent years, technical advances in the molecular analysis of fetal DNA (e.g., digital PCR and massively parallel sequencing (MPS)) has enabled the successful implementation of noninvasive testing into clinical practice, such as fetal sex assessment, RhD genotyping, and fetal chromosomal aneuploidy detection.With the ability to decipher the entire fetal genome from maternal plasma DNA, we foresee that an increased number of non-invasive prenatal tests will be available for detecting many single-gene disorders in the near future. This review briefly summarizes the technical aspects of the NIPT and application of NIPT in clinical practice.
MeSH term(s)	DNA/blood ; DNA/genetics ; Female ; Fetus/cytology ; Fetus/metabolism ; Humans ; Maternal-Fetal Exchange ; Polymerase Chain Reaction ; Pregnancy ; Prenatal Diagnosis/methods ; Sequence Analysis, DNA
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2014-01-20
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	80228-1
ISSN	1873-3492 ; 0009-8981
ISSN (online)	1873-3492
ISSN	0009-8981
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Article ; Online: Non-invasive prenatal testing using cell-free fetal DNA in maternal circulation.

Liao, Gary J W / Gronowski, Ann M / Zhao, Zhen

Clinica chimica acta; international journal of clinical chemistry

2013

Abstract	The identification of cell-free fetal DNA (cffDNA) in maternal circulation has made non-invasive prenatal testing (NIPT) possible. Maternal plasma cell free DNA is a mixture of maternal and fetal DNA, of which, fetal DNA represents a minor population in maternal plasma. Therefore, methods with high sensitivity and precision are required to detect and differentiate fetal DNA from the large background of maternal DNA. In recent years, technical advances in the molecular analysis of fetal DNA (e.g., digital PCR and massively parallel sequencing (MPS)) has enabled the successful implementation of noninvasive testing into clinical practice, such as fetal sex assessment, RhD genotyping, and fetal chromosomal aneuploidy detection. With the ability to decipher the entire fetal genome from maternal plasma DNA, we foresee that an increased number of non-invasive prenatal tests will be available for detecting many single-gene disorders in the near future. This review briefly summarizes the technical aspects of the NIPT and application of NIPT in clinical practice.
Language	English
Publishing date	2013-10-25
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80228-1
ISSN	1873-3492 ; 0009-8981
ISSN (online)	1873-3492
ISSN	0009-8981
DOI	10.1016/j.cca.2013.10.007
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Article ; Online: Prenatal assessment of fetal chromosomal and genetic disorders through maternal plasma DNA analysis.

Liao, Gary J W / Chiu, Rossa W K / Lo, Y M Dennis

Pathology

2012 Volume 44, Issue 2, Page(s) 69–72

Abstract: The existence of cell free DNA derived from the fetus in the plasma of pregnant women was first demonstrated in 1997. This discovery offered the possibility of non-invasive sampling of fetal genetic material simply through the collection of a maternal ... ...

Abstract	The existence of cell free DNA derived from the fetus in the plasma of pregnant women was first demonstrated in 1997. This discovery offered the possibility of non-invasive sampling of fetal genetic material simply through the collection of a maternal blood sample. Such cell free fetal DNA molecules in the maternal circulation have subsequently been shown to originate from the placenta and could be detected from about 7 weeks of gestation. It has been shown that cell free fetal DNA analysis could offer highly accurate assessment of fetal genotype and chromosomal makeup for some applications. Thus, cell free fetal DNA analysis has been incorporated as a part of prenatal screening programs for the prenatal management of sex-linked and sex-associated diseases, rhesus D incompatibility as well as the prenatal detection of Down's syndrome.Cell free fetal DNA analysis may lead to a change in the way prenatal assessments are made.
MeSH term(s)	Chromosome Disorders/blood ; Chromosome Disorders/diagnosis ; DNA/analysis ; DNA/blood ; Female ; Humans ; Pregnancy ; Prenatal Diagnosis/methods
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2012-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	7085-3
ISSN	1465-3931 ; 0031-3025
ISSN (online)	1465-3931
ISSN	0031-3025
DOI	10.1097/PAT.0b013e32834e8e29
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Article ; Online: Noninvasive prenatal diagnosis of fetal trisomy 21 by allelic ratio analysis using targeted massively parallel sequencing of maternal plasma DNA.

Liao, Gary J W / Chan, K C Allen / Jiang, Peiyong / Sun, Hao / Leung, Tak Y / Chiu, Rossa W K / Lo, Y M Dennis

PloS one

2012 Volume 7, Issue 5, Page(s) e38154

Abstract: Background: Plasma DNA obtained from a pregnant woman contains a mixture of maternal and fetal DNA. The fetal DNA proportion in maternal plasma is relatively consistent as determined using polymorphic genetic markers across different chromosomes in ... ...

Abstract	Background: Plasma DNA obtained from a pregnant woman contains a mixture of maternal and fetal DNA. The fetal DNA proportion in maternal plasma is relatively consistent as determined using polymorphic genetic markers across different chromosomes in euploid pregnancies. For aneuploid pregnancies, the observed fetal DNA proportion measured using polymorphic genetic markers for the aneuploid chromosome would be perturbed. In this study, we investigated the feasibility of analyzing single nucleotide polymorphisms using targeted massively parallel sequencing to detect such perturbations in mothers carrying trisomy 21 fetuses. Methodology/principal findings: DNA was extracted from plasma samples collected from fourteen pregnant women carrying singleton fetuses. Hybridization-based targeted sequencing was used to enrich 2 906 single nucleotide polymorphism loci on chr7, chr13, chr18 and chr21. Plasma DNA libraries with and without target enrichment were analyzed by massively parallel sequencing. Genomic DNA samples of both the mother and fetus for each case were genotyped by single nucleotide polymorphism microarray analysis. For the targeted regions, the mean sequencing depth of the enriched samples was 225-fold higher than that of the non-enriched samples. From the targeted sequencing data, the ratio between fetus-specific and shared alleles increased by approximately 2-fold on chr21 in the paternally-derived trisomy 21 case. In comparison, the ratio is decreased by approximately 11% on chr21 in the maternally-derived trisomy 21 cases but with much overlap with the ratio of the euploid cases. Computer simulation revealed the relationship between the fetal DNA proportion, the number of informative alleles and the depth of sequencing. Conclusions/significance: Targeted massively parallel sequencing of single nucleotide polymorphism loci in maternal plasma DNA is a potential approach for trisomy 21 detection. However, the method appears to be less robust than approaches using non-polymorphism-based counting of sequence tags in plasma.
MeSH term(s)	Alleles ; Computer Simulation ; DNA/blood ; DNA/genetics ; Down Syndrome/diagnosis ; Down Syndrome/genetics ; Female ; Fetus/metabolism ; High-Throughput Screening Assays ; Humans ; Mothers ; Polymorphism, Single Nucleotide/genetics ; Pregnancy ; Prenatal Diagnosis/methods ; Sequence Analysis, DNA
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2012-05-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0038154
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Noninvasive prenatal diagnosis of monogenic diseases by targeted massively parallel sequencing of maternal plasma: application to β-thalassemia.

Lam, Kwan-Wood G / Jiang, Peiyong / Liao, Gary J W / Chan, K C Allen / Leung, Tak Y / Chiu, Rossa W K / Lo, Y M Dennis

Clinical chemistry

2012 Volume 58, Issue 10, Page(s) 1467–1475

Abstract: Background: A genomewide genetic and mutational profile of a fetus was recently determined via deep sequencing of maternal plasma DNA. This technology could have important applications for noninvasive prenatal diagnosis (NIPD) of many monogenic diseases. ...

Abstract	Background: A genomewide genetic and mutational profile of a fetus was recently determined via deep sequencing of maternal plasma DNA. This technology could have important applications for noninvasive prenatal diagnosis (NIPD) of many monogenic diseases. Relative haplotype dosage (RHDO) analysis, a core step of this procedure, would allow one to elucidate the maternally inherited half of the fetal genome. For clinical applications, the cost and complexity of data analysis might be reduced via targeted application of this approach to selected genomic regions containing disease-causing genes. There is thus a need to explore the feasibility of performing RHDO analysis in a targeted manner. Methods: We performed target enrichment by using solution-phase hybridization followed by massively parallel sequencing of the β-globin gene region in 2 families undergoing prenatal diagnosis for β-thalassemia. We used digital PCR strategies to physically deduce parental haplotypes. Finally, we performed RHDO analysis with target-enriched sequencing data and parental haplotypes to reveal the β-thalassemic status for the fetuses. Results: A mean sequencing depth of 206-fold was achieved in the β-globin gene region by targeted sequencing of maternal plasma DNA. RHDO analysis was successful for the sequencing data obtained from the target-enriched samples, including a region in one of the families in which the parents had similar haplotype structures. Data analysis revealed that both fetuses were heterozygous carriers of β-thalassemia. Conclusions: Targeted sequencing of maternal plasma DNA for NIPD of monogenic diseases is feasible.
MeSH term(s)	Algorithms ; DNA/blood ; DNA/genetics ; Female ; Haplotypes ; Heterozygote ; Humans ; Male ; Microarray Analysis ; Pedigree ; Plasma ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Pregnancy ; Prenatal Diagnosis/methods ; Sequence Analysis/methods ; beta-Globins/genetics ; beta-Thalassemia/diagnosis ; beta-Thalassemia/genetics
Chemical Substances	beta-Globins ; DNA (9007-49-2)
Language	English
Publishing date	2012-08-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1373/clinchem.2012.189589
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Article ; Online: Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing.

Chan, Rebecca W Y / Jiang, Peiyong / Peng, Xianlu / Tam, Lai-Shan / Liao, Gary J W / Li, Edmund K M / Wong, Priscilla C H / Sun, Hao / Chan, K C Allen / Chiu, Rossa W K / Lo, Y M Dennis

Proceedings of the National Academy of Sciences of the United States of America

2014 Volume 111, Issue 49, Page(s) E5302–11

Abstract: We performed a high-resolution analysis of the biological characteristics of plasma DNA in systemic lupus erythematosus (SLE) patients using massively parallel genomic and methylomic sequencing. A number of plasma DNA abnormalities were found. First, ... ...

Abstract	We performed a high-resolution analysis of the biological characteristics of plasma DNA in systemic lupus erythematosus (SLE) patients using massively parallel genomic and methylomic sequencing. A number of plasma DNA abnormalities were found. First, aberrations in measured genomic representations (MGRs) were identified in the plasma DNA of SLE patients. The extent of the aberrations in MGRs correlated with anti-double-stranded DNA (anti-dsDNA) antibody level. Second, the plasma DNA of active SLE patients exhibited skewed molecular size-distribution profiles with a significantly increased proportion of short DNA fragments. The extent of plasma DNA shortening in SLE patients correlated with the SLE disease activity index (SLEDAI) and anti-dsDNA antibody level. Third, the plasma DNA of active SLE patients showed decreased methylation densities. The extent of hypomethylation correlated with SLEDAI and anti-dsDNA antibody level. To explore the impact of anti-dsDNA antibody on plasma DNA in SLE, a column-based protein G capture approach was used to fractionate the IgG-bound and non-IgG-bound DNA in plasma. Compared with healthy individuals, SLE patients had higher concentrations of IgG-bound DNA in plasma. More IgG binding occurs at genomic locations showing increased MGRs. Furthermore, the IgG-bound plasma DNA was shorter in size and more hypomethylated than the non-IgG-bound plasma DNA. These observations have enhanced our understanding of the spectrum of plasma DNA aberrations in SLE and may provide new molecular markers for SLE. Our results also suggest that caution should be exercised when interpreting plasma DNA-based noninvasive prenatal testing and cancer testing conducted for SLE patients.
MeSH term(s)	Adult ; Aged ; Biomarkers/blood ; Chromosome Aberrations ; CpG Islands ; DNA/blood ; DNA Methylation ; Epigenesis, Genetic ; Female ; Gene Expression Regulation ; Gene Library ; Genome, Human ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoglobulin G/analysis ; Lupus Erythematosus, Systemic/blood ; Lupus Erythematosus, Systemic/genetics ; Middle Aged ; Sequence Analysis, DNA
Chemical Substances	Biomarkers ; Immunoglobulin G ; DNA (9007-49-2)
Language	English
Publishing date	2014-12-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1421126111
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Article ; Online: Noninvasive prenatal diagnosis of fetal trisomy 21 by allelic ratio analysis using targeted massively parallel sequencing of maternal plasma DNA.

Gary J W Liao / K C Allen Chan / Peiyong Jiang / Hao Sun / Tak Y Leung / Rossa W K Chiu / Y M Dennis Lo

PLoS ONE, Vol 7, Iss 5, p e

2012 Volume 38154

Abstract: BACKGROUND: Plasma DNA obtained from a pregnant woman contains a mixture of maternal and fetal DNA. The fetal DNA proportion in maternal plasma is relatively consistent as determined using polymorphic genetic markers across different chromosomes in ... ...

Abstract	BACKGROUND: Plasma DNA obtained from a pregnant woman contains a mixture of maternal and fetal DNA. The fetal DNA proportion in maternal plasma is relatively consistent as determined using polymorphic genetic markers across different chromosomes in euploid pregnancies. For aneuploid pregnancies, the observed fetal DNA proportion measured using polymorphic genetic markers for the aneuploid chromosome would be perturbed. In this study, we investigated the feasibility of analyzing single nucleotide polymorphisms using targeted massively parallel sequencing to detect such perturbations in mothers carrying trisomy 21 fetuses. METHODOLOGY/PRINCIPAL FINDINGS: DNA was extracted from plasma samples collected from fourteen pregnant women carrying singleton fetuses. Hybridization-based targeted sequencing was used to enrich 2 906 single nucleotide polymorphism loci on chr7, chr13, chr18 and chr21. Plasma DNA libraries with and without target enrichment were analyzed by massively parallel sequencing. Genomic DNA samples of both the mother and fetus for each case were genotyped by single nucleotide polymorphism microarray analysis. For the targeted regions, the mean sequencing depth of the enriched samples was 225-fold higher than that of the non-enriched samples. From the targeted sequencing data, the ratio between fetus-specific and shared alleles increased by approximately 2-fold on chr21 in the paternally-derived trisomy 21 case. In comparison, the ratio is decreased by approximately 11% on chr21 in the maternally-derived trisomy 21 cases but with much overlap with the ratio of the euploid cases. Computer simulation revealed the relationship between the fetal DNA proportion, the number of informative alleles and the depth of sequencing. CONCLUSIONS/SIGNIFICANCE: Targeted massively parallel sequencing of single nucleotide polymorphism loci in maternal plasma DNA is a potential approach for trisomy 21 detection. However, the method appears to be less robust than approaches using non-polymorphism-based counting of sequence ...
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Noninvasive twin zygosity assessment and aneuploidy detection by maternal plasma DNA sequencing.

Leung, Tak Y / Qu, James Z Z / Liao, Gary J W / Jiang, Peiyong / Cheng, Yvonne K Y / Chan, K C Allen / Chiu, Rossa W K / Lo, Y M Dennis

Prenatal diagnosis

2013 Volume 33, Issue 7, Page(s) 675–681

Abstract: Objective: This study aimed to provide an individualized assessment of fetal trisomy 21 and trisomy 18 status for twin pregnancies by maternal plasma DNA sequencing.: Method: Massively parallel sequencing was performed on the plasma/serum DNA ... ...

Abstract	Objective: This study aimed to provide an individualized assessment of fetal trisomy 21 and trisomy 18 status for twin pregnancies by maternal plasma DNA sequencing. Method: Massively parallel sequencing was performed on the plasma/serum DNA libraries of eight twin pregnancies and 11 singleton pregnancies. The apparent fractional fetal DNA concentrations between genomic regions were assessed to determine the zygosities of the twin pregnancies and to calculate the fetal DNA concentrations of each individual member of dizygotic twin pairs. Z-scores were determined for the detection of trisomy 18 and trisomy 21. Results: Circulating DNA sequencing showed elevated chromosome 21 representation in one set of twins and elevated chromosome 18 representation in another pair of twins. Apparent fractional fetal DNA concentration analysis revealed both sets of twins to be dizygotic. The fractional fetal DNA concentrations for each individual fetus of the dizygotic twin pregnancies were determined. Incorporating the information about the fetal DNA fraction, we ascertained that each fetus contributed adequate amounts of DNA into the maternal circulation for the aneuploidy test result to be interpreted with confidence. Conclusion: Noninvasive prenatal assessment of fetal chromosomal aneuploidy for twin pregnancies can be achieved with the use of massively parallel sequencing of cell-free DNA in maternal blood.
MeSH term(s)	Chromosomes, Human, Pair 18/genetics ; DNA/blood ; DNA/chemistry ; Diseases in Twins/genetics ; Down Syndrome/genetics ; Female ; Fetus/chemistry ; Genetic Testing/methods ; Gestational Age ; High-Throughput Nucleotide Sequencing ; Humans ; Pregnancy ; Pregnancy, Twin ; Prenatal Diagnosis/methods ; Sequence Analysis, DNA ; Trisomy/genetics ; Trisomy 18 Syndrome ; Twins/genetics ; Twins, Dizygotic/genetics
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2013-04-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	82031-3
ISSN	1097-0223 ; 0197-3851
ISSN (online)	1097-0223
ISSN	0197-3851
DOI	10.1002/pd.4132
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Article ; Online: Noninvasive prenatal determination of twin zygosity by maternal plasma DNA analysis.

Qu, James Z Z / Leung, Tak Y / Jiang, Peiyong / Liao, Gary J W / Cheng, Yvonne K Y / Sun, Hao / Chiu, Rossa W K / Chan, K C Allen / Lo, Y M Dennis

Clinical chemistry

2012 Volume 59, Issue 2, Page(s) 427–435

Abstract: Background: The current methods for distinguishing the zygosities of twins include ultrasound scanning, which is nondefinitive, and amniocentesis, which is invasive. We explored the use of massively parallel sequencing of maternal plasma DNA for the ... ...

Abstract	Background: The current methods for distinguishing the zygosities of twins include ultrasound scanning, which is nondefinitive, and amniocentesis, which is invasive. We explored the use of massively parallel sequencing of maternal plasma DNA for the noninvasive prenatal assessment of the zygosities of twin pregnancies. Methods: Plasma DNA was extracted from blood collected from 8 women pregnant with twins. Target enrichment and massively parallel sequencing were performed for each plasma DNA library. Apparent fractional fetal DNA concentrations were calculated for multiple genomic regions by determining the ratio of minor to major alleles among single-nucleotide polymorphism sites. Variations in the apparent fractional fetal DNA concentrations between genomic regions were used to infer whether individual fetuses in a twin pair were genotypically different and hence dizygotic. Results: The extent of the variation in the apparent fractional fetal DNA concentration across chromosomes was 0.82-1.35 SDs for monozygotic twin pregnancies and 2.42-4.80 SDs for dizygotic twin pregnancies. The proportions of apparent fractional fetal DNA concentration values that deviated beyond the range expected for stochastic variation were 0.00%-1.93% for monozygotic twin pregnancies and 36.2%-78.1% for dizygotic twin pregnancies. After identifying a pair of twins as likely dizygotic, the method also allowed determination of the fractional fetal DNA concentrations contributed by the individual fetuses of a dizygotic twin pair. Conclusions: Noninvasive prenatal determination of twin zygosity by maternal plasma DNA sequencing is feasible. It is also possible to determine the relative fractional fetal DNA concentrations for each fetus for dizygotic twin pregnancies.
MeSH term(s)	DNA/blood ; DNA/genetics ; Female ; Gene Library ; Humans ; Maternal Serum Screening Tests ; Polymorphism, Single Nucleotide ; Pregnancy ; Prenatal Diagnosis/methods ; Sequence Analysis, DNA/methods ; Twins, Dizygotic/genetics ; Twins, Monozygotic/genetics
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2012-10-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1373/clinchem.2012.194068
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