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Article ; Online: Improving enrichment of circulating fetal DNA for genetic testing: size fractionation followed by whole gene amplification.

Jorgez, Carolina J / Bischoff, Farideh Z

2009 Volume 25, Issue 3, Page(s) 314–319

Abstract: Objective: Among the pitfalls of using cell-free fetal DNA in plasma for prenatal diagnosis is quality of the recovered DNA fragments and concomitant presence of maternal DNA (>95%). Our objective is to provide alternative methods for achieving ... ...

Abstract	Objective: Among the pitfalls of using cell-free fetal DNA in plasma for prenatal diagnosis is quality of the recovered DNA fragments and concomitant presence of maternal DNA (>95%). Our objective is to provide alternative methods for achieving enrichment and high-quality fetal DNA from plasma. Methods: Cell-free DNA from 31 pregnant women and 18 controls (10 males and 8 females) were size separated using agarose gel electrophoresis. DNA fragments of 100-300, 500-700 and 1,500-2,000 bp were excised and extracted, followed by whole genome amplification (WGA) of recovered fragments. Levels of beta-globin and DYS1 were measured. Results: Distribution of beta-globin size fragments was similar among pregnant women and controls. Among control male cases, distribution of size fragments was the same for both beta-globin and DYS1. Among maternal cases confirmed to be male, the smallest size fragment (100-300 bp) accounted for nearly 50% (39.76 +/- 17.55%) of the recovered DYS1-DNA (fetal) and only 10% (10.40 +/- 6.49%) of beta-globin (total) DNA. After WGA of plasma fragments from pregnant women, DYS1 sequence amplification was best observed when using the 100-300 bp fragments as template. Conclusions: Combination of electrophoresis for size separation and WGA led to enriched fetal DNA from plasma. This novel combination of strategies is more likely to permit universal clinical applications of cell-free fetal DNA.
MeSH term(s)	DNA/blood ; DNA/chemistry ; DNA/isolation & purification ; Electrophoresis, Agar Gel ; Female ; Genetic Testing ; Humans ; Male ; Nucleic Acid Amplification Techniques ; Pregnancy ; Prenatal Diagnosis/methods
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2009-09-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1066460-9
ISSN	1421-9964 ; 1015-3837
ISSN (online)	1421-9964
ISSN	1015-3837
DOI	10.1159/000235877
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Article ; Online: Stability of placental RNA using dried maternal blood spots.

Jorgez, Carolina J / Bischoff, Farideh Z

Reproductive biomedicine online

2008 Volume 17, Issue 5, Page(s) 716–721

Abstract: Having demonstrated successful recovery and detection of placental transcripts from dried blood spots (DBS), various preanalytical conditions were examined to determine optimal handling of samples. The role of several factors was explored, including ... ...

Abstract	Having demonstrated successful recovery and detection of placental transcripts from dried blood spots (DBS), various preanalytical conditions were examined to determine optimal handling of samples. The role of several factors was explored, including temperature (4 degrees C versus 25 degrees C), processing time (24 h to 8 weeks), and addition of preservatives (RNA later and formalin) that may interfere with stability and detection of placental transcripts in DBS. mRNA transcripts encoding human glyceraldehyde-3-phosphate dehydrogenase (GAPDH; internal control) and beta-human chorionic gonadotrophin (beta HCG; placental) were analysed by real-time-polymerase chain reaction using DBS from 23 pregnant women. GAPDH and beta HCG transcripts were detected in all samples 24 h after collection. Although treatment of blood with RNA later did not affect RNA recovery, formalin treatment negatively affected RNA recovery from DBS. Temperature did not have a significant effect on levels of either transcript. Storage time caused a significant decrease in GAPDH after 4 weeks (P = 0.014) and beta HCG after 1 week (P = 0.007). Decrease of beta HCG levels after 1 week followed by steady detectable levels for up to 4 weeks suggests two populations of circulating placental transcript exist, a population susceptible to degradation in blood versus a more stable form. Therefore, defining proper parameters for collection and storage of DBS further reinforces reliable analysis of target sequences for clinical testing.
MeSH term(s)	Chorionic Gonadotropin, beta Subunit, Human/genetics ; Female ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics ; Humans ; Placenta/metabolism ; Polymerase Chain Reaction ; Pregnancy ; RNA Stability ; RNA, Messenger/blood ; RNA, Messenger/genetics ; RNA, Messenger/isolation & purification
Chemical Substances	Chorionic Gonadotropin, beta Subunit, Human ; RNA, Messenger ; Glyceraldehyde-3-Phosphate Dehydrogenases (EC 1.2.1.-)
Language	English
Publishing date	2008-11-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2113823-0
ISSN	1472-6491 ; 1472-6483
ISSN (online)	1472-6491
ISSN	1472-6483
DOI	10.1016/s1472-6483(10)60321-5
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Zs.A 5792: Show issues

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Article ; Online: Endocervical fetal trophoblast for prenatal genetic diagnosis.

Bischoff, Farideh Z / Simpson, Joe Leigh

Current opinion in obstetrics & gynecology

2006 Volume 18, Issue 2, Page(s) 216–220

Abstract: Purpose of review: For over a decade, methods of first-trimester, noninvasive prenatal genetic diagnosis have been actively pursued by many investigators. Isolation of fetal trophoblast from endocervical specimens remains an attractive approach, given ... ...

Abstract	Purpose of review: For over a decade, methods of first-trimester, noninvasive prenatal genetic diagnosis have been actively pursued by many investigators. Isolation of fetal trophoblast from endocervical specimens remains an attractive approach, given the greater numbers of fetal cells than in maternal blood and the better potential for fetal-cell identification based on markers specific for a single cell type (trophoblasts). Recent findings: Current studies demonstrate feasibility in identification and molecular analysis of fetal trophoblast cells for prenatal genetic testing. Sampling methods involving lavage, cytobrush, or aspiration of cervical specimens, however, have limitations in the recovery of trophoblasts. Summary: Clinical applications await further systematic studies to determine safety and accuracy in recovery.
MeSH term(s)	Cervix Uteri/cytology ; Female ; Genetic Testing/methods ; Humans ; In Situ Hybridization, Fluorescence ; Oligonucleotide Array Sequence Analysis ; Pregnancy ; Prenatal Diagnosis/methods ; Specimen Handling/instrumentation ; Trophoblasts/cytology ; Vaginal Smears/methods
Language	English
Publishing date	2006-04
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1049382-7
ISSN	1473-656X ; 1040-872X
ISSN (online)	1473-656X
ISSN	1040-872X
DOI	10.1097/01.gco.0000192985.22718.17
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Zs.A 3048: Show issues

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Article: Improving Enrichment of Circulating Fetal DNA for Genetic Testing: Size Fractionation Followed by Whole Gene Amplification

Jorgez, Carolina J. / Bischoff, Farideh Z.

Fetal Diagnosis and Therapy

2009 Volume 25, Issue 3, Page(s) 314–319

Institution	Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Tex., and Biocept Inc., San Diego, Calif., USA
Abstract	Objective: Among the pitfalls of using cell-free fetal DNA in plasma for prenatal diagnosis is quality of the recovered DNA fragments and concomitant presence of maternal DNA (>95%). Our objective is to provide alternative methods for achieving enrichment and high-quality fetal DNA from plasma. Methods: Cell-free DNA from 31 pregnant women and 18 controls (10 males and 8 females) were size separated using agarose gel electrophoresis. DNA fragments of 100–300, 500–700 and 1,500–2,000 bp were excised and extracted, followed by whole genome amplification (WGA) of recovered fragments. Levels of β-globin and DYS1 were measured. Results: Distribution of β-globin size fragments was similar among pregnant women and controls. Among control male cases, distribution of size fragments was the same for both β-globin and DYS1. Among maternal cases confirmed to be male, the smallest size fragment (100–300 bp) accounted for nearly 50% (39.76 ± 17.55%) of the recovered DYS1-DNA (fetal) and only 10% (10.40 ± 6.49%) of β-globin (total) DNA. After WGA of plasma fragments from pregnant women, DYS1 sequence amplification was best observed when using the 100–300 bp fragments as template. Conclusions: Combination of electrophoresis for size separation and WGA led to enriched fetal DNA from plasma. This novel combination of strategies is more likely to permit universal clinical applications of cell-free fetal DNA.
Keywords	Cell-free fetal DNA ; Real-time PCR ; DYS1 ; Whole genome amplification ; β-Globin ; Gel extraction
Language	English
Publishing date	2009-09-22
Publisher	S. Karger AG
Publishing place	Basel, Switzerland
Document type	Article
Note	Original Paper
ZDB-ID	1066460-9
ISSN	1421-9964 ; 1015-3837
ISSN (online)	1421-9964
ISSN	1015-3837
DOI	10.1159/000235877
Database	Karger publisher's database

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Article: Heritability and molecular genetic studies of endometriosis.

Simpson, Joe Leigh / Bischoff, Farideh Z

Annals of the New York Academy of Sciences

2002 Volume 955, Page(s) 239–51; discussion 293–5, 396–406

Abstract: Endometriosis is well established as a condition showing heritable tendencies. Polygenic/multifactorial etiology appears far more likely to be the etiology than Mendelian inheritance. The current task is to determine the number and location of genes ... ...

Abstract	Endometriosis is well established as a condition showing heritable tendencies. Polygenic/multifactorial etiology appears far more likely to be the etiology than Mendelian inheritance. The current task is to determine the number and location of genes responsible for endometriosis. This paper shall review the basis for concluding that endometriosis is a genetic disorder of polygenic/multifactorial inheritance and outline selected strategies for identifying the number and location of causative genes. It shall also illustrate our approach to testing the hypothesis that endometriosis bears similarity to neoplasia and, hence, is a multistep phenomenon of clonal origin.
MeSH term(s)	DNA/genetics ; Endometriosis/genetics ; Female ; Gene Expression ; Genetic Linkage ; Genetic Predisposition to Disease ; Humans ; Oncogenes ; Quantitative Trait, Heritable
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2002-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ; Review
ZDB-ID	211003-9
ISSN	1749-6632 ; 0077-8923
ISSN (online)	1749-6632
ISSN	0077-8923
DOI	10.1111/j.1749-6632.2002.tb02785.x
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Article ; Online: Efficient capture of circulating tumor cells with a novel immunocytochemical microfluidic device.

Nora Dickson, Mary / Tsinberg, Pavel / Tang, Zhongliang / Bischoff, Farideh Z / Wilson, Timothy / Leonard, Edward F

Biomicrofluidics

2011 Volume 5, Issue 3, Page(s) 34119–3411915

Abstract: Ability to perform cytogenetic interrogations on circulating tumor cells (CTCs) from the blood of cancer patients is vital for progressing toward targeted, individualized treatments. CTCs are rare compared to normal (bystander) blood cells, found in ... ...

Abstract	Ability to perform cytogenetic interrogations on circulating tumor cells (CTCs) from the blood of cancer patients is vital for progressing toward targeted, individualized treatments. CTCs are rare compared to normal (bystander) blood cells, found in ratios as low as 1:10(9). The most successful isolation techniques have been immunocytochemical technologies that label CTCs for separation based on unique surface antigens that distinguish them from normal bystander cells. The method discussed here utilizes biotin-tagged antibodies that bind selectively to CTCs. The antibodies are introduced into a suspension of blood cells intending that only CTCs will display surface biotin molecules. Next, the cell suspension is passed through a microfluidic channel that contains about 9000 transverse, streptavidin coated posts. A CTC making contact with a post has the opportunity to engage in a biotin-streptavidin reaction that immobilizes the cell. Bystander blood cells remain in suspension and pass through the channel. The goal of the present study is to establish the technical performance of these channels as a function of antigen density and operating conditions, especially flow rate. At 18 μL/min, over 70% of cells are captured at antigen densities greater than 30 000 sites/cell while 50% of cells are captured at antigen densities greater than 10 000. It is found that lower flow rates lead to decreasing cell capture probabilities, indicating that some streamlines develop which are never close enough to a post to allow cell-post contact. Future modeling and streamline studies using computational fluid dynamics software could aid in optimization of channel performance for capture of rare cells.
Language	English
Publishing date	2011-08-22
Publishing country	United States
Document type	Journal Article
ISSN	1932-1058
ISSN (online)	1932-1058
DOI	10.1063/1.3623748
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Article: Re: Familial cryptic translocation (2;17) ascertained through recurrent spontaneous abortions: Bruyere H, Rajcan-Separovic E, Doyle J, Pantzar T, Langlois S.

Bacino, Carlos A / Bischoff, Farideh Z / Shaffer, Lisa G

American journal of medical genetics. Part A

2004 Volume 130A, Issue 4, Page(s) 439–440

MeSH term(s)	Abortion, Habitual/genetics ; Abortion, Habitual/pathology ; Chromosomes, Human, Pair 17/genetics ; Chromosomes, Human, Pair 2/genetics ; Female ; Humans ; In Situ Hybridization, Fluorescence ; Iran ; Pedigree ; Translocation, Genetic
Language	English
Publishing date	2004-09-23
Publishing country	United States
Document type	Comment ; Letter
ZDB-ID	2108614-X
ISSN	1552-4825
ISSN	1552-4825
DOI	10.1002/ajmg.a.30219
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Article: Recovery and amplification of placental RNA from dried maternal blood spots: utility for non-invasive prenatal diagnosis.

Jorgez, Carolina J / Simpson, Joe Leigh / Bischoff, Farideh Z

Reproductive biomedicine online

2006 Volume 13, Issue 4, Page(s) 558–561

Abstract: Methods utilizing circulating cell-free RNA in plasma have clinical applications for cancer and prenatal genetic analysis. Given these potential roles, the feasibility of detecting placental specific RNA in dried maternal blood spots after storage at ... ...

Abstract	Methods utilizing circulating cell-free RNA in plasma have clinical applications for cancer and prenatal genetic analysis. Given these potential roles, the feasibility of detecting placental specific RNA in dried maternal blood spots after storage at room temperature for varying lengths of time was investigated. Using real-time polymerase chain reaction (PCR), positive amplification of placental-specific beta-human chorionic gonadotrophin transcripts was demonstrated in nine of 11 dried blood samples from first and second trimester pregnancies stored at room temperature for up to 4 weeks. This work demonstrates feasibility in isolation and amplification of placental mRNA using dried maternal blood spots. With the development of fetal and placental RNA markers, this approach would allow simplified collection, transport, and storage of samples for prenatal genetic diagnosis and pregnancy related complications.
MeSH term(s)	Chorionic Gonadotropin, beta Subunit, Human/blood ; Chorionic Gonadotropin, beta Subunit, Human/genetics ; Female ; Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)/genetics ; Humans ; Nucleic Acid Amplification Techniques/methods ; Placenta/physiology ; Pregnancy ; Pregnancy Trimester, First ; Pregnancy Trimester, Second ; Prenatal Diagnosis/methods ; RNA/analysis ; RNA/blood ; RNA/isolation & purification
Chemical Substances	Chorionic Gonadotropin, beta Subunit, Human ; RNA (63231-63-0) ; Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+) (EC 1.2.1.9)
Language	English
Publishing date	2006-08-02
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2113823-0
ISSN	1472-6491 ; 1472-6483
ISSN (online)	1472-6491
ISSN	1472-6483
DOI	10.1016/s1472-6483(10)60645-1
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Zs.A 5792: Show issues

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Article: Cell-free fetal DNA in maternal blood: kinetics, source and structure.

Bischoff, Farideh Z / Lewis, Dorothy E / Simpson, Joe Leigh

Human reproduction update

2005 Volume 11, Issue 1, Page(s) 59–67

Abstract: The kinetics and structure of cell-free fetal DNA in maternal plasma is currently under investigation. Plasma fetal DNA seems quite stable albeit cleared rapidly following birth, suggesting continuous fetal DNA release into the maternal circulation ... ...

Abstract	The kinetics and structure of cell-free fetal DNA in maternal plasma is currently under investigation. Plasma fetal DNA seems quite stable albeit cleared rapidly following birth, suggesting continuous fetal DNA release into the maternal circulation during pregnancy. However, to understand better the kinetics of circulating DNA, studies to determine the biological (structural) form in which fetal and maternal DNA exist and the mechanisms underlying variation in plasma are warranted to ensure quantitative diagnostic reliability. It is likely that circulating fetal DNA is released from fetal and/or placental cells undergoing apoptosis. Thus, the majority of fetal DNA is proposed to circulate in membrane-bound vesicles (apoptotic bodies). This review summarizes the latest reports in this field.
MeSH term(s)	Aneuploidy ; Apoptosis/genetics ; Cell-Free System ; Chromosomes, Human, Y/genetics ; DNA/blood ; DNA/isolation & purification ; Female ; Fetal Blood/cytology ; Fetal Blood/physiology ; Fetus/cytology ; Humans ; Kinetics ; Male ; Maternal-Fetal Exchange ; Microscopy, Electron, Transmission ; Mothers ; Neoplasms/blood ; Neoplasms/genetics ; Placenta/physiology ; Polymerase Chain Reaction/methods ; Pregnancy ; Pregnancy Complications/diagnosis ; Prenatal Diagnosis/methods
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2005-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S. ; Review
ZDB-ID	1286738-x
ISSN	1460-2369 ; 1355-4786
ISSN (online)	1460-2369
ISSN	1355-4786
DOI	10.1093/humupd/dmh053
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Zs.A 4378: Show issues

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Article: Somatic DNA alterations in endometriosis: high frequency of chromosome 17 and p53 loss in late-stage endometriosis.

Bischoff, Farideh Z / Heard, Michael / Simpson, Joe Leigh

Journal of reproductive immunology

2003 Volume 55, Issue 1-2, Page(s) 49–64

Abstract: Problem: Genetic predisposition to endometriosis is well established, but the gene(s) involved largely remain unknown. Although endometriosis is considered a benign disease, it displays several features similar to malignancy: altered morphology, ... ...

Abstract	Problem: Genetic predisposition to endometriosis is well established, but the gene(s) involved largely remain unknown. Although endometriosis is considered a benign disease, it displays several features similar to malignancy: altered morphology, disregulated growth, invasion. We hypothesize endometriosis arises as result of somatic DNA alterations occurring in a multi-step process, analogous to origin of neoplasia. Since chromosome 17 and TP53 tumor suppressor gene (TSG) alterations occur frequently in premalignant and malignant tissues, including endometrial and ovarian epithelial carcinomas, we sought to determine if similar somatic changes occur in late stage endometriosis. Method of study: To determine the frequencies of monosomy for chromosome 17, as well as for perturbations of p53 and other loci on 17, two different approaches were used. Fluorescent in situ hybridization (FISH) analysis was used to detect monosomy for the 17 centromere and for the p53 locus. For FISH, archival tissue (n=6) and fresh endometriotic touch preparations were prepared from women (n=8) undergoing extirpation of advanced stage endometriosis. Direct-labeled probes specific for p53 (17p13.1) and for the chromosome 17 alpha-satellite centromere region (1711.1-q11.1) were used to compare single glandular and stromal cells from endometriosis and normal tissue. DNA analysis of polymorphic DNA loci were used to detect loss of heterozygosity (LoH) for other loci on 17. We assessed matched endometriotic and normal DNA (peripheral blood) from women with severe/late stage disease (n=15), studying these dinucleotide markers: HGH (located on 17q22-24), D17S250 (17q11.2-q12) and CHRNB1 (17p13.1). Results: Loss of the chromosome 17 centromere (monosomy) was shown by FISH in some cells from all 14 endometriosis specimens, although in no case did every cell show monosomy 17. In 12 of 14 specimens, significant proportions of cells not only were monosomic for the chromosome 17-centromere (8 to 42% of cells) but also showed loss of p53 locus. In the two remaining cases, p53 loss alone was observed in 8 and 14%. LoH for other alleles on chromosome 17 was observed less often, namely only 3 of 15 specimens for HGH, 1 of 15 for D17S250, and 0 of 15 for CHRNB1. Conclusions: Our study indicates that perturbations of chromosome 17 in general and the p53 locus in particular occur frequently in severe/late stage endometriosis. That not all cells show loss of whole chromosome 17 or the p53 locus suggests somatic mutation, perhaps occurring late in the pathogenesis of endometriosis. Clonal evolution of endometriosis must depend not only on somatic mutations for p53 but also on other oncogenes or TSG. Alternatively, the clone could begin with a germline or somatic mutation involving a nonneoplastic process, followed by one or more somatic mutations involving an oncogene or TSG like p53. Additional candidate genes clearly must be evaluated in order to determine the precise role chromosome 17 and p53 alterations play in endometriosis; however, additional genes seem unlikely to involve region connoted by HGH, D17S250 or CHRNB1.
MeSH term(s)	Chromosomes, Human, Pair 17/genetics ; DNA/genetics ; Endometriosis/genetics ; Female ; Genes, p53 ; Humans ; In Situ Hybridization, Fluorescence ; Loss of Heterozygosity ; Models, Genetic
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2003-02-21
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	424421-7
ISSN	1872-7603 ; 0165-0378
ISSN (online)	1872-7603
ISSN	0165-0378
DOI	10.1016/s0165-0378(01)00131-0
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