Detection of Y chromosome‐specific DNA in the plasma and urine of pregnant women using nested polymerase chain reaction

Al‐Yatama, Majda; Mustafa, Abu Salim; Ali, Sadiq; Abraham, Suresh K.; Khan, Zohra; Khaja, Nawal

doi:10.1002/pd.69

Cited by 62 publications

(44 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Therefore, from the 57 selected studies used in the meta-analysis, we extracted 80 data sets 37,56,57,60,61,67, 77. † References 6,[14][15][16][17]23,25,27,55,59,62,70,75,78,88. (eTable 2).…”

Section: Study Selectionmentioning

confidence: 99%

“…35,49,60 The remaining 4 data sets 14,15,79 showed poor and inconsistent performance (sensitivity: 6.3%, 32.3%, 38.2%, and 95.1%; specificity: 98.2%, 98.2%, 96%, and 87.9%; and PPV, 90.7% and NPV, 52.4% [across the 4 data sets]). The high specificity is likely an artifact; if no fetal DNA can be amplified, the test will not produce false-positive results.…”

Section: Sample Typementioning

confidence: 99%

“…The remaining 146 studies were read in their entirety (eTable 1, available at http://www.jama.com). A total of 74 studies 6,7,[14][15][16][17][18] were suitable for inclusion in the analyses (Figure 2). Interreviewer agreement was high.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Noninvasive Fetal Sex Determination Using Cell-Free Fetal DNA: A Systematic Review and Meta-Analysis

Devaney

Palomaki

Scott

et al. 2011

Obstetrical &Amp; Gynecological Survey

View full text Add to dashboard Cite

Context-Noninvasive prenatal determination of fetal sex using cell-free fetal DNA provides an alternative to invasive techniques for some heritable disorders. In some countries this testing has transitioned to clinical care, despite the absence of a formal assessment of performance.Objective-To document overall test performance of noninvasive fetal sex determination using cell-free fetal DNA and to identify variables that affect performance.Data Sources-Systematic review and meta-analysis with search of PubMed (January 1, 1997-April 17, 2011) to identify English-language human studies reporting primary data. References from review articles were also searched.Study Selection and Data Extraction-Abstracts were read independently to identify studies reporting primary data suitable for analysis. Covariates included publication year, sample type, DNA amplification methodology, Y chromosome sequence, and gestational age. Data were independently extracted by 2 reviewers. Disclaimer:The research that is the basis of this study was conducted prior to Dr Devaney starting at the National Institutes of Health (NIH), and the views expressed in the article do not necessarily represent the views of the NIH or the United States Government.Online-Only Material: eTables 1 and 2 are available at http://www.jama.com. Conclusions-Despite interstudy variability, performance was high using maternal blood. Sensitivity and specificity for detection of Y chromosome sequences was greatest using RTQ-PCR after 20 weeks' gestation. Tests using urine and tests performed before 7 weeks' gestation were unreliable. HHS Public AccessNoninvasive prenatal determination of fetal sex could provide an important alternative to invasive cytogenetic determination, which is currently the gold standard for ambiguous genitalia, X-linked conditions, and single-gene disorders such as congenital adrenal hyperplasia. Chorionic villus sampling and amniocentesis have small but measurable rates of procedure-related pregnancy loss. [1][2][3] The availability of a reliable noninvasive alternative to determine fetal sex would reduce unintended fetal losses and would presumably be welcomed by pregnant women carrying fetuses at risk for disorders. A much broader potential application for fetal sex detection is family balancing, which poses ethical concerns.Fetal sex determination can be performed by sonography at as early as 11 weeks' gestation, although not reliably. Test performance across published studies varies significantly. According to a review by Odeh et al, 4 fetal sex cannot be determined by ultrasound examination in 7.5% to 50% of pregnancies at 11 weeks' gestation, and this decreases to 3% to 24% at 13 weeks. When reported, the sex determination is incorrect as often as 40% of the time at 11weeks, although by 13 weeks, accuracy (when reported) is close to 100%. A subsequent prospective study reported that fetal sex could be determined by ultrasound 90% of the time, with 86% accuracy from 11 to 14 weeks' gestation. 5The presence of cell-free circul...

show abstract

Section: Study Selectionmentioning

confidence: 99%

Section: Sample Typementioning

confidence: 99%

See 1 more Smart Citation

Noninvasive Fetal Sex Determination Using Cell-Free Fetal DNA: A Systematic Review and Meta-Analysis

Devaney

Palomaki

Scott

et al. 2011

Obstetrical &Amp; Gynecological Survey

View full text Add to dashboard Cite

show abstract

“…However, maternal urine analysis was faced with technical difficulties, and it was suggested that the concentration of transrenal DNA might be too low for standard PCR protocols. On the basis of DNA isolation and amplification techniques some authors reported positive results (2,(5)(6)(7), whereas others did not (4,8,9 ). The reason for the differing outcomes was attributed to renal function, in particular glomerular permeability, small size of DNA fragments, and the presence of urinary nucleases.…”

mentioning

confidence: 99%

On Targeting Cell-Free DNA in Urine: A Protocol for Optimized DNA Analysis

Bauer¹,

Pertl

2009

Clinical Chemistry

View full text Add to dashboard Cite

This is not the first editorial in Clinical Chemistry dedicated to the testing of urine for cell-free DNA. In 2000 Lo (1 ) highlighted the findings of Botezatu et al. (2 ), who were the first to describe a transfer of DNA across the kidney barrier into urine. The origins of detected transrenal DNA sequences were carcinomas, blood transfusions, and, in pregnant women, the fetus. Following this first report, some pioneering work was done in transplant medicine. Urinary microchimerism was found in women after receiving kidney transplants from males (3,4 ). In a quantitative analysis it was demonstrated that transplant-derived DNA was increased during graft rejection, indicating a potential marker for transplant control (4 ).Later, attempts were made to detect cell-free fetal DNA in maternal urine. However, maternal urine analysis was faced with technical difficulties, and it was suggested that the concentration of transrenal DNA might be too low for standard PCR protocols. On the basis of DNA isolation and amplification techniques some authors reported positive results (2, 5-7 ), whereas others did not (4,8,9 ). The reason for the differing outcomes was attributed to renal function, in particular glomerular permeability, small size of DNA fragments, and the presence of urinary nucleases. A comprehensive review covering many aspects of transrenal DNA was published by Umansky and Tomei (10 ). It was reported that transrenal DNA appears in fragments of 150 -200 bp. Nearly a decade after the first report (2 ), another transformative report on this topic appears in this issue of Clinical Chemisty (11 ). Interestingly, Melkonyan and Umansky are among the authors of both papers.The current study, reported by Shekhtman et al. (11 ), aimed at optimizing the molecular technique of transrenal DNA analysis in urine. In a first set of experiments the investigators used a novel DNA isolation and purification technique based on the adsorption of nucleic acids to Q-Sepharose resin, which allows isolation of short (150 -200 bp) and very short (50 -150 bp) DNA fragments. A comparison with the silica-based method showed that Q-Sepharose resin was superior in DNA detection, as demonstrated by a 100% detection rate with the Q-Sepharose resin method vs 70% with the silica method. Shekhtman et al. (11 ) designed another experiment to characterize fetal transrenal DNA. They performed real-time PCR using 4 sets of primers to amplify sequences of 25-88 bp within the sex determining region Y (SRY) gene. These experiments showed that the assay diagnostic sensitivity was inversely correlated with the length of the PCR targets. The use of a short amplicon size of 25 bp led to a tremendous increase in the detection of fetal DNA in maternal urine, whereas it was completely undetectable with 88-bp fragments. The experimental validation was followed by a clinical study on pregnant women. The results of 173 urine samples obtained from pregnant women revealed a positive predictive value of 87.6% and a negative predictive value of 95.2%. A drawback of...

show abstract

“…Otherwise, it is difficult to explain how fetal DNA appears in the urine of pregnant women or how tumor-specific DNA markers appear in the urine of patients with tumors located outside of the urinary system. This original observation was reproduced in many laboratories (2)(3)(4)(5)(6)(7). At the same time, several groups could not detect fetal DNA in the urine of pregnant women (8,9 ), raising doubts about the concept of Tr-DNA.…”

mentioning

confidence: 99%

From Transrenal DNA to Stem Cell Differentiation: An Unexpected Twist

Umansky¹

2009

Clinical Chemistry

View full text Add to dashboard Cite

In this issue of Clinical Chemistry, Hung et al. describe the results of a study originally devoted to investigation of the transrenal DNA (Tr-DNA) 1 phenomenon. These authors report on the presence of donorderived, cell-free DNA and cells in the urine of sexmismatched hematopoietic stem cell transplant (HSCT) recipients (1 ).The term Tr-DNA defines DNA molecules that appear in the urine from sources located outside of the urinary system. The investigators who found such molecules in urine for the first time suggested that DNA fragments from cells dying throughout the body appear in the bloodstream as so-called cell-free circulating DNA (cfcDNA) and then cross the kidney barrier into the urine (2 ). Otherwise, it is difficult to explain how fetal DNA appears in the urine of pregnant women or how tumor-specific DNA markers appear in the urine of patients with tumors located outside of the urinary system. This original observation was reproduced in many laboratories (2-7 ). At the same time, several groups could not detect fetal DNA in the urine of pregnant women (8,9 ), raising doubts about the concept of Tr-DNA. The latter results can be explained by the fact that Tr-DNA fragments are shorter than cfcDNA, and shorter amplicons should be used for their detection (4, 7, 10 ), especially in prenatal models in which concentrations of fetal DNA in maternal urine are low. It is also important to remember that urinary DNA from other sources complicates analysis of Tr-DNA. Other sources of urinary DNA include epithelial cells shed from the organs of the urinary system, often lymphocytes and other white blood cells, and cell-free DNA released into the urine after chromatin degradation in cells dying in the kidney and bladder. Bacterial infection is another potential source of urinary DNA; hence urine is widely used for diagnosing sexually transmitted diseases (11, 12 ).As a model for investigation of the Tr-DNA phenomenon, Hung and colleagues studied HSCT recipients, whose plasma contains a significant amount of donor-specific cfcDNA. The primary goal of the study was to find out if there is a correlation between concentrations and sizes of cfcDNA in the plasma and Tr-DNA in the urine. To simplify detection of donor DNA in plasma and urine, the authors selected sexmismatched HSCT recipients. Twenty-one of 22 patients had more than 99% of donor lymphohematopoietic cells in the peripheral blood. To differentiate male and female DNA, a zinc finger-protein gene assay was designed based on the nucleotide difference between the zinc finger-protein genes located on chromosomes X and Y. In addition, Y chromosome-specific SRY sequences were used for male donor/female recipient patients. The contribution of donor-derived cfcDNA in plasma was in the range of 72.8%-79.3%, supporting the earlier conclusion about the predominantly hematopoietic origin of cfcDNA in plasma (13 ). These data indicate that only about 25% of cfcDNA is delivered to the bloodstream by other tissues. However, one should keep in mind that in spite of all preca...

show abstract

Detection of Y chromosome‐specific DNA in the plasma and urine of pregnant women using nested polymerase chain reaction

Cited by 62 publications

References 8 publications

Noninvasive Fetal Sex Determination Using Cell-Free Fetal DNA: A Systematic Review and Meta-Analysis

Noninvasive Fetal Sex Determination Using Cell-Free Fetal DNA: A Systematic Review and Meta-Analysis

On Targeting Cell-Free DNA in Urine: A Protocol for Optimized DNA Analysis

From Transrenal DNA to Stem Cell Differentiation: An Unexpected Twist

Contact Info

Product

Resources

About