Analysis of the Size Distributions of Fetal and Maternal Cell-Free DNA by Paired-End Sequencing

Fan, Hongxin; Blumenfeld, Yair J.; Chitkara, Usha; Hudgins, Louanne; Quake, Stephen R.

doi:10.1373/clinchem.2010.144188

Cited by 235 publications

(177 citation statements)

References 22 publications

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“…Such measurements, however, are often confounded by the challenge of sample handling: Any lysis of maternal lymphocytes after the blood is drawn would contribute disproportionately longer fragments than the typical circulating cell-free DNA, thereby artificially enhancing the apparent size difference between maternal and fetal DNA. Our own results have shown a slight enrichment of fetal DNA among the smaller fragments, but unfortunately not enough to be practically useful at this point (13 ).…”

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confidence: 68%

Sizing Up Cell-Free DNA

Quake

2012

Clinical Chemistry

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confidence: 68%

Sizing Up Cell-Free DNA

Quake

2012

Clinical Chemistry

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“…The third possible source is that cffDNA comes directly into maternal peripheral blood. The cffDNA in maternal peripheral blood comes mainly from apoptosis and the length of the DNA fragment is only about 162 bp, rarely reaching 340 bp (Fan et al, 2010). The cffDNA in maternal peripheral blood consists of small fragments that are unstable, and its concentration reduces at a constant speed after collecting blood because of the activity of DNases.…”

Section: Discussionmentioning

confidence: 99%

Isolation and analysis of cell-free fetal DNA from maternal peripheral blood in Chinese women

Yang¹,

Zhu²,

Qiu³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Non-invasive prenatal diagnosis is used to detect the genetic material of the fetus by isolating the cell-free fetal DNA (cffDNA) from maternal peripheral blood. In order to establish an isolation method for 18079 Isolation and analysis of cell free fetal DNA ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 18078-18089 (2015) cffDNA from maternal peripheral blood in Chinese women, the cffDNA was acquired with a two-step centrifugation using a QlAamp DNA Blood mini kit. The SRY gene of plasma DNA was amplified by polymerase chain reaction (PCR). Real-time quantitative PCR was used to measure the concentration of cffDNA in maternal peripheral blood in different pregnant women. The results of the SRY gene amplification of plasma DNA from pregnant women was the same as that of the amniocyte DNA. The average concentration of cffDNA in maternal peripheral blood of pregnant women in different gestational stages was 0.98 ng/mL (0.26-1.49 ng/mL), 1.43 ng/mL (0.46-2.34 ng/mL), and 1.95 ng/mL (0.65-6.81 ng/mL) from early, middle, and late gestational stages, respectively. The mean of cffDNA from total DNA in plasma in different stages of gestation was 22.28% (9.86-27.81%). The lowest concentration of DNA amplified by nested-PCR in our research was 10 -4 -10 -3 ng/µL. The isolation method for cffDNA from maternal peripheral blood was successfully established and further research into its applications will be conducted.

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“…Hence, a comprehensive and high-resolution size profile can be obtained. This approach has been used to elucidate the difference in size between fetal and maternal DNA in maternal plasma (13,14 ). Recently, PE deep sequencing of maternal plasma DNA has unveiled that plasma DNA molecules possess a fragmentation pattern reminiscent of nuclease-cleaved nucleosomes, with fetal DNA showing a reduction in a 166-bp peak and relative prominence of a 143-bp peak, compared with maternal DNA (13 ).…”

confidence: 99%

Nonhematopoietically Derived DNA Is Shorter than Hematopoietically Derived DNA in Plasma: A Transplantation Model

Zheng¹,

Chan²,

Sun³

et al. 2012

Clinical Chemistry

108

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BACKGROUND Plasma DNA is predominantly hematopoietic in origin. The size difference between maternal- and fetal-derived DNA in maternal plasma prompted us to investigate whether there was any discrepancy in molecular size between hematopoietically and nonhematopoietically derived DNA in plasma. METHODS Plasma DNA samples from 6 hematopoietic stem cell transplant recipients and 1 liver transplant recipient were analyzed by massively parallel paired-end sequencing. The size of each fragment was deduced from the alignment positions of the paired reads. In sex-mismatched transplant recipients, the reads from chromosome Y were used as markers for the male donor/recipient. For other transplant recipients, the reads of the donor- and recipient-specific alleles were identified from the single-nucleotide polymorphism genotypes. RESULTS In male patients receiving female hematopoietic stem cells, more chromosome Y–derived DNA molecules (nonhematopoietically derived) were ≤150 bp than the autosome-derived ones (mainly hematopoietically derived) (median difference, 9.9%). In other hematopoietic stem cell transplant recipients, more recipient-specific DNA molecules (nonhematopoietically derived) were ≤150 bp than the donor-specific ones (hematopoietically derived) (median difference, 14.8%). In the liver transplant recipient, more donor-derived DNA molecules (liver derived) were ≤150 bp than the recipient-derived ones (mainly hematopoietically derived) (difference, 13.4%). The nonhematopoietically derived DNA exhibited a reduction in a 166-bp peak compared with the hematopoietically derived DNA. A 10-bp periodicity in size distribution below approximately 143 bp was observed in both DNA populations. CONCLUSIONS Massively parallel sequencing is a powerful tool for studying posttransplantation chimerism. Plasma DNA molecules exhibit a distinct fragmentation pattern, with the nonhematopoietically derived molecules being shorter than the hematopoietically derived ones.

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Analysis of the Size Distributions of Fetal and Maternal Cell-Free DNA by Paired-End Sequencing

Cited by 235 publications

References 22 publications

Sizing Up Cell-Free DNA

Sizing Up Cell-Free DNA

Isolation and analysis of cell-free fetal DNA from maternal peripheral blood in Chinese women

Nonhematopoietically Derived DNA Is Shorter than Hematopoietically Derived DNA in Plasma: A Transplantation Model

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