Determination of fetal DNA fraction from the plasma of pregnant women using sequence read counts.

Abstract:

OBJECTIVE:This study introduces a novel method, referred to as SeqFF, for estimating the fetal DNA fraction in the plasma of pregnant women and to infer the underlying mechanism that allows for such statistical modeling. METHODS:Autosomal regional read counts from whole-genome massively parallel single-end sequencing of circulating cell-free DNA (ccfDNA) from the plasma of 25 312 pregnant women were used to train a multivariate model. The pretrained model was then applied to 505 pregnant samples to assess the performance of SeqFF against known methodologies for fetal DNA fraction calculations. RESULTS:Pearson's correlation between chromosome Y and SeqFF for pregnancies with male fetuses from two independent cohorts ranged from 0.932 to 0.938. Comparison between a single-nucleotide polymorphism-based approach and SeqFF yielded a Pearson's correlation of 0.921. Paired-end sequencing suggests that shorter ccfDNA, that is, less than 150 bp in length, is nonuniformly distributed across the genome. Regions exhibiting an increased proportion of short ccfDNA, which are more likely of fetal origin, tend to provide more information in the SeqFF calculations. CONCLUSION:SeqFF is a robust and direct method to determine fetal DNA fraction. Furthermore, the method is applicable to both male and female pregnancies and can greatly improve the accuracy of noninvasive prenatal testing for fetal copy number variation.

journal_name

Prenat Diagn

journal_title

Prenatal diagnosis

authors

Kim SK,Hannum G,Geis J,Tynan J,Hogg G,Zhao C,Jensen TJ,Mazloom AR,Oeth P,Ehrich M,van den Boom D,Deciu C

doi

10.1002/pd.4615

subject

Has Abstract

pub_date

2015-08-01 00:00:00

pages

810-5

issue

8

eissn

0197-3851

issn

1097-0223

journal_volume

35

pub_type

杂志文章
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  • Decreased first trimester PAPP-A is a predictor of adverse pregnancy outcome.

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    authors: Yaron Y,Heifetz S,Ochshorn Y,Lehavi O,Orr-Urtreger A

    更新日期:2002-09-01 00:00:00

  • Measurements of placental, decidual, and fetal proteins before and after chorionic villus sampling.

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    authors: Stabile I,Warren R,Rodeck C,Grudzinskas JG

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  • Can we predict 22q11 status of fetuses with tetralogy of Fallot?

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    更新日期:2002-03-01 00:00:00

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    更新日期:2003-01-01 00:00:00

  • Amiodarone treatment in pregnancy for dilatative cardiomyopathy with ventricular malignant extrasystole and normal maternal and neonatal outcome.

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  • Expression of fragile-X in a female fetus diagnosed after chorionic villus sampling.

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    pub_type: 杂志文章

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  • Diagnostic accuracy, work-up, and outcomes of pregnancies with clubfoot detected by prenatal sonography.

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  • Evaluation of long-term neurodevelopment in twin-twin transfusion syndrome after laser therapy.

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  • Second-trimester prenatal screening for trisomy 21 using biochemical markers: a 7-year experience in one cytogenetic laboratory.

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    更新日期:2006-04-01 00:00:00

  • First and early second-trimester diagnosis of fetal urinary tract anomalies using transvaginal sonography.

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    pub_type: 杂志文章

    doi:10.1002/pd.1970101005

    authors: Bronshtein M,Yoffe N,Brandes JM,Blumenfeld Z

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    pub_type: 杂志文章

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  • The utility of detailed first trimester ultrasound examination in abnormal fetal nuchal translucency.

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  • Current awareness in prenatal diagnosis.

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    更新日期:2001-01-01 00:00:00

  • Current controversies in prenatal diagnosis 2: prediction and prevention of adverse pregnancy outcomes requires a genomic rather than proteomic solution.

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    doi:10.1002/pd.4533

    authors: Chiu RW,Myatt L,Otaño L

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    更新日期:1999-08-01 00:00:00

  • Prenatal diagnosis of 46,XX/47,XXY mosaicism: a case report.

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    doi:10.1002/pd.1970030406

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  • Fetal diagnostic indications for second and third trimester outpatient pregnancy termination.

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    doi:10.1002/pd.4324

    authors: Hern WM

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    doi:10.1002/pd.1970110403

    authors: Mostello D,Hoechstetter L,Bendon RW,Dignan PS,Oestreich AE,Siddiqi TA

    更新日期:1991-04-01 00:00:00