Imaging single DNA molecules for high precision NIPT

Dahl, Fredrik A.; Ericsson, Olle; Karlberg, Olof; Karlsson, Filip; Howell, Mathias; Persson, Fredrik; Roos, Fredrik; Stenberg, Johan A.; Ahola, Tarja; Alftrén, Ida; Andersson, Björn; Barkenäs, Emelie; Brandner, Birgit D.; Dahlberg, Jenny; Elfman, Sara; Eriksson, Magnus; Forsgren, Per-Ola; Francois, Niels; Gousseva, Anna; Hakamali, Faizan; Janfalk-Carlsson, Åsa; Johansson, Henrik; Lundgren, Johanna; Mohsenchian, Atefeh; Olausson, Linus; Olofsson, Simon; Qureshi, Atif; Skarpås, Björn; Sävneby, Anna; Åström, Eva; Öhman, Ove; Westgren, Magnus; Kallner, Helena Kopp; Fianu-Jonasson, Aino; Syngelaki, Argyro; Nicolaides, Kypros H.

doi:10.1038/s41598-018-22606-0

Cited by 39 publications

(63 citation statements)

References 12 publications

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“…The Vanadis NIPT assay relies on a series of enzymatic steps that specifically generate labelled rolling circle replication products (RCPs) from chromosomal cfDNA targets, as previously described . Automated extraction of cfDNA from plasma was performed using the Vanadis Extract platform, followed by continued processing on the Vanadis Core platform to generate labelled RCPs, which were imaged and counted using the Vanadis View instrument.…”

Section: Methodsmentioning

confidence: 99%

“…The assay enables automated high precision cfDNA analysis from primary blood tubes. Previously, the Vanadis NIPT assay has been demonstrated to enable high precision measurement of aneuploidies and clinical classification of euploid and aneuploid trisomy 21 pregnancies and is here extended to trisomies 13 and 18. Targeted NIPT tests using PCR typically remove samples with low fetal fraction since these cannot be classified accurately, resulting in a high assay failure rate.…”

Section: Introductionmentioning

confidence: 99%

“…Targeted NIPT tests using PCR typically remove samples with low fetal fraction since these cannot be classified accurately, resulting in a high assay failure rate. Using direct quantification of targeted chromosomal fragment labelled by rolling circle replication, the Vanadis NIPT has been demonstrated to correctly classify reference samples well below 4% fetal fraction …”

Section: Introductionmentioning

confidence: 99%

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Clinical validation of a novel automated cell‐free DNA screening assay for trisomies 21, 13, and 18 in maternal plasma

Ericsson¹,

Ahola²,

Dahl³

et al. 2019

Prenatal Diagnosis

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ObjectiveTo evaluate clinical performance of a new automated cell‐free (cf)DNA assay in maternal plasma screening for trisomies 21, 18, and 13, and to determine fetal sex.MethodMaternal plasma samples from 1200 singleton pregnancies were analyzed with a new non–sequencing cfDNA method, which is based on imaging and counting specific chromosome targets. Reference outcomes were determined by either cytogenetic testing, of amniotic fluid or chorionic villi, or clinical examination of neonates.ResultsThe samples examined included 158 fetal aneuploidies. Sensitivity was 100% (112/112) for trisomy 21, 89% (32/36) for trisomy 18, and 100% (10/10) for trisomy 13. The respective specificities were 100%, 99.5%, and 99.9%. There were five first pass failures (0.4%), all in unaffected pregnancies. Sex classification was performed on 979 of the samples and 99.6% (975/979) provided a concordant result.ConclusionThe new automated cfDNA assay has high sensitivity and specificity for trisomies 21, 18, and 13 and accurate classification of fetal sex, while maintaining a low failure rate. The study demonstrated that cfDNA testing can be simplified and automated to reduce cost and thereby enabling wider population‐based screening.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Clinical validation of a novel automated cell‐free DNA screening assay for trisomies 21, 13, and 18 in maternal plasma

Ericsson¹,

Ahola²,

Dahl³

et al. 2019

Prenatal Diagnosis

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“…There are already laboratories that offer the test us-ing this method and, although the validation studies show results comparable with those obtained by MPSS, no largescale prospective validation study has yet been published in the general population. More recently, a proof-of-principle study on a method based on highly specific chromosomal fluorescent labeling has been published [22].…”

Section: Othersmentioning

confidence: 99%

Implementation of maternal blood cell-free DNA testing in early screening for aneuploidies

Gil

Nicolaides

2019

Medizinische Genetik

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Several externally blinded validation and implementation studies in the last 9 years have shown that it is now possible, through analysis of cell-free (cf) DNA in maternal blood, to effectively detect a high proportion of fetuses affected by trisomies 21, 18, and 13 at a much lower false-positive rate (FPR) than all other existing screening methods. This article is aimed at reviewing technical and clinical considerations for implementing cfDNA testing in routine practice, including methods of analysis, performance of the test, models for clinical implementation, and interpretation of results.

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“…The two main types of methods for prenatal cfDNA testing are targeted and genome-wide. Targeted approaches are based on the capture and amplification or enrichment of specific cfDNA fragments from chromosomes or regions of clinical interest, usually chromosomes 21,18,13, sex chromosomes and a select set of regions involved in microdeletion syndromes [4][5][6] . Genome-wide tests are based on massively parallel shotgun sequencing of maternal plasma cfDNA fragments 7,8 and have been applied to detect additional chromosome regions larger than 7-10 Mb.…”

Section: Introductionmentioning

confidence: 99%

Rare autosomal trisomies: comparison of detection through cell‐free DNA analysis and direct chromosome preparation of chorionic villus samples

Benn

Malvestiti²,

Grimi³

et al. 2019

Ultrasound in Obstet & Gyne

109

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Objective Direct chromosome preparations of chorionic villus samples (CVS) and cell‐free DNA (cfDNA) testing both involve analysis of the trophoblastic cell lineage. The aim of this study was to compare the spectrum of rare autosomal trisomies (RATs) detected by these two approaches and assess the available information on their clinical significance. Methods Data from 10 reports on genome‐wide cfDNA testing were pooled to determine which chromosomes were most frequently involved in RAT‐positive cases, and pregnancy outcome information was reviewed. CVS information was obtained from an updated database of 76 102 consecutive CVS analyses performed over a period of 18 years at TOMA laboratory, in which trophoblastic and mesenchymal layers were analyzed and amniotic fluid cell analysis was recommended for RAT‐positive cases. Chromosomes involved and presence of confined placental mosaicism, true fetal mosaicism and uniparental disomy (UPD) for imprinted chromosomes were assessed. Also evaluated were the frequency and types of RATs in products of conception. Results RATs were present in 634 of 196 662 (0.32%) cfDNA samples and 237 of 57 539 (0.41%) CVS trophoblast samples (P < 0.01). The frequency of RATs varied over 8‐fold between the cfDNA reports. Confirmation of abnormality through amniocentesis was more likely when RATs were ascertained through cfDNA (14 of 151; 9.3%) than through CVS trophoblasts (seven of 237; 3.0%) (P < 0.01). In cfDNA‐ascertained cases, trisomies 15, 16 and 22, which are associated with fetal loss, were identified proportionately more often. Of 151 cases with RAT identified by cfDNA and outcome information available, 41.1% resulted in normal live birth; 27.2% in fetal loss; 7.3% had phenotypic abnormality detected through ultrasound or other follow‐up evaluation; 2.0% had a clinically significant UPD; and 14.6% had fetal growth restriction or low birth weight. All autosomes were involved in trisomies in products of conception; the most common RATs detected were trisomies 16, 22 and 15 with a frequency of > 9% each. Conclusions Although there are strong parallels between RATs ascertained through cfDNA analysis and direct chromosome preparation of CVS, caution is needed in applying conclusions from CVS analysis to cfDNA testing, and vice versa. RATs identified through genome‐wide cfDNA tests have uncertain risks for fetal loss, growth restriction or fetal abnormality. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

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Imaging single DNA molecules for high precision NIPT

Cited by 39 publications

References 12 publications

Clinical validation of a novel automated cell‐free DNA screening assay for trisomies 21, 13, and 18 in maternal plasma

Clinical validation of a novel automated cell‐free DNA screening assay for trisomies 21, 13, and 18 in maternal plasma

Implementation of maternal blood cell-free DNA testing in early screening for aneuploidies

Rare autosomal trisomies: comparison of detection through cell‐free DNA analysis and direct chromosome preparation of chorionic villus samples

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