Genomic SNP array as a gold standard for prenatal diagnosis of foetal ultrasound abnormalities

Srebniak, Malgorzata I.; Boter, Marjan; Oudesluijs, Grétel; Cohen–Overbeek, Titia E.; Govaerts, L.; Diderich, Karin E. M.; Oegema, Renske; Knapen, Maarten F. C. M.; Laar, Ingrid M van de; Joosten, Marieke; Opstal, Diane Van; Galjaard, Robert-Jan H

doi:10.1186/1755-8166-5-14

Cited by 68 publications

(93 citation statements)

References 13 publications

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“…The cohort presented here includes cases published in our previous publications. 6,16 Since September 2012, SNP array testing is performed as a stand-alone first-tier test and therefore in only about 60 initial cases karyotyping was performed simultaneously to array. In some abnormal cases karyotyping was performed after array detected a pathogenic CNV to characterize the chromosome aberration and provide the risk for recurrence.…”

Section: Materials and Methods Materialsmentioning

confidence: 99%

“…In some abnormal cases karyotyping was performed after array detected a pathogenic CNV to characterize the chromosome aberration and provide the risk for recurrence. Initially cases (~200 cases) were selected by both gynecologists and clinical geneticists, 6 but since June 2011 array testing was performed in all cases of ultrasound anomalies (~800 cases) regardless of the severity of the phenotype.…”

Section: Materials and Methods Materialsmentioning

confidence: 99%

“…A total of 50-100 ng fetal DNA was tested with~300 K Illumina HumanCytoSNP-12 (HCS) array (San Diego, CA, USA), as described before. 6,16 The array profiles were analyzed with a 0.15 Mb resolution in UCSC (Human Mar. 2006 (NCBI36/hg18) Assembly) by using initially Karyo Studio (Illumina), then Genome Studio (Illumina) and different versions of Nexus Copy Number (BioDiscovery: versions 5.0 and higher (Hawthorne, CA, USA)).…”

Section: Snp Array and Reportingmentioning

confidence: 99%

“…2006 (NCBI36/hg18) Assembly) by using initially Karyo Studio (Illumina), then Genome Studio (Illumina) and different versions of Nexus Copy Number (BioDiscovery: versions 5.0 and higher (Hawthorne, CA, USA)). 6,16 We did not use a filter, but in our experience events smaller that 150 kb most of the time occurred to be noisy and therefore we estimated the working resolution at 150 kb level. Fetal and parental DNA was simultaneously tested to determine the inheritance of CNVs, mainly to avoid subsequent testing, which delays the final reports.…”

Section: Snp Array and Reportingmentioning

confidence: 99%

“…Fetuses with ultrasound abnormalities are known to carry not only the highest percentage of microscopically visible chromosome abnormalities 1-3 but also submicroscopic aberrations. [4][5][6][7][8][9][10][11] Before array implementation, these submicroscopic chromosome aberrations could only be detected if targeted testing was requested in case of specific ultrasound anomalies, for example, 22q11 deletion in fetuses with cardiac defects. 12 However, based on prenatal phenotyping by ultrasound examination, it is not always easy to obtain a clinical diagnosis and to determine which locus/loci should be investigated.…”

Section: Introductionmentioning

confidence: 99%

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Prenatal SNP array testing in 1000 fetuses with ultrasound anomalies: causative, unexpected and susceptibility CNVs

et al. 2015

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To evaluate the diagnostic value of single-nucleotide polymorphism (SNP) array testing in 1033 fetuses with ultrasound anomalies we investigated the prevalence and genetic nature of pathogenic findings. We reclassified all pathogenic findings into three categories: causative findings; unexpected diagnoses (UD); and susceptibility loci (SL) for neurodevelopmental disorders. After exclusion of trisomy 13, 18, 21, sex-chromosomal aneuploidy and triploidies, in 76/1033 (7.4%) fetuses a pathogenic chromosome abnormality was detected by genomic SNP array: in 19/1033 cases (1.8%) a microscopically detectable abnormality was found and in 57/1033 (5.5%) fetuses a pathogenic submicroscopic chromosome abnormality was detected. 58% (n = 44) of all these pathogenic chromosome abnormalities involved a causative finding, 35% (n = 27) a SL for neurodevelopmental disorder, and 6% (n = 5) a UD of an early-onset untreatable disease. In 0.3% of parental samples an incidental pathogenic finding was encountered. Our results confirm that a genomic array should be the preferred first-tier technique in fetuses with ultrasound anomalies. All UDs involved early-onset diseases, which is beneficial for the patients to know. It also seems that UDs occur at a comparable frequency among microscopic and submicroscopic pathogenic findings. SL were more often detected than in pregnancies without ultrasound anomalies.

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Section: Materials and Methods Materialsmentioning

confidence: 99%

Section: Materials and Methods Materialsmentioning

confidence: 99%

Section: Snp Array and Reportingmentioning

confidence: 99%

Section: Snp Array and Reportingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Prenatal SNP array testing in 1000 fetuses with ultrasound anomalies: causative, unexpected and susceptibility CNVs

et al. 2015

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Prenatal Diagnosis by Microarray Analysis

Vermeesch¹

2015

Genetic Disorders and the Fetus

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An economic analysis of prenatal cytogenetic technologies for sonographically detected fetal anomalies

Sutton

Longman

Odibo

2014

American J of Med Genetics Pt A

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When congenital anomalies are diagnosed on prenatal ultrasound, the current standard of care is to perform G-banded karyotyping on cultured amniotic cells. Chromosomal microarray (CMA) can detect smaller genomic deletions and duplications than traditional karyotype analysis. CMA is the first-tier test in postnatal evaluation of children with multiple congenital anomalies. Recent studies have demonstrated the utility of CMA in the prenatal setting and have advocated for widespread implementation of this technology as the preferred test in prenatal diagnosis. However, CMA remains significantly more expensive than karyotype. In this study, we performed an economic analysis of cytogenetic technologies in the prenatal diagnosis of sonographically-detected fetal anomalies comparing 4 strategies: 1) karyotype alone, 2) CMA alone, 3) karyotype and CMA, and 4) karyotype followed by CMA if the karyotype was normal. In a theoretical cohort of 1,000 patients, CMA alone and karyotype followed by CMA if the karyotype was normal identified a similar number of chromosomal abnormalities. In this model, CMA alone was the most cost effective strategy, although karyotype alone and CMA following a normal karyotype are both acceptable alternatives. This study supports the clinical utility of CMA in the prenatal diagnosis of sonographically-detected fetal anomalies.

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Genomic SNP array as a gold standard for prenatal diagnosis of foetal ultrasound abnormalities

Cited by 68 publications

References 13 publications

Prenatal SNP array testing in 1000 fetuses with ultrasound anomalies: causative, unexpected and susceptibility CNVs

Prenatal SNP array testing in 1000 fetuses with ultrasound anomalies: causative, unexpected and susceptibility CNVs

Prenatal Diagnosis by Microarray Analysis

An economic analysis of prenatal cytogenetic technologies for sonographically detected fetal anomalies

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