• bioimaging
• diagnosis
• quantum dot
• rare genetic disease
• therapy

• Quantum Dots/chemistry
• Humans
• Theranostic Nanomedicine/methods
• Rare Diseases/therapy
• Rare Diseases/genetics
• Genetic Diseases, Inborn/therapy
• Animals

• BACs-on-Beads technology (BoBs technology)
• abnormal
• amniotic fluid
• chromosome karyotype
• prenatal diagnosis

Most studies on chromosomal microarray analysis (CMA) and amniocentesis risks have not evaluated pregnancies with low risk for genetic diseases; therefore, the efficacy and safety of CMA and amniocentesis in this population are unclear. This study aimed to examine the benefits and risks of prenatal genetic diagnostic tests in pregnancies having low risk for chromosomal diseases.

In this retrospective study, we used clinical data from a large database of 30,830 singleton pregnancies at gestational age 16–23 weeks who underwent amniocentesis for karyotyping with or without CMA. We collected socio-demographic, medical and obstetric information, along with prenatal screening, CMA and karyotyping results. Fetal loss events were also analysed. CMA was performed in 5,837 pregnancies with normal karyotype (CMA cohort). In this cohort, 4,174 women had normal prenatal screening results and the risk for identifying genetic abnormalities with >10% risk for intellectual disability by CMA was 1:102, with no significant difference between maternal age groups. The overall post-amniocentesis fetal loss rate was 1:1,401 for the entire cohort (n = 30,830) and 1:1,945 for the CMA cohort (n = 5,837). The main limitation of this study is the relatively short follow-up of 3 weeks, which may not have been sufficient for detecting all fetal loss events.

The low risk for post-amniocentesis fetal loss, compared to the rate of severe genetic abnormalities detected by CMA, suggests that even pregnant women with normal prenatal screening results should consider amniocentesis with CMA.

• chromosomal microarray
• microdeletion
• microduplication
• prenatal diagnosis

• Amniocentesis
• Aneuploidy
• Chorionic Villi Sampling
• Chromosome Deletion
• Chromosome Duplication
• DNA Copy Number Variations
• Female
• Hong Kong
• Humans
• Incidence
• Microarray Analysis
• Pregnancy
• Prenatal Diagnosis
• Retrospective Studies

• Array-CGH
• Fetal malformations
• Molecular genetics
• Prenatal diagnosis
• Ultrasound

• chromosomal microarray analysis
• chromosome copy number
• fetus
• prenatal genetic testing
• syndromic malformations

• CNV
• array
• background risk
• prenatal diagnosis
• review
• submicroscopic chromosomal aberrations

• Chromosome Aberrations
• Cohort Studies
• DNA Copy Number Variations/genetics
• Down Syndrome/diagnosis
• Down Syndrome/genetics
• Female
• Humans
• Maternal Age
• Oligonucleotide Array Sequence Analysis/methods
• Pregnancy
• Risk
• Ultrasonography, Prenatal

• abnormal sonographic findings
• detection rate
• fetuses
• karyotype analysis
• obstetric ultrasound

• Adolescent
• Adult
• Amniotic Fluid/diagnostic imaging
• Chromosome Aberrations/embryology
• Chromosome Aberrations/statistics & numerical data
• Female
• Humans
• Middle Aged
• Pregnancy
• Reproducibility of Results
• Retrospective Studies
• Ultrasonography, Prenatal/methods
• Young Adult

Noninvasive prenatal testing (NIPT) using whole genome and targeted sequencing has become increasingly accepted for clinical detection of Trisomy 21 and sex chromosome aneuploidies. Few studies have shown that sub-chromosomal deletions or duplications associated with genetic syndromes can also be detected in the fetus noninvasively. There are still limitations on these methodologies such as the detection of variants of unknown clinical significance, high number of false positives, and difficulties to detect small aberrations. We utilized a recently developed targeted sequencing approach for the development of a NIPT assay, for large and small size deletions/duplications, which overcomes these existing limitations. Artificial pregnancies with microdeletion/microduplication syndromes were created by spiking DNA from affected samples into cell free DNA (cfDNA) from non-pregnant samples. Unaffected spiked samples and normal pregnancies were used as controls. Target Capture Sequences (TACS) for seven syndromes were designed and utilized for targeted capture enrichment followed by sequencing. Data was analyzed using a statistical pipeline to identify deletions or duplications on targeted regions. Following the assay development a proof of concept study using 33 normal pregnancies, 21 artificial affected and 17 artificial unaffected pregnancies was carried out to test the sensitivity and specificity of the assay. All 21 abnormal spiked-in samples were correctly classified as subchromosomal aneuploidies while the 33 normal pregnancies or 17 normal spiked-in samples resulted in a false positive result. We have developed an NIPT assay for the detection of sub-chromosomal deletions and duplications using the targeted capture enrichment technology. This assay demonstrates high accuracy, high read depth of the genomic region of interest, and can identify deletions/duplications as small as 0.5 Mb. NIPT of fetal microdeletion/microduplication syndromes can be of enormous benefit in the management of pregnancies at risk both for prospective parents and health care providers.

• Abnormalities, Multiple/diagnosis
• Abnormalities, Multiple/genetics
• Chromosome Deletion
• Chromosome Disorders/diagnosis
• Chromosome Disorders/genetics
• Chromosome Duplication/genetics
• Female
• Humans
• Male
• Pregnancy
• Prenatal Diagnosis/methods
• Reproducibility of Results
• Sensitivity and Specificity

• CMA
• chromosomal microarray analysis
• prenatal CMA
• prenatal diagnosis

• copy number variants
• cystic hygroma
• genomic microarray
• increased nuchal translucency
• prenatal diagnosis

• Abnormalities, Multiple
• Chromosome Duplication
• Chromosomes, Human, Pair 22
• Comparative Genomic Hybridization/methods
• DNA Copy Number Variations
• DiGeorge Syndrome
• Female
• Fetal Development/genetics
• Fetal Diseases/diagnostic imaging
• Fetal Diseases/genetics
• Genomics
• Humans
• Karyotype
• Karyotyping
• Lymphangioma, Cystic/diagnostic imaging
• Lymphangioma, Cystic/genetics
• Nuchal Translucency Measurement/methods
• Pregnancy
• Pregnancy Trimester, First/genetics
• Tissue Array Analysis

• Comparative Genomic Hybridization/methods
• Cytogenetic Analysis/methods
• Female
• Humans
• Karyotyping/methods
• Polymorphism, Single Nucleotide
• Pregnancy
• Prenatal Diagnosis/methods
• Ultrasonography, Prenatal/methods

• chromosomal abnormalities
• comparative genomic hybridization
• karyotype
• prenatal diagnosis

• Chromosome Aberrations
• Chromosome Disorders/diagnosis
• Comparative Genomic Hybridization
• Female
• Genetic Testing/methods
• Humans
• Karyotyping
• Pregnancy
• Prenatal Diagnosis/methods
• Sensitivity and Specificity

• microarray
• molecular karyotyping
• prenatal diagnosis

• Chromosomal microarray
• Prenatal diagnosis

• Array-based CGH
• Prenatal diagnostics
• Submicroscopic chromosomal abnormalities

• array comparative genomic hybridization (aCGH)
• chromosomal microarray (CMA)
• congenital anomalies
• cost-effectiveness analysis
• ultrasonic prenatal diagnosis

The application of microarray-based techniques for the diagnosis of genomic rearrangements has been steadily growing in popularity since its introduction in 2004. Given the many advantages of these techniques over conventional cytogenetics, there is increasing pressure towards their application in prenatal diagnosis. However, there remain several important issues that must be addressed. For example, microarray-based techniques (comparative genomic hybridization-based arrays and single nucleotide polymorphism-based arrays) allow detection of even very small genomic imbalances that can determine pathological clinical conditions. In addition, there are other copy number variations which represent normal variation, with no detectable effects on phenotype. Given the still incomplete knowledge of the changes in our genome and the associated phenotypes, microarray-based diagnosis is likely to find variants of uncertain and unknown clinical significance. The interpretation of these variants is now a major challenge for the medical geneticist, who often find it difficult to establish precise correlations between genotype and phenotype. There is sufficient available evidence to justify the use of microarray-based diagnostics for a select number of specific conditions, but there is also an inevitable trend towards ever wider application. It is very important that this drift does not progress in an unchecked and uncontrolled manner under the thrust of commercial interests. Therefore, we recommend that scientific societies be vigilant and take an advisory role in the adopting of these technologies as new scientific knowledge becomes available.

• Copy number variations
• Genomic microarray analysis
• Prenatal diagnosis

• conotruncal cardiac defects
• genes
• genetic heart disease
• congenital

The clinical utility of microarray technologies when used in the context of prenatal diagnosis lies in the technology's ability to detect submicroscopic copy number changes that are associated with clinically significant outcomes. We have carried out a systematic review of the literature to calculate the utility of prenatal microarrays in the presence of a normal conventional karyotype. Amongst 12 362 cases in studies that recruited cases from all prenatal ascertainment groups, 295/12 362 (2.4%) overall were reported to have copy number changes with associated clinical significance (pCNC), 201/3090 (6.5%) when ascertained with an abnormal ultrasound, 50/5108 (1.0%) when ascertained because of increased maternal age and 44/4164 (1.1%) for all other ascertainment groups (e.g. parental anxiety and abnormal serum screening result). When additional prenatal microarray studies are included in which ascertainment was restricted to fetuses with abnormal ultrasound scans, 262/3730 (7.0%) were reported to have pCNCs. © 2013 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd.

• array comparative genomic hybridization
• chromosomal microarray analysis
• copy number variant
• prenatal diagnosis
• low risk pregnancies

• Abnormal Karyotype
• Chromosome Aberrations
• Chromosome Disorders/diagnosis
• Chromosome Disorders/etiology
• Chromosome Disorders/genetics
• Female
• Genetic Testing
• Humans
• Maternal Age
• Microarray Analysis/methods
• Pregnancy
• Prenatal Diagnosis
• Ultrasonography, Prenatal

• Chromosome Disorders/diagnosis
• Female
• Humans
• In Situ Hybridization, Fluorescence
• Karyotyping/methods
• Microarray Analysis/methods
• Pregnancy
• Prenatal Diagnosis/methods
• Prospective Studies
• Ultrasonography, Prenatal/methods

The aim of this study was to develop an improved technique for DNA extraction from 1 ml of uncultured AF from patients with a gestational age less than 16 weeks and to allow the use of array-CGH without DNA amplification. The DNA extraction protocol was tested in a series of 90 samples including 41 of uncultured AF at less than 16 weeks of gestation. Statistical analyses were performed using linear regression. To evaluate the sensitivity and the specificity of array-CGH on 1 ml of uncultured AF, five samples with an abnormal karyotype (three with aneuploidy, two with structural abnormalities) and five with a normal karyotype were studied. This protocol was reproducible and we were able to show a great improvement with higher yield of DNA obtained from all patients, including those with a gestational age less than 16 weeks (p = 0.003). All chromosomal abnormalities were detected and characterized by array-CGH and normal samples showed normal profiles. This new DNA extraction protocol associated with array-CGH analysis could be used in prenatal testing even when gestational age is less than 16 weeks, especially in cases with abnormal ultrasound findings.

• Abnormal Karyotype
• Chromosome Aberrations
• Chromosome Disorders/diagnosis
• Chromosome Disorders/genetics
• DiGeorge Syndrome/genetics
• Echocardiography
• Female
• Fetal Diseases/diagnosis
• Fetal Diseases/genetics
• Genetic Testing/methods
• Humans
• Karyotyping
• Microarray Analysis/methods
• Pregnancy
• Prenatal Diagnosis/methods
• Retrospective Studies

Karyotyping is considered the gold standard for the genome-wide detection of genomic imbalances in prenatal diagnosis, but it has a number of inherent limitations, namely the time required to culture cell and the limited resolution(5 ~ 10 Mb). Although fluorescence in situ hybridization (FISH) can also be used as a rapid prenatal diagnosis for common aneuploidies, it is labor intensive, requires prior knowledge of the regions of interest, and can only be used to diagnose one or a few genomic regions simultaneously. Array comparative genomic hybridization (aCGH) can overcome the resolution, the locus-specific, and the time limitations of the karyotyping and FISH techniques and is currently the most powerful method for detecting chromosomal alterations in pre and postnatal clinical cases. Several investigations have suggested that the aCGH testing should be considered a first-tier test for the diagnosis of cytogenetic aberrations in the fetus.

This study used karyotyping, FISH, sequence-tagged site (STS) analysis and aCGH to diagnose a case of de novo duplication of chromosome 21q22.12 → q22.3 with other concomitant deletion and duplication of small fragments in 21q associated with Down syndrome prenatally.

FISH, aCGH and STS analysis are useful in prenatal investigation of the nature of de novo alterations of small fragments of the chromosome.

• Adult
• Chromosome Aberrations
• Chromosome Disorders/diagnosis
• Chromosomes, Human/genetics
• Down Syndrome/diagnosis
• Female
• Fetal Diseases/diagnosis
• Genetic Testing/methods
• Humans
• Karyotype
• Karyotyping
• Maternal Age
• Oligonucleotide Array Sequence Analysis
• Pregnancy
• Prenatal Diagnosis/methods
• Ultrasonography, Prenatal

• UL1 TR000150 NCATS NIH HHS
• R01HD05565101 NICHD NIH HHS
• RC2HD064525 NICHD NIH HHS
• R01 HD055651 NICHD NIH HHS
• R01HD055651-03S1 NICHD NIH HHS
• RC2 HD064525 NICHD NIH HHS

• Chromosome Aberrations
• Comparative Genomic Hybridization/methods
• Female
• Humans
• Male
• Pregnancy
• Prenatal Diagnosis/methods

• abnormal ultrasound
• microarray
• array cgh < prenatal cytogenetics
• prenatal
• congenital anomalies
• soft markers

• Adult
• Bone and Bones/abnormalities
• Brain/abnormalities
• Chromosome Aberrations
• Comparative Genomic Hybridization
• Congenital Abnormalities/diagnostic imaging
• Congenital Abnormalities/genetics
• Female
• Heart Defects, Congenital/diagnostic imaging
• Heart Defects, Congenital/genetics
• Holoprosencephaly/diagnostic imaging
• Holoprosencephaly/genetics
• Humans
• Karyotyping
• Microarray Analysis/methods
• Mutation/genetics
• Pregnancy
• Prenatal Diagnosis/methods
• Retrospective Studies
• Ultrasonography, Prenatal

• Chromosome Aberrations
• Comparative Genomic Hybridization
• Female
• Humans
• Infant, Newborn
• Karyotyping
• Pregnancy
• Prenatal Diagnosis/methods
• Sensitivity and Specificity
• Tissue Array Analysis

To describe the diagnostic performance of array comparative genomic hybridization (aCGH) as a potential first line diagnostic method in first trimester high risk pregnancies.

In a retrospective study we performed aCGH using a targeted array BAC platform (Constitutional Chip® 4.0, PerkinElmer, Turku Finland, median resolution 600 kB) and the Affymetrix Cytogenetics® Whole Genome 2.7 M array (at a resolution of 400kB) on 100 anonymized prenatal samples from first trimester high risk pregnancies with normal conventional karyotype. We studied the technical feasibility and turn-around-time as well as the detection rate of pathogenic submicroscopic chromosome anomalies and CNVs of unknown significance.

We obtained results in 98 of 100 samples in 3 to a maximum of 5 days after DNA extraction. At the given resolution we did not identify any additional pathogenic CNVs but two CNVs of unknown significance in the chromosomal regions 1q21.1q21.2 (deletion) and 5p15.33 (duplication) (2%).

In accordance with a growing number of reports this study supports the concept that aCGH at a resolution of 400-600kB may be used as a first line prenatal diagnostic test with high diagnostic safety and rapid turn-around time in high-risk first trimester pregnancies. Detection rate of CNVs of unknown significance, considered as a major hindrance for replacing conventional karyotyping by aCGH, is 2%, but the diagnosis of additional submicroscopic anomalies in this heterogeneous group of patients seems to be rare.

To demonstrate the usefulness of microarray testing in prenatal diagnosis based on our laboratory experience.

Prenatal samples received from 2004 to 2011 for a variety of indications (n = 5003) were tested using comparative genomic hybridization-based microarrays targeted to known chromosomal syndromes with later versions of the microarrays providing backbone coverage of the entire genome.

The overall detection rate of clinically significant copy number alterations (CNAs) among unbiased, nondemise cases was 5.3%. Detection rates were 6.5% and 8.2% for cases referred with abnormal ultrasounds and fetal demise, respectively. The overall rate of findings with unclear clinical significance was 4.2% but would reduce to 0.39% if only de novo CNAs were considered. In cases with known chromosomal rearrangements in the fetus or parent, 41.1% showed CNAs related to the rearrangements, whereas 1.3% showed clinically significant CNAs unrelated to the karyotype. Finally, 71% of the clinically significant CNAs found by microarray were below the resolution of conventional karyotyping of fetal chromosomes.

Microarray analysis has advantages over conventional cytogenetics, including the ability to more precisely characterize CNAs associated with abnormal karyotypes. Moreover, a significant proportion of cases studied by array will show a clinically significant CNA even with apparently normal karyotypes. © 2012 John Wiley & Sons, Ltd.

Novel methodologies for detection of chromosomal abnormalities have been made available in the recent years but their clinical utility in prenatal settings is still unknown. We have conducted a comparative study of currently available methodologies for detection of chromosomal abnormalities after invasive prenatal sampling. A multicentric collection of a 1-year series of fetal samples with indication for prenatal invasive sampling was simultaneously evaluated using three screening methodologies: (1) karyotype and quantitative fluorescent polymerase chain reaction (QF-PCR), (2) two panels of multiplex ligation-dependent probe amplification (MLPA), and (3) chromosomal microarray-based analysis (CMA) with a targeted BAC microarray. A total of 900 pregnant women provided informed consent to participate (94% acceptance rate). Technical performance was excellent for karyotype, QF-PCR, and CMA (~1% failure rate), but relatively poor for MLPA (10% failure). Mean turn-around time (TAT) was 7 days for CMA or MLPA, 25 for karyotype, and two for QF-PCR, with similar combined costs for the different approaches. A total of 57 clinically significant chromosomal aberrations were found (6.3%), with CMA yielding the highest detection rate (32% above other methods). The identification of variants of uncertain clinical significance by CMA (17, 1.9%) tripled that of karyotype and MLPA, but most alterations could be classified as likely benign after proving they all were inherited. High acceptability, significantly higher detection rate and lower TAT, could justify the higher cost of CMA and favor targeted CMA as the best method for detection of chromosomal abnormalities in at-risk pregnancies after invasive prenatal sampling.

• Adult
• Chromosome Aberrations
• Chromosome Disorders/genetics
• Female
• Humans
• Karyotype
• Oligonucleotide Array Sequence Analysis/economics
• Pregnancy
• Prenatal Diagnosis/economics
• Prenatal Diagnosis/methods
• Sensitivity and Specificity

• Chromosome Disorders/diagnosis
• Chromosome Disorders/genetics
• Cytogenetic Analysis/methods
• Cytogenetic Analysis/trends
• Female
• Humans
• Italy
• Microarray Analysis/methods
• Polymorphism, Single Nucleotide
• Pregnancy
• Prenatal Diagnosis/methods