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Concept: Aneuploidy

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BACKGROUND: Noninvasive prenatal detection of common fetal aneuploidies with cell-free DNA from maternal plasma has been achieved with high-throughput next-generation sequencing platforms. Turnaround times for previously tested platforms are still unsatisfactory for clinical applications, however, because of the time spent on sequencing. The development of semiconductor sequencing technology has provided a way to shorten overall run times. We studied the feasibility of using semiconductor sequencing technology for the noninvasive detection of fetal aneuploidy.METHODS: Maternal plasma DNA from 13 pregnant women, corresponding to 4 euploid, 6 trisomy 21 (T21), 2 trisomy 18 (T18), and 1 trisomy 13 (T13) pregnancies, were sequenced on the Ion Torrent Personal Genome Machine sequencer platform with 318 chips. The data were analyzed with the T statistic method after correcting for GC bias, and the T value was calculated as an indicator of fetal aneuploidy.RESULTS: We obtained a mean of 3 524 401 high-quality reads per sample, with an efficiency rate of 77.9%. All of the T21, T13, and T18 fetuses could be clearly distinguished from euploid fetuses, and the time spent on library preparation and sequencing was 24 h.CONCLUSIONS: Semiconductor sequencing represents a suitable technology for the noninvasive prenatal detection of fetal aneuploidy. With this platform, sequencing times can be substantially reduced; however, a further larger-scale study is needed to determine the imprecision of noninvasive fetal aneuploidy detection with this system.

Concepts: Pregnancy, Infant, Embryo, Fetus, Uterus, Fertility, Abortion, Aneuploidy

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Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly detrimental in oncology where rearrangements play diagnostic and prognostic roles. Here we describe the use of Hi-C as a tool for detection of both balanced and unbalanced chromosomal rearrangements in primary human tumour samples, with the potential to define chromosome breakpoints to bp resolution. In addition, we show copy number profiles can also be obtained from the same data, all at a significantly lower cost than standard sequencing approaches.

Concepts: Gene, Genetics, Cancer, Oncology, Tumor, Cytogenetics, Chromosomal translocation, Aneuploidy

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To review clinical validation or implementation studies of maternal blood cell-free (cf) DNA analysis and define the performance of screening for fetal trisomies 21, 18 and 13 and sex chromosome aneuploidies.

Concepts: DNA, Gene, Cancer, Eukaryote, Chromosome, Cytogenetics, Meiosis, Aneuploidy

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Purpose:Recent published studies have demonstrated the incremental value of the use of cell-free DNA for noninvasive prenatal testing with 100% sensitivity for trisomies 21 and 18 and a specificity of ≥99.7% for both. Data presented by two independent groups suggesting positive results by noninvasive prenatal testing were not confirmed by cytogenetic studies.Methods:Concordance of results among cases with noninvasive prenatal testing referred for cytogenetic prenatal and/or postnatal studies by karyotyping, fluorescence in situ hybridization, and/or oligo-single-nucleotide polymorphism microarray was evaluated for 109 consecutive specimens.Results:Cytogenetic results were positive for trisomy 21 in 38 of the 41 noninvasive prenatal testing-positive cases (true-positive rate: 93%) and for trisomy 18 in 16 of the 25 noninvasive prenatal testing-positive cases (true-positive rate: 64%). The true-positive rate was only 44% (7/16 cases) for trisomy 13 and 38% (6/16 cases) for sex chromosome aneuploidy.Conclusion:These findings raise concerns about the limitations of noninvasive prenatal testing and the need for analysis of a larger number of false-positive cases to provide true positive predictive values for noninvasive testing and to search for potential biological or technical causes. Our data suggest the need for a careful interpretation of noninvasive prenatal testing results and cautious transmission of the same to providers and patients.Genet Med advance online publication 07 August 2014Genetics in Medicine (2014); doi:10.1038/gim.2014.92.

Concepts: Positive predictive value, Chromosome, Type I and type II errors, Sensitivity and specificity, Cytogenetics, Aneuploidy, Trisomy, Karyotype

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With recent rapid advances in genomic technologies, precise delineation of structural chromosome rearrangements at the nucleotide level is becoming increasingly feasible. In this era of “next-generation cytogenetics” (i.e., an integration of traditional cytogenetic techniques and next-generation sequencing), a consensus nomenclature is essential for accurate communication and data sharing. Currently, nomenclature for describing the sequencing data of these aberrations is lacking. Herein, we present a system called Next-Gen Cytogenetic Nomenclature, which is concordant with the International System for Human Cytogenetic Nomenclature (2013). This system starts with the alignment of rearrangement sequences by BLAT or BLAST (alignment tools) and arrives at a concise and detailed description of chromosomal changes. To facilitate usage and implementation of this nomenclature, we are developing a program designated BLA(S)T Output Sequence Tool of Nomenclature (BOSToN), a demonstrative version of which is accessible online. A standardized characterization of structural chromosomal rearrangements is essential both for research analyses and for application in the clinical setting.

Concepts: DNA, Gene, Chromosome, Cytogenetics, Chromosomal translocation, Sequence, Aneuploidy, Metaphase

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Context: Recently, new clinically important information regarding Klinefelter syndrome (KS) has been published. We review aspects of epidemiology, endocrinology, metabolism, body composition, and neuropsychology with reference to recent genetic discoveries. Evidence Acquisition: PubMed was searched for “Klinefelter,” “Klinefelter’s,” and “XXY” in titles and abstracts. Relevant papers were obtained and reviewed, as well as other articles selected by the authors. Evidence Synthesis: KS is the most common sex chromosome disorder in males, affecting one in 660 men. The genetic background is the extra X-chromosome, which may be inherited from either parent. Most genes from the extra X undergo inactivation, but some escape and serve as the putative genetic cause of the syndrome. KS is severely underdiagnosed or is diagnosed late in life, roughly 25% are diagnosed, and the mean age of diagnosis is in the mid-30s. KS is associated with an increased morbidity resulting in loss of approximately 2 yr in life span with an increased mortality from many different diseases. The key findings in KS are small testes, hypergonadotropic hypogonadism, and cognitive impairment. The hypogonadism may lead to changes in body composition and a risk of developing metabolic syndrome and type 2 diabetes. The cognitive impairment is mainly in the area of language processing. Boys with KS are often in need of speech therapy, and many suffer from learning disability and may benefit from special education. Medical treatment is mainly testosterone replacement therapy to alleviate acute and long-term consequences of hypogonadism as well as treating or preventing the frequent comorbidity. Conclusions: More emphasis should be placed on increasing the rate of diagnosis and generating evidence for timing and dose of testosterone replacement. Treatment of KS should be a multidisciplinary task including pediatricians, speech therapists, general practitioners, psychologists, infertility specialists, urologists, and endocrinologists.

Concepts: Medicine, Endocrinology, Syndromes, Klinefelter's syndrome, Aneuploidy, Y chromosome, X chromosome, Mosaic

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We present rapid aneuploidy diagnosis of de novo partial trisomy 12q (12q24.21→qter) and partial monosomy 6q (6q27→qter) by aCGH using uncultured amniocytes in a fetus with coarctation of the aorta, ventriculomegaly and thickened nuchal fold. We discuss the association of TBX3, TBX5 and MED13L gene duplication with coarctation of the aorta, and the association of RNASET2 gene haploinsufficiency with ventriculomegaly in this case.

Concepts: DNA, Chromosome, Cytogenetics, Klinefelter's syndrome, Aneuploidy, Genetic disorders, Trisomy, Karyotype

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Context:Pseudohypoparathyroidism type 1b (PHP1b) is the result of end-organ resistance to PTH and other hormones such as TSH in the absence of any features of Albright’s hereditary osteodystrophy. Patients with PHP1b show imprinting abnormalities at the complex GNAS locus. The molecular cause of autosomal dominant familial PHP1b has been well-defined with identification of microdeletions within the GNAS locus or the nearby STX16, but the molecular mechanism of the GNAS imprinting defects in sporadic PHP1b cases remains elusive.Objective:We investigated the underlying molecular mechanism of GNAS imprinting defects in two patients with sporadic PHP1b.Results:We identified paternal uniparental disomy of the long arm of chromosome 20 (patUPD20) in two unrelated patients with sporadic PHP1b. This provides an explanation for the patients' GNAS methylation abnormalities and hormone resistance. Our data and a review of the six published cases of patUPD20 suggest that high birth weight and/or early-onset obesity and macrocephaly may also represent features of patUPD20.Conclusion:We suggest that patUPD20 should be considered in the evaluation of patients with sporadic PHP1b.

Concepts: DNA, Biology, Chromosome, Cytogenetics, Chromosomes, Aneuploidy, Pseudohypoparathyroidism, RIC8A

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OBJECTIVES: Karyotyping is a well-established method of investigating the genetic content of product of conceptions (POCs). Because of the high rate of culture failure and maternal cell contamination, failed results or 46,XX findings are often obtained. Different molecular approaches that are not culture dependent have been proposed to circumvent these limits. On the basis of the robust experience previously obtained with bacterial artificial chromosomes (BACs)-on-Beads™ (BoBs™), we evaluated the same technology that we had used for the analysis of prenatal samples on POCs. METHOD: KaryoLite™ BoBs™ includes 91 beads, each of which is conjugated with a composite of multiple neighboring BACs according to the hg19 assembly. It quantifies proximal and terminal regions of each chromosome arm. The study included 376 samples. RESULTS: The failure rate was 2%, and reproducibility >99%; false-positive and false-negative rates were <1% for non-mosaic aneuploidies and imbalances effecting all three BACs in a contig. Detection rate for partial terminal imbalances was 65.5%. The mosaic detection threshold was 50%, and the success rate in macerated samples was 87.8%. The aneuploidy detection rate in samples with cell growth failure was 27.8%, and maternal cell contamination was suspected in 23.1% of 46,XX cultured cells. CONCLUSION: KaryoLite™ BoBs™ as a 'first-tier' test in combination with other approaches showed beneficial, cost-effective and clearly enhanced POC testing. © 2012 John Wiley & Sons, Ltd.

Concepts: DNA, Gene, Cell nucleus, Bacteria, Chromosome, Failure, Aneuploidy, Y chromosome

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Purpose:A combination of oligonucleotide and single-nucleotide polymorphism probes on the same array platform can detect copy-number abnormalities and copy-neutral aberrations such as uniparental disomy and long stretches of homozygosity. The single-nucleotide polymorphism probe density in commercially available platforms varies widely, which may affect the detection of copy-neutral abnormalities.Methods:We evaluated the ability of array platforms with low (Oxford Gene Technology CytoSure ISCA uniparental disomy), mid-range (Agilent custom array), and high (Affymetrix CytoScan HD) single-nucleotide polymorphism probe density to detect copy-number variation, mosaicism, uniparental isodisomy, and absence of heterozygosity in 50 clinical samples.Results:All platforms reliably detected copy-number variation, mosaicism, and uniparental isodisomy; however, absence-of-heterozygosity detection varied significantly. The low-density array called absence-of-heterozygosity regions not confirmed by the other platforms and also overestimated the length of true absence-of-heterozygosity regions. Furthermore, the low- and mid-density platforms failed to detect some small absence-of-heterozygosity regions that were identified by the high-density platform.Conclusion:Variation in single-nucleotide polymorphism density can lead to major discrepancies in the detection of and confidence in copy-neutral abnormalities. Although suitable for uniparental disomy detection, copy-number plus single-nucleotide polymorphism arrays with 30,000 or fewer unique single-nucleotide polymorphism probes miscall absence-of-heterozygosity regions due to identity by descent.Genet Med advance online publication 4 April 2013Genetics in Medicine (2013); doi:10.1038/gim.2013.36.

Concepts: DNA, Gene, Genetics, Molecular biology, Copy number variation, Cytogenetics, Aneuploidy, Uniparental disomy