Recurrent Pregnancy Loss
Vincenzo Berghella in Obstetric Evidence Based Guidelines, 2022
Management of women with ≥2 RPLs should begin with genetic evaluation of products of conception (POCs) if possible (Figure 17.1) [15]. About 75% of early pregnancy losses in the first trimester result from random numeric chromosomal errors [16]. More than 50% of aneuploidies are trisomies; the most common single aneuploidy is 45,XO. Additionally, as maternal age increases, miscarriage associated with aneuploidy increases, accounting for up to 80% in those over 35 years of age [17]. Aneuploidy is typically considered sufficient explanation for pregnancy loss; this provides the couple with an explanation and has been shown to decrease self-blame [18]. Karyotype can be obtained directly from POCs; however, this test requires growing (dividing) cells to assess DNA in metaphase. Many times cells of abortuses do not grow in culture, especially those with aneuploidy. Potential pitfalls include culturing of maternal cell contaminants, falsely providing a “negative” test result (46,XX). Array comparative genomic hybridization (aCGH) does not require dividing cells and therefore can be useful in settings of culture failure. As such, aCGH has been suggested for use over karyotype.
Intracytoplasmic Sperm Injection
Botros Rizk, Ashok Agarwal, Edmund S. Sabanegh in Male Infertility in Reproductive Medicine, 2019
PGT: Originally, aneuploidy screening by PGT was done by cleavage stage embryo biopsy and chromosome analysis using fluorescence in situ hybridization (FISH); but this technique has stopped as not all chromosomes are analyzed and more importantly the incidence of mosaicism was found to be more frequent in day-3 embryo blastomeres. Currently IVF specialists conduct day-5 trophectoderm biopsy on blastocysts with more precise molecular diagnostic technologies including microarray technologies or next-generation sequencing (NGS) [54]. The diode LASER is used to get a small opening in the ZP and about three trophectoderm cells are aspirated with moderate suction for each blastocyst (Figure 19.3). The Microarray-based comparative genomic hybridization (aCGH) technique cannot be used to test balanced translocations (reciprocal or Robertsonian translocations, inversions, and insertions), and some unbalanced translocations such as point mutations, trinucleotide expansions, small deletions, and duplications because they are beyond the resolutions of the method while NGS can. The same concerns about embryo mosaicism, self-correction, and restriction of the abnormal cells in the trophectoderm are still present even after the use of the recent molecular diagnostic technologies [55].
Preimplantation Genetic Testing of Aneuploidies (PGT-A)
Carlos Simón, Carmen Rubio in Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
While aneuploidy may be more commonly seen in specific chromosomes at miscarriage, at the embryo stage it can affect any chromosome and thus a broader platform is required if PGT-A is to be clinically effective, accepted, and implemented widely. The development of novel technologies in the late 2000s facilitated the transition from FISH-based analysis to comprehensive chromosomal screening (CCS) methodologies. CCS is a catch-all term that includes array comparative genomic hybridization (aCGH), real-time quantitative PCR (RT-qPCR), and next-generation sequencing (NGS). NGS, at the time of writing, is the preferred platform in terms of current usage. In addition to identifying chromosome copy number differences across all chromosomes, these techniques also offer superior resolution and additional karyotype information, such as detection of segmental aneuploidy and embryonic mosaicism [14].
Extent of resection predicts risk of progression in adult pilocytic astrocytoma
Published in British Journal of Neurosurgery, 2019
Andrew J. Nelson, Rasheed Zakaria, Michael D. Jenkinson, Andrew R. Brodbelt
Molecular tumour charecteristics are being developed. Standardized assessment of proliferating cell nuclear antigen (PCNA) to investigate tumour cell growth kinetics in pilocytoc astrocytomas may be a useful, independent indicant of biological behaviour.18 Whole genome interrogation has shown single point aberrations of the mitogen-activating protein kinase (MAPK) pathway in nearly all cases.19 The most commonly observed mechanism gives rise to a transforming fusion protein with BRAF kinase domain.19 Whilst not yet commonplace, array comparative genomic hybridization (aCGH) analysis is being used to identify a variety of novel, subtle genomic changes which may liberate clinically useful diagnostic and therapeutic biomarkers.20 Although specific to supratentorial tumours, the histological characteristis of adult pilocytic astrocytomas are known to include nuclear abnormalities, mitoses and endothelial proliferation.6
Advances in genetic testing and optimization of clinical management in children and adults with epilepsy
Published in Expert Review of Neurotherapeutics, 2020
Marcello Scala, Amedeo Bianchi, Francesca Bisulli, Antonietta Coppola, Maurizio Elia, Marina Trivisano, Dario Pruna, Tommaso Pippucci, Laura Canafoglia, Simona Lattanzi, Silvana Franceschetti, Carlo Nobile, Antonio Gambardella, Roberto Michelucci, Federico Zara, Pasquale Striano
The array comparative genomic hybridization (array CGH) is a molecular cytogenetic method suitable for DNA copy number variants (CNVs) analysis, such as deletions or duplications. This technique is based on the quantitative comparison between test DNA extracted from peripheral blood lymphocytes of the proband and reference DNA from healthy donors, using competitive fluorescence in situ hybridization (FISH). The resolution power is variable, ranging from 1 Mb to 100 kb, but it is at least 100-fold higher than traditional cytogenetics. Rare CNVs, some of which involve known morbid genes, contribute to approximately 10% of infantile epilepsies and 5% of epileptic encephalopathies, overall [29]. In large cohorts, array CGH studies further showed recurrent deletions in 15q13.3, 16p13.11, and 15q11.2 in patients with focal epilepsies or generalized epilepsies with ID, suggesting that these rearrangements might represent susceptibility factors for these conditions [30–32]. When epilepsy is not associated with ID or dysmorphic features/malformations, the diagnostic impact of array CGH appears to be lower [33,34].
Determining the accuracy of next generation sequencing based copy number variation analysis in Hereditary Breast and Ovarian Cancer
Published in Expert Review of Molecular Diagnostics, 2022
Nihat Bugra Agaoglu, Busra Unal, Ozlem Akgun Dogan, Payam Zolfagharian, Pari Sharifli, Aylin Karakurt, Burak Can Senay, Tugba Kizilboga, Jale Yildiz, Gizem Dinler Doganay, Levent Doganay
CNVs can be detected by several different methods like array-comparative genomic hybridization (aCGH) and single nucleotide polymorphism array (SNP-array). Both are hybridization-based methods, and despite easy application, their resolution is low, and it is not possible to determine the breakpoint regions. On the other hand, methods like real-time PCR (qPCR), fluorescent in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA) can also be used to determine the CNV regions. The most significant disadvantage of these methods is that they can only be applied to the regions known to carry CNVs. Moreover, it is not cost-effective to apply these methods in genes with many exons like BRCA1 and BRCA2. Today with advanced analysis tools, in addition to SNVs, it is possible to determine structural variants like CNVs by next generation sequencing (NGS) in a single run [19,20]. The data generated by NGS can be used for prescreening of CNVs by bioinformatics algorithms in cancer predisposition genes [21–26]. There are different tools available for the interpretation of CNVs by NGS, and many of these tools use different methods like read depth, GC content and a combination of all these [24–26]. Although the results are promising, the reliability of the analysis tools are still controversial and the findings are still in need of validation for diagnostic purposes.
Related Knowledge Centers
- Copy Number Variation
- Cytogenetics
- DNA
- Fluorescence In Situ Hybridization
- Fluorophore
- G Banding
- Ploidy
- Chromosome
- Chromosome Regions
- Base Pair