A rapid and reliable chromosome analysis method for products of conception using interphase nuclei

Abstract

BackgroundKaryotype determination has a central role in the genetic workup of pregnancy loss, as aneuploidy (trisomy and monosomy) and polyploidy (triploidy and tetraploidy) are the cause in at least 50% of first trimester, 25% of second trimester, and 11% of third trimester miscarriages. There are several limitations with the current approaches of obtaining a karyotype using traditional cytogenetics, fluorescence in situ hybridization with a limited number of probes, and chromosomal microarray. These include culture failure, incomplete results, lower sensitivity, and longer reporting time.MethodsTo overcome current limitations, a novel molecular assay is developed with a Standard Resolution Interphase Chromosome Profiling probe set which is a variation of the recently developed High Resolution probe set. It generates a molecular karyotype that can detect all major changes commonly associated with pregnancy loss. Initial familiarization of signal patterns from the probe set was used, followed by validation of the method using 83 samples from miscarriages in a blind study from three different laboratories. Finally, the clinical utility of the method was tested on 291 clinical samples in two commercial reference laboratory settings on two different continents.ResultsThe new molecular approach not only identified all the chromosome changes observed by current methods, but also significantly improved abnormality detection by characterizing derivative chromosomes and finding subtle subtelomeric rearrangements, balanced and unbalanced. All Robertsonian translocations were also detected. The abnormality rate was 54% on clinical samples from commercial laboratory 1 and 63% from laboratory 2.ConclusionThe attributes of this method make it an ideal choice for the genetic workup of miscarriages, namely (1) near 100% successful results, (2) greater sensitivity than conventional chromosome analysis or FISH panels, (3) rapid reporting time, and (4) favorable comparisons with chromosomal microarray.

Applying high‐throughput sequencing to identify and evaluate foetal chromosomal deletion and duplication

“…In simulation experiments, about 40% of CNVs with 50‐400 kb could be detected under a foetal DNA concentration of 13% 22 . Taken together, foetal DNA concentration, the size of deletion and duplication fragments, statistical methods and coverage depth are key factors for detection accuracy of high‐throughput sequencing for foetal chromosomal deletions and duplications 23‐25 …”

Clinical application of single nucleotide polymorphism microarray analysis in pregnancy loss in Northwest China

“…The SNP probes are designed to help detect contamination of maternal cells in POCs, eliminating the need for the short tandem repeat test for samples in POC samples. In addition, for CNV analysis, the double validation of both the CNV probe and the SNP probe in the SNP array ensures the accuracy of copy number variation detection, which has been confirmed in several studies ( Shah et al, 2017 ; Babu et al, 2018 ; Smits et al, 2020 ). While the SNP array offers numerous advantages, it shares some limitations with aCGH and CNV-seq.…”

Polyploidy Phenomenon as a Cause of Early Miscarriages in Abortion Materials

“…Most chromosomal disorders are sporadic and have little risk of recurrence, but their analysis is important for couples and has a prognostic value in terms of the next pregnancy [ 18 ]. Chromosomal problems in the form of aneuploidy (trisomy-monosomy) and polyploidy (triploidy-tetraploidy) are determining factors in at least 50% of first trimester abortions, 25% of second, and 11% of third trimester miscarriages [ 19 ]. Cytogenetic analysis of conception products (POCs) can be done to identify the genetic cause of miscarriages, to predict recurrence risk, and to provide important information for genetic counseling and reproductive planning.…”