Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue

Abstract

BackgroundDetermination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on “rescue karyotyping”, wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH).MethodsA retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX).ResultsRescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p = 0.14) or gestational age at pregnancy loss (p = 0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants.ConclusionsRescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy loss.

Deletion 21pterq22.11: Report of a Patient with Dysmorphic Features, Hypertonia, and Café-au-Lait Macules and Review of the Literature

“…With the introduction of molecular methods for investigation, such as FISH, MLPA, and chromosomal microarray, a larger number of patients with these deletions are being identified. The precise breakpoints and deletion size determinations have allowed better genotype-phenotype correlations [Kudesia et al, 2014]. In this study, we report a patient with a deletion 21pterq22.11 due to a chromosome rearrangement in which the 21q22.11qter segment was translocated to 12p13.…”

Comprehensive genetic analysis of pregnancy loss by chromosomal microarrays: outcomes, benefits, and challenges

“…The superior diagnostic power of CMA compared with karyotyping is well established in the pediatric and prenatal literature; however, exploration of the use of this technology for studying POC samples has been somewhat limited to date. 9,10,12,14,15,18,[20][21][22][23][24][25][26][27][28] Specifically, CMA is a particularly attractive technology for use in the study of POC samples because it is performed using extracted cellular DNA, significantly improving the likelihood of obtaining a result. Unlike karyotype analysis, CMA can even be performed on DNA extracted from formalin-fixed and paraffin-embedded tissues (FFPE), a process that is undergone by nearly every POC sample subjected to histopathological evaluation.…”

Genetic Considerations in Recurrent Pregnancy Loss

“…Genetic testing of POCs using nonculturebased techniques such as array comparative genomic hybridization with or without reflex microsatellite single nucleotide polymorphism (SNP) analysis (Rajcan-Separovic et al 2010;Viaggi et al 2013;Mathur et al 2014) (discussed below) is more precise, more detailed, and more reliable than culture-based methods and should add to cost-efficiency and overall utility. Nonculture-based techniques have been used successfully in fresh and in preserved tissues (Kudesia et al 2014;Mathur et al 2014). …”