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

Rashmi Kudesia,Ankita Patel,Zev Williams,Marilyn Li,Janice Smith

doi:10.1186/1477-7827-12-19

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.

Highlights

Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL)
A critical initial step in the evaluation of recurrent pregnancy loss is to perform cytogenetic analysis of the products of conception (POCs) in order to determine whether aneuploidy was the cause of the loss
For the purpose of retrospectively or “rescue” karyotyping, we adapted array-based comparative genomic hybridization (aCGH) analysis of DNA extracted from paraffin embedded tissue, a technique widely used in analysis of tumor samples, to analysis of paraffin embedded POCs. This technique provides the potential to obtain detailed cytogenetic information from previously collected paraffin-embedded conceptual tissue. We propose this technique as a method of obtaining useful cytogenetic information for patients who require karyotype results but have had either no attempts or failed attempts at conventional karyotyping at the time of prior losses

Summary

Introduction

Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). Obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Diagnosing the cause of a pregnancy loss is Chromosomal abnormalities account for up to 75% of first trimester pregnancy losses [3,4,5,6,7,8,9,10] Given this high frequency, a critical initial step in the evaluation of recurrent pregnancy loss is to perform cytogenetic analysis of the products of conception (POCs) in order to determine whether aneuploidy was the cause of the loss. If aneuploidy was not the cause, a further work-up is indicated

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