Original article A clinical algorithm for efficient, high-resolution cytogenomic analysis of uncultured perinatal tissue samples Eric K. Morgen a, b , Georges Maire a, b , Elena Kolomietz a, b, * a Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Canada b Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada article info Article history: Received 10 November 2011 Accepted 17 April 2012 Available online 28 April 2012 Keywords: Oligonucleotide array comparative genomic hybridization Quantitative fluorescence polymerase chain reaction Products of conception Gestational trophoblastic disease Molecular diagnosis abstract Purpose: Cytogenetic analysis of solid tissue is indispensable in perinatal care, reproductive planning, and detection of gestational trophoblastic disease. Unfortunately, methods in common use suffer from drawbacks including culture artifact, low resolution, and high cost. We propose a new diagnostic algo- rithm based on direct genetic analysis of tissues (without cell culture) using QF-PCR and array CGH. Methods: Study samples consisted of specimens submitted to the cytogenetics laboratory between January and June of 2011 that were split and analyzed in parallel by our traditional algorithm (culture and G-banding, plus an interphase FISH aneuploidy panel for culture failures) and the proposed “no-culture” algorithm (first line QF-PCR, plus array CGH on normal QF-PCRs). Data on clinical impact, cost, and turnaround time were collected. Results: Forty specimens were included. The algorithms produced results that were fully concordant in 22 cases, partially concordant in 9 cases, and discordant in 9 cases. The no-culture algorithm detected new, clinically-significant abnormalities in 8 of 40 cases (20%), corrected the sex chromosome assortment in 1 case, reduced the analysis failure rate from 10% to 0%, and provided at least one of these three important benefits in 12 of 40 cases (30%). The algorithm also demonstrated a reduced cost per-specimen and per diagnosis, as well as improved turnaround time, with virtually all cases reported per guidelines. Conclusion: These striking results favor the “no-culture” algorithm, which may have the potential to replace standard cytogenetic methods in the clinical laboratory. Ó 2012 Elsevier Masson SAS. All rights reserved. 1. Introduction Cytogenetic analysis of solid tissue is an essential tool in peri- natal care and reproductive planning. According to current practice guidelines, it is indicated for the investigation of spontaneous abortions as well as congenital anomalies or growth retardation noted post-mortem (in autopsy specimens, stillbirths, and products of conception-POC) [1]. In many of these circumstances, combined cytogenetic and pathologic evaluation lends all of the benefits inherent in a clinical autopsy: providing closure to family members, improving care for future patients, and diagnosing conditions relevant to surviving family members [2,3]. The last is particularly important, encompassing i) screening for heritable syndromes or potentially-recurrent chromosomal abnormalities, ii) providing information for reproductive planning or workup of recurrent pregnancy loss, and iii) detecting gestational trophoblastic disease. 1.1. Reproductive planning Spontaneous abortions affect 12e13% of clinically-recognized pregnancies [4,5], 31% of biochemically-identified pregnancies [6], and are most often (50e70%) due to fetal chromosome abnormal- ities, of which 86% are numerical, 6% structural, and 8% other problems, including mosaicism [7]. Here, cytogenetic analysis offers valuable information: an aneuploid result provides a definite cause for pregnancy loss and may indicate a higher risk of a future aneuploid pregnancy [8], a euploid result can prompt evaluation for recurrent miscarriage [3], and structural anomalies e inherited in 50% [7] e necessitate cytogenetic evaluation of both partners prior to another pregnancy [3]. Cytogenetic analysis is also helpful in recurrent miscarriage, a condition defined by a history of three or more spontaneous abortions and which affects 1e2% of women [9]. Recurrent miscarriage has numerous potential causes that include endocrine, environmental, immunologic, anatomical, and genetic factors [10], but 50% of couples will have no identifiable cause [9]. These patients often undergo an expensive, time-consuming, multi-physician workup to rule out all possible etiologies [3]. For the 5% of cases with a cytogenetic abnormality detectable * Corresponding author. Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, 600 University Avenue, 6th floor Rm 6-500, Toronto, Ontario, Canada M5G 1X5. Tel.: þ1 416 586 4800x3969; fax: þ1 416 586 8882. E-mail address: ekolomietz@mtsinai.on.ca (E. Kolomietz). Contents lists available at SciVerse ScienceDirect European Journal of Medical Genetics journal homepage: http://www.elsevier.com/locate/ejmg 1769-7212/$ e see front matter Ó 2012 Elsevier Masson SAS. All rights reserved. doi:10.1016/j.ejmg.2012.04.005 European Journal of Medical Genetics 55 (2012) 446e454