Best diagnostic approach for the genetic evaluation of fetuses after intrauterine death in first, second or third trimester: QF-PCR, karyotyping and/or genome wide SNP array analysis

Abstract

BackgroundThe aim of this study was to evaluate the best diagnostic approach for the genetic analysis of samples from first, second and third trimester intrauterine fetal deaths (IUFDs). We examined a total of 417 IUFD samples from fetuses with and without congenital anomalies. On 414 samples, karyotyping (N = 46) and/or rapid aneuploidy testing by QF-PCR (N = 371) was performed). One hundred sixty eight samples with a normal test result were subsequently tested by genome wide Single Nucleotide Polymorphism (SNP) array analysis. Three samples were only analyzed by array.ResultsIn 50 (12.0%) samples an aneuploidy was detected by QF-PCR and/or karyotyping, representing 47.1% of first, 13.2% of second and 3.4% of third trimester pregnancies. Karyotyping and QF-PCR failed in 4 (8.7%) and 7 (1.9%) samples, respectively, concerning mostly contaminated amniotic fluid samples from third trimester pregnancies.Clinically relevant aberrations were identified in 4.2% (all fetuses with malformations) of the 168 samples tested by SNP array. Inherited copy number variants (CNVs) were detected in 5.4% and 8.9% showed CNVs of unknown clinical relevance as parental inheritance could not be studied yet. In a sample from a fetus suspect for Meckel-Grüber syndrome, the genotype information from the SNP array revealed various stretches of homozygosity, including one stretch encompassing the CEP290 gene. Subsequent CEP290 mutation analysis revealed a homozygous, pathogenic mutation in this gene.ConclusionsBased on our experience we recommend QF-PCR as the first-line test in IUFD samples of first and second trimester pregnancies to exclude aneuploidy before performing array analysis. The chance to detect aneuploidy in third trimester pregnancies is relatively low and therefore array analysis can be performed as a first-tier test. A tissue sample, instead of amniotic fluid, is preferred because of a higher success rate in testing.We emphasize the need for analysis of parental samples whenever a rare, unique CNV is detected to allow for better interpretation of such findings and to improve future pregnancy management. Furthermore, we illustrate the strength of SNP arrays for genotype analysis, even though we realize it is crucial to have detailed phenotypic information to make optimal use of the genotype data in finding candidate recessive genes that may be related to the fetal phenotype.

Stillbirths: recall to action in high-income countries

“…Whichever test is used, a perinatal pathology service is important to establish stillbirth phenotype and to assess the meaning of newly described genetic variations. 39,40 …”

Efficient and cost-effective genetic analysis of products of conception and fetal tissues using a QF-PCR/array CGH strategy; five years of data

“…In our cohort, 1.5% (40/2718) of samples were found to have a fully penetrant clinically significant submicroscopic (<10 Mb) CNV, whilst 0.3% (9/2718) were found to have a neurosusceptibility CNVs (nsCNV) >1 Mb in size. Other published cohorts found clinically significant submicroscopic imbalance in 0.6% [6], 0.8% [10], 1.6% [8] of samples, although the Levy study [10] included nsCNV and CNVs of unknown significance in this group. The patient vs patient aCGH strategy provides a significant cost reduction compared with patient vs control testing.…”

“…However, the clinical utility of arrays for investigating pregnancy loss is still being established; the extent to which submicroscopic imbalance contributes to pregnancy loss and/or fetal abnormalities is unknown. The application of arrays for testing of fetal tissues was first described in 2004 [5]; since then there have been a limited number of published clinical cohorts [6–11]. Interpreting and reporting copy number variants (CNV) detected by aCGH in miscarriage samples is complex, given potential implications for familial testing and future pregnancies, and best practice has yet to be determined.…”

“Donating our bodies to science”: A discussion about autopsy and organ donation in Turner syndrome

“…For individuals with TS, genetic analysis of the chromosomal complement is a critical component of autopsy. The karyotype or metaphase chromosome analysis, is the usual “gold standard” for diagnosis of TS, but is not always accessible from autopsy specimens due to the requirement for fresh peripheral blood and special cell preparations (Kooper, Faas, Feenstra, de Leeuw, & Smeets, 2014). Chromosomal microarray analysis (CMA) or single nucleotide polymorphism (SNP) microarrays are viable alternatives to karyotypes, because they can utilize purified genomic DNA from any tissue and may be ordered as clinical tests.…”