Usefulness of the SNP microarray technology to identify rare mutations in the case of perinatal death

Introduction

Genomic rearrangements such as microdeletions and microduplications, referred to as copy number variants (CNVs), play a fundamental role in human evolution and phenotypic variability. In particular, CNVs have been associated with a wide variety of complex disorders, including birth defects and neurodevelopmental disorders [1]. The SNP microarray technology has proven valuable to identify such rare CNVs providing a much higher resolution than traditional cytogenetic analysis. The relative low cost of this assay raises the possibility that this technique may become a standard tool to explore the genetic causes of unexplained foetal maldevelopment and death.

Clinical report and methods

Results

The SNP microarray analysis identified one duplication and two deletions in the female twin (Table 1 and Figure 1). The duplication at chr1p31.1 spans 298 kbp and includes exon 2–4 of the gene ST6GALNAC3. It is unclear whether the mutant gene directs the synthesis of a functional protein or in contrary is equivalent to a null mutant due to erratic splicing or additional exon-encoded domains. Two similar duplications spanning exon 2–3 are reported in the DGV database and ISCA consortium, respectively. Two duplications of the entire ST6GALNAC3 gene were identified by the ISCA consortium while a similar duplication was observed de novo in the Icelandic sample. These whole-gene duplications all have the potential to result in two independent, functional transcription units.

Figure 1

The intensity plot of the duplication at chr1p31.1 from Disease miner developed at deCODE Genetics.

The B allele frequencies (purple) and the Log R ratios (blue) are plotted on the y-axis and the genomic positions (hg18) are displayed on the x-axis. The green square indicates the duplication detected by the PennCNV algorithm. The known genes from the UCSC genome browser are displayed below the intensity plot.

A 163.5-kbp deletion is observed at chrXq27.3 in the intergenetic region more than 329 kbp from the nearest genes UBE2NL and SPANXN1, thus unlikely to affect expression directly (Table 1). Much larger deletions spanning the whole deleted region and neighbouring genes at Xq27.3 were reported by the ISCA consortium and found de novo in the Icelandic sample (n=74 and n=4, respectively). In addition, a number of smaller deletions were reported in this region in the DGV database. Both location and number of reported deletion carriers indicate that the deletion may be benign.

A 250.1-kbp deletion is observed at chr22q11.23 that eliminates the genes IGLL3, LRP5L, and CRYBB2P1 (Table 1). Numerous deletions (n>40) of the three genes – although with variable size and breakpoints – were found in the DGV database, the ISCA consortium database, the Danish and Icelandic samples which suggest that these genes are not vital for survival.

Discussion

In the present case report we identify three CNVs in a female twin of perinatal death using the SNP microarray technology and demonstrate the usefulness of the SNP microarray technology to detect CNVs that would escape detection by traditional cytogenetic analysis.

The three identified CNVs cannot unambiguously be causally linked to the death of the case twin, but several aspects deserve discussion.

The duplication at chr1q31.1 affects the gene ST6GALNAC3 that encodes an enzyme involved in the biosynthesis of gangliosides [4] that seems to be important for normal development and function. The genome wide association studies have previously associated SNPs in this gene with variability in human electroencephalogram [5], nicotine dependence [6], subcutaneous fat thickness [7], and elevated liver enzymes [8]. Also, ST6GALNAC3 is highly expressed during embryonic brain development in rat and mice [9], and in mice null-mutations in genes essential for the ganglioside biosynthesis lead to neurodegeneration and premature death [10].

The CNV at chr22q11.13 deletes three genes involved in the immune system, endocytotic process and eye lens generation, and might, therefore, be expected to affect key physiological processes. Nonetheless, the CNV itself is unlikely to affect human development as it is found in numerous healthy individuals.

The deletion at chrXq27.3 is located distantly from known genes, which argue against a functional impact on key physiological processes. Curiously, the 74 deletions spanning Xq27.3 reported by the ICSA consortium are interpreted as pathogenic, although the reason for this classification remains obscure.

The identified CNVs do hold a potential to affect biological processes, and, therefore, we cannot exclude that two or three of these genomic alterations in concert may confer liability to the severe physiological stress of the transfusion syndrome that the case twin was exposed to and thus contributed to the premature death.

Funding

This study was financed through grants to Dr. Werge from the Lundbeck Foundation (R34-A3243), the Danish National Advanced Technology Foundation (001-2009-2), the Danish Council for Independent Research in Medical Sciences, the Danish Psychiatric Research Foundation and the European Union (LSHM-CT-2006-037761). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.