Aneuploidy is a significant cause of developmental disease, with frequency close to 50% in spontaneous abortions and 0.5% in live born individuals (1
). Very few human chromosome aneuploidies are seen in liveborn individuals; however, mosaic aneuploidy is better tolerated. Uniparental disomy (UPD) is another mechanism for disturbance of human gene expression that can lead to human disease, and mosaic aneuploidy has been shown to be associated with UPD in some cases (4
). In this work, we demonstrate the utility of a genome-wide single nucleotide polymorphism (SNP) array to identify the mechanisms causing mosaic chromosome aneuploidy and UPD. This analysis provides a window into the mechanisms of aneuploidy occurrence by observation of the genotypes in the disomic and trisomic cell lines.
Chromosomal mosaicism is defined as the presence of two or more different chromosome complements within an individual developed from a single zygote. Mosaicism has been reported for many types of chromosome abnormalities including trisomy, monosomy, triploidy, deletions, duplications, rings and other types of structural rearrangements. Mosaic aneuploidy is the most common type of mosaicism (1
). Recent studies on early human embryos have demonstrated that over 50% of embryos generated by in vitro
fertilization are mosaic for a chromosome anomaly, underlining the high frequency of non-disjunction (8
). Mosaic aneuploidy can arise from meiotic events, with an abnormal zygote and loss of one copy of a trisomic chromosome in some cells during development, or mitotically, with a normal zygote, and a subsequent non-disjunction or anaphase lag during a somatic division. These different mechanisms have a profound effect on the developing fetus. In the cases where the non-disjunction occurred meiotically, it is likely that there is a trisomic constitution in the very early stages of development, where correct chromosome number might be very important (12
). Alternatively, in the cases of mitotic origin of the trisomy, early development proceeded normally, with trisomy originating further along in development, and possibly affecting only a subset of tissues. Previous work has shown that there is a chromosome-specific bias in the proportion of meiotically to mitotically occurring non-disjunctions (12
Another consequence of meiotically originating trisomies is the risk for UPD in the disomic cell line. In the case of a meiotic trisomy, with mitotic loss of one copy of the duplicated chromosome (also referred to as trisomy rescue), the cells that have lost one copy of the trisomic chromosome are at risk for UPD, where the chromosomes that remain are both from the same parent. UPD is well known to cause disease if the chromosome contains an imprinted gene, or if a recessive disease allele is uncovered. There are three primary mechanisms by which UPD can occur: (i) trisomy rescue, whereby there is mitotic loss of one of the three copies of the trisomic chromosome; (ii) monosomy duplication in which the lone copy of a chromosome pair is duplicated via non-disjunction or (iii) gamete complementation, whereby a gamete that is missing one chromosome pair unites with a gamete containing two copies of that pair, by chance (4
). Each of these mechanisms have been reported, although trisomy rescue is thought to be the most common of the three mechanisms (7
). UPD cannot be identified by standard cytogenetic techniques. Rather, when UPD is suspected based on clinical or cytogenetic features, analysis of specific chromosomes is undertaken using molecular markers or by analysis of methylation patterns for the chromosomal region of interest.
Chromosomal mosaicism can be identified cytogenetically, but identification of lower levels of mosaicism can be challenging, as many cells have to be counted. It has been estimated that analysis of 20 cells (standard for routine chromosome analysis) will detect 14% mosaicism (in the tissue being studied) with 95% confidence (14
). The level of mosaicism detected goes down when the number of cells is increased, however analysis of more cells is not normally carried out unless there is a suspicion for chromosomal mosaicism. In addition, for some types of mosaicism, the abnormal cells as well as the normal cells may not divide, so analysis of metaphases might provide a biased view of the true chromosome constitution of this individual. This metaphase bias against abnormal cells has been conclusively demonstrated for some abnormalities, such as the isochromosome 12p seen in patients with Pallister Killian syndrome (15
). Array analysis by comparative genomic hybridization or SNP array analysis offers several advantages for detection of mosaicism compared with chromosome analysis in which (i) a large number of cells can be surveyed at once, since DNA is extracted from a culture of many cells and (ii) both interphase and metaphase cells are analyzed, eliminating the culture bias introduced by analysis of metaphase cells only.
We have used a genome-wide SNP array for our genomic analyses. Genome-wide SNP arrays use a combination of intensity and genotyping data that provide high-resolution means to diagnose genomic abnormalities that cause clinical disease. The use of genome-wide SNP arrays permits the simultaneous evaluation of copy number to detect mosaic gains and losses, and UPD, in cases of isodisomy or isodisomic regions secondary to recombination. In the case of heterodisomy, UPD diagnosis by SNP array can be accomplished if parental DNA is analyzed.
Chimerism is similar to mosaicism in that it is defined by the presence of two genetically distinct cell lines; however, in the case of chimerism there is fusion of two different zygotes within a single embryo (16
). Chimerism is often recognized because there are both 46,XX and 46,XY cell lines, which sometimes manifest clinically, but are readily discernable cytogenetically. Cytogenetic analysis are unable to detect chimerism without a difference in sex chromosome constitution between the two cell lines. Detection in these instances requires molecular analysis if chimerism is suspected. The use of a genome-wide SNP array makes the differentiation of chimerism and mosaicism possible, as the additional presence of extra genotypes in the chimeras is readily detectable. In this study, we analyzed a phenotypic male with multiple clinical abnormalities and 46,XX and 46,XY cell lines, and demonstrate that his genotypes are consistent with chimerism. We are able to propose a mechanism for the origin of his 46,XX cell line, which explains his clinical abnormalities.
We present data on a cohort of patients with mosaic chromosome abnormalities to provide information on the timing and origin of the mosaicism, mechanism by which the abnormality occurred, and frequency of UPD in these patients. We have also studied 11 patients with UPD, both segmental and whole chromosome, and were able to diagnose the mechanism by which these occurred, and provide information relevant to recurrence risks for these individuals.