Utility of SNP arrays in detecting, quantifying, and determining meiotic origin of tetrasomy 12p in blood from individuals with Pallister–Killian syndrome

Abstract

Identification of the isochromosome 12p (i(12p)) associated with Pallister-Killian syndrome is complicated by the low frequency of this supernumerary chromosome in PHA stimulated peripheral blood lymphocytes, and frequently requires cytogenetic analysis of fibroblast cells. Recently, it has been shown that array CGH techniques are able to detect tetrasomy 12p in peripheral blood, even when not identified by traditional cytogenetic techniques. We studied 15 patients with a previous cytogenetic and clinical diagnosis of Pallister-Killian syndrome using genome-wide SNP arrays to investigate the ability of this platform to identify the i(12p) in blood and tissue. Array analysis verified tetrasomy 12p in all samples from fibroblasts, but was only able to detect it in 46% of blood samples. The genotyping information available from the SNP arrays allowed for the detection of as low as 5% mosaicism, as well as suggesting a Meiosis II origin for the isochromosome in the majority of patients. Analysis of the percentage of abnormal cells with patient age at time of study suggests that the frequency of the i(12p) decreased with age in blood, but not in fibroblasts. These highlight the power of SNP arrays in detecting and characterizing the isochromosome 12p in Pallister-Killian syndrome as well as underscoring the important utility of traditional cytogenetic techniques.

Somatic mosaicism: implications for disease and transmission genetics

“…SNP microarrays, meanwhile, measure the allele frequency of alternative alleles at polymorphic loci. Resolution is limited by availability of known polymorphic SNPs, but by searching for slight deviation from expected allele frequencies (0, 0.5, and 1), mosaicism for CNVs of modest size can be detected as low as 5% [58,59]. …”

Detection of structural mosaicism from targeted and whole-genome sequencing data

“…There are two possible explanations for the disparity in tissue distribution we observed, first, that the epithelium-derived mutational events occurred late, i.e., after the differentiation of lymphocytes and epithelial cells; or second, that these events occurred early, i.e., prior to the split between lymphocytes and epithelial cells with subsequent removal from blood cell lineages by purifying selection. Several lines of evidence suggest the second explanation is more likely: (1) existing precedent, as the second phenomenon has been directly observed in Pallister-Killian syndrome, in which the percentage of abnormal cells decreases with age in blood but not fibroblasts (Conlin et al 2012), and tissue-limited mosaicism has been observed in mosaic tetrasomies of Chromosomes 5p, 8p, 9p, and 18p (Choo et al 2002); (2) the clonality of events observed in both blood and saliva is not greater than the clonality of events in only saliva, which would be expected if events seen across tissue arose earlier in development; and (3) both observed LOH events are shared between tissues but only one of nine CNV events are shared between tissues, perhaps suggesting increased pathogenicity of CNV events compared to copy-neutral events, thus, more likely to be negatively selected in blood. Given these considerations underlying the disparity in tissue type and the observation that the majority of observed abnormalities were detected in saliva but not blood, it is possible that, compared to the sampling of saliva, the sampling of blood could lead to a substantial loss of power (possibly <50% power) to detect pathogenic structural mosaicism, resulting in missed diagnoses.…”

Pallister-Killian syndrome

“…The diagnosis of PKS can thus be frequently missed due to the tissue-specific nature of mosaicism, and usually is not detected in rapidly dividing cells such as the peripheral blood cells [6,22]. There are very few reported cases in which the isochromosome was diagnosed in peripheral lymphocytes [23]. The detection rate is 0–2% in lymphocytes, 50–100% in fibroblasts, and 100% in amniocytes and bone marrow cells [24].…”