Genome Wide SNP Analysis Reveals Frequent Uniparental Disomy (UPD) Due to Somatic Recombination in Acute Myeloid Leukemias.
Authors: Raghavan Manoj , Lillington Debra , Skoulakis Spyros , Debernardi Silvana , Chaplin Tracy , Foot Nicola J. , Lister T. Andrew , Young Bryan D. 
Published: April 2020

Many cases of AML have either a normal karyotype or non-recurrent chromosomal abnormalities and hence their pathogenesis remains obscure. The introduction of array-based analysis of single nucleotide polymorphisms (SNPs) allows the rapid determination of genome-wide allelic information at a high density for a DNA sample. High-resolution SNP genotype analysis was performed on 64 presentation AML samples with full karyotype information as follows: normal karyotype [40], t(8;21) [5], t(15;17) [4], inv16 [3], 11q23 [2],−7 [3],+8 [2] and other structural abnormalities [7]. Using the 10K SNP array (Affymetrix, Inc., Santa Clara) 9, a mean call rate of 93.3% yielded more than 10,000 SNP genotype calls per sample.

Large unexpected regions of homozygosity were observed in 12 AMLs (18.75%). These regions ranged in size from 16 million base pairs to 113 million base pairs and would have been visible in the karyotypes if due to deletion. Remission bone marrow samples from 5 of those patients were subjected to SNP genotype analysis. The SNP call data demonstrated clearly that the homozygosity seen in the leukemic DNA was not present in the respective remission bone marrow DNA. Fluorescence in situ hybridisation (FISH) demonstrated 2 signals for probes within regions of homozygosity. Furthermore, hybridisation signal values on the SNP arrays demonstrated that regions of homozygosity did not differ from the rest of the chromosome. It was therefore concluded that such homozygous regions corresponded to uniparental disomy (UPD) due to somatic recombination events occurring during development of the leukemias. There appears to be a non-random distribution of UPD with 5 events on chromosome 11, 2 on chromosome 6, 2 on chromosome 9 and 1 on chromosomes 13, 19 and 21. As expected for somatic recombination, homozygosity continued to the telomere in most cases. Any parental bias in UPD could be evidence of a role for imprinted genes. This issue was investigated using the H19 gene, which is located at 11p15 and is normally methylated only on the paternal allele. Two leukemias exhibited UPD including 11p15 and the methylation status of the H19 gene was therefore determined by bisulfite sequencing. One leukemia with UPD11p exhibited a homozygous methylated paternal pattern, while the other example of UPD11p showed a homozygous non-methylated maternal pattern. These data show that the UPD seen on 11p is not restricted to a single parental origin. In a previous analysis, the leukemia with UPD19q was shown to be homozygous for a CEBPA mutation and FISH demonstrated 2 copies of the CEBPA gene. This gene is located at 19q13.1, within the area of UPD and we conclude that the mutation occurred prior to the UPD. We can therefore speculate that an important consequence of UPD could be to unmask pre-existing mutations. A total of 8 different chromosomal regions have been shown to be affected by UPD in this study and this may suggest that there are at least this number of mutational targets. The discovery of widespread, somatically acquired, UPD in leukemias has potentially important clinical implications. 20% of the normal karyotype AMLs was found to have UPD, and this could offer a valuable new approach to the classification of this important subgroup of AML. The prognostic consequences of such cryptic abnormalities for the patient are uncertain, and larger studies will be required to assess the clinical significance of this phenomenon.