Case Study: Chromosome Genomic Array Testing ("Virtual Karyotype") Confirms Loss of Heterozygosity Originally Detected by Hla Typing.

Publication Type:

Journal Article


Human immunology, Volume 74, p.6-6 (2013)




2013, Clinical Research Division, December 2013, Immunology


Aim: A 25 year old male AML patient in relapse was refered to our transplant center, having undergone a haploidentical transplant from a sib at another center. Bone marrow was collected, DNA from the sorted blast fraction isolated and HLA typed using rSSO (Luminex). Only the paternal haplotype shared with the sibling donor was detected in the blast cells, suggesting loss of heterozygosity (LOH), since both the patient’s original maternal haplotype and the donor’s unshared haplotype were absent. Chimerism testing confirmed that the blast cells were entirely of patient origin. Buccal sample DNA was HLA typed and the patient’s original germline type was confirmed. We decided to run both marrow and buccal samples by chromosome genomic array testing (CGAT) to confirm our HLA results. Methods: DNA from the blast fraction was isolated using QIAamp DNA Blood MiniKit; DNA from the buccal sample was isolated using QIAamp DNA MicroKit. Both samples were run in Luminex rSSO assays. Cyto- ScanHD (Affymetrix) was run using DNA from unsorted bone marrow (Qiagen Gentra Puregene kit) and the results compared with the genomic profile obtained using the buccal sample DNA. Results: Only the paternal haplotype was detected by Luminex rSSO in the DNA from the blast fraction (A*33:03g, C*16:02g, B*51:08g, DRB1*12, DQB1*03:01g), while both paternal and maternal haplotypes were present in buccal DNA. For whole bone marrow cells, the CGAT array plot clearly showed copy neutral LOH on the short arm of chromosome 6 from 6p21.2 to the telemere. For the buccal cells, the CGAT profile showed no LOH for the ‘‘virtual karyotype’’ of chromosome 6. Conclusions: Both HLA and CGAT assays confirmed LOH for the entire HLA region on the short arm of chromosome 6 in this patient’s blast cells, an example of copy number neutral acquired uniparental disomy. The graphic output of the CGAT dramatically illustrates this acquired somatic mutation.


PT: J; CT: 39th Annual Meeting of the American-Society-for-Histocompatibility-and-Immunogenetics (ASHI); CY: NOV 17-21, 2013; CL: Chicago, IL; SP: Amer Soc Histocompatibil & Immunogenet; NR: 0; TC: 0; J9: HUM IMMUNOL; SU: S; PG: 1; GA: 239YC