Case Study: Saliva Dna Not Equivalent to Buccal Swab Dna as a Surrogate for a Germline Sample.

Publication Type:

Journal Article


Human immunology, Volume 74, p.4-4 (2013)




2013, Clinical Research Division, December 2013, Immunology


Aim: Saliva is fast becoming an alternative to buccal cells as a source of DNA for HLA typing prior to hematopoietic cell transplant (HCT), either when a peripheral blood sample is not an option or as a source of germline DNA. We describe the case of a 47 year old male aplastic anemia patient, previously typed at another center and subsequently referred to our center for HLA typing. Initial SBT on saliva and peripheral blood lymphocytes showed dropout of the expected maternal haplotype. A buccal swab sample was obtained for further typing. Methods: Saliva was collected using an Oragene kit and DNA extracted with the QIAgen EZ1 DNA Tissue kit. Buccal cells were collected using sterile swabs (Cap-Shure) and DNA extracted using QIAamp DNA microkit. HLA typing was performed by SBT with Atria reagents on an ABI 3130xl and analyzed with Conexio Assign software. Both samples were also tested with rSSO and by Chromosome Genomic Array Testing (CGAT). Results: Initial typing of the patient’s saliva sample by SBT generated the type A*03:01, C*04:JERF, B*XX, DRB1*01:01 (with possible 2nd alleles at A, C, and DRB1). Based on external typing, it appeared that the patient had lost the maternal haplotype, suggesting loss of heterozygosity (LOH), confirmed by CGAT "virtual keryotyping" of chromosome 6, which also revealed copy neutral uniparental disomy. The array plot clearly showed  40Mb LOH from 6p21.1 to the telemere, which included the entire HLA region. Typing of buccal sample revealed a heterozygous A*03:01, 02:01, C*04:JERF, 02:02, B*35:BJTR, B*27:EKN, DRB1*01:01, 09:01 type. Conclusions: Since this aplastic anemia patient had never been transplanted, the LOH must have occurred at some time between the initial external typing and our more recent typing. This case indicates that caution must be used even when testing patients who do not suffer from hematological malignancies, especially when relying on saliva samples as a DNA source for either germline sample or for confirmatory HLA typing.


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