Can you perform single-cell HLA typing?

We occasionally get inquiries as to whether we can perform HLA sequencing and typing from single-cell samples or samples with very low cell counts (i.e. blastomeres, etc.).  Unfortunately, we cannot run HLA typing from samples with low, or single, cell counts.

In general, we use GenDx NGSgo-MX11-3 and NGSgo-AmpX library preparation kits for HLA sequencing and typing.  These library prep kits require a minimum DNA concentration of ca. 30 ng/uL in 30 uL.  We typically need about 5M (5×10^6) cells to get this DNA yield.  Single-cells and samples with low cell count simply do not contain sufficient DNA mass to reach the minimum DNA concentration to perform HLA sequencing.

Furthermore, some experiments with low cell count samples have shown that HLA allele amplifications were effective for some short length Class I alleles but not for longer Class II alleles.  And there were significant unexpected allele imbalances, probably due to low initial DNA sample concentrations.

Thus, at the present time, we can accept samples with a sufficient cell count (5M cells) but not single or low cell count samples.