Table 2.

The profiles and somatic mutations of HLA-A allele–lacking granulocytes

Case no.	HLA-LLs				SNP array	Mutated genes
	Lost allele	Lineage combination pattern	% in the total G population	6pLOH frequency in HLA− granulocytes, %	CNV	Targeted sequencing, n = 15	WES, n = 5	Median VAF
1	A24	GM	49.6	96	NE	DNMT3A, ZRSR2, TET2	NE	0.36
2	A31	GMB	99.7	36 (Discrepancy)	6pLOH*	DNMT3A	NE	0.19
3	A2	GMBT	94.2	46† (Discrepancy)	6pLOH*	LRCH1, PRR5L	NE	0.11
4	A31	GMB	99.0	99	6pLOH	CBL	NE	0.33
5	A2	GMBT	62.1	75† (Discrepancy)	6pLOH	(−)	NE	—
6	A2	GMBT	5.5	70† (Discrepancy)	6pLOH*	(−)	NE	—
7	A2	GM	6.4	92	6pLOH	(−)	NE	—
8	A2	GMB	9.8	96	6pLOH	(−)	NE	—
9	A24	GMBT	40.9	99	6pLOH	(−)	NE	—
10	A31	GMBT	98.6	33 (Discrepancy)	6pLOH	(−)	NE	—
11	A24	GMB	25.1	92†	6pLOH	(−)	(−)	—
12	A2	GMBT	97.7	92†	6pLOH*	(−)	11 genes (PPAP2B, MYSM1, FER1L5, SP5, OR2AT4, PEX5, FAM154B, SRRM2, GPR56, NLRP4, COX4I2)	0.45
13	A2	GMBT	99.8	99	6pLOH	(−)‡	2 genes (ZNF502, DHX35)	0.49
14	A2	GMBT	98.6	99	6pLOH	(−)‡	5 genes (GPT, ZNF462, CTCRTA1, OLFM4, SERPINF1)	0.22
15	A31	GMB	98.6	99	6pLOH	(−)	3 genes (EDEM3, ATXN1L, AKAP10), 11pLOH	0.44

“(Discrepancy)” indicates the presence of a discrepancy in the percentage between 6pLOH⁺ cells and HLA-LLs. —, not calculated; (−), not detected;

6pLOH, copy-number neutral loss of heterozygosity in chromosome 6p; CNV, copy-number variant; GM, granulocytes, monocytes; GMB, granulocytes, monocytes, B cells; GMBT, granulocytes, monocytes, B cells, and T cells; NE, not evaluated; SNP, single-nucleotide polymorphism; VAF, variant allele frequency; WES, whole-exome sequencing.

^*Breakpoints of 6pLOH resided between the HLA-A and -C alleles were revealed by HLA-allelic sequencing.

^†6pLOH frequencies were estimated by HLA sequencing.

^‡Previous targeted sequencing failed to reveal any mutations in 106 genes, most of which are known to be recurrently mutated in myeloid malignancies.⁷