The lymphocyte genome is prone to many threats, including programmed mutation during differentiation¹, antigen-driven proliferation and residency in diverse microenvironments. Here, after developing protocols for expansion of single-cell lymphocyte cultures, we sequenced whole genomes from 717 normal naive and memory B and T cells and haematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells, with higher burdens in memory cells than in naive cells, and with T cells accumulating mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for approximately half of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every on-target IGHV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than in stem cells, with around 15% of deletions being attributable to off-target recombinase-activating gene activity. DNA damage from ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory cells. The mutation burden and signatures of normal B cells were broadly similar to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes that are active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.

淋巴细胞基因组容易受到许多威胁，包括分化过程中的程序性突变¹，抗原驱动的增殖和在不同微环境中的驻留。在这里，在制定了单细胞淋巴细胞培养扩增方案后，我们对 717 个正常幼稚和记忆 B 细胞和 T 细胞以及造血干细胞的全基因组进行了测序。与造血干细胞相比，所有淋巴细胞亚群都携带更多的点突变和结构变异，记忆细胞的负担高于幼稚细胞，并且 T 细胞在整个生命过程中以更高的速度积累突变。免疫多样化的脱靶效应约占淋巴细胞中额外分化相关突变的一半。记忆 B 细胞平均获得了 18 个全基因组范围内的脱靶突变，用于每个靶标IGHV生发中心反应过程中的突变。淋巴细胞的结构变异比干细胞高 16 倍，约 15% 的缺失可归因于脱靶重组酶激活基因活性。紫外线照射和其他零星突变过程造成的 DNA 损伤在某些记忆细胞中产生了成百上千个突变。正常 B 细胞的突变负荷和特征与许多 B 细胞癌症中所见的大致相似，这表明淋巴细胞的恶性转化源于在正常个体发育过程中活跃的相同突变过程。正常淋巴细胞的突变图谱记录了免疫多样化过程中程序化基因组工程的脱靶效应和分化的后果，