<em>Subtype Dependent Drug Resistance Alterations in Relapsed Childhood B-ALL: A Children's Oncology Group Study</em>

Introduction The survival rate for children with B-cell acute lymphoblastic leukemia (B-ALL) now approaches 90%. However, given the poor prognosis of those who relapse, B-ALL remains a leading cause of cancer related mortality in children. To discover underlying mechanisms of treatment failure, previous genomic profiling has identified somatic alterations in 12 genes that drive treatment resistance. However, these studies were underpowered to detect association between these alterations and known genetic subtypes (e.g., hyperdiploid, ::, ::, etc.) that would indicate cooperativity in driving clonal evolution. Results We performed whole genome sequencing (WGS) of diagnosis/remission/relapse specimens of 181 B-ALL cases (age 0-18 years) enrolled on a recently completed clinical trial for relapsed B-ALL (AALL1331). Somatic aberrations including SNV, Indel, structural variations (SV), copy number variations (CNV) were identified from WGS and fusion genes were detected from RNAseq data. By integrating these cases with 146 previously published cases (totaling N=327 with WGS/WES; N=255 with WGS), we aimed to identify novel resistance drivers and to discover associations between genetic subtypes and resistance drivers. Here, we report two novel somatic alterations to be enriched in relapsed B-ALL (Table 1), an intergenic deletion in chr1 (named ) and promoter alteration (which results in overexpression of ). Importantly, we also discovered statistically significant (with FDR corrected P value<0.2) associations between resistance drivers and subtypes that confirmed previously known associations such as / in :: and promoter alteration in hyperdiploid ALL. We also discovered novel associations including in ::, in hyperdiploid, in ::, in , mismatch repair deficiency (MMR) in ::, in and , and promoter alteration in  subtypes. In addition to these novel findings, our data also revealed high frequency nested :: fusions in other subtypes, which was validated using single cell sequencing. Conclusion Together, our study features NGS of the largest cohort of relapsed childhood ALL samples, identifies novel resistance markers for :: subtype, and uncovers novel associations between resistance drivers and subtypes. These finding may shape future clinical management of childhood ALL.

引言 B细胞急性淋巴细胞白血病（B - ALL）患儿的生存率现已接近90%。然而，鉴于复发患者预后不良，B - ALL仍然是儿童癌症相关死亡的主要原因。为了发现治疗失败的潜在机制，先前的基因组分析已确定了12个驱动治疗耐药的基因的体细胞改变。然而，这些研究不足以检测这些改变与已知遗传亚型（例如，超二倍体等）之间的关联，而这种关联可能表明在驱动克隆进化方面存在协同作用。 结果 我们对181例B - ALL病例（年龄0 - 18岁）的诊断/缓解/复发样本进行了全基因组测序（WGS），这些病例参加了一项最近完成的复发B - ALL临床试验（AALL1331）。从WGS中鉴定出包括单核苷酸变异（SNV）、插入缺失（Indel）、结构变异（SV）、拷贝数变异（CNV）在内的体细胞畸变，并从RNA测序数据中检测到融合基因。通过将这些病例与146例先前发表的病例整合（总计N = 327例有WGS/全外显子组测序（WES）；N = 255例有WGS），我们旨在识别新的耐药驱动因素，并发现遗传亚型与耐药驱动因素之间的关联。在此，我们报告了两种在复发B - ALL中富集的新型体细胞改变（表1），1号染色体上的一个基因间缺失（命名为）和启动子改变（导致的过表达）。重要的是，我们还发现耐药驱动因素与亚型之间存在具有统计学意义（错误发现率校正后的P值<0.2）的关联，这证实了先前已知的关联，例如在::中的/以及超二倍体ALL中的启动子改变。我们还发现了一些新的关联，包括在::中的，在超二倍体中的，在::中的，在中的，在::中的错配修复缺陷（MMR），在和中的，以及在亚型中的启动子改变。除了这些新发现外，我们的数据还揭示了在其他亚型中高频嵌套的::融合，这已通过单细胞测序得到验证。 结论 总之，我们的研究对最大规模的儿童复发ALL样本队列进行了新一代测序（NGS），确定了::亚型的新型耐药标志物，并揭示了耐药驱动因素与亚型之间的新关联。这些发现可能会影响儿童ALL未来的临床管理。