The technology has been used in fields such as investigating the functional heterogeneity of the human T cell ( 10), comparing TCR repertoire of different tissues ( 11, 12), analyzing the effect of genetic background on TCR repertoire ( 13), identifying autoimmune-disease-related T cells ( 14– 16), quantifying minimal residual disease in blood cancer ( 17), and predicting the responses of vaccination ( 18) or immunotherapy ( 19– 21). The application of HTS in TCR repertoire analysis (TCR-seq) began 10 years ago ( 4– 6) and has been widely used in basic and translational research ( 2, 7– 9) due to its high resolution and throughput. However, TCR spectratyping is limited by its low resolution because it cannot provide precise information on the individual clonotype ( 1– 3). Before the wide application of high throughput sequencing (HTS), spectratyping assays was the commonly used method for assessing the TCR repertoire. The human T cell repertoire is generated by somatic rearrangement of the variable (V), diversity (D), and joining (J) segments on the T cell receptor (TCR) loci during T cell development, and a diverse TCR repertoire is pivotal to human health. These data demonstrate that accurate immune repertoire information can improve our understanding of the adaptive immunity in leukemia and lead to better treatment management of the patients. These T cells were stimulated and emerged at the time of induction treatment and further expanded during consolidation treatment, possibly to fight against infections.

Our result shows that high-avidity T cells, such as those targeting known pathogens, are largely selected during chemotherapy, despite the global immunosuppression. We also interrogated how chemotherapy affected the TCR repertoire of patients with B-cell acute lymphoblastic leukemia. We then used the optimized system to detect the minimal residual disease of T cell acute lymphoblastic leukemia and showed a higher sensitivity compared with flow cytometry. These TRB reference materials could be used as independent positive controls to assess the accuracy of the experimental system, and they can also be used as spike-in materials to calibrate the residual biases of the experimental system. We assessed the stability of the optimized system by repeating the experiments in different batches and by remixing the TRB templates in different ratios. In this study, we designed and synthesized 611 T cell receptor (TCR) beta chain ( TRB) templates and used them as reference materials to optimize the multiplex PCR experimental system to enrich the TRB repertoire. 4Department of Computer Science, City University of Hong Kong, Hong Kong, ChinaĪccurate T cell receptor repertoire profiling has provided novel biological and clinical insights in widespread immunological settings however, there is a lack of reference materials in the community that can be used to calibrate and optimize the various experimental systems in different laboratories.3Hematology and Oncology Department, Shenzhen Children's Hospital, Shenzhen, China.1BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.Jinghua Wu 1,2 †, Xie Wang 2 †, Liya Lin 2 †, Xuemei Li 2 †, Sixi Liu 3, Wei Zhang 2,4, Lihua Luo 1,2, Ziyun Wan 2, Mingyan Fang 2, Yi Zhao 2, Xiaodong Wang 3, Huirong Mai 3, Xiuli Yuan 3, Feiqiu Wen 3, Changgang Li 3 * and Xiao Liu 2,5 *

Immune repertoire notation