B-other ALL classification by Targeted RNA-sequencing

We present a comprehensive genetic study of 144 pediatric B-other Acute Lymphoblastic Leukemia cases diagnosed and treated at Boldrini Children's Hospital (Brazil). We performed a targeted RNA-sequencing to evaluated the benefits of introducing genomic technologies into routine diagnostics. Targeted RNA-sequencing further classified 66.7% B-other cases. All 'classical' and novel ALL subgroups, except for iAMP21, hyper- and hypodiploid cases were identified. In addition, clinically important genetic alterations as druggable lesions and prognostic factors were found. Here, we uploaded files that contain: 

1. Gene expression data from the entire cohort studied, n=184 (Log2+1 TPM normalized gene expression data). Tab-delimited file (.csv) that contains a row for gene, a column for each sample, and expression values for each gene in each sample.  Annotation labels are in the first three rows and in the first column.

2. A subset of 23 BAM (Binary Alignment/Map) files for representative ALL cases, including BCR-ABL1, ETV6-RUNX1, TCF3-PBX1, KMT2A-r, High-Hyperdiploidy; DUX4-r, iAMP21, PAX5-driven, ABL-class fusion, JAK2-fusion, EPOR-fusion, CRLF2-high, ZNF384-r, MEF2D-r, NUTM1-r, B-'rest', IKZF1del, and ERGdel.

3- Genetic information of the 23 BAM files provided (tab-delimited file, .txt).

本研究针对巴西博尔德里尼儿童医院（Boldrini Children's Hospital）收治的144例儿科B-其他型急性淋巴细胞白血病（Acute Lymphoblastic Leukemia, ALL）病例开展了一项全面的遗传学研究。我们通过靶向RNA测序（targeted RNA-sequencing）评估了将基因组技术纳入常规临床诊断的应用价值。靶向RNA测序可进一步对66.7%的B-其他型病例完成分型。本研究共鉴定出所有经典及新型急性淋巴细胞白血病（ALL）亚型，仅iAMP21、超二倍体与低二倍体病例未被覆盖。此外，本研究还发现了多项具有临床重要性的遗传学改变，包括可靶向治疗的病变及预后相关因素。

本次上传的数据集包含以下内容：
1. 全队列基因表达数据集：涵盖本研究全部184例样本，数据为经Log2+1转换的TPM（Transcripts Per Million，转录本每百万）标准化基因表达量。文件为制表符分隔格式的.csv文件，每行对应一个基因，每列对应一个受试样本，单元格内存储各基因在对应样本中的表达值；文件前3行及第1列为注释标签。
2. 23份代表性急性淋巴细胞白血病病例的BAM（Binary Alignment/Map）文件子集，涵盖的亚型及遗传学改变包括：BCR-ABL1、ETV6-RUNX1、TCF3-PBX1、KMT2A重排（KMT2A-r）、超高二倍体；DUX4重排（DUX4-r）、iAMP21、PAX5驱动型、ABL类融合、JAK2融合、EPOR融合、CRLF2高表达、ZNF384重排（ZNF384-r）、MEF2D重排（MEF2D-r）、NUTM1重排（NUTM1-r）、B-其他未分类型（B-'rest'）、IKZF1缺失（IKZF1del）及ERG缺失（ERGdel）。
3. 上述23份BAM文件对应的遗传学信息文件：为制表符分隔的文本文件（.txt格式）。