Targeted sequencing of 252 genes based on their relevance in lymphoid malignancies

Dataset description Data consists of CRAM file from capture-based gene panel sequencing (Twist Bioscience) of 252 genes selected based on their relevance in lymphoid malignancies. The panel also included genome-wide backbone probes for copy-number analysis. The preprared libraries were then subsequenlty equenced in paired-end mode (2x150bp) on the Illumina NovaSeq 6000 (Illumina Inc.). BALSAMIC was used to analyze the FASTQ files and aligning them to reference genome. Trimmed reads were mapped to the reference genome hg19 using BWA MEM v0.7.15 4. The resulting SAM files were converted to BAM files and sorted using samtools v1.6. Duplicated reads were marked using Picard tools MarkDuplicate v2.17.0. And finally converted to CRAM files using samtools v1.6. Note: CRAM is a sequencing read file format that is highly space efficient by using reference-based compression of sequence data and offers both lossless and lossy modes of compression: https://www.ebi.ac.uk/ena/cram/ Data Access Statement The data is under restricted access and can be accessed upon request through the email-adress below. The targeted sequence datasets are only to be used for research aimed at advancing the understanding of genetic factors in the chronic lymphocytic leukemia. Applications aimed at method development including bioinformatics would not be considered as acceptable for use of this dataset.数据集说明 本数据集包含基于捕获式基因面板测序（Twist Bioscience公司）的CRAM格式测序文件，该测序靶向252个与淋巴系统恶性肿瘤相关的基因。该基因面板还包含用于拷贝数分析的全基因组骨架探针。制备好的文库随后在Illumina NovaSeq 6000测序仪（Illumina公司）上以双端测序模式（2×150bp）进行测序。 使用BALSAMIC工具对FASTQ文件进行分析，并将序列比对至参考基因组。采用BWA MEM v0.7.15将修剪后的测序读段比对至hg19参考基因组。生成的SAM格式文件经samtools v1.6转换为BAM格式文件并完成排序。使用Picard工具的MarkDuplicate v2.17.0标记重复测序读段，最终通过samtools v1.6将文件转换为CRAM格式文件。 注：CRAM是一种基于参考序列压缩测序数据的测序读段文件格式，具有极高的空间利用率，同时支持无损与有损两种压缩模式：https://www.ebi.ac.uk/ena/cram/ 数据获取声明 本数据集采用受限访问模式，可通过下方邮箱地址提交申请获取。 本靶向测序数据集仅可用于旨在加深慢性淋巴细胞白血病遗传因素认知的研究。包括生物信息学在内的方法开发类应用，均不被视为本数据集的可接受使用场景。