Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing (ALL_SNP). Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing (ALL_SNP)

We evaluated linked-read whole genome sequencing (WGS) for detection of structural chromosomal rearrangements in primary samples of varying DNA quality from 12 patients diagnosed with ALL. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements, aneuploidy assessment and gene deletions. Additional RNA-sequencing and copy number aberrations (CNA) data from Illumina Infinium arrays were also generated and assessed against the linked-read WGS data. RNA-sequencing data was used to support structural chromosomal rearrangements detected in the linked-read WGS data by detecting expressed fusion genes as a consequence of the rearrangements. Illumina Infinium arrays (450k array and/or SNP array) were used to assess CNA status to further support the findings in the linked-read WGS data. The processed CNA data from the primary ALL patient samples has been deposited to GEO. RNA-sequencing, linked-read WGS data, and raw SNP array data from the primary ALL patient samples will not be deposited because the patient/parent consent does not cover depositing data that may be used for large-scale determination of germline variants in a repository. The ALL samples were collected 10-20 years ago from pediatric patients aged 2-15 years, some whom have deceased. The linked-read WGS data and the RNA-sequencing data sets generated in the study are available upon reasonable request from the corresponding author [e-mail]. Overall design: The Illumina HumanOmni2.5 Exome-8v1 SNP array was used to detect copy number changes in peditric ALL samples. LogR files with the extension ".cn" are submitted to GEO and can be visualized in IGV. 450k methylation data for these ALL samples was submitted previously in GSE49031.

我们针对12名确诊急性淋巴细胞白血病（acute lymphoblastic leukemia, ALL）患者的不同DNA质量原代样本，评估了连锁读段全基因组测序（linked-read whole genome sequencing, WGS）在染色体结构重排检测中的应用效能。连锁读段WGS可在碱基对分辨率下实现精准的等位基因特异性数字核型分析，能够检测涵盖复杂重排、非整倍体评估及基因缺失在内的多种结构变异。
本研究同时生成了基于Illumina Infinium芯片的转录组测序（RNA-sequencing）与拷贝数畸变（copy number aberrations, CNA）数据，并与连锁读段WGS数据开展比对验证。转录组测序数据可通过检测重排事件导致的表达融合基因，佐证连锁读段WGS检测到的染色体结构重排结果；研究同时使用Illumina Infinium芯片（包括450K芯片和/或SNP芯片）评估拷贝数畸变状态，以进一步验证连锁读段WGS的检测发现。
本研究中急性淋巴细胞白血病原代患者样本的已处理拷贝数畸变数据已提交至基因表达汇编（Gene Expression Omnibus, GEO）。但急性淋巴细胞白血病原代患者样本的转录组测序数据、连锁读段WGS数据以及原始SNP芯片数据均不予存入数据库，原因是患者或其监护人的知情同意未涵盖将此类数据提交至数据库以用于大规模生殖系变异（germline variants）检测的相关用途。
本研究的急性淋巴细胞白血病样本采集自10至20年前，受试者为2至15岁的儿科患者，其中部分患者已离世。
本研究生成的连锁读段WGS数据与转录组测序数据集，可通过向通讯作者[e-mail]提出合理申请获取。
研究设计概述：本研究使用Illumina HumanOmni2.5 Exome-8v1 SNP芯片检测儿科急性淋巴细胞白血病样本的拷贝数变化。扩展名为".cn"的LogR文件已提交至GEO，可在整合基因组浏览器（Integrative Genomics Viewer, IGV）中进行可视化。上述急性淋巴细胞白血病样本的450K甲基化数据此前已提交至GSE49031数据集。