Accurate Detection Of Leukemia Molecular Abnormalities Based On High-throughput Sequencing Data

Leukemia is one of the major malignant blood tumor that harm people's health,such as acute lymphoid leukemia(ALL)and acute myeloid leukemia(AML).ALL is a common hematologic tumor in children.With the wide application of high-throughput sequencing,e.g.whole genome sequencing(WGS),whole exome sequencing(WES),gene-panel sequencing and RNA sequencing(RNA-seq),more and more biological molecules are detected as potential clinical markers and drug targets.However,subject to the limitations of detection technology,limitations of data analysis methods,and decentralized cohort studies,many of the molecular markers have not been effectively detected.For example,about 25% B-ALL patients(B-other)still can't detected any molecular abnormalities.How to accurately detect molecular abnormalities from highthroughput sequencing data of leukemia patients has always been a very practical issue.In this work,we first developed an integrated analysis method that can be used for the analysis of gene-panel sequencing data.It provides a series of methods for data quality control,multi-platform sequence alignment,sequencing data preprocessing,gene mutation detection,variants annotation,and visualization.In addition,based on the previously published WES data of 172 cases B-cell ALL(B-ALL)and its RNA-seq,we constructed a tumor gene mutation detection method for ALL RNA-seq data.Meanwhile,based on the method,six candidate tumor-associated mutations,PAK4,CELSR3,MINK1,NR4A1,BOD1L1,and VCP were found in the 130 cases T-ALL RNA-seq.Next,we also analyzed the 1,285 cases B-ALL RNA-seq data from public sequence databases,and built the BRVar database,the largest transcriptome variants datasets and tumor gene mutation profile available in B-ALL.Moreover,two novel hotspot mutations,ZEB2 H1038R(n=17)and TRRAP E3107K(n=6)were found in the integrated dataset.Then,we also examined the involvement of fusion genes in B-ALL and T-ALL.18 fusion genes that were not reported in T-ALL using 130 T-ALL RNA-seq and RT-PCR,in which rearrangements of ZBTB16-ABL1,TRA-SALL2,and NKX2-1 involved rearrangements are recurrent event.In the 1285 B-ALL RNA-seq data,we found that NUTM1 involved rearrangements(n=10)are highly recurrent in B-ALL.Besides,we also found four cases ZNF362 rearrangements and one case TCF4-HLF that respectively similar to the ZNF384 rearrangements and TCF3-HLF.