Benchmarking of Whole Genome Sequencing (WGS) and Whole Transcriptome Sequencing (WTS) As Diagnostic Tools for the Genetic Characterization of Acute Myeloid Leukemia (AML) and Acute Lymphoblastic Leukemia (ALL) in Adults

ETV6 一致性 全基因组测序 生物 断点 髓系白血病 融合基因 遗传学 DNA测序 计算生物学 融合转录本 肿瘤科 染色体易位 医学 基因组 癌症研究 基因
作者
Claudia Haferlach,Wencke Walter,Manja Meggendorfer,Anna Stengel,Constance Baer,Stephan Hütter,Niroshan Nadarajah,Heiko Müller,Wolfgang Kern,Torsten Haferlach
出处
期刊:Blood [Elsevier BV]
卷期号:138 (Supplement 1): 273-273 被引量:3
标识
DOI:10.1182/blood-2021-150260
摘要

Abstract Background: In AML and ALL the application of WHO classification and ELN guidelines requires a combination of cytogenetics and targeted sequencing for specific mutations to determine the diagnostic and prognostic subgroup. WGS and WTS have emerged as comprehensive techniques that allow the simultaneous analysis and identification of all genetic alterations in a single approach with possible turnaround times of 1 week. Aim: Evaluate the accuracy of WGS and WTS in providing all relevant genetic information in a clinical setting. Patients and Methods: The cohort comprised 738 AML, 293 BCP-ALL and 124 T-ALL. The diagnosis was established following WHO guidelines. WGS (100x, 2x151bp) and WTS (50 Mio reads, 2x101bp) were performed on a NovaSeq instrument. Variants were called with Strelka2, Manta and GATK using a tumor w/o normal pipeline, fusions with Arriba, STAR-Fusion and Manta. Results: The combination of WGS and WTS detected all chromosomal and molecular abnormalities in the AML and ALL cohorts relevant for disease stratification and prognostication as identified by chromosome banding analysis (CBA) and targeted panel sequencing (TPS). A very high concordance between CBA and WGS was revealed for the detection of balanced structural variants (SV) with the added benefit of WGS to also detect cytogenetically cryptic rearrangements (i.e.: ETV6-MN1, NUP98-KDM5A), which all were confirmed either by FISH or RT-PCR. Fusion calling by WTS identified 96% of the WHO subtype defining rearrangements and detected 20 additional fusion transcripts relevant for disease stratification (e.g. EP300-ZNF384, TCF3-HLF) including 9 fusion transcripts that led to prognostic reassignment or could serve as a potential treatment target. Breakpoints of unbalanced SV can occur in repetitive sequences of the genome, hampering the detection by WGS. However, adding copy number alteration (CNA) calls to the analyses allows also reliable identification of unbalanced SV. WGS outperformed CBA in cases with insufficient in vitro proliferation due to suboptimal pre-analytics (i.e. longer transport time) and identified 36 chromosomal aberrations in 12 cases with CBA not evaluable. WGS's independence of in vitro cell proliferation was most impactful in ALL: 40 T-ALL cases showed a normal karyotype according to CBA. WGS detected SVs in 16 (40%) and CNAs in 20 (50%) of these cases, confirming the normal karyotype for only 9 samples. In the BCP-ALL cohort, CNV analysis identified 29 low hypodiploid and 16 high hyperdiploid karyotypes, 6 of which were missed by CBA. Due to the higher resolution and unrestricted, genome-wide assessment, WGS detected relevant gene deletions (RB1, ERG, PAX5, CDKN2A, IKZF1, ETV6, BTG1) in 59% of ALL cases, providing additional diagnostic and prognostic information. In the AML cohort CBA and WGS detected 795 CNA concordantly. In addition WGS called 54 CNA with size 1-5 MB (below the detection limit of CBA), i.e. 3 BCOR deletions in inv(3)(q21q26) cases and 67 CNA with size > 5 MB, which were missed by CBA. 35 CNA were missed by WGS due to small clone sizes (median 6% as determined by FISH). WGS detected copy neutral loss of heterozygosity (CN-LOH) in AML most frequently on 21q (n=17), 4q (n=15), 13q (n=15), 11q (n=13) and in T-ALL on 9p (n=19), mostly encompassing CDKN2A/B deletions. Expression profiling provided additional diagnostic information for 57 ALL cases (41 BCR-ABL1-like, 16 DUX4 rearranged) that can only insufficiently be obtained by WGS or CBA. WGS reliably detected all gene mutations with a VAF > 15% (n = 647) identified by TPS encompassing especially all mutations in genes relevant for WHO diagnosis and prognostication. 26/171 mutations with a VAF < 15% were missed by WGS. Evaluation of WGS data for 121 genes recurrently mutated in hematologic neoplasms revealed an additional 2 mutations per sample on average (range: 0-9) which might qualify as targets for therapy. Conclusions: WGS and WTS provide all necessary genetic information to accurately determine the diagnostic and prognostic subgroup according to WHO and ELN guidelines in AML and ALL. Compared to today's gold standards, these novel methods provide a comprehensive genome wide characterization with higher resolution that directly identifies genes of impact, offering the basis for targeted treatment selection and monitoring of residual disease. Both can be implemented with automated analysis pipelines, consequently reducing time and error rates. Figure 1 Figure 1. Disclosures Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Kern: MLL Munich Leukemia Laboratory: Other: Part ownership. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership.

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
PDF的下载单位、IP信息已删除 (2025-6-4)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
刚刚
Yy完成签到 ,获得积分10
3秒前
Nayvue发布了新的文献求助10
5秒前
feng完成签到,获得积分10
5秒前
淡淡的小蘑菇完成签到 ,获得积分10
8秒前
G_Serron完成签到,获得积分10
9秒前
swordshine完成签到,获得积分10
9秒前
Anonymous完成签到,获得积分10
13秒前
medzhou完成签到,获得积分10
17秒前
儒雅的千秋完成签到,获得积分10
25秒前
普鲁卡因发布了新的文献求助10
28秒前
小雯完成签到,获得积分10
29秒前
搞怪梦寒完成签到,获得积分20
30秒前
喵了个咪完成签到 ,获得积分10
31秒前
mc完成签到 ,获得积分10
33秒前
量子星尘发布了新的文献求助10
36秒前
37秒前
37秒前
虚幻谷波完成签到,获得积分10
39秒前
ruochenzu发布了新的文献求助10
42秒前
小马甲应助搞怪梦寒采纳,获得10
44秒前
firewood完成签到 ,获得积分10
45秒前
天天快乐应助普鲁卡因采纳,获得10
47秒前
orixero应助NXK采纳,获得10
47秒前
bjr完成签到 ,获得积分10
49秒前
研友_LwlAgn完成签到,获得积分10
53秒前
陈昊完成签到,获得积分10
1分钟前
1分钟前
tian发布了新的文献求助10
1分钟前
1分钟前
1分钟前
龙舞星完成签到,获得积分10
1分钟前
1分钟前
王涉发布了新的文献求助10
1分钟前
普鲁卡因发布了新的文献求助10
1分钟前
量子星尘发布了新的文献求助10
1分钟前
柚子完成签到,获得积分10
1分钟前
1分钟前
马儿饿了要吃草完成签到,获得积分10
1分钟前
1分钟前
高分求助中
【提示信息,请勿应助】关于scihub 10000
Les Mantodea de Guyane: Insecta, Polyneoptera [The Mantids of French Guiana] 3000
徐淮辽南地区新元古代叠层石及生物地层 3000
The Mother of All Tableaux: Order, Equivalence, and Geometry in the Large-scale Structure of Optimality Theory 3000
Handbook of Industrial Diamonds.Vol2 1100
Global Eyelash Assessment scale (GEA) 1000
Picture Books with Same-sex Parented Families: Unintentional Censorship 550
热门求助领域 (近24小时)
化学 材料科学 医学 生物 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 遗传学 基因 物理化学 催化作用 冶金 细胞生物学 免疫学
热门帖子
关注 科研通微信公众号,转发送积分 4038128
求助须知:如何正确求助?哪些是违规求助? 3575831
关于积分的说明 11373827
捐赠科研通 3305610
什么是DOI,文献DOI怎么找? 1819255
邀请新用户注册赠送积分活动 892655
科研通“疑难数据库(出版商)”最低求助积分说明 815022