Prognostic potential of low-level mutations in meylodysplastic syndrome

骨髓增生异常综合征低水平突变的预后潜力

基本信息

批准号：
8787719
负责人：
G. Mike Makrigiorgos
金额：
$ 22.84万
依托单位：
DANA-FARBER CANCER INST
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-01-01 至 2016-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8787719
关键词：
Accounting Acute Myelocytic Leukemia Address Biological Biological Assay Biological Markers Blood Bone Marrow Diseases CBL gene Cancerous Clinical Clinical Data Collection Cytogenetics DNA DNA Sequence Alteration Data Detection Disease ETV6 gene EZH2 gene Event Future Genes Genetic Fingerprintings Genotype Health Hematopoiesis International Lung Malignant Neoplasms Malignant neoplasm of pancreas Methods Modeling Multivariate Analysis Mutation Mutation Detection NRAS gene Outcome Pancreas Patients Prevalence Process Prognostic Factor Prognostic Marker Public Health RUNX1 gene Risk Sampling Solid Somatic Mutation Syndrome System TP53 gene Technology Testing Time Validation Work base cancer therapy clinical phenotype clinically significant deep sequencing digital falls improved new technology next generation sequencing prevent prognostic prognostic value tumor

项目摘要

DESCRIPTION (provided by applicant): Accumulating evidence suggests that, if they go undetected, somatic low-level mutations in heterogeneous tumors or pre-cancerous syndromes can have profound clinical consequences. Furthermore, they may comprise important biomarkers and 'missed opportunities' for optimized therapy that could be applied had the mutation been known. We shall examine this hypothesis for the specific case of myelo-dysplastic syndromes (MDS). MDS are a collection of pre-cancerous, clonal bone marrow disorders with an increased risk of progression to acute myeloid leukemia (AML). Collaborators Ebert and Bejar demonstrated that mutations in TP53, RUNX1, ASLX1, EZH2, ETV6, are associated with decreased overall survival and are independent prognostic factors of outcome in multivariate analysis. Overall, mutations in MDS patients are of growing significance as biomarkers for 'personalization' of therapy beyond the established International Prognostic Scoring System (IPSS) which is based on clinical features and cytogenetics. While MDS is clearly a genetically heterogeneous disease, it is still not clear whether rare sub-clones influence clinical phenotype. This study aims first, to determine the prevalence of specific mutations that are below detection by existing technologies, and second to determine whether any identified mutations alter clinical phenotype. We shall employ COLD-PCR, a method developed by our group for enriching and detecting low-level DNA mutations, in conjunction with amplicon-based next-generation-sequencing. COLD-PCR increases the sensitivity of Illumina-based amplicon sequencing from the current ~2-5% down to 0.04% abundance, i.e. 'deep-sequencing' becomes 'ultra-deep-sequencing' using COLD-PCR. DNA from a group of 287 MDS patients will be screened via COLD-PCR-Illumina for mutations in the prognostic/potentially prognostic genes. Data from two groups of patients (poor outcome vs. favorable outcome, similar IPSS score) will be analyzed (a) accounting for both, low-level (0.04- 5% abundance) and high level (>5% abundance) mutations; and (b) accounting only for high level mutations, as practice has been until now. Results will be compared for their correlation with outcome/survival. The revised application contains additional data that fully validate our hypothesis for the first gene examined, NRAS. The ability to identify prognostic low-level mutations in MDS patients will enable better prediction of outcome and the fine-tuning of treatment for these patients. The approach addresses a problem common to all heterogeneous tumors (e.g. lung, pancreatic CA). Therefore relevance to Public Health is high.

描述（由申请人提供）：累积证据表明，如果未被发现，则在异质肿瘤或癌前综合症中的体细胞低水平突变可能会带来深远的临床后果。此外，它们可能包括重要的生物标志物和“错过的机会”，以优化治疗，如果知道该突变，则可以应用。我们将检查有关髓塑性综合征（MDS）的特定情况的这一假设。 MDS是癌前，克隆骨髓疾病的集合，其进展到急性髓样白血病（AML）的风险增加。合作者Ebert和Bejar表明，TP53，Runx1，Aslx1，Ezh2，ETV6中的突变与总体生存的降低相关，并且是多变量分析中结果的独立预后因素。总体而言，作为基于临床特征和细胞遗传学的既定国际预后评分系统（IPSS），MDS患者的突变作为“个性化”治疗的生物标志物的重要性越来越重要。虽然MDS显然是一种遗传性异构疾病，但尚不清楚罕见的亚基是否影响临床表型。这项研究的目的是首先确定现有技术低于检测到的特定突变的普遍性，其次是确定任何已鉴定的突变是否改变了临床表型。我们将采用Cold-PCR，这是我们小组与基于扩增子的下一代后期结合使用的小组开发的一种用于丰富和检测低级DNA突变的方法。 Cold-PCR将基于Illumina的扩增子测序的灵敏度从当前的〜2-5％降低到0.04％的丰度，即使用COLD-PCR变为“深度深”'。来自287例MDS患者的DNA将通过冷PCR-乳腺癌筛选，以在预后/潜在的预后基因中进行突变。将分析两组患者的数据（结果差与有利结果，类似的IPS得分）（a）对低水平（0.04-5％丰度）和高水平（> 5％的丰度突变）进行分析；（b）仅针对高级突变，因为迄今为止的实践一直存在。结果将与结果/生存的相关性进行比较。修订后的应用程序包含其他数据，可以完全验证我们对第一个基因NRAS的假设。在MDS患者中鉴定预后低水平突变的能力将使这些患者更好地预测结果和对治疗的微调。该方法解决了所有异质肿瘤（例如肺，胰腺CA）常见的问题。因此，与公共卫生相关。

项目成果

期刊论文数量（5）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（2）

DMSO Increases Mutation Scanning Detection Sensitivity of High-Resolution Melting in Clinical Samples.

DOI：
10.1373/clinchem.2015.245357
发表时间：
2015-11
期刊：
Clinical chemistry
影响因子：
9.3
作者：
Song C;Castellanos-Rizaldos E;Bejar R;Ebert BL;Makrigiorgos GM
通讯作者：
Makrigiorgos GM

Enriching mutant sequences by modulating the denaturation time during PCR.

通过调节 PCR 过程中的变性时间来富集突变序列。

DOI：
10.1373/clinchem.2014.221465
发表时间：
2014
期刊：
Clinical chemistry
影响因子：
9.3
作者：
Murphy,DerekM;Castellanos-Rizaldos,Elena;Makrigiorgos,GMike
通讯作者：
Makrigiorgos,GMike

Elimination of unaltered DNA in mixed clinical samples via nuclease-assisted minor-allele enrichment.

DOI：
10.1093/nar/gkw650
发表时间：
2016-11-02
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Song C;Liu Y;Fontana R;Makrigiorgos A;Mamon H;Kulke MH;Makrigiorgos GM
通讯作者：
Makrigiorgos GM

Single-tube, highly parallel mutation enrichment in cancer gene panels by use of temperature-tolerant COLD-PCR.

DOI：
10.1373/clinchem.2014.228361
发表时间：
2015-01
期刊：
Clinical chemistry
影响因子：
9.3
作者：
Castellanos-Rizaldos E;Richardson K;Lin R;Wu G;Makrigiorgos MG
通讯作者：
Makrigiorgos MG

COLD-PCR amplification of bisulfite-converted DNA allows the enrichment and sequencing of rare un-methylated genomic regions.

DOI：
10.1371/journal.pone.0094103
发表时间：
2014
期刊：
PloS one
影响因子：
3.7
作者：
Castellanos-Rizaldos E;Milbury CA;Karatza E;Chen CC;Makrigiorgos GM;Merewood A
通讯作者：
Merewood A