Whole Genome Sequencing for Genomic Evaluation and Risk Stratification of Patients with Myelodysplastic Syndromes

该提案的目标是改善遗传分析和风险分层的患者， 骨髓增生异常综合征（MDS）使用临床全基因组测序。MDS是一种异质性 一组克隆性骨髓疾病，由于骨髓衰竭或进展为急性髓系疾病而常常是致命的 白血病（AML）。因此，准确预测进展风险对于MDS患者的管理至关重要 为了延长生存期，并尽量减少与更多相关的发病率和死亡率的可能性， 积极的治疗骨髓增生异常综合征患者骨髓细胞中期染色体核型分析 是MDS风险评估算法的重要组成部分，用于检测染色体缺失， 重复和非整倍体与不同的临床结果相关。尽管染色体核型分析 虽然它已经被有效地使用了几十年，但它有几个缺点。这些包括低基因组分辨率和高 失败率可能导致某些患者的遗传风险特征不完整。我们最近开发了 经验证的ChromoSeq，一种稳健的CAP/CLIA兼容的全基因组测序（WGS）检测方法，用于遗传 骨髓恶性肿瘤患者的特征分析。我们表明，该方法对临床诊断的敏感性为100%。 AML中的相关细胞遗传学异常，并在高达25%的患者中确定了其他细胞遗传学事件 标准细胞遗传学未检测到的。这些发现包括新的风险定义染色体 在近15%的患者中发现异常，从而更好地预测临床结果。虽然MDS AML和AML是密切相关的疾病，它们共享许多特征，基因组特征和细胞免疫学特征。 MDS的组成不同。此外，使用ChromoSeq结果形成现有MDS风险组， 未经临床验证。我们假设优化ChromoSeq全基因组 MDS样本的测序分析将提高遗传分析和风险分层的准确性 MDS患者。在这里，我们建议使用回顾性和前瞻性临床MDS样本的组合 验证ChromoSeq用于MDS患者的遗传分析和风险评估。我们将首先使用回溯 MDS样品，以优化和验证我们现有的CAP/CLIA兼容的ChromoSeq WGS检测， 检测低频率突变、拷贝数改变（CNA）和拷贝中性杂合性丢失 （CNLOH），其在MDS中常见（Aim 1; UH2组分）。然后，我们将使用一个前瞻性MDS队列， 建立ChromoSeq检测用于MDS患者基因组分析和风险评估的临床有效性。 该项目将扩大CAP/CLIA兼容的ChromoSeq检测试剂盒在MDS样本中的使用， 用于未来的干预性临床试验和该恶性肿瘤患者的常规临床试验。

The goal of this proposal is to improve genetic profiling and risk stratification for patients with myelodysplastic syndromes (MDS) using clinical whole-genome sequencing. MDS is a heterogenous group of clonal bone marrow disorders that are often fatal due to marrow failure or progression to acute myeloid leukemia (AML). Accurate prediction progression risk is therefore critical for the management of MDS patients in order to prolong survival and minimize the potential for morbidity and mortality associated with more aggressive treatments. Cytogenetic analysis of bone marrow cells from MDS patients via metaphase karyotyping is an essential component of MDS risk assessment algorithms, and is used to detect chromosomal deletions, duplications, and aneuploidies that are associated with differential clinical outcomes. Although karyotyping has been used effectively for decades, it has several disadvantages. These include low genomic resolution and high failure rates that can result in incomplete genetic risk profiles for some patients. We recently developed and validated ChromoSeq, a robust CAP/CLIA-compliant whole-genome sequencing (WGS) assay for genetic profiling of patients with myeloid malignancies. We showed that this method was 100% sensitivity for clinically relevant cytogenetic abnormalities in AML and identified additional cytogenetic events in up to 25% of patients that were not detected by standard cytogenetics. These findings included new risk-defining chromosomal abnormalities in almost 15% of patients, which resulted in better prediction of clinical outcomes. Although MDS and AML are closely related diseases that share many features, the genomic characteristics and cellular composition of MDS is distinct. In addition, the use of ChromoSeq results to form existing MDS risk groups has not been clinically validated. We hypothesize that optimization of the ChromoSeq whole-genome sequencing assay for MDS samples will improve the accuracy of genetic profiling and risk stratification of MDS patients. Here we propose to use a combination of retrospective and prospective clinical MDS samples to validate ChromoSeq for genetic profiling and risk assessment in MDS patients. We will first use retrospective MDS samples to optimize and validate our existing CAP/CLIA-compliant ChromoSeq WGS assay to improve the detection of low frequency mutations, copy number alterations (CNAs) and copy neutral loss of heterozygosity (CNLOH), which are common in MDS (Aim 1; UH2 component). We will then use a prospective MDS cohort to establish the clinical validity of ChromoSeq assay for genomic profiling and risk assessment of MDS patients. This project will expand the use of the CAP/CLIA-compliant ChromoSeq assay to MDS samples so that it may be used for future interventional clinical trials and routine clinical testing of patients with this malignancy.