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

这项提案的目标是改善慢性阻塞性肺病患者的基因图谱和风险分层 骨髓增生异常综合征(MDS)的临床全基因组测序。MDS是一个异质的 一组克隆性骨髓疾病，通常因骨髓衰竭或进展为急性髓系而致命 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。 为了延长存活期，并最大限度地减少与更多 积极的治疗。MDS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， 与不同的临床结果相关的重复和非整倍体。尽管核型分析已经 几十年来，它一直被有效地使用，但也有几个缺点。这些问题包括低基因组分辨率和高基因组分辨率 失败率可能会导致某些患者的遗传风险谱不完整。我们最近开发了和 经过验证的ChromoSeq，一种符合CAP/CLIA标准的健壮的全基因组测序(WGS)分析方法 髓系恶性肿瘤患者的侧写。结果表明，该方法对临床诊断的敏感性为100%。 AML的相关细胞遗传学异常，并在多达25%的患者中发现了额外的细胞遗传学事件 这是标准细胞遗传学没有检测到的。这些发现包括新的定义风险的染色体 几乎15%的患者出现异常，这导致了对临床结果的更好预测。尽管MDS 和AML是密切相关的疾病，具有许多共同的特征、基因组特征和细胞 MDS的组成各不相同。此外，使用ChromoSeq结果组成现有的MDS风险小组 未经临床验证。我们假设ChromoSeq全基因组的优化 对MDS样本进行测序将提高遗传图谱和风险分层的准确性 在MDS患者中。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患者的遗传图谱和风险评估。我们将首先使用回顾 MDS样本以优化和验证我们现有的符合CAP/CLIA标准的ChromoSeq WGS分析，以改进 检测低频突变、拷贝数改变(CNA)和拷贝中性杂合性丢失 (CNLOH)，这在MDS中很常见(目标1；UH2组件)。然后，我们将使用预期的MDS队列来 建立ChromoSeq分析方法用于MDS患者基因组图谱和风险评估的临床有效性。 该项目将把符合CAP/CLIA标准的ChromoSeq检测扩大到MDS样本，以便它可以 将用于未来的介入临床试验和对这种恶性肿瘤患者的常规临床测试。

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.