Chronic lymphocytic leukemia (CLL) is characterized by multiple copy number alterations (CNAs) and somatic mutations that are central to disease prognosis, risk stratification, and mechanisms of therapy resistance. Fluorescence in situ hybridization (FISH) panels are widely used in clinical applications as the gold standard for screening prognostic chromosomal abnormalities in CLL. DNA sequencing is an alternative approach to identifying CNAs but is not an established method for clinical CNA screening. We sequenced DNA from 509 individuals with CLL or monoclonal B-cell lymphocytosis (MBL), the precursor to CLL, using a targeted sequencing panel of 59 recurrently mutated genes in CLL and additional amplicons across regions affected by clinically relevant CNAs [i.e., del(17p), del(11q), del(13q), and trisomy 12]. We used the PatternCNV algorithm to call CNA and compared the concordance of calling clinically relevant CNAs by targeted sequencing to that of FISH. We found a high accuracy of calling CNAs via sequencing compared to FISH. With FISH as the gold standard, the specificity of targeted sequencing was >95%, sensitivity was >86%, positive predictive value was >90%, and negative predictive value was >84% across the clinically relevant CNAs. Using targeted sequencing, we were also able to identify other common CLL-associated CNAs, including del(6q), del(14q), and gain 8q, as well as complex karyotype, defined as the presence of 3 or more chromosomal abnormalities, in 26 patients. In a single and cost-effective assay that can be performed on stored DNA samples, targeted sequencing can simultaneously detect CNAs, somatic mutations, and complex karyotypes, which are all important prognostic features in CLL.
慢性淋巴细胞白血病（CLL）的特征在于多种拷贝数变异（CNAs）和体细胞突变，这些改变对疾病预后、风险分层及治疗耐药机制至关重要。荧光原位杂交（FISH）检测组合作为筛查CLL预后相关染色体异常的金标准，在临床实践中被广泛应用。DNA测序是识别CNAs的替代方法，但尚未成为临床CNA筛查的成熟技术。本研究对509例CLL或CLL前体状态——单克隆B淋巴细胞增多症（MBL）患者的DNA进行了靶向测序，测序组合涵盖59个CLL常见突变基因，并额外覆盖了具有临床意义的CNA区域[包括del(17p)、del(11q)、del(13q)和12号染色体三体]。我们采用PatternCNV算法进行CNA判定，并将靶向测序与FISH在临床相关CNA检测方面的一致性进行比较。结果显示，与FISH相比，测序检测CNAs具有较高的准确性。以FISH为金标准，靶向测序对临床相关CNAs的特异性>95%、敏感性>86%、阳性预测值>90%、阴性预测值>84%。通过靶向测序，我们还检测到其他常见CLL相关CNAs，包括del(6q)、del(14q)和8q扩增，并在26例患者中发现复杂核型（定义为存在3个及以上染色体异常）。靶向测序作为一种可在储存DNA样本上实施的单次经济型检测方案，能够同步检测CNAs、体细胞突变和复杂核型——这些均为CLL重要的预后特征指标。
肿瘤(癌症)患者之家