Background

Kinase domain mutations in BCR-ABL1 are associated with resistance to tyrosine kinase inhibitors in patients with chronic myeloid leukaemia. Next-generation sequencing (NGS) allows detection of low-level kinase domain mutations, but its relevance in clinical practice remains debated. We aimed to examine the clinical effects of low-level kinase domain mutations identified using NGS in patients with chronic myeloid leukaemia.

Methods

In this population-based study, we included consecutive patients newly diagnosed with chronic myeloid leukaemia treated with first-line tyrosine kinase inhibitors, and patients identified at the time of resistance to first-line treatment with imatinib at six institutions (teaching hospitals and district hospitals) in southeast England. We screened patients for BCR-ABL1 kinase domain mutations using NGS, irrespective of patient response to tyrosine kinase inhibitor therapy. When we detected a mutation with NGS, we retrospectively analysed all previous samples to establish the date of first occurrence and subsequent kinetics of the mutant subclone (or subclones). The primary endpoints of this study were progression-free and event-free survival at 5 years.

Findings

Between Feb 1, 2007, and Dec 31, 2014, we screened 121 patients with chronic myeloid leukaemia for BCR-ABL1 kinase domain mutation. 99 consecutive patients were newly diagnosed, with available sequential RNA stored. The remaining 22 patients were diagnosed between June 1, 1999, and June 30, 2006, and were screened at the time of resistance to first-line treatment with imatinib. Imatinib was the first-line treatment for 111 patients, nilotinib for seven patients, and dasatinib for three patients. We detected a kinase domain mutation in 25 (21%) of 121 patients. Low-level kinase domain mutations were first identified in 17 (68%) of 25 patients with mutation. For patients with a complete cytogenetic response, 13 (14%) of 93 patients screened had a mutation. Five (71%) of the seven patients with a clinically relevant mutation lost complete cytogenetic response compared with 15 (17%) of 86 patients without a clinically relevant mutation (80 patients without mutation and six patients with a tyrosine kinase inhibitor-sensitive mutation, p=0·0031). Patients harbouring a mutant clone had poorer 5-year progression-free survival (65·3% [95% CI 40·5–81·8] vs 86·9% [75·8–93·2]; p=0·0161) and poorer 5-year event-free survival (22·2% [CI 5·6–45·9] vs 62·0% [50·4–71·6]; p<0·0001) than did patients without a mutation. We identified a kinase domain mutation in four (10%) of 41 patients with samples available at 3 months after starting first-line tyrosine kinase inhibitor treatment; all four subsequently progressed to accelerated phase disease compared with only three (8%) of 37 without a mutation (p<0·0001).

Interpretation

NGS reliably and consistently detected early appearance of kinase domain mutations that would not otherwise be detected by Sanger sequencing. For the first time, to our knowledge, we report the presence of kinase domain mutations after only 3 months of therapy, which could have substantial clinical implications. NGS will allow early clinical intervention and our findings will contribute to the establishment of new recommendations on the frequency of kinase domain mutation analysis to improve patient clinical care.

Funding

None.

中文翻译：

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下一代测序鉴定的慢性骨髓性白血病患者低水平BCR-ABL1激酶结构域突变的影响：一项基于人群的研究

背景

BCR-ABL1中的激酶结构域突变与慢性粒细胞白血病患者对酪氨酸激酶抑制剂的耐药性有关。下一代测序（NGS）可以检测低水平的激酶结构域突变，但其在临床实践中的相关性仍存在争议。我们旨在检查使用NGS鉴定的低水平激酶结构域突变在慢性粒细胞白血病患者中的临床效果。

方法

在这项基于人群的研究中，我们纳入了六家机构（教学医院和地区医院）连续接受一线酪氨酸激酶抑制剂治疗的新近诊断出患有慢性粒细胞白血病的患者，以及在对伊马替尼一线治疗产生抗药性时确定的患者）在英格兰东南部。无论患者对酪氨酸激酶抑制剂治疗的反应如何，我们均使用NGS筛选了患者的BCR-ABL1激酶结构域突变。当我们检测到NGS突变时，我们回顾性分析了所有先前的样品，以确定突变亚克隆（或亚克隆）的首次出现日期和后续动力学。这项研究的主要终点是5年无进展生存率和无事件生存率。

发现

在2007年2月1日至2014年12月31日期间，我们对121例慢性粒细胞白血病患者进行了BCR-ABL1筛查激酶结构域突变。新诊断了99例连续患者，并存储了可用的顺序RNA。其余22位患者在1999年6月1日至2006年6月30日之间被诊断出，并在对伊马替尼的一线治疗产生抗药性时进行了筛查。伊马替尼是一线治疗的111例患者，尼洛替尼治疗7例，达沙替尼治疗3例。我们在121位患者中有25位（21％）检测到了激酶结构域突变。在25例突变患者中，有17例（68％）首先发现了低水平的激酶结构域突变。对于具有完全细胞遗传学应答的患者，筛选出的93名患者中有13名（14％）具有突变。在7个具有临床相关突变的患者中，有5个（71％）失去了完全的细胞遗传学反应，而在86个无临床相关突变的患者中（80个无突变和6个酪氨酸激酶抑制剂敏感性突变的患者中，有15个（17％）， p = 0·0031）。携带突变克隆的患者的5年无进展生存期较差（65·3％[95％CI 40·5–81·8]vs 86·9％[75·8–93·2]；p = 0·0161）和5年无事件生存期较差（22·2％[CI 5·6-45·9] vs 62·0％[50·4-71·6]； p <0·0001 ）比没有突变的患者要多。我们在开始一线酪氨酸激酶抑制剂治疗后3个月获得样本的41名患者中，有4名（10％）发现了激酶结构域突变；所有这四个随后发展为加速期疾病，而没有突变的37个中只有三个（8％）（p <0·0001）。

解释

NGS可靠且一致地检测到激酶结构域突变的早期出现，而Sanger测序则无法检测到。据我们所知，我们仅报道了仅治疗3个月后就存在激酶结构域突变的情况，这可能具有重大的临床意义。NGS将允许早期的临床干预，我们的发现将有助于就激酶结构域突变分析的频率提出新的建议，以改善患者的临床护理。

资金

没有。