Predicting osimertinib‐treatment outcomes through EGFR mutant‐fraction monitoring in the circulating tumor DNA of EGFR T790M‐positive patients with non‐small cell lung cancer (WJOG8815L)

The WJOG8815L phase II clinical study involves patients with non‐small cell lung cancer (NSCLC) that harbored the EGFR T790M mutation, which confers resistance to EGFR tyrosine kinase inhibitors (TKIs). The purpose of this study was to assess the predictive value of monitoring EGFR genomic alterations in circulating tumor DNA (ctDNA) from patients with NSCLC that undergo treatment with the third‐generation EGFR‐TKI osimertinib. Plasma samples of 52 patients harboring the EGFR T790M mutation were obtained pretreatment (Pre), on day 1 of treatment cycle 4 (C4) or cycle 9 (C9), and at diagnosis of disease progression or treatment discontinuation (PD/stop). CtDNA was screened for EGFR‐TKI‐sensitizing mutations, the EGFR T790M mutation, and other genomic alterations using the cobas EGFR Mutation Test v2 (cobas), droplet digital PCR (ddPCR), and targeted deep sequencing. Analysis of the sensitizing—and T790M—EGFR mutant fractions (MFs) was used to determine tumor mutational burden. Both MFs were found to decrease during treatment, whereas rebound of the sensitizing EGFR MF was observed at PD/stop, suggesting that osimertinib targeted both T790M mutation‐positive tumors and tumors with sensitizing EGFR mutations. Significant differences in the response rates and progression‐free survival were observed between the sensitizing EGFR MF‐high and sensitizing EGFR MF‐low groups (cutoff: median) at C4. In conclusion, ctDNA monitoring for sensitizing EGFR mutations at C4 is suitable for predicting the treatment outcomes in NSCLC patients receiving osimertinib (Clinical Trial Registration No.: UMIN000022076).

Abbreviations

CIs

confidence intervals

ctDNA

circulating tumor DNA

ddPCR

droplet digital PCR

EGFR

epidermal growth factor receptor

MFs

mutant fractions

NGS

next‐generation sequencing

NSCLC

non‐small cell lung cancer

ORR

overall response rate

OS

overall survival

PD

progressive disease

PFS

progression‐free survival

PR

partial response

SD

stable disease

TKI

tyrosine kinase inhibitor

     

Mutation status and burden can improve prognostic prediction of patients with lower‐risk myelodysplastic syndromes

Patients with lower‐risk myelodysplastic syndromes (LR‐MDS) as defined by the International Prognostic Scoring System (IPSS) have more favorable prognosis in general, but significant inter‐individual heterogeneity exists. In this study, we examined the molecular profile of 15 MDS‐relevant genes in 159 patients with LR‐MDS using next‐generation sequencing. In univariate COX regression, shorter overall survival (OS) was associated with mutation status of ASXL1 (P = .001), RUNX1 (P = .031), EZH2 (P = .049), TP53 (P = .016), SRSF2 (P = .046), JAK2 (P = .040), and IDH2 (P = .035). We also found significantly shorter OS in patients with an adjusted TET2 variant allele frequency (VAF) ≥18% versus those with either an adjusted TET2 VAF <18% or without TET2 mutations (median: 20.4 vs 47.8 months; P = .020; HR = 2.183, 95%CI: 1.129‐4.224). After adjustment for IPSS, shorter OS was associated with mutation status of ASXL1 (P < .001; HR = 4.306, 95% CI: 2.144‐8.650), TP53 (P = .004; HR = 4.863, 95% CI: 1.662‐14.230) and JAK2 (P = .002; HR = 5.466, 95%CI: 1.848‐16.169), as well as adjusted TET2 VAF ≥18% (P = .008; HR = 2.492, 95% CI: 1.273‐4.876). Also, OS was increasingly shorter as the number of mutational factors increased (P < .001). A novel prognostic scoring system incorporating the presence/absence of the four independent mutational factors into the IPSS further stratified LR‐MDS patients into three prognostically different groups (P < .001). The newly developed scoring system redefined 10.1% (16/159) of patients as a higher‐risk group, who could not be predicted by the currently prognostic models. In conclusion, integration of the IPSS with mutation status/burden of certain MDS‐relevant genes may improve the prognostication of patients with LR‐MDS and could help identify those with worse‐than‐expected prognosis for more aggressive treatment.     

Identification of the sequence variations of 15 autosomal STR loci in a Chinese population

Background: DNA sequence variation including base(s) changes and insertion or deletion in the primer binding region may cause a null allele and, if this changes the length of the amplified fragment out of the allelic ladder, off-ladder (OL) alleles may be detected.

Aim: In order to provide accurate and reliable DNA evidence for forensic DNA analysis, it is essential to clarify sequence variations in prevalently used STR loci.

Subjects and methods: Suspected null alleles and OL alleles of PlowerPlex16® System from 21?934 unrelated Chinese individuals were verified by alternative systems and sequenced.

Results: A total of 17 cases with null alleles were identified, including 12 kinds of point mutations in 16 cases and a 19-base deletion in one case. The total frequency of null alleles was 7.751?×?10^?4. Eight hundred and forty-four OL alleles classified as being of 97 different kinds were observed at 15 STR loci of the PowerPlex®16 system except vWA. All the frequencies of OL alleles were under 0.01.

Conclusion: Null alleles should be confirmed by alternative primers and OL alleles should be named appropriately. Particular attention should be paid to sequence variation, since incorrect designation could lead to false conclusions.     

汉族脑梗死患者阿司匹林抵抗基因单核苷酸多态性的分布特征

目的 研究汉族脑梗死患者人群中阿司匹林抵抗相关基因重要位点单核苷酸多态性（SNPs）的分布频率,并将其分布与在其他人群中的分布进行比较。方法 选取475例汉族脑梗死患者为研究对象,采用荧光染色原位杂交技术检测GPⅢa PLA2 (rs5918)、PEAR1 (rs12041331)和PTGS1 (rs10306114) 3个位点的基因型,统计分析相关位点基因型和等位基因分布频率,并与相关数据库收录的其他人群进行比较。结果 在汉族脑梗死患者人群中GPⅢa PLA2 (rs5918)位点上存在2种基因型,为TT（98.74%）和TC（1.26%）,其中T、C等位基因频率分别为99.37%、0.63%;PTGS1 (rs10306114)位点上仅存在1种基因型,即AA（100%）;PEAR1 (rs12041331)位点上GG、GA、AA 3种基因型均存在,分别占42.32%、43.79%、13.89%。结论 在汉族脑梗死患者人群中,阿司匹林抵抗相关的GPⅢa PLA2 (rs5918)和PTGS1 (rs10306114)位点上突变情况极少,均以野生型纯合子为主,而PEAR1 (rs12041331)位点上突变多见。     

Utility of next‐generation sequencing methods to identify the novel HLA alleles in potential stem cell donors from Chinese Marrow Donor Program

The human leucocyte antigen (HLA) is the most polymorphic region of the human genome. Compared with Sanger‐sequencing‐based typing (SBT) methods, next‐generation sequencing (NGS) has significantly higher throughput and depth sequencing characteristics, having dramatic impacts on HLA typing in clinical settings. Here, we performed NGS technology with Ion Torrent S5 platform to evaluate the potential four novel HLA alleles detected in five donors from Chinese Marrow Donor Program (CMDP, Shaanxi Province) during routine Sanger SBT testing. We also predicted the highest estimated relative frequency novel allele‐bearing haplotypes according to their phenotypes and HaploStats database. NGS assays, as it provided the phase‐defined and complete sequencing information, undoubtedly increase novel allele identification which will greatly enrich HLA database and provide more information for donor selection.     

HLA -A, -C, -B, -DRB1, -DQB1 and -DPB1 allele and haplotype frequencies in 4514 healthy Norwegians

We report HLA-A, -C, -B, -DRB1, -DQB1 and -DPB1 allele frequencies and estimated haplotype frequencies from 4514 healthy Norwegians who volunteered to participate in the Norwegian Bone Marrow Donor Registry. HLA genotyping was conducted on a Next Generation Sequencing platform. Data were analyzed using Arlequin and Pypop software. No significant deviations from Hardy-Weinberg Equilibrium were noted at any of the loci studied. We discuss the representability for the Norwegian population and argue that the presented HLA data could serve as a Norwegian reference panel.     

B亚型中Bx新等位基因的鉴定

目的对ABO血型中B亚型分子遗传背景的研究,发现并鉴定ABO新等位基因。方法对5份血型血清学鉴定为B亚型的样本,采用PCR-SSP、ABO基因第6及第7外显子直接测序方法进行基因定型;并对目的B亚型样本进行RT-PCR、巢式PCR扩增、测序,分析其cDNA结构的差异。结果5份血清学为B亚型的样本中,血清学鉴定为Bx的个体发现了一个新的B等位基因。该等位基因与B101等位基因相比,差异仅在于第7外显子的B基因序列中nt721位C>T突变。其余4份B亚型样本的ABO基因第6、7外显子都未发现新的点突变。结论首次在中国汉族人中发现一个721C>T新变异的B等位基因,该等位基因nt721位由C转变为T,241位氨基酸由精氨酸转变为色氨酸,可导致糖基转移酶活性的降低,表明ABO基因的第241位氨基酸对决定糖基转移酶活性是至关重要的。     

CD14基因-260A/G位点多态性与前列腺癌易感性的研究

目的研究CD14基因-260A/G位点多态性与前列腺癌易感性的关系。方法提取168例前列腺癌患者和208例对照组的外周血DNA标本,应用聚合酶链反应-连接酶特异检测技术（polymerase chain reaction-ligase detection reaction,PCR-LDR）分析前列腺癌患者CD14-260A/G位点多态性,比较不同基因型和前列腺癌易感性的关系,并探讨不同基因型与前列腺癌患者年龄、体重指数（body mass index,BMI）、吸烟、饮酒及肿瘤家族史的关系。结果总体来说CD14基因-260A/G多态性与前列腺癌易感性之间无显著相关性（P=0.284,OR=1.27,95%CI=0.82～1.94）;饮酒（P=0.003）和肿瘤家族史（P〈0.001）与前列腺癌的发生密切相关;在分层分析中,年龄〈70岁的男性携带CD14-260G（AG＋GG）等位基因者能增加前列腺癌的易感性（P=0.011,OR=2.93,95%CI=1.28～6.70）。结论 CD14基因-260A/G位点多态性在总体上与前列腺癌易感性无显著相关性,但在年龄小于70岁男性中,携带有CD14-260G等位基因者患前列腺癌的危险性却明显增高。