Variant allelic frequencies of driver mutations can identify gliomas with potentially false-negative MGMT promoter methylation results.
Variant allelic frequencies of driver mutations can identify gliomas with potentially false-negative MGMT promoter methylation results.
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DOI：
10.1186/s40478-023-01680-0
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发表时间：
2023-11-02
影响因子：
7.1
通讯作者：
中科院分区：
文献类型：
--
作者：
MGMT 启动子甲基化测试对于神经胶质瘤的预后和预测替莫唑胺反应是必需的。准确的结果取决于足够的肿瘤细胞构成，但细胞构成的组织学估计是主观的。我们试图确定驱动突变变异等位基因频率 (VAF) 是否可以作为细胞结构的更客观指标，并识别可能的假阴性 MGMT 样本。在691例成人型弥漫性胶质瘤中，通过焦磷酸测序（N = 445）或DNA甲基化芯片（N = 246）评估MGMT启动子甲基化；通过下一代测序评估 TERT 和 IDH 驱动突变的 VAF。 MGMT 结果与 VAF 相关进行分析。通过焦磷酸测序，所有具有驱动突变 VAF ≥0.325 的神经胶质瘤中有 56% 具有 MGMT 启动子甲基化，而 VAF < 0.325 的胶质瘤中只有 37% (p< 0.0001)。 VAF VAF ≥0.325 的样品的平均 MGMT 启动子焦磷酸测序得分为 19.3%，而 VAF < 0.325 的样品的平均 MGMT 启动子焦磷酸测序得分为 12.7% (p < 0.0001)。神经胶质瘤亚型之间的最佳 VAF 截止值不同（IDH 野生型胶质母细胞瘤：0.12–0.18，IDH 突变型星形细胞瘤：~0.33，IDH 突变型和 1p/19q 共缺失少突胶质细胞瘤：0.3–0.4）。甲基化阵列对较低 VAF 下的 MGMT 启动子甲基化比焦磷酸测序更敏感。当 VAF 较低时，显微镜检查往往会高估肿瘤细胞结构。使用甲基化阵列和液滴数字 PCR (ddPCR) 重新测试低 VAF 病例证实其中一部分最初是假阴性。我们的结论是，在评估 MGMT 启动子甲基化测试时，驱动突变 VAF 是一个有用的质量保证指标，因为它可以帮助识别可能的假阴性病例。在线版本包含可在 10.1186/s40478-023-01680-0 获取的补充材料。
MGMT promoter methylation testing is required for prognosis and predicting temozolomide response in gliomas. Accurate results depend on sufficient tumor cellularity, but histologic estimates of cellularity are subjective. We sought to determine whether driver mutation variant allelic frequency (VAF) could serve as a more objective metric for cellularity and identify possible false-negative MGMT samples. Among 691 adult-type diffuse gliomas, MGMT promoter methylation was assessed by pyrosequencing (N = 445) or DNA methylation array (N = 246); VAFs of TERT and IDH driver mutations were assessed by next generation sequencing. MGMT results were analyzed in relation to VAF. By pyrosequencing, 56% of all gliomas with driver mutation VAF ≥ 0.325 had MGMT promoter methylation, versus only 37% with VAF < 0.325 (p < 0.0001). The mean MGMT promoter pyrosequencing score was 19.3% for samples with VAF VAF ≥ 0.325, versus 12.7% for samples with VAF < 0.325 (p < 0.0001). Optimal VAF cutoffs differed among glioma subtypes (IDH wildtype glioblastoma: 0.12–0.18, IDH mutant astrocytoma: ~0.33, IDH mutant and 1p/19q co-deleted oligodendroglioma: 0.3–0.4). Methylation array was more sensitive for MGMT promoter methylation at lower VAFs than pyrosequencing. Microscopic examination tended to overestimate tumor cellularity when VAF was low. Re-testing low-VAF cases with methylation array and droplet digital PCR (ddPCR) confirmed that a subset of them had originally been false-negative. We conclude that driver mutation VAF is a useful quality assurance metric when evaluating MGMT promoter methylation tests, as it can help identify possible false-negative cases. The online version contains supplementary material available at 10.1186/s40478-023-01680-0.
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影响因子：
64.8
作者：
Capper D;Jones DTW;Sill M;Hovestadt V;Schrimpf D;Sturm D;Koelsche C;Sahm F;Chavez L;Reuss DE;Kratz A;Wefers AK;Huang K;Pajtler KW;Schweizer L;Stichel D;Olar A;Engel NW;Lindenberg K;Harter PN;Braczynski AK;Plate KH;Dohmen H;Garvalov BK;Coras R;Hölsken A;Hewer E;Bewerunge-Hudler M;Schick M;Fischer R;Beschorner R;Schittenhelm J;Staszewski O;Wani K;Varlet P;Pages M;Temming P;Lohmann D;Selt F;Witt H;Milde T;Witt O;Aronica E;Giangaspero F;Rushing E;Scheurlen W;Geisenberger C;Rodriguez FJ;Becker A;Preusser M;Haberler C;Bjerkvig R;Cryan J;Farrell M;Deckert M;Hench J;Frank S;Serrano J;Kannan K;Tsirigos A;Brück W;Hofer S;Brehmer S;Seiz-Rosenhagen M;Hänggi D;Hans V;Rozsnoki S;Hansford JR;Kohlhof P;Kristensen BW;Lechner M;Lopes B;Mawrin C;Ketter R;Kulozik A;Khatib Z;Heppner F;Koch A;Jouvet A;Keohane C;Mühleisen H;Mueller W;Pohl U;Prinz M;Benner A;Zapatka M;Gottardo NG;Driever PH;Kramm CM;Müller HL;Rutkowski S;von Hoff K;Frühwald MC;Gnekow A;Fleischhack G;Tippelt S;Calaminus G;Monoranu CM;Perry A;Jones C;Jacques TS;Radlwimmer B;Gessi M;Pietsch T;Schramm J;Schackert G;Westphal M;Reifenberger G;Wesseling P;Weller M;Collins VP;Blümcke I;Bendszus M;Debus J;Huang A;Jabado N;Northcott PA;Paulus W;Gajjar A;Robinson GW;Taylor MD;Jaunmuktane Z;Ryzhova M;Platten M;Unterberg A;Wick W;Karajannis MA;Mittelbronn M;Acker T;Hartmann C;Aldape K;Schüller U;Buslei R;Lichter P;Kool M;Herold-Mende C;Ellison DW;Hasselblatt M;Snuderl M;Brandner S;Korshunov A;von Deimling A;Pfister SM
通讯作者：
Pfister SM
影响因子：
3.9
作者：
Hosoya, Tomohiro;Takahashi, Masamichi;Honda-Kitahara, Mai;Miyakita, Yasuji;Ohno, Makoto;Yanagisawa, Shunsuke;Omura, Takaki;Kawauchi, Daisuke;Tamura, Yukie;Kikuchi, Miyu;Nakano, Tomoyuki;Yoshida, Akihiko;Igaki, Hiroshi;Matsushita, Yuko;Ichimura, Koichi;Narita, Yoshitaka
通讯作者：
Narita, Yoshitaka
影响因子：
7.3
作者：
Gempt, J.;Withake, F.;Aftahy, A. K.;Meyer, H. S.;Barz, M.;Delbridge, C.;Liesche-Starnecker, F.;Prokop, G.;Pfarr, N.;Schlegel, J.;Meyer, B.;Zimmer, C.;Menze, B. H.;Wiestler, B.
通讯作者：
Wiestler, B.
影响因子：
45.3
作者：
Gilbert, Mark R.;Wang, Meihua;Mehta, Minesh P.
通讯作者：
Mehta, Minesh P.
影响因子：
15.9
作者：
Kitange, Gaspar J.;Carlson, Brett L.;Sarkaria, Jann N.
通讯作者：
Sarkaria, Jann N.