A systematic assessment of cell type deconvolution algorithms for DNA methylation data.
A systematic assessment of cell type deconvolution algorithms for DNA methylation data.
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DOI：
10.1093/bib/bbac449
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发表时间：
2022-11-19
影响因子：
9.5
通讯作者：
中科院分区：
文献类型：
--
作者：
我们对计算反褶积方法进行了系统评估，这些方法在从大量甲基化数据估计细胞类型比例方面发挥重要作用。提出的框架methylDeConv（可作为R包提供）集成了几种甲基化谱的反卷积方法（Illumina HumanMethylation450和MethylationEPIC阵列），并提供不同细胞类型特异性CpG选择，以构建包含主要免疫细胞亚群，上皮细胞和无细胞dna的扩展参考文库。我们通过模拟和基准数据集比较了不同反卷积算法的性能，并进一步研究了乳腺癌中估计的细胞类型比例与癌症治疗和黑色素瘤甲基化病例研究中亚型之间的关系。我们的结果表明，基于扩展参考库的反褶积对于获得非血液组织中细胞比例的准确估计至关重要。
We performed systematic assessment of computational deconvolution methods that play an important role in the estimation of cell type proportions from bulk methylation data. The proposed framework methylDeConv (available as an R package) integrates several deconvolution methods for methylation profiles (Illumina HumanMethylation450 and MethylationEPIC arrays) and offers different cell-type-specific CpG selection to construct the extended reference library which incorporates the main immune cell subsets, epithelial cells and cell-free DNAs. We compared the performance of different deconvolution algorithms via simulations and benchmark datasets and further investigated the associations of the estimated cell type proportions to cancer therapy in breast cancer and subtypes in melanoma methylation case studies. Our results indicated that the deconvolution based on the extended reference library is critical to obtain accurate estimates of cell proportions in non-blood tissues.
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影响因子：
12.3
作者：
Jaffe AE;Irizarry RA
通讯作者：
Irizarry RA
影响因子：
7.7
作者：
Hannon E;Dempster EL;Mansell G;Burrage J;Bass N;Bohlken MM;Corvin A;Curtis CJ;Dempster D;Di Forti M;Dinan TG;Donohoe G;Gaughran F;Gill M;Gillespie A;Gunasinghe C;Hulshoff HE;Hultman CM;Johansson V;Kahn RS;Kaprio J;Kenis G;Kowalec K;MacCabe J;McDonald C;McQuillin A;Morris DW;Murphy KC;Mustard CJ;Nenadic I;O'Donovan MC;Quattrone D;Richards AL;Rutten BP;St Clair D;Therman S;Toulopoulou T;Van Os J;Waddington JL;Wellcome Trust Case Control Consortium (WTCCC);CRESTAR consortium;Sullivan P;Vassos E;Breen G;Collier DA;Murray RM;Schalkwyk LS;Mill J
通讯作者：
Mill J
影响因子：
10.9
作者：
Danaher P;Warren S;Lu R;Samayoa J;Sullivan A;Pekker I;Wallden B;Marincola FM;Cesano A
通讯作者：
Cesano A
影响因子：
30.8
作者：
Corces, M. Ryan;Buenrostro, Jason D.;Wu, Beijing;Greenside, Peyton G.;Chan, Steven M.;Koenig, Julie L.;Snyder, Michael P.;Pritchard, Jonathan K.;Kundaje, Anshul;Gkeenleaf, William J.;Majeti, Ravindra;Chang, Howard Y.
通讯作者：
Chang, Howard Y.
影响因子：
5.7
作者：
Bauer M;Linsel G;Fink B;Offenberg K;Hahn AM;Sack U;Knaack H;Eszlinger M;Herberth G
通讯作者：
Herberth G