Fig 1.
An endometrial cancer patient with tumor-normal paired samples.
(A) The immunohistochemical result show subclonal immunohistochemical loss of MMR expression in a variable proportion of tumor cells in tumor sample. (B) MS length distributions in paired samples. T, N represents the mean of MS length distribution in tumor sample and normal sample, respectively. U1 and U2 respectively represent the mean value of MS distribution in each clone. MSIsensor distribution represents the MS length distribution curve fitted based on the statistical test assumption of MSIsensor.
Fig 2.
(A) Algorithmist flow of scMSI. (B) Variables shown in (A).
Fig 3.
Probability graphical model of scMSI.
are the mean matrix and precision matrix related to the input variable L. A is a matrix, and each element Agk in A is a binary vector of "1 of K". And Agk = 1 means that the length distribution of MS in the g-th clone belongs to the k-th cluster in the mixed model. β, m are the parameters of the conjugate prior distribution related to μ, and w, v are the parameters of the conjugate prior distribution related to ∧. Blue text marks hyper-parameters; orange marks observed variables; black marks latent variables.
Table 1.
Comparison results of scMSI and MSIsensor for different proportions of primary clones.
Table 2.
Performance comparison of scMSI and MSIsensor in different sequencing depths.
Table 3.
Comparison results of scMSI and MSIsensor for different clone numbers.
Table 4.
Comparison of test results among scMSI, MSIsensor, MSIsensor-pro, mSINGS, MANTIS and IHC for the patient cohort.
Fig 4.
IHC detection map and PCR microsatellite detection site length distribution map of case 1.
(A) BAT26 microsatellite length distribution map (B) NR24 microsatellite length distribution map (C) BAT25 microsatellite length distribution map (D) NR27 microsatellite length distribution map (E) NR21 microsatellite length distribution map (F) The figures of clonal immunohistochemical loss of MMR expression in tumor cells: clonal loss of MLH1 and PMS2 expression in the majority of tumor cells.
Fig 5.
IHC detection map and PCR microsatellite detection site length distribution map of case 2.
(A) BAT26 microsatellite length distribution map (B) NR24 microsatellite length distribution map (C) BAT25 microsatellite length distribution map (D) NR27 microsatellite length distribution map (E) NR21 microsatellite length distribution map (F) The figures of clonal immunohistochemical loss of MMR expression in tumor cells: clonal loss of PMS2 protein alone in focal tumor cells.
Table 5.
Cases with clonal MMR deficiencies.
Table 6.
Detection of clonal microsatellite status for case 1.
Table 7.
Detection of clonal microsatellite status for case 2.