Additional file 1: of Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data

Supplementary information. A.xls file including supplementary tables. (XLS 25 kb

Characteristics of the 50 patients and transplant.

<p>Characteristics of the 50 patients and transplant.</p

Clusters of immunologic variables correlated to aGVHD, cGVHD, and relapse by multivariate analysis.

<p>Clusters of immunologic variables correlated to aGVHD, cGVHD, and relapse by multivariate analysis.</p

Comparison of immunological variables between patients with and without acute GVHD.

<p>Comparison of immunological variables between patients with and without acute GVHD.</p

Steroid effect on lymphocyte subsets and index of B/T cell neogenesis at day +90.

<p>Steroid effect on lymphocyte subsets and index of B/T cell neogenesis at day +90.</p

Univariate analysis of immunological variables associated with relapse.

<p>Univariate analysis of immunological variables associated with relapse.</p

Characteristics of the 50 patients and transplant.

<p>Characteristics of the 50 patients and transplant.</p

Comparison of immunological variables between patients with and without chronic GVHD.

<p>Comparison of immunological variables between patients with and without chronic GVHD.</p

Clonogenic assays of CB-CD34+ cells.

<p>Results of statistical analysis of methylcellulose-based clonogenic assay performed on CB-CD34+ cells plated after 14 days of co-culture with human MSCs. (A) CFU-GEMM count; (B) BFU-E count; (C) CFU-GM count. Values are reported as mean ± SD. The results derive from three independent experiments. Abbreviations: BFU-E, Burst forming unit-erythroid; CFU, Colony forming unit; E, erythrocyte; GM, granulocyte-monocyte; GEMM, granulocyte-erythrocyte-monocyte-megakaryocyte.</p

Gene expression profiles analysis of MSCs after co-culturing with CB-CD34+ cells.

<p>(A) Supervised analysis of MSCs-alone vs. MSCs after 10 days of co-culture with CB-CD34+ cells. A heat map of the genes differentially expressed in a statistically significant manner after co-culture (corrected p value <0.05) is plotted. (B) Gene Set Enrichment Analysis (GSEA) of MSCs-alone vs. MSCs maintained for 10 days in co-culture with CB-CD34+ cells. Top 10 gene sets from hallmark gene sets, canonical/KEGG pathways and oncogenic signatures are plotted. Please refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172430#pone.0172430.s013" target="_blank">S4 Table</a> for the complete GSEA details.</p