Additional file 18: of Metagenomic characterization of ambulances across the USA

Figure S24. Boxplots of dataset performance for random forest training (80/20 split) for city class. Classes underwent down sampling and were optimized in terms of mean ROC score. Shown are kappa and balanced accuracy, averaged over classes. (DOCX 113 kb

Transcriptome Profiling of Pediatric Core Binding Factor AML

<div><p>The t(8;21) and Inv(16) translocations disrupt the normal function of core binding factors alpha (CBFA) and beta (CBFB), respectively. These translocations represent two of the most common genomic abnormalities in acute myeloid leukemia (AML) patients, occurring in approximately 25% pediatric and 15% of adult with this malignancy. Both translocations are associated with favorable clinical outcomes after intensive chemotherapy, and given the perceived mechanistic similarities, patients with these translocations are frequently referred to as having CBF-AML. It remains uncertain as to whether, collectively, these translocations are mechanistically the same or impact different pathways in subtle ways that have both biological and clinical significance. Therefore, we used transcriptome sequencing (RNA-seq) to investigate the similarities and differences in genes and pathways between these subtypes of pediatric AMLs. Diagnostic RNA from patients with t(8;21) (N = 17), Inv(16) (N = 14), and normal karyotype (NK, N = 33) were subjected to RNA-seq. Analyses compared the transcriptomes across these three cytogenetic subtypes, using the NK cohort as the control. A total of 1291 genes in t(8;21) and 474 genes in Inv(16) were differentially expressed relative to the NK controls, with 198 genes differentially expressed in both subtypes. The majority of these genes (175/198; binomial test <i>p</i>-value < 10⁻³⁰) are consistent in expression changes among the two subtypes suggesting the expression profiles are more similar between the CBF cohorts than in the NK cohort. Our analysis also revealed alternative splicing events (ASEs) differentially expressed across subtypes, with 337 t(8;21)-specific and 407 Inv(16)-specific ASEs detected, the majority of which were acetylated proteins (p = 1.5x10^-51 and p = 1.8x10^-54 for the two subsets). In addition to known fusions, we identified and verified 16 <i>de novo</i> fusions in 43 patients, including three fusions involving <i>NUP98</i> in six patients. Clustering of differentially expressed genes indicated that the homeobox (<i>HOX</i>) gene family, including two transcription factors (<i>MEIS1</i> and <i>NKX2-3</i>) were down-regulated in CBF compared to NK samples. This finding supports existing data that the dysregulation of <i>HOX</i> genes play a central role in biology CBF-AML hematopoiesis. These data provide comprehensive transcriptome profiling of CBF-AML and delineate genes and pathways that are differentially expressed, providing insights into the shared biology as well as differences in the two CBF subsets.</p></div

Additional file 25: of Metagenomic characterization of ambulances across the USA

Figure S8. Volcano plot of the p-value versus log2-fold change (LFC) of HUMAnN2 pathway abundances resulting from a DESeq2 differential abundance analysis for surface class with FDR correction (Benjamini-Hochberg correction, α = 0.01). Class combinations were selected based on overlap data classification performance. Points vary in color based on pathway superclass and size based on the proportion of genes in that class with p < α. Genes in the 95th percentile of absolute LFC are labeled. (PDF 273 kb

Identification of gene-fusion events in pediatric AML samples.

<p>(A) Gene-fusion events were detected using four gene fusion detection methods. (B) 69 putative fusion events shown in a circular plot. Red: intra-chromosomal fusion event; Blue: inter-chromosomal fusion event. (C) three fusion variants of NUP98. (D) Two in-frame fusions.</p

Comparison of expression profiles for those with and without <i>FLT3</i>/ITD mutation.

<p>(A) PCA for the two groups. (B) Genes with the most significant adjust <i>p</i>-value between the two groups.</p

Co-expression of t(8;21)-specific genes.

<p>(A) Heatmaps showing the clustering of 827 t(8;21)-specific genes in 64 pediatric AML samples. (B) Co-expressed genes were determined based on the coefficient of determination (R2 > 0.6). The co-expression gene networks were generated using Cytoscape 2.8.3[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138782#pone.0138782.ref019" target="_blank">19</a>]. Node color is based on the fold change of the differentially expressed gene (red: up-regulated; green: down-regulated), and node size corresponds to the degree of the node (i.e., the number of edges incident to it). (C) Gene expression of the HOX gene family for three types of cytogenetic abnormalities, where NK is separated into two groups based on the mutation of FLT3/ITD.</p

Differentially expressed genes characterize different cytogenetic abnormalities.

<p>(A) Principal component analysis for samples with different cytogenetic abnormalities. (B-D) Circular plots were drawn with the in-house software application OmicCircos[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138782#pone.0138782.ref018" target="_blank">18</a>] to represent the t(8;21)-specific, Inv(16)-specific, and normal-specific differentially expressed genes. The track from outside to inside are the symbols of differentially expressed genes with high significance (p-value < 1.0E-08); genome positions by chromosomes (black lines are cytobands); average expression level for the samples with specific cytogenetic abnormalities (yellow); average expression level for the remaining samples (pink); fold change (red: up-regulated; blue: down-regulated); and the p-values associated with the expression patterns between one subtype and the remaining samples.</p

Most significantly up- and down-regulated genes in the three cytogenetic categories.

<p>Most significantly up- and down-regulated genes in the three cytogenetic categories.</p

Alternative splicing for pediatric AML samples.

<p>Alternative splicing events detected by MATS for three cytogenetic abnormalities. Five different alternative splicing events were detected: skipped exon (SE), alternative 5’ splice site (A5SS), alternative 3’ splice site (A3SS), mutually exclusive exons (MXE) and retained intron (RI). All events were further separated into two groups based on whether the alternative exon was included (A) or skipped (B) in the samples.</p

Rare coding variants identified in the 111 target candidate genes using whole exome sequencing in nine patients with suspected MODY.

a<p>SIFT: − tolerated, + not tolerated/PolyPhen-2: − benign, + possibly damaging, ++ probably damaging/Align-GVGD: the Grantham variation (GV), and the Grantham deviation (GD) are combined to provide graded classifiers from most likely to interfere with function (class C65) to least likely (class C0).</p>b<p>Allele frequencies from the interim analysis of phase I of the 1000 Genomes Project, 2010.08.04 sequence index, which included 629 samples (SNPs released in November 2010, indels released in February 2011).</p><p>Abbreviation: Chr, chromosome number; 1000 G, the 1000 Genomes Project; n.a, not analysed due to insufficient number of alignments to make prediction.</p