Additional file 1: Table S1. of Copy number variants and rasopathies: germline KRAS duplication in a patient with syndrome including pigmentation abnormalities

Gene content of the ~10.5-Mb chromosome 12p duplication between nt 23,728,536 and nt 34,189,943 (NCBI Build hg19), including 49 protein coding genes, two microRNA genes, and one long non coding RNA gene. (DOCX 24 kb

Allelic analyses of the 23 tag SNPs genotyped in CCALD and AMN patients.

a<p>: The Fisher's exact test was used for SNP with a Minor Allele Frequency (MAF)<0.10.</p>b<p>: Permutation-based empirical <i>P</i> value were calculated for SNP showing a trend of association (<i>P</i> value<0.10).</p

Tagging of the <i>CD1 locus</i>.

<p>A) Allelic association results of the tag SNPs genotyped in CCALD and AMN patients: each black dot represents a tag SNP; -log₁₀<i>P</i> is plotted for each of the 21 tag SNPs; the five <i>CD1</i> genes are indicated by black boxes; B) LD between the corresponding tag SNPs: LD is represented by shades of grey as a function of r² values (black diamond for r²≥0.90, white diamond for r² = 0). Associated tag SNPs are marked with an asterisk.</p

Allelic analyses of <i>CD1D</i> and <i>CD1B</i> variants in the CCALD and AMN patients.

a<p>: The Fisher's exact test was used for SNP with a Minor Allele Frequency (MAF)<0.10.</p>b<p>: Permutation-based empirical <i>P</i> value were calculated for SNP showing a trend of association (<i>P</i> value<0.10).</p

Modification of miRNAs expression in SVRs and NRs.

<p>Total RNAs was extracted and analyzed for miRNAs content by RT q-PCR. The ΔCt for each miRNA was calculated and normalized to the ΔCt value of SNORD44, in each biopsy. The histograms represent the mean expression of miRNAs/SNORD44 within the groups of patients NRs, SVRs and RRs normalized to the expression of the same miRNA within the group of normal patients. The association of miRNAs expression with viral response was calculated using the Wald test. 1A- Out of 851 miRNAs, 20 miRNAs were particularly deregulated between NRs and SVRs in the screen group (p<0.05 with at least a 2-fold difference between NRs and SVRs or p<0.01). 1B- The expression of the 20 miRNAs previously selected was assessed by RT q-PCR, in the validation group, independently. N = normal non-infected patients, NR = non-responders, RR = responders-relapsers, SVR = sustained virological responders.</p

Differentially expressed miRNAs between NRs, SVRs and RR, prior to treatment.

<p>Differentially expressed miRNAs between NRs, SVRs and RR, prior to treatment.</p

Identification of a 3 miRNAs signature (mir-99a, mir-23a and mir-181a*) predictor of SVR and selective analysis of miRNAs expression in NRs and SVRs.

<p>2A- The receiver Operator Curves (ROC) were calculated for each miRNAs and for the signature based on the combination of the 3 miRNAs. 2B- The sensibility (Se), specificity (Spe), positive predictive value (PPV) and negative predictive value (NPV) were calculated for each miRNA isolated and for the combination of the 3 miRNAs. 2C- The expression of mir-122, mir-196b, mir-296-5p, mir-448, mir-431 and mir-128 was analyzed by RT q-PCR in the total group of patients (n = 111). The ΔCp (ΔCp_<i>t</i> = 2^{<i>ΔCpsample</i>}) for each miRNAs was calculated and normalized to the ΔCp value of SNORD44 in each biopsy. The histograms represent the mean expression of miRNA/SNORD44 within the groups of patients NRs, SVRs and RRs normalized to the expression of the same miRNA within the group of normal patients. The association of mRNAs expression with viral response was calculated using the Wald test. N = normal un-infected patients, NR = non-responders, RR = responders-relapsers, SVR = sustained virological responders.</p

Modification of miRNAs expression in the serum of patients with chronic hepatitis C.

<p>3A- Mir-23a, mir-99a, mir-181a*, mir-217 and mir-122 were detected by RT-q-PCR in 68 serums (NR = 26, RR = 10, RR = 32). The ΔCt for each miRNAs were calculated and normalized to the ΔCt value of <i>c</i>.<i>elegans</i> mir-39. The histograms represent the mean expression of miRNAs/mir-39 within the groups of patients NRs, RRs and SVRs. 3B- Correlation between mir-122 and alanine amino transferase, in the serum. The correlation was assessed using the Spearman correlation test. NR = non-responders, RR = responders-relapsers, SVR = sustained virological responders.</p