Additional file 1: of Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans

Supplementary figures. (PDF 2303 kb

Additional file 2: of Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans

Supplementary tables. (XLSX 1030 kb

Differentially triggered genes by <i>M. leprae</i> sonicate in whole blood of T1R-affected and T1R-free leprosy patients.

<p><b>A</b>: The distribution of ΔFC values of 532 gene probes (corresponding to 462 genes) that were induced by <i>M. leprae</i> antigen with |FC|≥2. Probes outside the cut-off values of ΔFC≥1.3 and ΔFC≤1/1.3 are indicated in red. These 50 probes which represent the extreme decile (9.4%) of the ΔFC values tagged 44 genes. These 44 genes are the T1R-specific gene set. <b>B</b>: Mean fold changes of the 532 |FC|≥2 gene probes for T1R-free leprosy patients (mean FC_LEP) plotted against the mean fold changes of the same probes for T1R-affected leprosy patients (mean FC_T1R). Each dot represents a single gene. Open circles represent the T1R gene set. The insert displays genes with mean FC of −5 to +10.</p

Overrepresented Gene Ontology terms amongst the 572 genes regulated by <i>M. leprae</i> sonicate in the samples from former leprosy patients with and without T1R.

a<p>Number of genes assigned to one GO term or pathway.</p>b<p>Percentage of genes assigned to one GO term or pathway from the total number of processed genes.</p>c<p><i>P</i>-value derived from a modified Fisher's exact test.</p>d<p><i>P</i>-value corrected for multiple testing by Benjamini-Hochberg correction.</p

SNPs investigated in this study together with the PCR primers and detection method.

<p>Chrom: Chromosome.</p><p>SNP: single nucleotide polymorphism.</p><p>NCBI AN: NCBI Accession Number.</p><p>AA: Amino Acid.</p><p>Dig: Digestion.</p><p>AT: Annealing Temperature.</p><p>FS: Fragment size.</p><p>DFS: Digestion Fragment size.</p

Associations between reduced sperm counts and the most common <i>MTHFR</i> haplotypes.

<p>Associations between reduced sperm counts and the most common <i>MTHFR</i> haplotypes.</p

Haplotype organisation of the <i>MTHFR</i> gene in the CEPH pedigrees.

<p>The haplotype block pattern was constructed using the Haploview program using data from the HapMap project. The number in each cell represents the LD parameter D' (x100). Each cell is colour graduated relative to the strength of LD between two markers. Red cells without numbers refer to pairs of SNPs in significant and maximum LD (i.e. D' = 1). Blue cells also represent pairs of SNPs with D' = 1, although in these case the observed LD levels are not statistically significant. The entire gene lies within a large haplotype block, within which two minor blocks can be identified. The rs numbers are the SNP ID in the NCBI SNP database. The marker rs1801131 (E429A) is located in haplotype block 1, marker rs2066472 (not shown) is located within haplotype block 2 and the markers A222V is located between these two haplotype blocks.</p

Molecular pathways overrepresented amongst the 572 genes regulated by <i>M. leprae</i> sonicate in the samples from former leprosy patients with and without T1R.

a<p>Number of genes assigned to one pathway.</p>b<p>Percentage of genes assigned to one GO term or pathway from the total number of processed genes.</p>c<p><i>P</i>-value derived from a modified Fisher's exact test.</p>d<p><i>P</i>-value corrected for multiple testing by Benjamini-Hochberg correction</p

Summary of published associations between the <i>MTHFR</i> C665T variant and unexplained male infertility.

<p>Summary of published associations between the <i>MTHFR</i> C665T variant and unexplained male infertility.</p

Associations between reduced sperm counts and the most common <i>MTRR</i> haplotypes.

<p>Associations between reduced sperm counts and the most common <i>MTRR</i> haplotypes.</p