Genes and transcribed Single Nucleotide Polymorphisms (SNP) used in ASE assay.

a<p>Different transcribed SNPs were used to obtain ASE data for the CEU/CHB and YRI datasets due to MAF differences in the populations used.</p>b<p>Only the CEU population was analysed due to the low MAF observed for transcribed SNPs in the YRI and CHB populations.</p

<i>Cis</i>-association of SNPs with ASE data.

<p>Hapmap populations used: CEU (blue), CHB (green) and YRI population (yellow) unrelated individuals. Dots represent the results using a LM and crosses represent SNPs associated with ASE data which are in complete LD with the transcribed SNP (T-test results). Coordinates are in NCBI Build 35. Horizontal lines reflect a multiple testing adjusted gene-wide statistical significance threshold of 5%. Vertical lines represent the 5′ prime (grey) and 3′ prime(black) of the gene.</p

Multi-population <i>cis</i>-mapping (CEU, CHB, YRI).

<p>For the CHI3L2 gene, only CEU and CHB populations were pooled. Horizontal lines reflect a multiple testing adjusted gene-wide statistical significance threshold of 5%.</p

Additional file 1: of Heterogeneous ribonuclear protein A3 (hnRNP A3) is present in dipeptide repeat protein containing inclusions in Frontotemporal Lobar Degeneration and Motor Neurone disease associated with expansions in C9orf72 gene

Selected clinical, pathological and genetic details on cases studied. (XLSX 17 kb

Additional file 2: of Pathological tau deposition in Motor Neurone Disease and frontotemporal lobar degeneration associated with TDP-43 proteinopathy

File S1. Clinical histories and neuropathological findings in patients #35 and 41. (DOCX 21 kb

Additional file 1: Figure S1. of Pathological tau deposition in Motor Neurone Disease and frontotemporal lobar degeneration associated with TDP-43 proteinopathy

α-synuclein (a-c) pathology in cingulate gyrus (a), CA2 region of hippocampus (b) and substantia nigra (c) and TDP-43 pathology in anterior horn cells of the spinal cord (d-f), with fine, particulate accumulations of TDP-43 (d,e) or skein-like structures (e,f) being present in affected cells in which the nucleus has been ‘cleared’ of its normal immunoreactivity. Immunoperoxidase, x400 microscope magnification. (DOCX 6504 kb

Haplotype Transmission Disequilibrium Test (TDT) of association with severe malaria in Gambian, Kenyan and Malawian child-parental trios.

<p>The table shows the common haplotypes (frequency higher than 5%) within each LD block identified in the gene, their frequency and the results of family-based test of association with severe malaria in the three populations of affected child-parental trios. Freq: frequency of the haplotype in trio parents. These are not unbiased estimates of the population frequencies. OR: Odds Ratio comparing the risk of the untransmitted versus the transmitted haplotype. All other abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004206#pone-0004206-t002" target="_blank">Table 2</a>.</p

The <i>IRF1</i> locus and Single Nucleotide Polymorphisms (SNPs) tested for association with severe malaria in child-parental trios.

<p>From top to bottom, the figure shows: human chromosome 5 with its G-banding patterns (black, grey and black bands) where the location of the 5q31.1 band is indicated; genes contained within a 642 kb segment of the 5q31.1 band known as the “Th2 cytokine cluster”; <i>IRF1</i> gene region, where the arrow indicates the direction of transcription, horizontal lines indicate intergenic regions, white boxes indicate 5′ and 3′ un-transcribed regions (UTR), black boxes indicate exons and diagonal lines indicate introns; SNPs that were tested for severe malaria in our study populations and their location with respect to the <i>IRF1</i> gene region. Coordinates quoted (Mb) are based on Ensembl release 40.</p

Single marker Transmission Disequilibrium Test (TDT) of association with severe malaria in Gambian, Kenyan and Malawian child-parental trios.

<p>The table shows the SNPs tested in association analysis with severe malaria and results of the TDT in the three populations of affected child-parental trios. Inform is the number of informative trios. OR: Odds Ratio comparing the risk of the minor vs major allele. LCL and UCL: Lower and Upper Confidence Limits of a 95% Confidence Interval respectively. TDT P: P-value for the family-based test of association. P-values<0.05 are shown in bold.</p

Minor allele frequency of <i>HBB</i> and <i>IRF1</i> Single Nucleotide Polymorphisms (SNPs) in trio parents from The Gambia, Kenya and Malawi.

<p>The table shows the SNPs that have been genotyped in the affected child parental trio studies and their frequency in trio parents from The Gambia, Kenya and Malawi. These are not unbiased estimates of the population frequencies. Chr coord is the SNP chromosome coordinate (chromosome: base pair) based on Ensemble release 40. Location: location of the SNP with respect to the <i>HBB</i> or <i>IRF1</i> locus. Alleles: minor and major alleles (major allele is shown in brackets). MAF: Minor Allele Frequency in pedigree parents (The Gambia, N = 1100; Kenya, N = 408; Malawi, N = 404). StE: Standard Error of the MAF. MAF comparison: P-values of Yates corrected χ² Test for comparison of MAF between populations; a P-value<0.05 is considered statistically significant. G: The Gambia. K: Kenya. M: Malawi.</p