Distribution of ATXN2 repeat sizes, represented as polyQ triplet numbers.

<p>Turkish ALS patients are represented in red and healthy controls in blue bars; numbers of the individuals having the relevant alleles are shown on the top of each bar.</p

Characteristics of CNV calls.

<p>Characteristics of CNV calls.</p

Distribution of LRR values of controls and individuals with CNV at SNP level.

<p>LRRs of all individuals were extracted and plotted. “<i>Cont</i>” indicates control individuals and “<i>CNV</i>” indicates individuals with a CNV. “*” indicates the significance level between controls and CNV. 4 SNPs, including one upstream, one downstream and two within the CNV region, were selected and LRRs were plotted for (a) intergenic reigon on chromosome 11, (b) MAP4K3 gene, (c) HLA-B gene and (d) EPHA3 gene.</p

CNV call validation via LRR values.

<p>LRR values of controls and individuals with CNV for particular SNPs were extracted to check CNV calls of PennCNV tool. Average LRR values of each SNP for both groups were calculated and plotted. Consecutive SNPs in chromosome position line do not demonstrate the exact distance. The CNVs detected by PennCNV were shown by black bars. (a) Loss of an intergenic region on chromosome 11 between rs1916207 and rs554110 (chr11: 50,545,009–50,586,426), (b) gain of MAP4K3 gene between rs12151392 and rs2373530 (chr2: 39,372,016–39,428,488), (c) homozygous loss of HLA-B gene between rs9295976 and rs28367708 (chr6: 31,389,749–31,393,270), (d) loss of EPHA3 gene between rs2063589 and rs870899 (chr3: 89,485,137–89,499,861) (NCBI37/hg19).</p

The frequency of ATXN2 expansion sizes in ALS and controls (in the genotypic model).

a<p>Fisher’s exact test.</p

Association results of CNVs observed in analysis with p<0.05 (Fisher’s Exact Test).

<p>loss* Homozygous deletion.</p

Clinical characteristics of four Turkish ALS patients with ATXN2 expansions.

<p>AO: age of onset, AD: age at death. UE: upper extremity, LE: lower extremity, ULE: upper and lower extremity.</p>*<p>GWA- genotyped.</p

Summary Statistics of CNV screening in 115 ALS patients and 106 controls.

<p>Summary Statistics of CNV screening in 115 ALS patients and 106 controls.</p

Haplotype block analysis of ATXN2 locus on chromosome 12q (110,300,000–110,550,000).

<p>Genotyped SNPs located in 250 kb region were analyzed by Haploview 4.2 in order to identify haplotype blocks with ALS risk. A 136 kb large haplotype block, highlighted in red, was observed in the analysis. The frequencies of haplotypes defined in this haplotype block, the p-values and permutation p-values are shown.</p