Effect of DNA isolation on copy number determination by ddPCR for cerebellar samples.

<p>(A) <i>EIF2C1</i> and (B) <i>TSC2</i>. The medians and interquartile ranges from the original results, and repeats after overnight SC extractions from 25 mg and 5 mg starting material, and Puregene, are shown. n = 6, except 5 mg SC, where n = 4.</p

Demographic details of individuals whose brains were used.

<p>Demographic details of individuals whose brains were used.</p

Whole genome sequencing coverage in relation to GC content.

<p>The mean normalized coverage per 100 kb window of PD3 cerebellum is shown, after 25 mg overnight SC isolation and Puregene isolation.</p

Chromosome 1 in aCGH.

<p>The 10 Mb moving average and the aberration calls by ADM2 (after raising threshold to 12, with FZ off) are plotted for each sample. Losses are green, gains are red. </p><p></p><p></p><p>(A) Brain DNA hybridised against PBL reference DNA. Cerebellar samples are orange, and FC green. The moving average of a male to female DNA reference hybridisation is also shown (dark blue).</p><p></p><p></p><p>(B) Genome isochores. GC content range for each 100 kb isochore is 30–65% (blue to orange).</p><p></p><p></p><p>(C) Cerebellar DNA hybridised against FC DNA of the same brain for three PD cases with overnight SC extraction. PD1 = purple, PD2 = black, PD4 = green. Data for PD2 are derived after combining the dye-flip hybridisation pair.</p><p></p><p></p><p>(D) Hybridisations between DNA from the same brain as follows.</p><p>(1–3) Hybridisations of SC-isolated cerebellar DNA, with Puregene-isolated DNA from same cerebellum as reference. (1) PD3, 5 mg SC; (2) PD3, 25mg SC; (3) PD4, 25 mg SC.</p><p>(4) PD1, Puregene-isolated DNA, cerebellar (test) with FC as reference. Note the absence of waves and losses. This sample combination, but with spin column extraction, had led to waves and losses (PD1 in panel C).</p><p></p><p></p><p></p> <p>(A) Brain DNA hybridised against PBL reference DNA. Cerebellar samples are orange, and FC green. The moving average of a male to female DNA reference hybridisation is also shown (dark blue).</p> <p>(B) Genome isochores. GC content range for each 100 kb isochore is 30–65% (blue to orange).</p> <p>(C) Cerebellar DNA hybridised against FC DNA of the same brain for three PD cases with overnight SC extraction. PD1 = purple, PD2 = black, PD4 = green. Data for PD2 are derived after combining the dye-flip hybridisation pair.</p> <p>(D) Hybridisations between DNA from the same brain as follows.</p> <p>(1–3) Hybridisations of SC-isolated cerebellar DNA, with Puregene-isolated DNA from same cerebellum as reference. (1) PD3, 5 mg SC; (2) PD3, 25mg SC; (3) PD4, 25 mg SC.</p> <p>(4) PD1, Puregene-isolated DNA, cerebellar (test) with FC as reference. Note the absence of waves and losses. This sample combination, but with spin column extraction, had led to waves and losses (PD1 in panel C).</p

Additional file 1: of Distinct clinical and neuropathological features of G51D SNCA mutation cases compared with SNCA duplication and H50Q mutation

A, Double immunofluorescence images of ubiquitin (green) with α-synuclein (red) in a representative G51D case (CA3), the duplication case (SN) and the H50Q case (EC). B, Representative immunofluorescence image of α-synuclein (red) and p62 (green) in G51D (CA1), the duplication case (substantia nigra) and the H50Q case (Temporal cortex). Scale bar represents 50 μm. (TIF 5,615 kb