Characterization of the samples included in this study.

<p>Characterization of the samples included in this study.</p

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: FigureS1. of Genotype-phenotype correlations and expansion of the molecular spectrum of AP4M1-related hereditary spastic paraplegia

Expression of the AP4M1 gene in several regions of the human brain throughout development and aging. Note the higher expression levels during fetal development (birth is marked with a vertical solid line). Data from the Human Brain Transcriptome (HBT) project ( http://hbatlas.org ). CBC - cerebellar cortex, MD - mediodorsal nucleus of the thalamus, STR - striatum, AMY - amygdala, HIP - hippocampus, and NCX – neocortex. (PDF 68 kb

Overview of clinical and genetic features of atypical PKAN cases.

<p>PANK2 transcript: ENST00000316562.</p

Table_1_The Diagnostic Value of MRI Pattern Recognition in Distal Myopathies.DOCX

<p>Objective: Distal myopathies are a diagnostically challenging group of diseases. We wanted to understand the value of MRI in the current clinical setting and explore the potential for optimizing its clinical application.</p><p>Methods: We retrospectively audited the diagnostic workup in a distal myopathy patient cohort, reassessing the diagnosis, whilst documenting the usage of MRI. We established a literature based distal myopathies MRI pattern template and assessed its diagnostic utility in terms of sensitivity, specificity, and potential impact on the diagnostic workup.</p><p>Results: Fifty-five patients were included; in 38 with a comprehensive set of data the diagnostic work-up was audited. The median time from symptoms onset to diagnosis was 12.1 years. The initial genetic diagnostic rate was 39%; 18% were misdiagnosed as neuropathies and 13% as inclusion body myositis (IBM). Based on 21 publications we established a MRI pattern template. Its overall sensitivity (50%) and specificity (32%) were low. However in some diseases (e.g., MYOT-related myopathy, TTN-HMERF) MRI correctly identified the causative gene. The number of genes suggested by MRI pattern analysis was smaller compared to clinical work up (median 1 vs. 9, p < 0.0001) but fewer genes were correctly predicted (5/10 vs. 7/10). MRI analysis ruled out IBM in all cases.</p><p>Conclusion: In the diagnostic work-up of distal myopathies, MRI is useful in assisting genetic testing and avoiding misdiagnosis (IBM). The overall low sensitivity and specificity limits its generalized use when traditional single gene test methods are applied. However, in the context of next generation sequencing MRI may represent a valuable tool for interpreting complex genetic results.</p

MRM conditions for the analysis of vitamin B5 and isotopically-labelled vitamin B5 including retention times, collision energy, precursor ions and their respective quantifier and qualifier ions.

<p>MRM conditions for the analysis of vitamin B5 and isotopically-labelled vitamin B5 including retention times, collision energy, precursor ions and their respective quantifier and qualifier ions.</p

Antibodies used for ICC and Western blotting.

<p>Antibodies used for ICC and Western blotting.</p