UCSC Genome browser view of CNVs in the <i>NRXN1</i> region.

<p>CNVs observed in the vicinity of the <i>NRXN1-alpha</i> transcription start site are shown. Note that most CNVs observed in ASD patients include exon 1 of <i>NRXN1-alpha</i> while only 1 control CNV extends into exon 1. Produced with custom tracks listing CNV calls and uploaded to <a href="http://genome.ucsc.edu" target="_blank">http://genome.ucsc.edu</a>.</p

Top Significant Biological Functions identified by Ingenuity IPA and literature searches.

<p>The right-tailed Fisher's exact test was used to calculate P-values representing the probability that selecting genes associated with that pathway or network is due to chance alone. Each functional category represents a collection of associated subcategories, each of which has an associated P-value. For example, within ‘Neurological Disease,’ are subcategories of genes associated with seizures, Huntington Disease, schizophrenia, etc. The P-value range given represents the range of P-values generated for each subcategory. In the first line, 14 genes were associated with a function in Neurological Disease by Ingenuity software. An additional 4 genes were identified as having neurological functions in the literature, giving a total of 18 with known or suspected roles in neurological disease.</p

Confirmation of CNV calls by quantitative PCR.

<p>A summary of the PCR validation result is shown. Sequence SNP CNVs were discovered in this work using SNVs present on this array for sequence variant confirmation in the same cohort.</p

UCSC Genome Browser View of CNVs in the GABR Region on chromosome 15q12.

<p>Duplications were called by both PennCNV and by CNAM in this region, however the number of duplications called by each program differed, with many additional duplications called by CNAM. Produced with custom tracks listing CNV calls and uploaded to <a href="http://genome.ucsc.edu" target="_blank">http://genome.ucsc.edu</a>.</p

Workflow for CNV analysis for samples analyzed on the custom array.

<p>The same process was used for both CNAM and PennCNV analyses. All samples used for CNV analysis in this study had to meet the quality control measures described. Only unrelated cases and controls were used for the final statistical analysis.</p

Published CNVs observed in our sample population.

*<p>Denotes CNVs contiguous with the chromosome 15q11.2–13.1 CNV shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052239#pone-0052239-t003" target="_blank">Table 3</a>.</p

Manhattan plot of CNVs called both by PennCNV and CNAM.

<p>Association statistics across all regions covered on the Illumina custom array are shown. Since the array used was not a genome-wide array, the width of each chromosome on the plot is not proportional to the chromosome length. Adjacent chromosomes are displayed in alternating red and blue colors to aid in distinguishing them.</p

Additional file 1: of Variants in CXCR4 associate with juvenile idiopathic arthritis susceptibility

Supplemental Data: Table S1. The clinical characteristics of samples in each JIA cohort. Table S2. Genome-wide significant associations at the HLA locus (p < 5×10-8 in the discovery cohort).Table S3. Association results for top SNPs in known JIA associated genes PTPN22, IL2RA, ANTXR2. TableS4. The most significantly associated SNPs at CXCR4 locus on chromosome 2q22.1. Table S5 . Genomewideassociation results for imputed SNPs (p < 1×10-4 in combined analysis) in the vicinity of CXCR4 in our JIA cohort. Table S6. Primers used in Sanger sequencing validation of rare variants at CXCR4 locus. Figure S1. Genome-wide association results for JIA. Figure S2. Regional association plot for the 2q22.1 region. Figure S3. CXCR4 tissue-specific gene expression levels. Figure S4. CXCR4 expression levels stratified by SNP genotype. (DOC 466 kb

Additional file 1: Table S1. of Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

Tagging and coverage of MHC region markers. Table S2: Tagging and coverage of Tx-specific genes. Table S3: Untranslated regions (UTRs) considered in the TxArray design. Table S4: Loss-of-function variants included in the TxArray. Table S5: Copy number polymorphisms (CNPs) and variations (CNVs) included in the TxArray. (DOCX 54 kb