Additional file 2: Table S2. of Identification of functional single nucleotide polymorphisms in the branchpoint site

List of primer sequences utilized in the study. (XLSX 10 kb

The analysis results based on the early-AFP group are shown.

<p>Panel A shows the scatter plot of REHH plotted against all core haplotype frequency (circled dot indicates the selected core haplotype “rs1074014-rs1072877-rs1564582-rs11212724-rs11211725”). Panel B shows the haplotype bifurcation diagram, which visualizes the breakdown of LD at increasing distances from core haplotypes at the selected core region. The root of each diagram is a core haplotype, identified by a dark blue circle. Panel C illustrates how the REHH value varies by the selected core haplotype. Panel D shows the table of core haplotype, and the dot in the observed haplotype sequence represents the allele that matches the ancestral. Panel E presents the theoretical phylogenetic tree of different core haplotypes. Gray squares represent haplotypes that are not present in the observed data, but are missing links in the phylogeny. The area of the squares is proportional to the frequency of the haplotype.</p

Case-control association test results for 4 runs of homozygosity (ROH) regions nominally associated with the risk of autism (unadjusted p-value <0.01) in the discovery sample.

*<p>R_Case = prevalence rate of the ROH marker in cases; R_Ctrl = prevalence rate of the ROH marker in controls;</p>Δ<p>Unadjusted p-values based on the Fisher’s exact tests.</p

The association findings for age of first phrase (AFP) are presented as –log₁₀ p-values (unadjusted by multiple tests) across the whole autosome.

<p>The arrow indicates the ROH region at 11q22.3.</p

Case-only association test results for age of first phrase (only unadjusted p-value <1×10⁻⁵ were shown).

*<p>Bonferroni-corrected p-value.</p

Demographic features of cases in the discovery population.

1<p>Maternal and paternal education: 1≤6 years, 2 = 7−9 years; 3 = 10−12 years, 4 = 13−16 years, 5 = >16 years.</p>2<p>SRST: Total social responsiveness score assessed by the Autism Diagnostic Interview-revised.</p>3<p>SCQ: social communication quotient total score.</p>4<p>FSTBEH: Stereotype behavior/interest score assessed by the Autism Diagnostic Interview-revised.</p>5<p>The unit of age of phrase is month.</p>6<p>VIQ = verbal IQ; PIQ = performance IQ.</p>7<p>The unit of paternal/maternal age is year.</p

Linkage disequilibrium patterns in the 11q22.3 region are shown.

<p>Linkage disequilibrium patterns in the 11q22.3 region are shown.</p

The distribution of runs of homozygosity (ROH) regions (by length of the ROH region) is shown.

<p>Age of first phrase (AFP) was classified into early-AFP and late-AFP groups by the k-means clustering algorithm.</p

The analysis results based on the late age of first phrase (late-AFP) group are shown.

<p>Panel A shows the scatter plot of REHH plotted against all core haplotype frequency (circled dot indicates the selected core haplotype “rs1074014-rs1072877-rs1564582-rs11212724-rs11211725”). Panel B shows the haplotype bifurcation diagram, which visualizes the breakdown of LD at increasing distances from core haplotypes at the selected core region. The root of each diagram is a core haplotype, identified by a dark blue circle. Panel C illustrates how the REHH value varies by the selected core haplotype. Panel D shows the table of core haplotype, and the dot in the observed haplotype sequence represents the allele that matches the ancestral. Panel E presents the theoretical phylogenetic tree of different core haplotypes. Gray squares represent haplotypes that are not present in the observed data, but are missing links in the phylogeny. The area of the squares is proportional to the frequency of the haplotype.</p

Additional file 15: of An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation population-optimized human arrays

Sequence information of the primers used for qPCR. (XLSX 11 kb