Overview of non-HDL-C associations in the region around <i>LDLR</i>.

<p>Plot <b>A</b> is a 0.8Mb overview centered on <i>LDLR</i> and plot <b>B</b> is a 70kb overview around the <i>LDLR</i> gene. Black circles show-log₁₀<i>P</i> as a function of build 36 coordinates for associations with non-HDL-C and red crosses correspond to non-HDL-C associations after adjusting for the four variants rs17248720, rs72658867, rs200238879 and rs17248748 that are indicated by vertical broken lines in plot b. Genes are shown in blue and recombination rates are reported in cM/Mb.</p

RNA sequencing data from blood demonstrates increased expression and abnormal splicing characterized by intron 14 retention in carriers of the splice region variant rs72658867-A.

<p><b>A.</b> Normalized average <i>LDLR</i> exon coverage for non-carriers (<i>N</i> = 238, in blue) and heterozygotes (<i>N</i> = 15, in red) of rs72658867-A demonstrates increased expression of <i>LDLR</i> transcripts in heterozygotes by ~22%, <i>P</i> = 0.0075. The X-axis is the exon number corresponding to RefSeq transcript NM_000527 for <i>LDLR</i>. The Y-axis shows the median normalized coverage (normalized for each individual to the total number of aligned reads). The error bars are based on the median absolute deviation within each group and is calculated separately for each exon. <b>B.</b> Using the same samples as in a) preferential intron 14 retention is observed in heterozygous carriers of rs72658867-A (shown in red). The X-axis is the genomic position in Mb (hg18/Build36). The Y-axis is the median count of normalized reads as in a). The structure of all <i>LDLR</i> RefSeq transcript variants is shown. The upper panel shows the full length gene whereas the lower panel shows the exons 13, 14 and 15 and the intron retention in intron 14. <b>C.</b> Quantitation of the proportion of transcripts with intron 14 retention in heterozygotes. The Y-axis corresponds to the proportion of RNA sequencing reads that are spliced from exon 14 to exon 15 (correctly spliced) out of the total number of reads that cover the last base of exon 14 (individuals that do not have coverage at this position are omitted). Median proportion: 1.00 (non-carriers); 0.70 (heterozygotes). Mean proportion: 0.95 (non-carriers); 0.71 (heterozygotes). Mann-Whitney test for location shift gives <i>P</i> = 6.0×10⁻⁹.</p

Association of <i>LDLR</i> splice region variant rs72658867-A and intronic variant rs17248748-T with non-HDL-C in Denmark, Netherlands and Iran.

<p>Shown are association results for rs72658867-A and rs17248748-T with non-HDL-C, TG and HDL-C in replication samples from Denmark, Netherlands and Iran.</p><p>^aAssociation results are adjusted for the variants rs17248748-T and rs6511720-T (r² = 0.96 with rs17248720-T in Europeans in the 1000G Phase 3 data).</p><p>^bAssociation results are adjusted for the variants rs72658867-A and rs6511720-T (r² = 0.96 with rs17248720-T in Europeans in the 1000G Phase 3 data).</p><p>^cAll replication samples combined for each trait.</p><p>^dReplication samples combined with Icelandic samples, # non-HDL-C = 139,385, # TG = 100,350, # HDL = 139,753.</p><p>^eEffect (β) in mmol/l given with respect to allele A for rs72658867 and allele T for rs17248748.</p><p>^fEffect (β) in % change is given with respect to the allele A for rs72658867 and allele T for rs17248748.</p><p>^g<i>P</i>_<i>het</i> = <i>P</i>-value for a test of heterogeneity in the combined effect estimate.</p><p>Association of <i>LDLR</i> splice region variant rs72658867-A and intronic variant rs17248748-T with non-HDL-C in Denmark, Netherlands and Iran.</p

Association of <i>LDLR</i> sequence variants with CAD and age at diagnosis of CAD in Iceland.

<p>Association results for rs17248720, rs17248748, rs200238879 and rs72658867 with CAD (coronary artery disease) and age at diagnosis of CAD. Association results for each variant is presented with and without adjusting for the other three variants in the table.</p><p>^aFreq A1 = allellic frequency of A1.</p><p>^bOR is given with respect to allele A1.</p><p>^cEffect (β) is given in years with respect to allele A1.</p><p>Association of <i>LDLR</i> sequence variants with CAD and age at diagnosis of CAD in Iceland.</p

Relevance in population surveys of study place and time to (i) the mean general population serum folate level, and (ii) the excess plasma homocysteine level in the TT versus CC <i>MTHFR</i> C677T genotype.

a<p>Mean folate levels average all who were surveyed; SE denotes the standard error due only to within-survey variation. Between-survey variation in folate levels is illustrated in <a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1001177#pmed-1001177-g001" target="_blank">Figure 1</a>.</p>b<p>From inverse-variance-weighted averages of within-study differences in log homocysteine; <a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1001177#pmed.1001177.s001" target="_blank">Figure S1</a>, Table S2 in <a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1001177#pmed.1001177.s006" target="_blank">Text S1</a>.</p>c<p>Mainly of Japanese, Chinese, or Korean populations; none of South Asians.</p

Effects of folic acid on major coronary events (nonfatal myocardial infarction or coronary death) in a meta-analysis of the published results of all large randomized trials of homocysteine reduction.

<p>Data for the VITATOPS trial are for myocardial infarction only. Data for FAVORIT are for all cardiovascular disease outcomes. Symbols and conventions as in <a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1001177#pmed-1001177-g002" target="_blank">Figure 2</a>.</p

Homozygote CHD OR (TT versus CC <i>MTHFR</i> C677T genotype) in 19 unpublished datasets, yielding 24 parts that are classified by genotyping panel size.

<p>For these datasets, being unpublished introduces a negligible bias (less than 0.3% for each OR and about 0.1% for the overall OR: eAppendix 1). Black squares indicate OR (with areas inversely proportional to the variance of log OR), and horizontal lines indicate 99% CIs. The subtotals and their 99% CIs are indicated by black diamonds. The overall OR and its 95% CI is indicated by a white diamond. The weight (defined as the inverse of the variance of the maximum likelihood estimate of the log OR) and the product of the weight times OR indicates how much each study has contributed to the subtotals and totals. Because the weights and products are approximately additive, they can be used to estimate the effects of ignoring particular studies, or of grouping studies in different ways.</p

Mean serum folate concentrations in 81 population surveys, by calendar year and region.

<p>White squares, no folate supplementation; black squares, after folate supplementation; broken vertical line, 1995–1996, when folate supplementation began in the United States, Canada, Australia, New Zealand (US & ANZ), and some but not all European countries. No Asian surveys were in supplemented populations.</p

Homozygote CHD OR (TT versus CC <i>MTHFR</i> C677T genotype) in each probable folate status category, from meta-analyses of 86 published studies, 14 large (i.e., variance of log OR less than 0.05) and 72 smaller studies.

<p>Black squares indicate OR (with areas inversely proportional to the variance of log OR in each subdivision), and horizontal lines indicate 99% CIs. The overall OR and its 95% CI are indicated by a black diamond. Average homocysteine difference (in the non-CHD general population) for all areas and periods is weighted in proportion to the numbers of TT CHD cases in all 86 studies.</p

Additional file 3: of Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6

Video S1. (Quicktime) Video to illustrate the DORV phenotype finding in an Adamts6 mutant heart. (MOV 1983 kb