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Målet med denna studie var att undersöka och utvärdera effekten av systematiserad träning av avkodnings- och ordläsningsförmåga med ett lässpel hos elever i årskurs två med låg läsförmåga. Sex elever som presterade inom stanine 1-3 på ordavkodning i mitten av årskurs två deltog i studien. Studien hade en single subject design med två beselinegrupper med tre elever i varje grupp. På testet före interventionen presterade ingen av eleverna över stanine 3 på ordläsning. Testen efter interventionen visade att alla eleverna hade förbättrat sin avkodning och läsförmåga. Detta indikerar att en intervention med systematisk träning av avkodning och ordläsningsförmåga i den här åldern har god effekt.

Additional file 1: Read length distribution and assembly coverage. (A) Distribution of read lengths as generated by the 454 Genome Sequencer FLX/Titanium. The read length in base pairs (bp) is on the horizontal axis and the read count is on the vertical axis. The plot displays a bimodal curve with one peak at 250 bp and another one at 500 bp, typical for each one of the two platform types used for sequencing. (B) Shows the number of assembly positions on the vertical axis with a certain level of coverage on the horizontal axis. The plot shows that the average coverage is around 47 times. (PDF 55 KB)

Additional file 5: Evolutionary analyses of a recently acquired Giardia gene. Evolutionary analyses of a recently acquired Giardia gene. (A) A maximum likelihood tree of an acetyl transferase gene (GLP15_874). Only representatives of the homologs showing the highest similarity to the Giardia sequences are included. The tree is based on 139 unambiguously aligned amino acid positions. (B) Alignment of conserved hypothetical proteins from G. intestinalis GS (GL50581_4454) and WB (GL50803_10192) to all detected bacterial homologs. A putative amino acid sequence from a G. intestinalis P15 pseudogene is included and the positions of frameshift and in-frame termination codons are indicated. (C) A maximum likelihood tree based on 137 unambiguously aligned amino acid positions in the alignment shown in (B). Accession numbers are shown in parentheses. Only bootstrap values >50% are shown in the trees. Unambiguously aligned regions were identified manually and removed. Representative homologs with high sequence similarity to these genes were selected using the BLAST-EXPLORER software. (PDF 337 KB)

Additional file 7: VSP extended polyadenylation signal and VSP phylogenetic tree. (A) Comparative analysis of the extended polyadenylation sequence of VSP genes. The conservation of the VSP polyadenylation motif was investigated using the MEME software. Downstream regions (200 bp) of VSP genes were extracted and queried for the presence of conserved motifs. The VSP genes of all three Giardia isolates carries a very similar conserved motif that extends over at least 16 bp and is strictly positioned 0-15 bp from the translational stop codon. The P15 motif is more strictly conserved and carries a few more semi-conserved positions for a longer motif than the corresponding motifs in WB and GS. (B) A phylogenetic tree of VSP genes from P15 and WB. The VSP phylogenetic tree is based on a clustalw2 protein alignment of 156 VSP genes from WB and P15. VSP genes were selected for alignment by all-against-all BLASTP, and only VSP genes that showed at least 65% protein identity to the best-matching non-identical hit were used for the alignment (n = 156). In order to improve the alignment, sequences were trimmed (190 aa were removed from the 5' part of all sequences). Subsequent clustering was performed using maximum likelihood as implemented in the software RAxML version 7.0.4 using with the rapid bootstrap setting (-f a). The tree was rendered using the ape package for R. Black dots represent nodes with > = 50% bootstrap support. The gene id (genbank locus tag) is indicated at the tip of the branch. Blue labels represent genes from WB while black labels represent genes from P15. The tree revealed two primary groups (A and B), which are distinguished based on their distance in the tree. (PDF 172 KB)

Additional file 8: Synteny breaks and PCR primers. Experimental verification of 10 examples of structural variation discovered in the P15 genome. (PDF 785 KB)

Additional file of Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate

Additional file 6: Non-coding RNA conservation. Conservation of non-coding RNAs across the three Giardia genomes. Non-coding RNAs are generally well conserved, with P15-WB pairs showing the greatest similarity. Examples of ultraconserved non-coding RNAs across all genomes include GLsR2 and GLsR8. (PDF 93 KB)

BACKGROUND: Genome-wide association studies have so far identified 56 loci associated with risk of coronary artery disease (CAD). Many CAD loci show pleiotropy; that is, they are also associated with other diseases or traits. OBJECTIVES: This study sought to systematically test if genetic variants identified for non-CAD diseases/traits also associate with CAD and to undertake a comprehensive analysis of the extent of pleiotropy of all CAD loci. METHODS: In discovery analyses involving 42,335 CAD cases and 78,240 control subjects we tested the association of 29,383 common (minor allele frequency >5%) single nucleotide polymorphisms available on the exome array, which included a substantial proportion of known or suspected single nucleotide polymorphisms associated with common diseases or traits as of 2011. Suggestive association signals were replicated in an additional 30,533 cases and 42,530 control subjects. To evaluate pleiotropy, we tested CAD loci for association with cardiovascular risk factors (lipid traits, blood pressure phenotypes, body mass index, diabetes, and smoking behavior), as well as with other diseases/traits through interrogation of currently available genome-wide association study catalogs. RESULTS: We identified 6 new loci associated with CAD at genome-wide significance: on 2q37 (KCNJ13-GIGYF2), 6p21 (C2), 11p15 (MRVI1-CTR9), 12q13 (LRP1), 12q24 (SCARB1), and 16q13 (CETP). Risk allele frequencies ranged from 0.15 to 0.86, and odds ratio per copy of the risk allele ranged from 1.04 to 1.09. Of 62 new and known CAD loci, 24 (38.7%) showed statistical association with a traditional cardiovascular risk factor, with some showing multiple associations, and 29 (47%) showed associations at p < 1 × 10(-4) with a range of other diseases/traits. CONCLUSIONS: We identified 6 loci associated with CAD at genome-wide significance. Several CAD loci show substantial pleiotropy, which may help us understand the mechanisms by which these loci affect CAD risk.

Supplemental Digital Content is available in the text., Rationale: Abdominal aortic aneurysm (AAA) is a complex disease with both genetic and environmental risk factors. Together, 6 previously identified risk loci only explain a small proportion of the heritability of AAA. Objective: To identify additional AAA risk loci using data from all available genome-wide association studies. Methods and Results: Through a meta-analysis of 6 genome-wide association study data sets and a validation study totaling 10 204 cases and 107 766 controls, we identified 4 new AAA risk loci: 1q32.3 (SMYD2), 13q12.11 (LINC00540), 20q13.12 (near PCIF1/MMP9/ZNF335), and 21q22.2 (ERG). In various database searches, we observed no new associations between the lead AAA single nucleotide polymorphisms and coronary artery disease, blood pressure, lipids, or diabetes mellitus. Network analyses identified ERG, IL6R, and LDLR as modifiers of MMP9, with a direct interaction between ERG and MMP9. Conclusions: The 4 new risk loci for AAA seem to be specific for AAA compared with other cardiovascular diseases and related traits suggesting that traditional cardiovascular risk factor management may only have limited value in preventing the progression of aneurysmal disease.

Background Genome-wide association studies have so far identified 56 loci associated with risk of coronary artery disease (CAD). Many CAD loci show pleiotropy; that is, they are also associated with other diseases or traits. Objectives This study sought to systematically test if genetic variants identified for non-CAD diseases/traits also associate with CAD and to undertake a comprehensive analysis of the extent of pleiotropy of all CAD loci. Methods In discovery analyses involving 42,335 CAD cases and 78,240 control subjects we tested the association of 29,383 common (minor allele frequency >5%) single nucleotide polymorphisms available on the exome array, which included a substantial proportion of known or suspected single nucleotide polymorphisms associated with common diseases or traits as of 2011. Suggestive association signals were replicated in an additional 30,533 cases and 42,530 control subjects. To evaluate pleiotropy, we tested CAD loci for association with cardiovascular risk factors (lipid traits, blood pressure phenotypes, body mass index, diabetes, and smoking behavior), as well as with other diseases/traits through interrogation of currently available genome-wide association study catalogs. Results We identified 6 new loci associated with CAD at genome-wide significance: on 2q37 (KCNJ13-GIGYF2), 6p21 (C2), 11p15 (MRVI1-CTR9), 12q13 (LRP1), 12q24 (SCARB1), and 16q13 (CETP). Risk allele frequencies ranged from 0.15 to 0.86, and odds ratio per copy of the risk allele ranged from 1.04 to 1.09. Of 62 new and known CAD loci, 24 (38.7%) showed statistical association with a traditional cardiovascular risk factor, with some showing multiple associations, and 29 (47%) showed associations at p < 1 × 10−4 with a range of other diseases/traits. Conclusions We identified 6 loci associated with CAD at genome-wide significance. Several CAD loci show substantial pleiotropy, which may help us understand the mechanisms by which these loci affect CAD risk.