27 research outputs found
Limitations of the Human Reference Genome for Personalized Genomics
<div><p>Data from the 1000 genomes project (1KGP) and Complete Genomics (CG) have dramatically increased the numbers of known genetic variants and challenge several assumptions about the reference genome and its uses in both clinical and research settings. Specifically, 34% of published array-based GWAS studies for a variety of diseases utilize probes that overlap unanticipated single nucleotide polymorphisms (SNPs), indels, or structural variants. Linkage disequilibrium (LD) block length depends on the numbers of markers used, and the mean LD block size decreases from 16 kb to 7 kb,when HapMap-based calculations are compared to blocks computed from1KGP data. Additionally, when 1KGP and CG variants are compared, 19% of the single nucleotide variants (SNVs) reported from common genomes are unique to one dataset; likely a result of differences in data collection methodology, alignment of reads to the reference genome, and variant-calling algorithms. Together these observations indicate that current research resources and informatics methods do not adequately account for the high level of variation that already exists in the human population and significant efforts are needed to create resources that can accurately assess personal genomics for health, disease, and predict treatment outcomes.</p> </div
Venn diagrams illustrating the overlap in SNP calls between the 1KGP and CG.
<p><b>A</b>. For the full call sets. <b>B</b>. For the matched set of 32 genomes.</p
A comparison of the Linkage disequilibrium patterns of BRCA1 and JAK2 using HapMap and 1000 Genomes data.
<p>A comparison of the Linkage disequilibrium patterns of BRCA1 and JAK2 using HapMap and 1000 Genomes data.</p
List of Probes on Common array platforms adversely affected by variants detected through sequencing and not probed on the array.
<p>List of Probes on Common array platforms adversely affected by variants detected through sequencing and not probed on the array.</p
The LD block structure of two genes for the HapMap data and the 1KGP data.
<p><b>A.</b> The BRCA1 gene using the HapMap data. <b>B.</b> The BRCA1 gene using the 1KGP data. <b>C.</b> The JAK2 gene using the HapMap data. <b>D.</b> The Jak2 gene using the 1KGP data.</p
Problematic probes on microarrays.
<p>The number of probes on the Affymetrix Axiom CEU (blue) and Illumina 2.5 M(red) arrays that are found to contain an un-probed SNP for sub-samples of the 1KGP SNPs.</p
Reads from HEK293-GFP-PBmut mapped to hg19+pb-ef1-neo
Reads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-GFP-PBmut, filtered, quality trimmed and mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters
Reads from HEK293-GFP-PBwt mapped to hg19+pb-ef1_neo.
Reads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-GFP-PBwt, mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters
<i>Dnmt3c</i><sup><i>rahu</i></sup> mutants up-regulate retrotransposons belonging to L1 and ERVK families.
<p><b>(A)</b> Volcano plot of differential RNA-seq values for various classes of retrotransposons. RNA-seq was performed on testis RNA samples from six 14-<i>dpp</i> animals from a single litter: three <i>Dnmt3c</i><sup><i>rahu</i></sup> mutants and three heterozygotes (same mice analyzed in <b><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006964#pgen.1006964.g005" target="_blank">Fig 5A</a></b>). Q-value is the Benjamini-Hochberg-adjusted p-value from DESeq2. Retrotransposons with expression fold change of >2 (up or down) and q < 0.01 are depicted as large, colored circles. <b>(B)</b> Heatmap showing the z-score of differentially expressed retrotransposon families (with expression fold change >2 and q < 0.01) in individual <i>Dnmt3c</i><sup><i>rahu</i></sup> mutants (x, y, z) and their heterozygous littermates (x′, y′, z′). Labels on rows indicate the retrotransposon family, followed by superfamily, followed by class, and then in parentheses the log<sub>2</sub> fold change of median expression in mutant versus heterozygote. Rows with greater than two-fold change in median expression (up or down) are in bold. The log<sub>2</sub> fold changes are also provided in the bar graph at left (greater than two-fold change shown as black bars). <b>(C)</b> Correlation between differentially expressed retrotransposon families in 14-<i>dpp</i> <i>Dnmt3c</i><sup><i>rahu</i></sup> mutants and 20-<i>dpp</i> <i>Dnmt3l</i> mutants. The regression line is shown and <i>r</i> is the Pearson correlation coefficient.</p
DNMT3C is a putative DNA methyltransferase with similarity to DNMT3B.
<p><b>(A)</b> Schematics of DNMT3C and DNMT3B showing the location of conserved domains and the <i>rahu</i> mutation (asterisk). <b>(B)</b> Cladogram of Clustal Omega aligned human and mouse DNMT3 family sequences rooted with HhaI. <b>(C)</b> Motif IX in Clustal Omega aligned sequences showing the location of the <i>rahu</i> mutation (asterisk). DNMT3L proteins do not contain Motif IX. Amino acids identical to those in DNMT3C are shaded gray. Amino acid positions refer to DNMT3C. <b>(D)</b> Homology-based model of DNMT3C carboxy-terminal domain (cytosine methyltransferase domain and the preceding four amino acid residues) with E692 depicted in red. <b>(E)</b> Crystal structure of the DNMT3A carboxy-terminal domain dimer (PDB ID:2QRV), with monomers depicted in two shades of blue. The DNMT3A amino acid equivalent to the glutamic acid that is mutated in <i>Dnmt3c</i><sup><i>rahu</i></sup> mutants (DNMT3A E861) is shown in red.</p