A recurrent translocation is mediated by homologous recombination between HERV-H elements

<p>Abstract</p> <p>Background</p> <p>Chromosome rearrangements are caused by many mutational mechanisms; of these, recurrent rearrangements can be particularly informative for teasing apart DNA sequence-specific factors. Some recurrent translocations are mediated by homologous recombination between large blocks of segmental duplications on different chromosomes. Here we describe a recurrent unbalanced translocation casued by recombination between shorter homologous regions on chromosomes 4 and 18 in two unrelated children with intellectual disability.</p> <p>Results</p> <p>Array CGH resolved the breakpoints of the 6.97-Megabase (Mb) loss of 18q and the 7.30-Mb gain of 4q. Sequencing across the translocation breakpoints revealed that both translocations occurred between 92%-identical human endogenous retrovirus (HERV) elements in the same orientation on chromosomes 4 and 18. In addition, we find sequence variation in the chromosome 4 HERV that makes one allele more like the chromosome 18 HERV.</p> <p>Conclusions</p> <p>Homologous recombination between HERVs on the same chromosome is known to cause chromosome deletions, but this is the first report of interchromosomal HERV-HERV recombination leading to a translocation. It is possible that normal sequence variation in substrates of non-allelic homologous recombination (NAHR) affects the alignment of recombining segments and influences the propensity to chromosome rearrangement.</p

Differential expression analysis with global network adjustment

&lt;p&gt;Background: Large-scale chromosomal deletions or other non-specific perturbations of the transcriptome can alter the expression of hundreds or thousands of genes, and it is of biological interest to understand which genes are most profoundly affected. We present a method for predicting a gene’s expression as a function of other genes thereby accounting for the effect of transcriptional regulation that confounds the identification of genes differentially expressed relative to a regulatory network. The challenge in constructing such models is that the number of possible regulator transcripts within a global network is on the order of thousands, and the number of biological samples is typically on the order of 10. Nevertheless, there are large gene expression databases that can be used to construct networks that could be helpful in modeling transcriptional regulation in smaller experiments.&lt;/p&gt; &lt;p&gt;Results: We demonstrate a type of penalized regression model that can be estimated from large gene expression databases, and then applied to smaller experiments. The ridge parameter is selected by minimizing the cross-validation error of the predictions in the independent out-sample. This tends to increase the model stability and leads to a much greater degree of parameter shrinkage, but the resulting biased estimation is mitigated by a second round of regression. Nevertheless, the proposed computationally efficient “over-shrinkage” method outperforms previously used LASSO-based techniques. In two independent datasets, we find that the median proportion of explained variability in expression is approximately 25%, and this results in a substantial increase in the signal-to-noise ratio allowing more powerful inferences on differential gene expression leading to biologically intuitive findings. We also show that a large proportion of gene dependencies are conditional on the biological state, which would be impossible with standard differential expression methods.&lt;/p&gt; &lt;p&gt;Conclusions: By adjusting for the effects of the global network on individual genes, both the sensitivity and reliability of differential expression measures are greatly improved.&lt;/p&gt

Abstract 516: Chromosome 18p Deletion Inhibits Platelet Aggregation

Inappropriate platelet function is a significant risk factor for cardiovascular disease, the leading cause of death in the United States. Although abnormal platelet function has a strong genetic component, very few human genes have been linked to platelet function. Mice with a homozygous deletion of EMILIN2 (Elastin Microfibril Interface Located Protein2) gene, located on Chromosome 18p, have a significant decrease in platelet function and clot formation. However, deletion or inactivation of only one copy of a gene is most relevant to human disease modeling. Our hypothesis is that blood samples from people with single 18p deletions that include EMILIN2 will have decreased platelet function compared to healthy individuals. We conducted a case-control study of nine adult individuals with chromosome 18p deletions matched with healthy men and women (n=20). Routine coagulation measurements were performed on a STAGO STA-R instrument. Platelet aggregation was measured with whole blood impedance aggregometry and Thromboelastography with PlateletMapping using the manufacturers’ protocols. There was no significant difference in platelet count, prothrombin time, partial thromboplastin time, d-dimer, or fibrinogen between individuals with a single 18p gene copy number and normal controls. However, platelet aggregation was impaired in individuals with 18p deletions compared to normal controls in response to collagen and arachidonic acid (ASPI), respectively ( p &lt;0.0001, Figure 1). Moreover, Thromboelastography with PlateletMapping was decreased in individuals with 18p deletions compared to normal controls for ADP and ASPI, ( p &lt;0.001). Individuals with one copy of 18p have decrease platelet function compared to normal controls. These results identify a novel human genetic loci linked to a specific phenotype of platelet function. Future will studies will determine if this gene can be used for diagnostic or therapeutics for cardiovascular disease. </jats:p

Identification of Cryptic Rearrangements in Patients with 18q− Deletion Syndrome

SummaryThe majority of patients with 18q− syndrome appear cytogenetically to have a terminal deletion of the long arm of chromosome 18. These 18q− patients are diagnosed by use of standard cytogenetic banding techniques, which have resolution insufficient for precise genotyping. In our effort to obtain a thorough genotype, we have analyzed the DNA from 35 patients who originally were diagnosed as having de novo terminal deletions of chromosome 18. Molecular analysis was performed with polymorphic markers throughout the 18q− region. Cytogenetic FISH was performed with two human 18q telomeric probes, a chromosome 18–specific α-satellite probe, and whole chromosome 18–specific paint. Of 35 patients previously reported to have terminal deletions of 18q, we found that 5 (14%) have more-complex cryptic rearrangements and that 3 (9%) retain the most distal portion of 18q, consistent with an interstitial rather than a terminal deletion. These findings indicate that a standard karyotype can lead to insufficient characterization in 18q− syndrome. This has important ramifications for phenotype mapping of this syndrome, as well as for proper prognosis