Genomic characterization of large rearrangements of the LDLR gene in Czech patients with familial hypercholesterolemia

<p>Abstract</p> <p>Background</p> <p>Mutations in the <it>LDLR </it>gene are the most frequent cause of Familial hypercholesterolemia, an autosomal dominant disease characterised by elevated concentrations of LDL in blood plasma. In many populations, large genomic rearrangements account for approximately 10% of mutations in the <it>LDLR </it>gene.</p> <p>Methods</p> <p>DNA diagnostics of large genomic rearrangements was based on Multiple Ligation dependent Probe Amplification (MLPA). Subsequent analyses of deletion and duplication breakpoints were performed using long-range PCR, PCR, and DNA sequencing.</p> <p>Results</p> <p>In set of 1441 unrelated FH patients, large genomic rearrangements were found in 37 probands. Eight different types of rearrangements were detected, from them 6 types were novel, not described so far. In all rearrangements, we characterized their exact extent and breakpoint sequences.</p> <p>Conclusions</p> <p>Sequence analysis of deletion and duplication breakpoints indicates that intrachromatid non-allelic homologous recombination (NAHR) between <it>Alu </it>elements is involved in 6 events, while a non-homologous end joining (NHEJ) is implicated in 2 rearrangements. Our study thus describes for the first time NHEJ as a mechanism involved in genomic rearrangements in the <it>LDLR </it>gene.</p

Chromosomal Inversions between Human and Chimpanzee Lineages Caused by Retrotransposons

The long interspersed element-1 (LINE-1 or L1) and Alu elements are the most abundant mobile elements comprising 21% and 11% of the human genome, respectively. Since the divergence of human and chimpanzee lineages, these elements have vigorously created chromosomal rearrangements causing genomic difference between humans and chimpanzees by either increasing or decreasing the size of genome. Here, we report an exotic mechanism, retrotransposon recombination-mediated inversion (RRMI), that usually does not alter the amount of genomic material present. Through the comparison of the human and chimpanzee draft genome sequences, we identified 252 inversions whose respective inversion junctions can clearly be characterized. Our results suggest that L1 and Alu elements cause chromosomal inversions by either forming a secondary structure or providing a fragile site for double-strand breaks. The detailed analysis of the inversion breakpoints showed that L1 and Alu elements are responsible for at least 44% of the 252 inversion loci between human and chimpanzee lineages, including 49 RRMI loci. Among them, three RRMI loci inverted exonic regions in known genes, which implicates this mechanism in generating the genomic and phenotypic differences between human and chimpanzee lineages. This study is the first comprehensive analysis of mobile element bases inversion breakpoints between human and chimpanzee lineages, and highlights their role in primate genome evolution

Diagnostic performance of a novel coronary CT angiography algorithm : Prospective multicenter validation of an intracycle CT motion correction algorithm for diagnostic accuracy

OBJECTIVE. Motion artifact can reduce the diagnostic accuracy of coronary CT angiography (CCTA) for coronary artery disease (CAD). The purpose of this study was to compare the diagnostic performance of an algorithm dedicated to correcting coronary motion artifact with the performance of standard reconstruction methods in a prospective international multicenter study. SUBJECTS AND METHODS. Patients referred for clinically indicated invasive coronary angiography (ICA) for suspected CAD prospectively underwent an investigational CCTA examination free from heart rate\u2013lowering medications before they underwent ICA. Blinded core laboratory interpretations of motion-corrected and standard reconstructions for obstructive CAD (= 50% stenosis) were compared with ICA findings. Segments unevaluable owing to artifact were considered obstructive. The primary endpoint was per-subject diagnostic accuracy of the intracycle motion correction algorithm for obstructive CAD found at ICA. RESULTS. Among 230 patients who underwent CCTA with the motion correction algorithm and standard reconstruction, 92 (40.0%) had obstructive CAD on the basis of ICA findings. At a mean heart rate of 68.0 \ub1 11.7 beats/min, the motion correction algorithm reduced the number of nondiagnostic scans compared with standard reconstruction (20.4% vs 34.8%; p < 0.001). Diagnostic accuracy for obstructive CAD with the motion correction algorithm (62%; 95% CI, 56\u201368%) was not significantly different from that of standard reconstruction on a per-subject basis (59%; 95% CI, 53\u201366%; p = 0.28) but was superior on a per-vessel basis: 77% (95% CI, 74\u201380%) versus 72% (95% CI, 69\u201375%) (p = 0.02). The motion correction algorithm was superior in subgroups of patients with severely obstructive (= 70%) stenosis, heart rate = 70 beats/min, and vessels in the atrioventricular groove. CONCLUSION. The motion correction algorithm studied reduces artifacts and improves diagnostic performance for obstructive CAD on a per-vessel basis and in selected subgroups on a per-subject basis

Selective Referral Using CCTA Versus Direct Referral for Individuals Referred to Invasive Coronary Angiography for Suspected CAD : a Randomized, Controlled, Open-Label Trial

Objectives: This study compared the safety and diagnostic yield of a selective referral strategy using coronary computed tomographic angiography (CCTA) compared with a direct referral strategy using invasive coronary angiography (ICA) as the index procedure. Background: Among patients presenting with signs and symptoms suggestive of coronary artery disease (CAD), a sizeable proportion who are referred to ICA do not have a significant, obstructive stenosis. Methods: In a multinational, randomized clinical trial of patients referred to ICA for nonemergent indications, a selective referral strategy was compared with a direct referral strategy. The primary endpoint was noninferiority with a multiplicative margin of 1.33 of composite major adverse cardiovascular events (blindly adjudicated death, myocardial infarction, unstable angina, stroke, urgent and/or emergent coronary revascularization or cardiac hospitalization) at a median follow-up of 1-year. Results: At 22 sites, 823 subjects were randomized to a selective referral and 808 to a direct referral strategy. At 1 year, selective referral met the noninferiority margin of 1.33 (p = 0.026) with a similar event rate between the randomized arms of the trial (4.6% vs. 4.6%; hazard ratio: 0.99; 95% confidence interval: 0.66 to 1.47). Following CCTA, only 23% of the selective referral arm went on to ICA, which was a rate lower than that of the direct referral strategy. Coronary revascularization occurred less often in the selective referral group compared with the direct referral to ICA (13% vs. 18%; p &lt; 0.001). Rates of normal ICA were 24.6% in the selective referral arm compared with 61.1% in the direct referral arm of the trial (p &lt; 0.001). Conclusions: In stable patients with suspected CAD who are eligible for ICA, the comparable 1-year major adverse cardiovascular events rates following a selective referral and direct referral strategy suggests that both diagnostic approaches are similarly effective. In the selective referral strategy, the reduced use of ICA was associated with a greater diagnostic yield, which supported the usefulness of CCTA as an efficient and accurate method to guide decisions of ICA performance. (Coronary Computed Tomographic Angiography for Selective Cardiac Catheterization [CONSERVE]; NCT01810198