Structural Variation Evolution at the 15q11-q13 Disease-Associated Locus

The impact of segmental duplications on human evolution and disease is only just starting to unfold, thanks to advancements in sequencing technologies that allow for their discovery and precise genotyping. The 15q11-q13 locus is a hotspot of recurrent copy number variation associated with Prader-Willi/Angelman syndromes, developmental delay, autism, and epilepsy and is mediated by complex segmental duplications, many of which arose recently during evolution. To gain insight into the instability of this region, we characterized its architecture in human and nonhuman primates, reconstructing the evolutionary history of five different inversions that rearranged the region in different species primarily by accumulation of segmental duplications. Comparative analysis of human and nonhuman primate duplication structures suggests a human-specific gain of directly oriented duplications in the regions flanking the GOLGA cores and HERC segmental duplications, representing potential genomic drivers for the human-specific expansions. The increasing complexity of segmental duplication organization over the course of evolution underlies its association with human susceptibility to recurrent disease-associated rearrangements.

A high-resolution map of small-scale inversions in the gibbon genome

Gibbons are the most speciose family of living apes, characterized by a strikingly diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics and deep in silico analysis of a southern white-cheeked gibbon genome providing the first comprehensive map of 238 previously hidden small-scale inversions. We determined that more than half are gibbon-specific, at least 5-fold higher than shown for other primate lineage specific inversions, with a significant high number of small heterozygous inversions, suggesting that accelerated evolution of inversions may have played a role in the high sympatric diversity of gibbons. Although the precise mechanisms underlying these inversions are not yet understood, it is clear that segmental duplication-mediated NAHR only accounts for a small fraction of events. Several genomic features including gene density and repeat (e.g. LINE1) content might render these regions more break-prone and susceptible to inversion formation. In the attempt to characterize interspecific variation between southern and northern white-cheeked gibbons, we identify several large assembly errors in the current GGSC Nleu3.0/nomLeu3 reference genome comprising over 49 megabases of DNA. Finally, we provide a list of 182 candidate genes potentially involved in gibbons diversification and speciation.

A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information

BACKGROUND

Human mitochondrial DNA has an important role in the cellular energy production through oxidative phosphorylation. Therefore, this process may be the cause and have an effect on mitochondrial DNA mutability, functional alteration, and disease onset related to a wide range of different clinical expressions and phenotypes. Although a large part of the observed variations is fixed in a population and hence expected to be benign, the estimation of the degree of the pathogenicity of any possible human mitochondrial DNA variant is clinically pivotal.

METHODS

In this scenario, the establishment of standard criteria based on functional studies is required. In this context, a "data and text mining" pipeline is proposed here, developed using the programming language R, capable of extracting information regarding mitochondrial DNA functional studies and related clinical assessments from the literature, thus improving the annotation of human mitochondrial variants reported in the HmtVar database.

RESULTS

The data mining pipeline has produced a list of 1,073 Pubmed IDs (PMIDs) from which the text mining pipeline has retrieved information on 932 human mitochondrial variants regarding experimental validation and clinical features.

CONCLUSIONS

The application of the pipeline will contribute to supporting the interpretation of pathogenicity of human mitochondrial variants by facilitating diagnosis to clinicians and researchers faced with this task.

Reshaping of vertebrae during treatment with neridronate or pamidronate in children with osteogenesis imperfecta

BACKGROUND/AIMS

Osteogenesis imperfecta (OI) is a hereditary disease causing increased bone fragility. Pamidronate (PAM), which has to be administered as a 3-day course according to the original protocol by Glorieux, is the most frequently used therapy. Other bisphosphonates like neridronate (NER), which can be infused during an outpatient visit, have also proven to be effective. This is the first analysis comparing the effect of PAM and NER using vertebral morphometry.

METHODS

28 patients with OI type III and IV were retrospectively analyzed by matched pairs.

RESULTS

No differences were detected between patients treated with PAM or NER at the start of therapy: mean age 4.4 years (p = 0.730), mean height 86.8 cm/85.3 cm (p = 0.854), lumbar vertebral area 208.9 mm(2)/206.0 mm(2) (p = 0.555), and in all vertebral indices. After 1 year of treatment (mean 1.16 years; p = 0.854) both groups showed a significant increase in the vertebral area and improved vertebral indices. Again there were no differences between the groups in the vertebral area (p = 0.590).

CONCLUSION

In this study there was no difference between patients treated with PAM or NER regarding vertebral morphometry during the first year of therapy. Because of the possibility of an outpatient setting, NER is convenient for these children.

[Reconstructive surgery of the mitral and tricuspid valves with a Cosgrove-Edwards flexible ring]

BACKGROUND

Mitral and tricuspid valve asymmetric annular dilation represents the most important mechanism which produces insufficiency. Recent computerized in vitro and in vivo three-dimensional models have been developed in order to better understand the competing factors (annular dilation, displacement of papillary muscles, left and right ventricular geometry). The leading cause of mitral and tricuspid competence is a sphincteric action of both annuli, during systole and diastole, the loss of which produces asymmetric dilation and therefore the absence of cusp coaptation. The Cosgrove-Edwards dynamic ring corrects, alone or in combination with other procedures on the valves, this patho-anatomic feature in a physiological way by restoring the normal annular dimensions and the sphincteric movements during the cardiac cycle.

METHODS

Between June 1998 and May 1999, 30 adult patients underwent mitral (n = 20, Group I) or tricuspid valve repair (n = 10, Group II). Regurgitation was due to a degenerative disease in 13 Group I patients and to ischemic (n = 3), congenital (n = 2) or dilated cardiomyopathy (n = 2) in the others. In Group II the leading cause of insufficiency was functional regurgitation in 7 patients and organic in 3. Associated procedures were carried out in 4 Group I patients and in all Group II patients. Regurgitation was evaluated by transesophageal echocardiography before, during and 3 months after operation. The maximal regurgitant area (MRA) and the grade of insufficiency were evaluated using the equation: MRA < 2 cm2 = grade 0, MRA > 2 < 4 cm2 = 1+, MRA > 4 < 7 cm2 = grade 2+, MRA > 7 < 10 cm2 = 3+, MRA > 10 cm2 = 4+.

RESULTS

The operative mortality was 0%. One Group I patient died 3 months after operation due to bronchopneumonia. No patient was reoperated on for plasty failure in both groups during the follow-up. Mitral insufficiency was absent (grade 0) in 17 Group I patients and mild (grade 1+) in 3 at the end of operation. At 3-month postoperative transesophageal echocardiographic control mitral insufficiency was absent in 14 patients, mild (1+) in 4 and moderate (2+) in 2. MRA was 3 cm2 in the 2 patients operated on for dilated cardiomyopathy and < 3 cm2 in the others. Preoperative tricuspid insufficiency of grade 4+ in all Group II patients became absent in 9 of them either at the end of operation or at 3-month postoperative control.

CONCLUSIONS

The Cosgrove-Edwards dynamic ring as isolated device or in combination with other plasty mitral or tricuspid procedures is a safe, simple, and reproducible method to restore the distorted motion of valvular annuli. It preserves the sphincteric mechanism of the valve and allows for the coaptation of cusps. Although in a small number of patients and for a short period of follow-up our experience corroborates what other more consistent series of patients operated on have shown.

[Effects of naloxone on plasma levels of atrial natriuretic factor and noradrenaline during water load in moderate heart failure]

BACKGROUND

The aim of our study was to evaluate the effects of endogenous opioids on the secretion of atrial natriuretic factor (ANF) in moderate chronic heart failure (HF).

METHODS

We evaluated the effects of i.v. volume load (NaCl 0.9% at 0.25 ml/Kg/min for 60 minutes) on heart rate (HR), on mean arterial pressure (MAP) and on the plasma levels of beta-endorphin (beta-end), met-enkephalin (Met-enk), dynorphin (Dyn), atrial natriuretic factor (ANF) and noradrenaline (NA) in 10 patients (age 58 +/- 9) with HF in NYHA class II (group I) and in 8 healthy control subjects (age 54 +/- 10) group II). The volume load was repeated after at least three days during infusion of naloxone (2 micrograms/Kg/min), evaluating the above mentioned hemodynamic and hormonal parameters.

RESULTS

The acute volume expansion caused an increase in ANF concentration (from 51.7 +/- 19.7 to 67.4 +/- 36.9 pg/ml; p < 0.05) and in beta-end (from 11.9 +/- 5.3 to 16.6 +/- 7.5 fmol/ml; p < 0.05), In group I. In group II an isolated increase in ANF was observed (from 14.1 +/- 7.8 to 21.9 +/- 7.9 pg/ml; p < 0.02). No significant changes were detected for HR, MAP, Dyn, Met-enk and NA. In group I the percent increase of ANF is less than in group II (30 vs 55%; p < 0.05). The volume load infused during naloxone infusion caused a significant increase in HR (from 73 +/- 6 to 78 +/- 9 bpm; p < 0.05) and in NA (from 311 +/- 123 to 415 +/- 142 pg/ml; p < 0.05) In group I. In group II, an increase in ANF was detected (from 13.8 +/- 6.0 to 23.6 +/- 5.0 pg/ml; p < 0.01).

CONCLUSIONS

Our data suggest that in moderate HF beta-end stimulates the secretion of ANF and inhibits the activity of the sympatho-adrenergic system during acute volume expansion.