iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types

Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants) as determined using high-throughput RNA-sequencing and genotyping arrays, respectively. Using iPSCs from a family of individuals, we show that iPSC-derived cardiomyocytes demonstrate gene expression patterns that cluster by genetic background, and can be used to examine variants associated with physiological and disease phenotypes. The iPSCORE collection contains representative individuals for risk and non-risk alleles for 95% of SNPs associated with human phenotypes through genome-wide association studies. Our study demonstrates the utility of iPSCORE for examining how genetic variants influence molecular and physiological traits in iPSCs and derived cell lines.

Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics

Induced pluripotent stem cells (iPSCs) show variable methylation patterns between lines, some of which reflect aberrant differences relative to embryonic stem cells (ESCs). To examine whether this aberrant methylation results from genetic variation or non-genetic mechanisms, we generated human iPSCs from monozygotic twins to investigate how genetic background, clone, and passage number contribute. We found that aberrantly methylated CpGs are enriched in regulatory regions associated with MYC protein motifs and affect gene expression. We classified differentially methylated CpGs as being associated with genetic and/or non-genetic factors (clone and passage), and we found that aberrant methylation preferentially occurs at CpGs associated with clone-specific effects. We further found that clone-specific effects play a strong role in recurrent aberrant methylation at specific CpG sites across different studies. Our results argue that a non-genetic biological mechanism underlies aberrant methylation in iPSCs and that it is likely based on a probabilistic process involving MYC that takes place during or shortly after reprogramming.

[Clinical assessment of peritoneal drainages for necrotizing enterocolitis. A Bayesian approach]

AIM

To assess effectiveness of peritoneal drainages for necrotizing enterocolitis.

MATERIAL AND METHODS

Retrospective cohort study (years 2000 to 2006). Laparotomy or patient's death were considered as failure.

STUDY VARIABLES

sex, gestational age, weight at delivery, Apgar score at minutes 1 and 5, modified Bell score, radiology and ventilatory status.

RESULTS

25 patients were diagnosed with necrotizing enterocolitis and treated with peritoneal drainages. Sample's Bell score was: 13(52%) Ia, 6 (24%) IIa, 5 (20%) IIb, and 1 (4%) IIIa. Mean gestational age was 31.8 (+/- 4.2) weeks, and mean weight 1,564 (+/- 810) g. Patients classified as Bell I presented statistically significat differences compared with Bell II-III as for radiology (unspecific), delivery weight (lower) and ventilatory status (higher mechanical ventilation rates). For the 12 patients with Bell scores II-III, peritoneal drains were enough for 5 cases (41.7%) and failed in 7 (58.3%), who were operated on. Multivariate analysis (logistic regression) was not able to show any conection with collected variables. However, a bayesian analysis using data from similar studies showed that the probability for drainage success rate to be higher than 50% is 99%.

CONCLUSIONS

In our centre, 52% of peritoneal drainages were used in patinets with low clinical suspect for necrotizing enetrocolitis, maybe in relation with their lower body weight and need for ventilatory support. In patients affected with necrotizing enterocolitis, drainages were effective in 41.7%. Although limited for its retrospective nature, our study suggests that peritoneal drainages can be curative in, at least, 50% of patients with necrotizing enterocolitis without pneumoperitoneum and clinical signs of peritonitis.

[Evidence-based medicine in Spanish pediatric surgery reports]

INTRODUCTION

Pediatric surgical literature is characterized by a high prevalence of observational studies and a paucity of randomized controlled trial, comparing mainly medical therapies.

AIMS

To asses scientific evidence level produced by spanish pediatric surgeons.

MATERIAL AND METHODS

Articles reported in Cirugía Pediátrica, surgical reports in Anales Españoles de Pediatría, and reports from spanish authors published in the Journal of Pediatric Surgery, Pediatric Surgery International and European Journal of Pediatric Surgery, from 1997 to 2002. Internal validity was assessed through the critial guides from Sackett, and evidence level was classified through the Oxford Centre for Evidence Based Medicine classification.

RESULTS

94.5% on therapy reports, 61.5% on diagnosis, 83.3% on prognosis and 52.2% on risk factors or etiology, were classified as level 4 (descriptive studies). Only four randomized controlled trials were found, all of them comparing medical therapies (analgesia, antibiotics and surgical stress control).

CONCLUSIONS

Our results are similar to those offered by previous reviews, showing up a low level of scientific evidence in most articles. Diffusion of guides on reporting descriptive studies may improve the evidence level of our reports.

[Acute epiglottitis caused by Haemophilus influenzae type b in children: presentation of 21 cases]

BACKGROUND

The aim of this paper is to review the epidemiological, clinical and therapeutical characteristics of Haemophilus influenzae type b (Hib) epiglottitis in children at a time when an efficient and safe vaccination is available.

METHODS

The clinical histories of 21 children admitted to Children's Hospital La Fe (1971-1996) with a clinical diagnosis of epiglottitis and isolation of the microorganism in blood cultures (20 cases) and surface culture of the epiglotis (one case) are reviewed.

RESULTS

The annual average was 4/100,000 children under 5 years of age. Evolution prior to diagnosis was > 12 hours in 52.4% of the cases. More males were affected (52.4% vs 47.6%). All the children except one (95.2%) were under 5 years of age; 81% were under 3 years of age and 1 child was 6 years and 8 months old. Respiratory distress (100%) and fever > or = 38 degrees C (85.7%) were the most common clinical manifestations. General health was affected in 71.4% of the cases and 66.7% had leucocytosis on admission. The clinical diagnosis was confirmed by direct visualization of the epiglotis in 76.1% of the cases. Hib was isolated in blood culture in 20 cases (95.2%). The strains produced beta-lactamases and were ampicillin-resistant in 57.1%. 19 children (90.5%) required endotracheal intubation. Initial empiric antibiotic therapy was third generation cephalosporins (cefotaxime or ceftriaxone) alone or combined with ampicillin. One child died (4.8%).

CONCLUSIONS

Pediatricians must still be aware of this serious infection in order to diagnosis and treat it as early as possible.

Laparoscopic cholecystectomy: use and preparation for Operation Desert Shield

While stationed at Winn army hospital, Fort Stewart, Georgia as backfill surgeons during the initial stages of Operation Desert Shield, we performed eight laparoscopic cholecystectomies (LC) over a 2 1/2 week period. Our patients included four active duty soldiers, three dependents, and one retiree. There were no complications. The average hospital stay was 2 days, and the average time to return to duty was 10 days for LC compared to 5 and 30 days, respectively, with standard cholecystectomy (SC). Performing LC whenever possible can return soldiers back to duty in one-third the time and greatly reduce health care costs by reducing the hospital stay.