Molecular diagnosis of long QT syndrome at 10 days of life by rapid whole genome sequencing
2014; 11 (10): 1707-1713
Self-reported history of childhood smoking is associated with an increased risk for peripheral arterial disease independent of lifetime smoking burden.
2014; 9 (2)
Triiodothyronine supplementation and cytokines during cardiopulmonary bypass in infants and children
JOURNAL OF THORACIC AND CARDIOVASCULAR SURGERY
2012; 144 (4): 938-?
Atherosclerotic disorders are well known to be associated with obesity, lipid profile, smoking, hypertension and other medical comorbidities, and large cohort studies have explored the childhood correlates to these adult risk factors. However, there has been little investigation into the childhood risk factors for peripheral arterial disease (PAD). We endeavored to better understand the role of smoking in childhood in the risk for PAD in a well described cohort of 1,537 adults at high risk for cardiovascular disease. In a multivariate regression model, we observed an increased risk of PAD among those who reported a history of smoking during childhood (OR?=?2.86; 95% CI, 1.99-4.11; P<0.001), which remained statistically significant after controlling for lifetime smoking burden (OR?=?1.55; 95% CI, 1.00-2.41; P?=?0.049). Our novel observation of disproportionate risk of PAD conferred by a history of childhood smoking may reflect an unrecognized biological mechanism such as a unique susceptibility to vascular injury or an unaccounted for covariate such as secondhand smoke exposure in childhood. This observation suggests further investigation is required into the pathophysiology of smoking in the developing vasculature and the need for detailed clinical data about patterns of childhood smoking and smoke exposure.
View details for DOI 10.1371/journal.pone.0088972
View details for PubMedID 24558458
Rare copy number variants in isolated sporadic and syndromic atrioventricular septal defects
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
2012; 158A (6): 1279-1284
The Triiodothyronine Supplementation in Infants and Children Undergoing Cardiopulmonary Bypass (TRICC) study demonstrated a shortened time to extubation in children younger than 5 months old undergoing cardiopulmonary bypass for congenital heart surgery with triiodothyronine supplementation. Cardiopulmonary bypass precipitates a systemic inflammatory response that affects recovery, and triiodothyronine is related to cytokine mediators of inflammation. We sought to investigate the preoperative cytokine levels by age and relationship to the triiodothyronine levels and to examine the effect of the cytokine levels on the time to extubation.We measured 6 cytokines at preoperative time 0 and 6 and 24 hours after crossclamp removal in 76 subjects.The preoperative cytokine levels were related to both the triiodothyronine levels and the patient age. The postoperative cytokine levels were predictive of the triiodothyronine levels at 6, 12, 24, and 72 hours. Preoperative CCL4 was associated with an increased chance of early extubation. Inclusion of the cytokines did not change the relationship of triiodothyronine to the time to extubation, and the postoperative course of interleukin-6 was independently associated with a decreased chance of early extubation.The preoperative and postoperative cytokine levels, in particular, interleukin-1?, showed complex time-dependent relationships with triiodothyronine. The data suggest that cytokine-mediated suppression of triiodothyronine plays an important role in determining the clinical outcome after cardiopulmonary bypass.
View details for DOI 10.1016/j.jtcvs.2012.05.063
View details for Web of Science ID 000309111600030
View details for PubMedID 22743177
Relationships of the Location and Content of Rounds to Specialty, Institution, Patient-Census, and Team Size
2010; 5 (6)
Atrioventricular septal defects (AVSDs) are a frequent but not universal component of Down syndrome (DS), while AVSDs in otherwise normal individuals have no well-defined genetic basis. The contribution of copy number variation (CNV) to specific congenital heart disease (CHD) phenotypes including AVSD is unknown. We hypothesized that de novo CNVs on chromosome 21 might cause isolated sporadic AVSDs, and separately that CNVs throughout the genome might constitute an additional genetic risk factor for AVSD in patients with DS. We utilized a custom oligonucleotide arrays targeted to CNV hotspots that are flanked by large duplicated segments of high sequence identity. We assayed 29 euploid and 50 DS individuals with AVSD, and compared to general population controls. In patients with isolated-sporadic AVSD we identified two large unique deletions outside of chromosome 21 not seen in the expanded set of 8,635 controls, each overlapping with larger deletions associated with similar CHD reported in the DECIPHER database. There was a small duplication in one patient with DS and AVSD. We conclude that isolated sporadic AVSDs may be occasionally associated with large de novo genomic structural variation outside of chromosome 21. The absence of CNVs on chromosome 21 in patients with isolated sporadic AVSD suggests that sub-chromosomal duplications or deletions of greater than 150?kbp on chromosome 21 do not cause sporadic AVSDs. Large CNVs do not appear to be an additive risk factor for AVSD in the DS population.
View details for DOI 10.1002/ajmg.a.35315
View details for Web of Science ID 000304133700007
View details for PubMedID 22529060
Self-Reported History of Childhood Smoking Is Associated with an Increased Risk for Peripheral Arterial Disease Independent of Lifetime Smoking Burden
2014; 9 (2)
Ebstein anomaly and Trisomy 21: A rare association.
Annals of pediatric cardiology
2014; 7 (1): 67-69
Existing observational data describing rounds in teaching hospitals are 15 years old, predate duty-hour regulations, are limited to one institution, and do not include pediatrics. We sought to evaluate the effect of medical specialty, institution, patient-census, and team participants upon time at the bedside and education occurring on rounds.Between December of 2007 and October of 2008 we performed 51 observations at Lucile Packard Children's Hospital, Seattle Children's Hospital, Stanford University Hospital, and the University of Washington Medical Center of 35 attending physicians. We recorded minutes spent on rounds in three location and seven activity categories, members of the care team, and patient-census.Results presented are means. Pediatric rounds had more participants (8.2 vs. 4.1 physicians, p<.001; 11.9 vs. 2.4 non-physicians, p<.001) who spent more minutes in hallways (96.9 min vs. 35.2 min, p<.001), fewer minutes at the bedside (14.6 vs. 38.2 min, p = .01) than internal medicine rounds. Multivariate regression modeling revealed that minutes at the bedside per patient was negatively associated with pediatrics (-2.77 adjusted bedside minutes; 95% CI -4.61 to -0.93; p<.001) but positively associated with the number of non-physician participants (0.12 adjusted bedside minutes per non physician participant; 95% CI 0.07 to 0.17; p = <.001). Education minutes on rounds was positively associated with the presence of an attending physician (2.70 adjusted education minutes; 95% CI 1.27 to 4.12; p<.001) and with one institution (1.39 adjusted education minutes; 95% CI 0.26 to 2.53; p = .02).Pediatricians spent less time at the bedside on rounds than internal medicine physicians due to reasons other than patient-census or the number of participants in rounds. Compared to historical data, internal medicine rounds were spent more at the bedside engaged in patient care and communication, and less upon educational activities.
View details for DOI 10.1371/journal.pone.0011246
View details for Web of Science ID 000279058300029
View details for PubMedID 20574534
A near null variant of 12/15-LOX encoded by a novel SNP in ALOX15 and the risk of coronary artery disease
2008; 198 (1): 136-144
This is a case report of a patient with Trisomy 21 with Ebstein anomaly, a ventricular septal defect, and acquired pulmonary vein stenosis; a rare combination, diagnosed during a routine neonatal examination.
View details for DOI 10.4103/0974-2069.126569
View details for PubMedID 24701093
Common polymorphisms of ALOX5 and ALOX5AP and risk of coronary artery disease
2008; 123 (4): 399-408
Murine genetic models suggest that function of the 12/15-LOX enzyme promotes atherosclerosis. We tested the hypothesis that exonic and/or promoter single nucleotide polymorphisms (SNPs) in the human 12/15-LOX gene (ALOX15) alter the risk of symptomatic coronary artery disease (CAD).We resequenced ALOX15 and then genotyped a common promoter and a less common novel coding SNP (T560M) in 1809 subjects with CAD and 1734 controls from Kaiser Permanente including a subset of participants of the Coronary Artery Risk Development in Young Adults study. We found no association between the promoter SNP and the risk of CAD. However, heterozygote carriers of the 560M allele had an increased risk of CAD (adjusted OR, 1.62; P=0.02) compared to non-carriers. In vitro studies demonstrated a 20-fold reduction in the catalytic activity of 560M when compared to 560T. We then genotyped T560M in 12,974 participants of the Atherosclerosis Risk in Communities study and similarly found that heterozygote carriers had an increased risk of CAD compared to non-carriers (adjusted HR, 1.31; P=0.06). In both population studies, homozygote carriers were rare and associated with a non-significant decreased risk of CAD compared to non-carriers (adjusted OR, 0.55; P=0.63 and HR, 0.93; P=0.9).A coding SNP in ALOX15 (T560M) results in a near null variant of human 12/15-LOX. Assuming a co-dominant mode of inheritance, this variant does not protect against CAD. Assuming a recessive mode of inheritance, the effect of this mutation remains unclear, but is unlikely to provide a protective effect to the degree suggested by mouse knockout studies.
View details for DOI 10.1016/j.atheroscierosis.2007.09.003
View details for Web of Science ID 000255491800016
View details for PubMedID 17959182
Brucellosis and sacroiliitis: A common presentation of an uncommon pathogen
JOURNAL OF THE AMERICAN BOARD OF FAMILY MEDICINE
2008; 21 (2): 158-161
Recent human genetic studies suggest that allelic variants of leukotriene pathway genes influence the risk of clinical and subclinical atherosclerosis. We sequenced the promoter, exonic, and splice site regions of ALOX5 and ALOX5AP and then genotyped 7 SNPs in ALOX5 and 6 SNPs in ALOX5AP in 1,552 cases with clinically significant coronary artery disease (CAD) and 1,583 controls from Kaiser Permanente including a subset of participants of the coronary artery risk development in young adults study. A nominally significant association was detected between a promoter SNP in ALOX5 (rs12762303) and CAD in our subset of white/European subjects (adjusted odds ratio per minor allele, log-additive model, 1.32; P = 0.002). In this race/ethnic group, rs12762303 has a minor allele frequency of 15% and is tightly linked to variation at the SP1 variable tandem repeat promoter polymorphism. However, the association between CAD and rs12762303 could not be reproduced in the atherosclerosis risk in communities study (hazard rate ratio per minor allele; 1.08, P = 0.1). Assuming a recessive mode of inheritance, the association was not significant in either population study but our power to detect modest effects was limited. No significant associations were observed between all other SNPs and the risk of CAD. Overall, our findings do not support a link between common allelic variation in or near ALOX5 or ALOX5AP and the risk of CAD. However, additional studies are needed to exclude modest effects of promoter variation in ALOX5 on the risk of CAD assuming a recessive mode of inheritance.
View details for DOI 10.1007/s00439-008-0489-5
View details for Web of Science ID 000254959600008
View details for PubMedID 18369664
Polymorphisms in hypoxia inducible factor 1 and the initial clinical presentation of coronary disease
AMERICAN HEART JOURNAL
2007; 154 (6): 1035-1042
Musculoskeletal problems are the most common chief complaint in ambulatory medicine across all specialties, and back pain is one of the top 10 problems encountered by the general practitioner. The differential diagnosis of lower back pain is exhaustive, but a history significant for constitutional symptoms or unusual exposures should prompt a work-up for an infectious cause. We describe the case of a 25-year-old man with a Brucella abortus sacroiliitis and possible orchiitis after consumption of unpasteurized cheese imported from El Salvador. The patient was successfully treated with gentamycin, rifampin, and doxycycline. Though the presentations of brucellosis are myriad, osteoarticular involvement of the axial skeleton is the most common presentation of this zoonotic infection. In the United States brucellosis is rarely encountered and is typically limited to people who are exposed during travel to endemic areas. Here we review briefly the epidemiology and presentation of a Brucella infection and current recommendations for treatment.
View details for DOI 10.3122/jabfm.2008.02.070170
View details for Web of Science ID 000253993300012
View details for PubMedID 18343865
Comparative genomics: a tool to functionally annotate human DNA.
Methods in molecular biology (Clifton, N.J.)
2007; 366: 229-251
Only some patients with coronary artery disease (CAD) develop acute myocardial infarction (MI), and emerging evidence suggests vulnerability to MI varies systematically among patients and may have a genetic component. The goal of this study was to assess whether polymorphisms in genes encoding elements of pathways mediating the response to ischemia affect vulnerability to MI among patients with underlying CAD.We prospectively identified patients at the time of their initial clinical presentation of CAD who had either an acute MI or stable exertional angina. We collected clinical data and genotyped 34 polymorphisms in 6 genes (ANGPT1, HIF1A, THBS1, VEGFA, VEGFC, VEGFR2).The 909 patients with acute MI were significantly more likely than the 466 patients with stable angina to be male, current smokers, and hypertensive, and less likely to be taking beta-blockers or statins. Three polymorphisms in HIF1A (Pro582Ser, rs11549465; rs1087314; and Thr418Ile, rs41508050) were significantly more common in patients who presented with stable exertional angina rather than acute MI, even after statistical adjustment for cardiac risk factors and medications. The HIF-mediated transcriptional activity was significantly lower when HIF1A null fibroblasts were transfected with variant HIF1A alleles than with wild-type HIF1A alleles.Polymorphisms in HIF1A were associated with development of stable exertional angina rather than acute MI as the initial clinical presentation of CAD.
View details for DOI 10.1016/j.ahj.2007.07.042
View details for Web of Science ID 000251396200006
View details for PubMedID 18035072
Genomic sequencing of Pleistocene cave bears
2005; 309 (5734): 597-600
The availability of an increasing number of vertebrate genomes has enabled comparative methods to infer functional sequences based on evolutionary constraint. Although this has proved powerful for gene identification, significant progress has also been made in uncovering gene regulatory sequences such as distant acting transcriptional enhancers. These pursuits have led to the development of a variety of valuable databases and resources that should serve as a routine toolbox for biological discovery.
View details for PubMedID 17568128
Human-zebrafish non-coding conserved elements act in vivo to regulate transcription
NUCLEIC ACIDS RESEARCH
2005; 33 (17): 5437-5445
Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to the amplification of mitochondrial sequences. Here we describe metagenomic libraries constructed with unamplified DNA extracted from skeletal remains of two 40,000-year-old extinct cave bears. Analysis of approximately 1 megabase of sequence from each library showed that despite significant microbial contamination, 5.8 and 1.1% of clones contained cave bear inserts, yielding 26,861 base pairs of cave bear genome sequence. Comparison of cave bear and modern bear sequences revealed the evolutionary relationship of these lineages. The metagenomic approach used here establishes the feasibility of ancient DNA genome sequencing programs.
View details for DOI 10.1126/science.1113485
View details for Web of Science ID 000230735200044
View details for PubMedID 15933159
The DNA sequence and comparative analysis of human chromosome 5
2004; 431 (7006): 268-274
Whole genome comparisons of distantly related species effectively predict biologically important sequences--core genes and cis-acting regulatory elements (REs)--but require experimentation to verify biological activity. To examine the efficacy of comparative genomics in identification of active REs from anonymous, non-coding (NC) sequences, we generated a novel alignment of the human and draft zebrafish genomes, and contrasted this set to existing human and fugu datasets. We tested the transcriptional regulatory potential of candidate sequences using two in vivo assays. Strict selection of non-genic elements which are deeply conserved in vertebrate evolution identifies 1744 core vertebrate REs in human and two fish genomes. We tested 16 elements in vivo for cis-acting gene regulatory properties using zebrafish transient transgenesis and found that 10 (63%) strongly modulate tissue-specific expression of a green fluorescent protein reporter vector. We also report a novel quantitative enhancer assay with potential for increased throughput based on normalized luciferase activity in vivo. This complementary system identified 11 (69%; including 9 of 10 GFP-confirmed elements) with cis-acting function. Together, these data support the utility of comparative genomics of distantly related vertebrate species to identify REs and provide a scaleable, in vivo quantitative assay to define functional activity of candidate REs.
View details for DOI 10.1093/nar/gki853
View details for Web of Science ID 000232593700016
View details for PubMedID 16179648
Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding conservation with non-mammalian vertebrates, suggesting that they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. We also completely sequenced versions of the large chromosome-5-specific internal duplications. These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy.
View details for DOI 10.1038/nature02919
View details for Web of Science ID 000223864000030
View details for PubMedID 15372022