Ethical Considerations Related to Return of Results from Genomic Medicine Projects: The eMERGE Network (Phase III) Experience

We examined the Institutional Review Board (IRB) process at 9 academic institutions in the electronic Medical Records and Genomics (eMERGE) Network, for proposed electronic health record-based genomic medicine studies, to identify common questions and concerns. Sequencing of 109 disease related genes and genotyping of 14 actionable variants is being performed in ~28,100 participants from the 9 sites. Pathogenic/likely pathogenic variants in actionable genes are being returned to study participants. We examined each site’s research protocols, informed-consent materials, and interactions with IRB staff. Research staff at each site completed questionnaires regarding their IRB interactions. The time to prepare protocols for IRB submission, number of revisions and time to approval ranged from 10–261 days, 0–11, and 11–90 days, respectively. IRB recommendations related to the readability of informed consent materials, specifying the full range of potential risks, providing options for receiving limited results or withdrawal, sharing of information with family members, and establishing the mechanisms to answer participant questions. IRBs reviewing studies that involve the return of results from genomic sequencing have a diverse array of concerns, and anticipating these concerns can help investigators to more effectively engage IRBs.

Long-term alterations in monocyte function after elective cardiac surgery

Optimal immunological homoeostasis determines the long-term recovery of patients in the postoperative period. The functional adaptability of monocytes plays a pivotal role in adjusting the host's response to an insult, immunostasis and long-term health, and may help to determine successful recovery. We undertook a longitudinal analysis of the functional adaptability of monocytes in 20 patients undergoing heart surgery with cardiopulmonary bypass, as a model of severe stress. Using each patient's pre-cardiopulmonary bypass data as a baseline, we investigated the characteristics of peripheral blood monocytes' functional plasticity in-vitro before elective bypass, and three months afterwards. Approximately 30% of subjects showed diminished monocyte plasticity, as demonstrated by decreased monocyte differentiation into dendritic cells three months after bypass. Diminished monocyte functional plasticity was related to over-production of macrophage colony-stimulating factor. Adding a neutralising antibody to macrophage colony-stimulating factor corrected the monocytes' differentiation defect. Finally, patients with reduced monocyte plasticity had significantly elevated serum C-reactive protein, with a concomitant increase in cytomegalovirus IgG antibody titres, suggestive of the acquisition of immuno-suppressive traits. Our study shows that severe surgical stress resulted in a lasting immunological defect in individuals who had seemingly recovered.

Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers

OBJECTIVE

The objective of this study is to develop an algorithm to accurately identify children with severe early onset childhood obesity (ages 1-5.99 years) using structured and unstructured data from the electronic health record (EHR).

INTRODUCTION

Childhood obesity increases risk factors for cardiovascular morbidity and vascular disease. Accurate definition of a high precision phenotype through a standardize tool is critical to the success of large-scale genomic studies and validating rare monogenic variants causing severe early onset obesity.

DATA AND METHODS

Rule based and machine learning based algorithms were developed using structured and unstructured data from two EHR databases from Boston Children's Hospital (BCH) and Cincinnati Children's Hospital and Medical Center (CCHMC). Exclusion criteria including medications or comorbid diagnoses were defined. Machine learning algorithms were developed using cross-site training and testing in addition to experimenting with natural language processing features.

RESULTS

Precision was emphasized for a high fidelity cohort. The rule-based algorithm performed the best overall, 0.895 (CCHMC) and 0.770 (BCH). The best feature set for machine learning employed Unified Medical Language System (UMLS) concept unique identifiers (CUIs), ICD-9 codes, and RxNorm codes.

CONCLUSIONS

Detecting severe early childhood obesity is essential for the intervention potential in children at the highest long-term risk of developing comorbidities related to obesity and excluding patients with underlying pathological and non-syndromic causes of obesity assists in developing a high-precision cohort for genetic study. Further such phenotyping efforts inform future practical application in health care environments utilizing clinical decision support.

Programmed intermittent epidural boluses for maintenance of labor analgesia: an impact study

INTRODUCTION

The aim of this impact study was to compare the analgesic efficacy and side effect profile of programmed intermittent epidural boluses (PIEB)+patient-controlled epidural analgesia (PCEA) to continuous epidural infusion (CEI)+PCEA for maintenance labor analgesia after the introduction of PIEB at our institution.

METHODS

We conducted a retrospective analysis after replacing the background CEI with PIEB for our labor PCEA. Pre-change pump settings were CEI 12mL/h with PCEA (12mL bolus, lockout 15min); PIEB settings were a 9mL bolus every 45min with PCEA (10mL bolus, lockout 10min). We compared medical records of all women receiving epidural or combined spinal-epidural labor analgesia for vaginal delivery for two months before PIEB implementation to a two-month period of PIEB utilization following a five-month introductory familiarization period. The primary outcome was the proportion of women requiring rescue clinician boluses.

RESULTS

Fewer patients in the PIEB group required rescue clinician boluses compared to the CEI group (12% vs. 19%, P=0.012). Time to first rescue bolus request and total bolus dose were not different. Peak (median [IQR]) pain scores were 2[0-5] with CEI and 0[0-4] with PIEB. There was no difference in instrumental delivery rates.

CONCLUSIONS

Using PIEB compared to CEI as the background maintenance epidural analgesia method in conjunction with PCEA reduced the number of women requiring clinician rescue boluses while providing comparable labor analgesia. The findings of this clinical care impact study confirm the results of randomized controlled studies and suggest PIEB may be a preferable technique to CEI for the maintenance of labor analgesia.

Spatial atmospheric atomic layer deposition of InxGayZnzO for thin film transistors

We have investigated the nucleation and growth of InGaZnO thin films by spatial atmospheric atomic layer deposition. Diethyl zinc (DEZ), trimethyl indium (TMIn), triethyl gallium (TEGa), and water were used as Zn, In, Ga and oxygen precursors, respectively. The vaporized metal precursors have been coinjected in the reactor. The metal composition of InGaZnO has been controlled by varying the TMIn or TEGa flow to the reactor, for a given DEZ flow and exposure time. The morphology of the films changes from polycrystalline, for ZnO and In-doped ZnO, to amorphous for In-rich IZO and InGaZnO. The use of these films as the active channel in TFTs has been demonstrated and the influence of In and Ga cations on the electrical characteristics of the TFTs has been studied.

Detection of low HCV viraemia by repeated HCV RNA testing predicts treatment failure to triple therapy with telaprevir

BACKGROUND

Early on-treatment virological response is one of the most important predictors for sustained virological response (SVR) to treatment of chronic hepatitis C virus (HCV) genotype 1 infection with triple therapy including HCV protease inhibitors (PI). Treatment duration (24 vs. 48 weeks) is based on HCV RNA results at weeks 4 and 12 of PI therapy when HCV RNA must be 'undetectable' to allow shorter therapy.

AIM

To analyse the reliability of HCV RNA measurements at key decision time points (weeks 4 and 12) and the predictive value of concordant or discordant assay results for SVR.

METHODS

Weeks 4 and 12 samples of patients receiving telaprevir-containing triple therapy were initially tested with the AmpliPrep/COBAS-TaqMan_HCV-Test-v1.0 (limit of detection; LOD = 15IU/mL) and retested with the AmpliPrep/COBAS-TaqMan_HCV-Test-v2.0 (LOD = 15IU/mL) and the High_Pure/COBAS-TaqMan_HCV-Test-v2.0 (LOD = 20IU/mL).

RESULTS

Concordance among the three test results in classifying samples as HCV RNA 'undetectable' or 'detectable' was only 55% at week 4, but 85% at week 12. Retesting of 'undetectable' week 4 samples with the respective other assays revealed positive HCV RNA results in 32-50%. In 30%, HCV RNA was 'undetectable' by all three tests at week 4 and all of these patients achieved SVR. In contrast, treatment failure occurred in 62% of patients with at least one 'detectable' result, including cases with one or two other 'undetectable' tests at week 4.

CONCLUSIONS

A single 'undetectable' HCV RNA result at week 4 is not always associated with achieving SVR. Repeated testing in difficult-to-treat patients may identify those at risk for treatment failure.

EMR-linked GWAS study: investigation of variation landscape of loci for body mass index in children

Common variations at the loci harboring the fat mass and obesity gene (FTO), MC4R, and TMEM18 are consistently reported as being associated with obesity and body mass index (BMI) especially in adult population. In order to confirm this effect in pediatric population five European ancestry cohorts from pediatric eMERGE-II network (CCHMC-BCH) were evaluated.

METHOD

Data on 5049 samples of European ancestry were obtained from the Electronic Medical Records (EMRs) of two large academic centers in five different genotyped cohorts. For all available samples, gender, age, height, and weight were collected and BMI was calculated. To account for age and sex differences in BMI, BMI z-scores were generated using 2000 Centers of Disease Control and Prevention (CDC) growth charts. A Genome-wide association study (GWAS) was performed with BMI z-score. After removing missing data and outliers based on principal components (PC) analyses, 2860 samples were used for the GWAS study. The association between each single nucleotide polymorphism (SNP) and BMI was tested using linear regression adjusting for age, gender, and PC by cohort. The effects of SNPs were modeled assuming additive, recessive, and dominant effects of the minor allele. Meta-analysis was conducted using a weighted z-score approach.

RESULTS

The mean age of subjects was 9.8 years (range 2-19). The proportion of male subjects was 56%. In these cohorts, 14% of samples had a BMI ≥95 and 28 ≥ 85%. Meta analyses produced a signal at 16q12 genomic region with the best result of p = 1.43 × 10(-) (7) [p (rec) = 7.34 × 10(-) (8)) for the SNP rs8050136 at the first intron of FTO gene (z = 5.26) and with no heterogeneity between cohorts (p = 0.77). Under a recessive model, another published SNP at this locus, rs1421085, generates the best result [z = 5.782, p (rec) = 8.21 × 10(-) (9)]. Imputation in this region using dense 1000-Genome and Hapmap CEU samples revealed 71 SNPs with p < 10(-) (6), all at the first intron of FTO locus. When hetero-geneity was permitted between cohorts, signals were also obtained in other previously identified loci, including MC4R (rs12964056, p = 6.87 × 10(-) (7), z = -4.98), cholecystokinin CCK (rs8192472, p = 1.33 × 10(-) (6), z = -4.85), Interleukin 15 (rs2099884, p = 1.27 × 10(-) (5), z = 4.34), low density lipoprotein receptor-related protein 1B [LRP1B (rs7583748, p = 0.00013, z = -3.81)] and near transmembrane protein 18 (TMEM18) (rs7561317, p = 0.001, z = -3.17). We also detected a novel locus at chromosome 3 at COL6A5 [best SNP = rs1542829, minor allele frequency (MAF) of 5% p = 4.35 × 10(-) (9), z = 5.89].

CONCLUSION

An EMR linked cohort study demonstrates that the BMI-Z measurements can be successfully extracted and linked to genomic data with meaningful confirmatory results. We verified the high prevalence of childhood rate of overweight and obesity in our cohort (28%). In addition, our data indicate that genetic variants in the first intron of FTO, a known adult genetic risk factor for BMI, are also robustly associated with BMI in pediatric population.

Association of common variants in the human eyes shut ortholog (EYS) with statin-induced myopathy: evidence for additional functions of EYS

INTRODUCTION

Of the nearly 38 million people in the USA who receive statin therapy, 0.1-0.5% experience severe or life-threatening myopathic side effects.

METHODS

We performed a genome-wide association study (GWAS) in a group of patients with severe statin myopathy versus a statin-tolerant group to identify genetic susceptibility loci.

RESULTS

Replication studies in independent groups of severe statin myopathy (n = 190) and statin-tolerant controls (n = 130) resulted in the identification of three single-nucleotide polymorphisms (SNPs), rs9342288, rs1337512, and rs3857532, in the eyes shut homolog (EYS) on chromosome 6 suggestive of an association with risk for severe statin myopathy (P = 0.0003-0.0008). Analysis of EYS cDNA demonstrated that EYS gene products are complex and expressed with relative abundance in the spinal cord as well as in the retina.

CONCLUSION

Structural similarities of these EYS gene products to members of the Notch signaling pathway and to agrin suggest a possible functional role in the maintenance and regeneration of the structural integrity of skeletal muscle.

Genetic risk for malignant hyperthermia in non-anesthesia-induced myopathies

Malignant hyperthermia (MH) is a pharmacogenetic, autosomal dominantly inherited disorder of skeletal muscle triggered by volatile anesthetics and infrequently by extreme exertion and heat exposure. MH has variable penetrance with an incidence ranging from 1 in 5000 to 1 in 50,000-100,000 anesthesias. Mutations in the ryanodine receptor gene, RYR1, are found in 50-70% of cases. We hypothesized that a portion of patients with drug-induced muscle diseases, unrelated to anesthesia, such as severe statin myopathy, have underlying genetic liability that may include RYR1 gene mutations. DNA samples were collected from 885 patients in 4 groups: severe statin myopathy (n=197), mild statin myopathy (n=163), statin-tolerant controls (n=133), and non-drug-induced myopathies of unknown etiology characterized by exercise-induced muscle pain and weakness (n=392). Samples were screened for 105 mutations and variants in 26 genes associated with 7 categories of muscle disease including 34 mutations and variants in the RYR1 gene. Disease-causing mutations or variants in RYR1 were present in 3 severe statin myopathy cases, 1 mild statin myopathy case, 8 patients with non-drug-induced myopathy, and none in controls. These results suggest that disease-causing mutations and certain variants in the RYR1 gene may contribute to underlying genetic risk for non-anesthesia-induced myopathies and should be included in genetic susceptibility screening in patients with severe statin myopathy and in patients with non-statin-induced myopathies of unknown etiology.

Evaluation of genetic association between an ITGAM non-synonymous SNP (rs1143679) and multiple autoimmune diseases

Many autoimmune diseases (ADs) share similar underlying pathology and have a tendency to cluster within families, supporting the involvement of shared susceptibility genes. To date, most of the genetic variants associated with systemic lupus erythematosus (SLE) susceptibility also show association with others ADs. ITGAM and its associated 'predisposing' variant (rs1143679, Arg77His), predicted to alter the tertiary structures of the ligand-binding domain of ITGAM, may play a key role for SLE pathogenesis. The aim of this study is to examine whether the ITGAM variant is also associated with other ADs. We evaluated case-control association between rs1143679 and ADs (N=18,457) including primary Sjögren's syndrome, systemic sclerosis, multiple sclerosis, rheumatoid arthritis, juvenile idiopathic arthritis, celiac disease, and type-1 diabetes. We also performed meta-analyses using our data in addition to available published data. Although the risk allele 'A' is relatively more frequent among cases for each disease, it was not significantly associated with any other ADs tested in this study. However, the meta-analysis for systemic sclerosis was associated with rs1143679 (p(meta)=0.008). In summary, this study explored the role of ITGAM in general autoimmunity in seven non-lupus ADs, and only found association for systemic sclerosis when our results were combined with published results. Thus ITGAM may not be a general autoimmunity gene but this variant may be specifically associated with SLE and systemic sclerosis.

C8orf13/BLK association with systemic lupus erythematosus across different ethnicities (136.28)

SLE is a complex autoimmune disease with immunological abnormalities that targets B cell functions and development. Previous genome-wide association studies identified C8orf13/BLK as a novel SLE risk factor. BLK (B lymphoid tyrosine kinase) has been shown to have potential effects on B cell develoment. The main objectives of this study are to: 1.) assess this association in independent populations and 2.) determine if BLK risk alleles correlate with alteration in peripheral blood B cell development and protein expression. We genotyped 52 SNPs within the C8orf13/BLK region in European-derived, Asian and African American populations. rs13277113 is associated with SLE in all three populations. A few novel upstream SNPs within the intergenic region demonstrate a stronger association in Asians. Flow cytometry data suggests there is a significant difference in BLK expression and T2 cells B cell numbers between high-risk and non-risk individuals based on the risk haplotype. Our results suggest that the BLK genetic polymorphisms alter immune system development and function to increase the risk for SLE development. Supported by NIH RR020143, RR015577, NIAID-DAIT-BAA-05-11, AI031584, AR053483, AR48940, AI063274, AR052125, AR043247 and OCAST # HR08-037.

Family dynamics, parental-fetal attachment and infant temperament

Family dynamics, parental-fetal attachment and infant temperament The purpose of this longitudinal study of families having their first or second baby was to explore relationships among family dynamics, paternal- and maternal-fetal attachment, and infant temperament. Data were collected from 156 women and 62 of their partners during the third trimester of pregnancy. One year later, when the infant was 8-9 months old, 75 of the women and 30 of their partners participated. In a hierarchical multiple regression analysis, after controlling for demographic variables, mutuality in the family was associated with greater maternal- and paternal-fetal attachment. Family dynamics were stable across the transition to parenthood except for an increase in role conflict reported by mothers. Sensitivity to specific family experiences by clinicians can provide assistance to families during these periods.

Formation of the compact confomer of kinesin requires a COOH-terminal heavy chain domain and inhibits microtubule-stimulated ATPase activity

Full-length Drosophila kinesin heavy chain from position 1 to 975 was expressed in Escherichia coil (DKH975) and is a dimer. The sedimentation coefficient of DKH975 shifts from 5.4 S at 1 M NaCl to approximately 6.9 S at <0.2 M NaCl. This transition of DKH975 between extended and compact conformations is essentially identical to that for the heavy chain dimer of bovine kinesin (Hackney, D. D., Levitt, J. D., and Suhan, J. (1992) J. Biol. Chem. 267, 8696-8701). Thus the capacity for undergoing the 7 S/5 S transition is an intrinsic property of the heavy chains and requires neither light chains nor eukaryotic post-translational modification. DKH960 undergoes a similar transition, indicating that the extreme COOH-terminal region is not required. More extensive deletions from the COOH-terminal (DKH945 and DKH937) result in a shift in the midpoint for the transition to lower salt concentrations. DKH927 and shorter constructs remaining extended even in the absence of added salt. Thus the COOH-terminal approximately 50 amino acids are required for the formation of the compact conformation. Separately expressed COOH-terminal tail segments and NH2-terminal head/neck segments interact in a salt-dependent manner that is consistent with the compact conformer being produced by the interaction of domains from these regions of the heavy chain dimer. The microtubule-stimulated ATPase rate of DKH975 in the compact conformer is strongly inhibited compared with the rate of extended DKH894 (4 s-1 and 35 s-1, respectively, for kcat at saturating microtubules).

The role of the serotonin transporter gene in cigarette smoking

Data from twin studies have suggested that cigarette smoking has a significant heritable component. The serotonin transporter gene (5-HTT) is a plausible candidate gene for smoking predisposition because of its association with psychological traits relevant to smoking behavior. The present investigation evaluated the associations of smoking practices and smoking cessation with a common polymorphism in the upstream regulatory region of 5-HTT that is manifested as either an inserted (long) variant or a deleted (short) variant. The short variant of the polymorphism is associated with reduced transcription of the gene promoter and diminished uptake. A case-control study design (268 smokers and 230 controls) was used to evaluate the associations of 5-HTT genotype with smoking status. Case series analysis of smokers was used to evaluate the role of 5-HTT in age at smoking initiation, previous quitting history, current smoking rate, and 12-month quit rate following a minimal-contact smoking cessation program. There were no significant differences in the distribution of 5-HTT genotypes in smokers as compared with nonsmokers in either Caucasians or African Americans, nor was the 5-HTT genotype associated with the smoking outcome variables. However, the results did reveal significant racial differences in the distribution of 5-HTT genotypes: Caucasians were significantly more likely to carry the short variant of the 5-HTT gene than were African Americans (P = 0.005). These findings suggest that the 5-HTT gene may not play a significant role in cigarette smoking practices.

Advantages and limitations of current soft intraocular lenses

We report our clinical experience with six soft intraocular lenses: (1) STAAR silicone, (2) CooperVision/Schlegel silicone, (3) IOLAB silicone, (4) Allergan Medical Optics (AMO) silicone, (5) Fyodorov silicone, and (6) Alcon hydrogel (IOGEL). We found that these soft intraocular lenses have several common design problems. The single-size design of five of the six soft lenses can lead to a windshield-wiper decentration effect in lenses too small for larger eyes. We observed several instances in which the one-piece lenses became decentered, subluxed, and vaulted anteriorly against the iris or posteriorly away from the iris as postoperative capsulozonular changes occurred. We found that the insertion methods for these soft lenses need refining to reduce the risk of intraocular damage and wound stretching if the lenses are to be folded and inserted through a small 3.0 mm to 3.5 mm incision. The surface and physical characteristics of these lenses may also require further study. We observed folding grooves, sebacium deposits, and rust from the insertion instrument on some lenses inside the postoperative eye and pigment dispersion associated with hydrogel lenses. We conclude that small diameter polymethylmethacrylate implants are the best choice for small incision cataract surgery at this time.

Glare disability devices for cataractous eyes: a consumer's guide

We evaluated five commercially available glare testers to determine how accurately each device predicted outdoor Snellen acuity in cataract patients. Predicted outdoor Snellen acuity was compared to actual Snellen outdoor acuity for the Miller-Nadler glare tester, the brightness acuity tester (BAT), the InnoMed true vision analyzer (TVA), the VisTech VCT 8000, and the EyeCon 5. All five devices were evaluated in a single series of eyes. We ranked the five glare testers as follows based upon their ability to predict outdoor Snellen acuity within one Snellen line: (1) BAT (73%), (2) TVA (69%), (3) VisTech VCT 8000 (56%), (4) Miller-Nadler (47%), and (5) EyeCon 5 (15%). All five devices were also evaluated for their capacity to provide false negative or false positive results and for testing time per eye, test difficulty level for the patient, versatility, upgrading capacity, examining room adaptability, and price. We concluded that glare testing of cataract patients is necessary to measure visual disability and that glare testing devices vary in their ability to predict outdoor vision.