Idiopathic Pulmonary Fibrosis Is Associated with Common Genetic Variants and Limited Rare Variants.

Rationale: Idiopathic pulmonary fibrosis (IPF) is a rare, irreversible, and progressive disease of the lungs. Common genetic variants, in addition to nongenetic factors, have been consistently associated with IPF. Rare variants identified by candidate gene, family-based, and exome studies have also been reported to associate with IPF. However, the extent to which rare variants, genome-wide, may contribute to the risk of IPF remains unknown. Objectives: We used whole-genome sequencing to investigate the role of rare variants, genome-wide, on IPF risk. Methods: As part of the Trans-Omics for Precision Medicine Program, we sequenced 2,180 cases of IPF. Association testing focused on the aggregated effect of rare variants (minor allele frequency ⩽0.01) within genes or regions. We also identified individual rare variants that are influential within genes and estimated the heritability of IPF on the basis of rare and common variants. Measurements and Main Results: Rare variants in both TERT and RTEL1 were significantly associated with IPF. A single rare variant in each of the TERT and RTEL1 genes was found to consistently influence the aggregated test statistics. There was no significant evidence of association with other previously reported rare variants. The SNP heritability of IPF was estimated to be 32% (SE = 3%). Conclusions: Rare variants within the TERT and RTEL1 genes and well-established common variants have the largest contribution to IPF risk overall. Efforts in risk profiling or the development of therapies for IPF that focus on TERT, RTEL1, common variants, and environmental risk factors are likely to have the largest impact on this complex disease.

Incidence and Progression of Fibrotic Lung Disease in an At-Risk Cohort.

Rationale: Relatives of patients with familial interstitial pneumonia (FIP) are at increased risk for pulmonary fibrosis and develop preclinical pulmonary fibrosis (PrePF). Objectives: We defined the incidence and progression of new-onset PrePF and its relationship to survival among first-degree relatives of families with FIP. Methods: This is a cohort study of family members with FIP who were initially screened with a health questionnaire and chest high-resolution computed tomography (HRCT) scan, and approximately 4 years later, the evaluation was repeated. A total of 493 asymptomatic first-degree relatives of patients with FIP were evaluated at baseline, and 296 (60%) of the original subjects participated in the subsequent evaluation. Measurements and Main Results: The median interval between HRCTs was 3.9 years (interquartile range, 3.5-4.4 yr). A total of 252 subjects who agreed to repeat evaluation were originally determined not to have PrePF at baseline; 16 developed PrePF. A conservative estimate of the annual incidence of PrePF is 1,023 per 100,000 person-years (95% confidence interval, 511-1,831 per 100,000 person-years). Of 44 subjects with PrePF at baseline, 38.4% subjects had worsening dyspnea compared with 15.4% of those without PrePF (P = 0.002). Usual interstitial pneumonia by HRCT (P < 0.0002) and baseline quantitative fibrosis score (P < 0.001) are also associated with worsening dyspnea. PrePF at the initial screen is associated with decreased survival (P < 0.001). Conclusions: The incidence of PrePF in this at-risk population is at least 100-fold higher than that reported for sporadic idiopathic pulmonary fibrosis (IPF). Although PrePF and IPF represent distinct entities, our study demonstrates that PrePF, like IPF, is progressive and associated with decreased survival.

MUC5B variant is associated with visually and quantitatively detected preclinical pulmonary fibrosis.

BACKGROUND: Relatives of patients with familial interstitial pneumonia (FIP) are at increased risk for pulmonary fibrosis. We assessed the prevalence and risk factors for preclinical pulmonary fibrosis (PrePF) in first-degree relatives of patients with FIP and determined the utility of deep learning in detecting PrePF on CT. METHODS: First-degree relatives of patients with FIP over 40 years of age who believed themselves to be unaffected by pulmonary fibrosis underwent CT scans of the chest. Images were visually reviewed, and a deep learning algorithm was used to quantify lung fibrosis. Genotyping for common idiopathic pulmonary fibrosis risk variants in MUC5B and TERT was performed. FINDINGS: In 494 relatives of patients with FIP from 263 families of patients with FIP, the prevalence of PrePF on visual CT evaluation was 15.6% (95% CI 12.6 to 19.0). Compared with visual CT evaluation, deep learning quantitative CT analysis had 84% sensitivity (95% CI 0.72 to 0.89) and 86% sensitivity (95% CI 0.83 to 0.89) for discriminating subjects with visual PrePF diagnosis. Subjects with PrePF were older (65.9, SD 10.1 years) than subjects without fibrosis (55.8 SD 8.7 years), more likely to be male (49% vs 37%), more likely to have smoked (44% vs 27%) and more likely to have the MUC5B promoter variant rs35705950 (minor allele frequency 0.29 vs 0.21). MUC5B variant carriers had higher quantitative CT fibrosis scores (mean difference of 0.36%), a difference that remains significant when controlling for age and sex. INTERPRETATION: PrePF is common in relatives of patients with FIP. Its prevalence increases with age and the presence of a common MUC5B promoter variant. Quantitative CT analysis can detect these imaging abnormalities.

Sunlight radiation as a villain and hero: 60 years of illuminating research.

In the 60 years since the inaugural edition of the International Journal of Radiation Biology, much of our understanding of the biological effects of solar radiation has changed. Earlier in the century, sunlight played a 'hero's' role in reducing disabling rickets, while today debate still continues on the amount of sun required before exposure reveals the 'villainous' side of solar radiation. Although knowledge of the ultra violet (UV) component of sunlight as a carcinogen has become widespread, skin cancer rates are still rising yearly. Twentieth century attitudes have seen an about-face in the field of dermatological sun protection, with sunscreens changing from recipes designed to promote a 'healthy tan' to formulations proven to block both ultraviolet B (UVB) and more recently, ultraviolet A (UVA), to minimize premature sun-aging and skin cancer risk. In the early 1960s, DNA was first found to exist within mitochondria, while recently the connections between mitochondrial changes and UV radiation exposure have been expanded. Sixty years ago, understanding of the endocrine systems of mammals was enjoying its infancy. Early discoveries that light, particularly natural light, could have profound effects on functions such as sleep patterns and hormonal balance were made, while today more advanced knowledge has led to lighting improvements having pronounced effects on human wellbeing. Photosensitization 60 years ago was a health concern for both humans and their domestic animals, while today chemically engineered photosensitizing drugs can be administered along with highly directed light to pinpoint delivery targets for drug action. Life on earth is inextricably bound up with solar radiation. This article attempts to outline many of the ways in which our opinions about solar radiation have changed since the journal's inception.

Lyme Disease Testing in a High-Incidence State: Clinician Knowledge and Patterns.

OBJECTIVES: Lyme disease (LD) incidence is increasing, but data suggest some clinicians are not fully aware of recommended procedures for ordering and interpreting diagnostic tests. The study objective was to assess clinicians' knowledge and practices regarding LD testing in a high-incidence region. METHODS: We distributed surveys to 1,142 clinicians in the University of Vermont Medical Center region, of which 144 were completed (12.6% response rate). We also examined LD laboratory test results and logs of calls to laboratory customer service over a period of 2.5 years and 6 months, respectively. RESULTS: Most clinicians demonstrated basic knowledge of diagnostic protocols, but many misinterpreted Western blot results. For example, 42.4% incorrectly interpreted a positive immunoglobulin M result as an overall positive test in a patient with longstanding symptoms. Many also reported receiving patient requests for unvalidated tests. CONCLUSIONS: Additional education and modifications to LD test ordering and reporting systems would likely reduce errors and improve patient care.

Polypharmacy and sun exposure: Implications for mitochondrial DNA deletions in skin.

Most somatic cells contain many copies of mitochondrial DNA (mtDNA). Because of both the high copy number and the lack of repair mechanisms available to mtDNA, damage to it largely goes unrepaired, and can accumulate over time. Large scale deletions are a recognised type of damage sustained by mtDNA as a consequence of exposure to the ultraviolet light in sunlight. A group of patients were identified as having abnormally high levels of either a 4977 base pair deletion (mtDNA4977) or 3895 base pair deletion (mtDNA3895), in mtDNA from sun exposed skin or skin suspected to be a non-melanoma skin cancer, but not in their non-sun exposed skin biopsies. In three of the four cases, skin cancer was ruled out due to histological testing. Additional factors from these patients' medical histories were studied, and it was noted that they shared diagnoses for multiple pathologies common to an older population, and that they were being treated with the same or related pharmaceuticals, including some that had been known to cause dermal side effects. Investigation into the biochemistry underlying the symptoms, the effects of sun exposure and side effects of the prescribed pharmaceuticals revealed a possible synergistic relationship leading to the localised high levels of mtDNA deletions.

Mitochondrial DNA deletion percentage in sun exposed and non sun exposed skin.

The percentages of mitochondrial genomes carrying the mtDNA3895 and the mtDNA4977 (common) deletion were quantified in sun exposed and non sun exposed skin biopsies, for five cohorts of patients varying either in sun exposure profile, age or skin cancer status. Non-melanoma skin cancer diagnoses are rising in Ireland and worldwide [12] but most risk prediction is based on subjective visual estimations of sun exposure history. A quantitative objective test for pre-neoplastic markers may result in better adherence to sun protective behaviours. Mitochondrial DNA (mtDNA) is known to be subject to the loss of a significant proportion of specific sections of genetic code due to exposure to ultraviolet light in sunlight. Although one such deletion has been deemed more sensitive, another, called the mtDNA4977 or common deletion, has proved to be a more useful indicator of possible risk in this study. Quantitative molecular analysis was carried out to determine the percentage of genomes carrying the deletion using non sun exposed and sun exposed skin biopsies in cohorts of patients with high or low sun exposure profiles and two high exposure groups undergoing treatment for NMSC. Results indicate that mtDNA deletions correlate to sun exposure; in groups with high sun exposure habits a significant increase in deletion number in exposed over non sun exposed skin occurred. An increase in deletion percentage was also seen in older cohorts compared to the younger group. The mtDNA3895 deletion was detected in small amounts in exposed skin of many patients, the mtDNA4977 common deletion, although present to some extent in non sun exposed skin, is suggested to be the more reliable and easily detected marker. In all cohorts except the younger group with relatively lower sun exposure, the mtDNA4977 deletion was more frequent in sun exposed skin samples compared to non-sun exposed skin.

Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia.

BACKGROUND: Fibrotic idiopathic interstitial pneumonias (fIIP) are a group of fatal lung diseases with largely unknown etiology and without definitive treatment other than lung transplant to prolong life. There is strong evidence for the importance of both rare and common genetic risk alleles in familial and sporadic disease. We have previously used genome-wide single nucleotide polymorphism data to identify 10 risk loci for fIIP. Here we extend that work to imputed genome-wide genotypes and conduct new RNA sequencing studies of lung tissue to identify and characterize new fIIP risk loci. RESULTS: We performed genome-wide genotype imputation association analyses in 1616 non-Hispanic white (NHW) cases and 4683 NHW controls followed by validation and replication (878 cases, 2017 controls) genotyping and targeted gene expression in lung tissue. Following meta-analysis of the discovery and replication populations, we identified a novel fIIP locus in the HLA region of chromosome 6 (rs7887 P meta = 3.7 × 10(-09)). Imputation of classic HLA alleles identified two in high linkage disequilibrium that are associated with fIIP (DRB1*15:01 P = 1.3 × 10(-7) and DQB1*06:02 P = 6.1 × 10(-8)). Targeted RNA-sequencing of the HLA locus identified 21 genes differentially expressed between fibrotic and control lung tissue (Q < 0.001), many of which are involved in immune and inflammatory response regulation. In addition, the putative risk alleles, DRB1*15:01 and DQB1*06:02, are associated with expression of the DQB1 gene among fIIP cases (Q < 1 × 10(-16)). CONCLUSIONS: We have identified a genome-wide significant association between the HLA region and fIIP. Two HLA alleles are associated with fIIP and affect expression of HLA genes in lung tissue, indicating that the potential genetic risk due to HLA alleles may involve gene regulation in addition to altered protein structure. These studies reveal the importance of the HLA region for risk of fIIP and a basis for the potential etiologic role of auto-immunity in fIIP.

The Cost-Effectiveness of Real-Time Continuous Glucose Monitoring (RT-CGM) in Type 2 Diabetes.

BACKGROUND: This analysis models the cost-effectiveness of real-time continuous glucose monitoring (RT-CGM) using evidence from a randomized controlled trial (RCT) that demonstrated RT-CGM reduced A1C, for up to 9 months after using the technology, among patients with type 2 diabetes not on prandial insulin. RT-CGM was offered short-term and intermittently as a self-care tool to inform patients' behavior. METHOD: The analyses projected lifetime clinical and economic outcomes for RT-CGM versus self-monitoring of blood glucose by fingerstick only. The base-case analysis was consistent with the RCT (RT-CGM for 2 weeks on/1 week off over 3 months). A scenario analysis simulated outcomes of an RT-CGM "refresher" after the active intervention of the RCT. Analyses used the IMS CORE Diabetes Model and were conducted from a US third-party payer perspective, including direct costs obtained from published sources and inflated to 2011 US dollars. Costs and health outcomes were discounted at 3% per annum. RESULTS: Life expectancy (LE) and quality-adjusted life expectancy (QALE) from RT-CGM were 0.10 and 0.07, with a cost of $653/patient over a lifetime. Incremental LE and QALE from a "refresher" were 0.14 and 0.10, with a cost of $1312/patient over a lifetime, and incremental cost-effectiveness ratios were $9319 and $13 030 per LY and QALY gained. CONCLUSIONS: RT-CGM, as a self-care tool, is a cost-effective disease management option in the US for people with type 2 diabetes not on prandial insulin. Repeated use of RT-CGM may result in additional cost-effectiveness.

Rare variants in RTEL1 are associated with familial interstitial pneumonia.

RATIONALE: Up to 20% of cases of idiopathic interstitial pneumonia cluster in families, comprising the syndrome of familial interstitial pneumonia (FIP); however, the genetic basis of FIP remains uncertain in most families. OBJECTIVES: To determine if new disease-causing rare genetic variants could be identified using whole-exome sequencing of affected members from FIP families, providing additional insights into disease pathogenesis. METHODS: Affected subjects from 25 kindreds were selected from an ongoing FIP registry for whole-exome sequencing from genomic DNA. Candidate rare variants were confirmed by Sanger sequencing, and cosegregation analysis was performed in families, followed by additional sequencing of affected individuals from another 163 kindreds. MEASUREMENTS AND MAIN RESULTS: We identified a potentially damaging rare variant in the gene encoding for regulator of telomere elongation helicase 1 (RTEL1) that segregated with disease and was associated with very short telomeres in peripheral blood mononuclear cells in 1 of 25 families in our original whole-exome sequencing cohort. Evaluation of affected individuals in 163 additional kindreds revealed another eight families (4.7%) with heterozygous rare variants in RTEL1 that segregated with clinical FIP. Probands and unaffected carriers of these rare variants had short telomeres (<10% for age) in peripheral blood mononuclear cells and increased T-circle formation, suggesting impaired RTEL1 function. CONCLUSIONS: Rare loss-of-function variants in RTEL1 represent a newly defined genetic predisposition for FIP, supporting the importance of telomere-related pathways in pulmonary fibrosis.

Prevalence and incidence of hypoparathyroidism in the United States using a large claims database.

Hypoparathyroidism is a rare endocrine disorder whose incidence and prevalence have not been well defined. This study aimed to 1) estimate the number of insured adult patients with hypoparathyroidism in the United States and 2) obtain physician assessment of disease severity and chronicity. Prevalence was estimated through calculation of diagnoses of hypoparathyroidism in a large proprietary health plan claims database over a 12-month period from October 2007 through September 2008 and projected to the US insured population. Incidence was also calculated from the same database by determining the proportion of total neck surgeries resulting in either transient (≤6 months) or chronic (>6 months) hypoparathyroidism. A physician primary market research study was conducted to assess disease severity and determine the percentage of new nonsurgical patients with hypoparathyroidism. Incidence data were entered into an epidemiologic model to derive an estimate of prevalence. The diagnosis-based prevalence approach estimated 58,793 insured patients with chronic hypoparathyroidism in the United States. The surgical-based incidence approach yielded 117,342 relevant surgeries resulting in 8901 cases over 12 months. Overall, 7.6% of surgeries resulted in hypoparathyroidism (75% transient, 25% chronic). The prevalence of chronic hypoparathyroidism among insured patients included in the surgical database was estimated to be 58,625. The physician survey found that 75% of cases treated over the past 12 months were reported due to surgery and, among all thyroidectomies and parathyroidectomies and neck dissections performed in a year, 26% resulted in transient hypoparathyroidism and 5% progressed to a chronic state. In conclusion, the two claims-based methods yielded similar estimates of the number of insured patients with chronic hypoparathyroidism in the United States (~58,700). The physician survey was consistent with those calculations and confirmed the burden imposed by hypoparathyroidism.

Food insecurity and household eating patterns among vulnerable American-Indian families: associations with caregiver and food consumption characteristics.

OBJECTIVE: To identify factors associated with food insecurity and household eating patterns among American-Indian families with young children. DESIGN: Cross-sectional survey among households with young children that were receiving emergency food services. We collected information on food insecurity levels, household eating patterns, experiences with commercial and community food sources and demographics, and used multivariate regression techniques to examine associations among these variables. SETTING: Four Southwestern American-Indian reservation communities. SUBJECTS: A total of 425 parents/caregivers of young children completed the survey. RESULTS: Twenty-nine per cent of children and 45 % of adults from households participating in the survey were classified as 'food insecure'. Larger household size was associated with increased food insecurity and worse eating patterns. Older respondents were more likely than younger respondents to have children with food insecurity (relative risk = 2·19, P < 0·001) and less likely to have healthy foods available at home (relative risk = 0·45, P < 0·01). Consumption of food from food banks, gas station/convenience stores or fast-food restaurants was not associated with food insecurity levels. Respondents with transportation barriers were 1·46 times more likely to be adult food insecure than respondents without transportation barriers (P < 0·001). High food costs were significantly associated with greater likelihoods of adult (relative risk = 1·47, P < 0·001) and child (relative risk = 1·65, P < 0·001) food insecurity. CONCLUSIONS: Interventions for American-Indian communities must address challenges such as expense and limited transportation to accessing healthy food. Results indicate a need for services targeted to older caregivers and larger households. Implications for innovative approaches to promoting nutrition among American-Indian communities, including mobile groceries and community gardening programmes, are discussed.

The Family Spirit trial for American Indian teen mothers and their children: CBPR rationale, design, methods and baseline characteristics.

The purpose of this paper is to describe the rationale, design, methods and baseline results of the Family Spirit trial. The goal of the trial is to evaluate the impact of the paraprofessional-delivered "Family Spirit" home-visiting intervention to reduce health and behavioral risks for American Indian teen mothers and their children. A community based participatory research (CBPR) process shaped the design of the current randomized controlled trial of the Family Spirit intervention. Between 2006 and 2008, 322 pregnant teens were randomized to receive the Family Spirit intervention plus Optimized Standard Care, or Optimized Standard Care alone. The Family Spirit intervention is a 43-session home-visiting curriculum administered by American Indian paraprofessionals to teen mothers from 28 weeks gestation until the baby's third birthday. A mixed methods assessment administered at nine intervals measures intervention impact on parental competence, mother's and children's social, emotional and behavioral risks for drug use, and maladaptive functioning. Participants are young (mean age = 18.1 years), predominantly primiparous, unmarried, and challenged by poverty, residential instability and low educational attainment. Lifetime and pregnancy drug use were ~2-4 times higher and ~5-6 times higher, respectively, than US All Races. Baseline characteristics were evenly distributed between groups, except for higher lifetime cigarette use and depressive symptoms among intervention mothers. If study aims are achieved, the public health field will have new evidence supporting multi-generational prevention of behavioral health disparities affecting young American Indian families and the utility of indigenous paraprofessional interventionists in under-resourced communities.

Fatherhood roles and drug use among young American Indian men.

BACKGROUND: High rates of substance abuse among young American Indian (AI) fathers pose multigenerational challenges for AI families and communities. OBJECTIVE: The objective of this study was to describe substance use patterns among young AI fathers and examine the intersection of substance use with men's fatherhood roles and responsibilities. METHODS: As part of a home-visiting intervention trial for AI teen mothers and their children, in 2010 we conducted a descriptive study of fatherhood and substance use on three southwestern reservations. Substance use and parenting data were collected from n = 87 male partners of adolescent mothers using audio computer-assisted self-interviews. RESULTS: Male partners were on average 22.9 years old, primarily living with their children (93%), unmarried (87%), and unemployed (70%). Lifetime substance use was high: 80% reported alcohol; 78% marijuana; 34% methamphetamines; 31% crack/cocaine; and 16% reported drinking binge in the past 6 months. Substance use was associated with history of alcohol abuse among participants' fathers (but not mothers); participants' poor relationships with their own fathers; unemployment status; and low involvement in child care. CONCLUSION: Drug and alcohol abuse may be obstructing ideal fatherhood roles among multiple generations of AI males. SCIENTIFIC SIGNIFICANCE: Targeting drug prevention among young AI men during early fatherhood may provide special opportunity to reduce substance use and improve parenting. Intergenerational approaches may hold special promise.

Comparative effectiveness research and healthcare reform: topics of the day.

The International Society for Pharmacoeconomics and Outcomes Research recently sponsored the 16th Annual International Meeting. Participants included industry, clinical practice, government, academia and health research professionals. The purpose of the conference is to share information on increasing the efficiency, effectiveness and fairness with which available healthcare resources are used to improve health.

Examining correlates of methamphetamine and other drug use in pregnant American Indian adolescents.

American Indian and Alaska Native (AI/AN) adolescents have high rates of pregnancy, as well as alcohol, marijuana, cocaine, and, increasingly, methamphetamine (meth) use. The progression of adolescent drug use to meth use could have devastating impacts on AI communities, particularly when youth are simultaneously at risk for teen childbearing. In order to inform future prevention efforts, this study explores correlates of meth use in a sample of pregnant AI teens, with a focus on sociodemographic, familial, and cultural factors and use of other drugs.

Aged men display blunted biorhythmic variation of muscle performance and physiological responses.

Aging is known to disrupt the "biological clock" that governs physiological variables at rest. This study sought to determine whether aged men demonstrated biorhythmic variation in muscle performance during resistance exercise and physiological responses to that stimulus. Ten aged (75.6 +/- 1.6 yr; mean +/- SE) men completed an isokinetic testing protocol of knee extensors and flexors at 0800, 1200, 1600, and 2000 h. Although time of day variation in peak torque was detectable, significant (P < or = 0.05) oscillation was established only in the knee flexors at 3.14 rad/s. Heart rate, blood pressure, and rectal temperature displayed no significant variation, but trends (P < 0.10) in oscillation of postexercise blood pressure and rectal temperature were noted. Temporal patterns in biorhythmic variation of muscle performance, as well as thermal and cardiovascular measures, emulated those observed in a previous study involving young men where the magnitude of variation was sufficient to achieve statistical significance. Similar to our earlier findings in young men, however, pre- and postexercise testosterone and cortisol concentrations demonstrated significant variation among aged men. These data confirm the blunting of biorhythmic variation in muscle performance and physiological variables, except for circulating hormones, in aged men.