Project Baby Bear: Rapid precision care incorporating rWGS in 5 California children's hospitals demonstrates improved clinical outcomes and reduced costs of care.

Genetic disorders are a leading contributor to mortality in neonatal and pediatric intensive care units (ICUs). Rapid whole-genome sequencing (rWGS)-based rapid precision medicine (RPM) is an intervention that has demonstrated improved clinical outcomes and reduced costs of care. However, the feasibility of broad clinical deployment has not been established. The objective of this study was to implement RPM based on rWGS and evaluate the clinical and economic impact of this implementation as a first line diagnostic test in the California Medicaid (Medi-Cal) program. Project Baby Bear was a payor funded, prospective, real-world quality improvement project in the regional ICUs of five tertiary care children's hospitals. Participation was limited to acutely ill Medi-Cal beneficiaries who were admitted November 2018 to May 2020, were <1 year old and within one week of hospitalization, or had just developed an abnormal response to therapy. The whole cohort received RPM. There were two prespecified primary outcomes-changes in medical care reported by physicians and changes in the cost of care. The majority of infants were from underserved populations. Of 184 infants enrolled, 74 (40%) received a diagnosis by rWGS that explained their admission in a median time of 3 days. In 58 (32%) affected individuals, rWGS led to changes in medical care. Testing and precision medicine cost $1.7 million and led to $2.2-2.9 million cost savings. rWGS-based RPM had clinical utility and reduced net health care expenditures for infants in regional ICUs. rWGS should be considered early in ICU admission when the underlying etiology is unclear.

Daily temperature fluctuations unpredictably influence developmental rate and morphology at a critical early larval stage in a frog.

BACKGROUND: Environmental temperature has profound consequences for early amphibian development and many field and laboratory studies have examined this. Most laboratory studies that have characterized the influence of temperature on development in amphibians have failed to incorporate the realities of diel temperature fluctuations (DTF), which can be considerable for pond-breeding amphibians. RESULTS: We evaluated the effects of different ecologically relevant ranges of DTF compared with effects of constant temperatures on development of embryos and larvae of the Korean fire-bellied toad (Bombina orientalis). We constructed thermal reaction norms for developmental stage, snout-vent length, and tail length by fitting a Gompertz-Gaussian function to measurements taken from embryos after 66 hours of development in 12 different constant temperature environments between 14°C and 36°C. We used these reaction norms as null models to test the hypothesis that developmental effects of DTF are more than the sum of average constant temperature effects over the distribution of temperatures experienced. We predicted from these models that growth and differentiation would be positively correlated with average temperature at low levels of DTF but not at higher levels of DTF. We tested our prediction in the laboratory by rearing B. orientalis embryos at three average temperatures (20°C, 24°C, and 28°C) and four levels of thermal variation (0°C, 6°C, 13°C, and 20°C). Several of the observed responses to DTF were significantly different from both predictions of the model and from responses in constant temperature treatments at the same average temperatures. At an average temperature of 24°C, only the highest level of DTF affected differentiation and growth rates, but at both cooler and warmer average temperatures, moderate DTF was enough to slow developmental and tail growth rates. CONCLUSIONS: These results demonstrate that both the magnitude of DTF range and thermal averages need to be considered simultaneously when parsing the effects of changing thermal environments on complex developmental responses, particularly when they have potential functional and adaptive significance.

Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization.

Genetic disorders are a leading cause of morbidity and mortality in infants. Rapid whole-genome sequencing (rWGS) can diagnose genetic disorders in time to change acute medical or surgical management (clinical utility) and improve outcomes in acutely ill infants. We report a retrospective cohort study of acutely ill inpatient infants in a regional children's hospital from July 2016-March 2017. Forty-two families received rWGS for etiologic diagnosis of genetic disorders. Probands also received standard genetic testing as clinically indicated. Primary end-points were rate of diagnosis, clinical utility, and healthcare utilization. The latter was modelled in six infants by comparing actual utilization with matched historical controls and/or counterfactual utilization had rWGS been performed at different time points. The diagnostic sensitivity of rWGS was 43% (eighteen of 42 infants) and 10% (four of 42 infants) for standard genetic tests (P = .0005). The rate of clinical utility of rWGS (31%, thirteen of 42 infants) was significantly greater than for standard genetic tests (2%, one of 42; P = .0015). Eleven (26%) infants with diagnostic rWGS avoided morbidity, one had a 43% reduction in likelihood of mortality, and one started palliative care. In six of the eleven infants, the changes in management reduced inpatient cost by $800,000-$2,000,000. These findings replicate a prior study of the clinical utility of rWGS in acutely ill inpatient infants, and demonstrate improved outcomes and net healthcare savings. rWGS merits consideration as a first tier test in this setting.

Ecological and developmental context of natural selection: maternal effects and thermally induced plasticity in the frog Bombina orientalis.

Variation in fitness generated by differences in functional performance can often be traced to morphological variation among individuals within natural populations. However, morphological variation itself is strongly influenced by environmental factors (e.g., temperature) and maternal effects (e.g., variation in egg size). Understanding the full ecological context of individual variation and natural selection therefore requires an integrated view of how the interaction between the environment and development structures differences in morphology, performance, and fitness. Here we use naturally occurring environmental and maternal variation in the frog Bombina orientalis in South Korea to show that ovum size, average temperature, and variance in temperature during the early developmental period affect body sizes, shapes, locomotor performance, and ultimately the probability of an individual surviving interspecific predation in predictable but nonadditive ways. Specifically, environmental variability can significantly change the relationship between maternal investment in offspring and offspring fitness so that increased maternal investment can actually negatively affect offspring over a broad range of environments. Integrating environmental variation and developmental processes into traditional approaches of studying phenotypic variation and natural selection is likely to provide a more complete picture of the ecological context of evolutionary change.

Maternal effects on offspring growth and development depend on environmental quality in the frogBombina orientalis.

Differences in maternal investment and initial offspring size can have important consequences for offspring growth and development. To examine the effects of initial size variability in the frogBombina orientalis, we reared larvae (N=360) in one of two treatments representing different levels of environmental quality. We used snout-vent length at the feeding stage (stage 25, Gosner 1960) as a measure of maternal investment. In a "low quality" treatment, larvae were reared with two conspecific tadpoles and food was limited, whereas in a "high quality" treatment, larvae were reared individually and were fed ad libitum. Among tadpoles reared in the low quality treatment, individuals that were initially small had smaller body sizes through metamorphosis and longer larval periods than individuals that were initially large. Among tadpoles reared in the high quality treatment, initial size had only a weak influence on later larval size, and did not significantly affect metamorphic size of the duration of the larval period. This interaction between maternal investment and rearing conditions suggests that production of initially small offspring could be advantageous if these offspring develop in relatively benign environments, but disadvantageous if environments are more severe. These findings are discussed in light of previous studies that have demonstrated such interactions in organisms with complex life cycles.

Female-specific increase in primordial germ cells marks sex differentiation in threespine stickleback (Gasterosteus aculeatus).

Gonadal sex differentiation is increasingly recognized as a remarkably plastic process driven by species-specific genetic or environmental determinants. Among aquatic vertebrates, gonadal sex differentiation is a frequent endpoint in studies of endocrine disruption with little appreciation of underlying developmental mechanisms. Work in model organisms has highlighted the diversity of master sex-determining genes rather than uncovering any broad similarities prompting the highly conserved developmental decision of testes versus ovaries. Here we use molecular genetic markers of chromosomal sex combined with traditional histology to examine the transition of the bipotential gonads to ovaries or testes in threespine stickleback (Gasterosteus aculeatus). Serially-sectioned threespine stickleback fry were analyzed for qualitative and quantitative indications of sexual differentiation, including changes in gonadal morphology, number of germ cells and the incidence of gonadal apoptosis. We show that threespine stickleback sampled from anadromous and lacustrine populations are differentiated gonochorists. The earliest sex-specific event is a premeiotic increase in primordial germ cell number followed by a female-specific spike in apoptosis in the undifferentiated gonad of genetic females. The data suggest that an increase in PGC number may direct the undifferentiated gonad toward ovarian differentiation.