Long-read whole genome sequencing (lrWGS) shows promise as an all-in-one test to detect clinically relevant variants and variants difficult to detect by current short-read whole genome sequencing (srWGS) pipelines. Comparisons between lrWGS and srWGS (or exome sequencing) pipelines will become commonplace as lrWGS is more widely adopted for clinical testing, particularly for individuals not diagnosed by srWGS. However, the sensitivity of lrWGS for detecting variants previously identified and prioritized by clinical srWGS has yet to be assessed. As part of the SeqFirst-neo study, a subset of critically ill newborns and their parents who underwent clinical srWGS also underwent lrWGS on the Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) platforms. In total, 134 families were sequenced across multiple technologies including 128 families with clinical srWGS who were sequenced on both lrWGS platforms. We compared the variants reported by clinical testing with the variants identified by lrWGS. Among the 128 families sequenced on all three platforms, 89 SNV/indels and 14 SV/CNVs clinically reported by the srWGS testing pipeline were evaluated. All variants assessed in probands were ultimately detected by both lrWGS platforms, although three events were not detected prior to application of an updated variant caller, highlighting the rapid evolution of lrWGS variant calling. Additionally, breakpoint coordinates and event sizes often differed substantially between calls from srWGS and events called in lrWGS data. Our work demonstrates that while most clinically reported variants from srWGS can be detected by lrWGS pipelines, challenges remain when attempting direct comparisons, particularly for SV/CNVs.

(Abstracted from JAMA 2025;333(3):232–240 Newborn screening (NBS) checks for congenital conditions that can be treated before symptoms start and lead to irreversible effects; these include conditions such as metabolic disease, cystic fibrosis, hearing impairment, endocrine disorders, hemoglobinopathies, severe combined immunodeficiency, and other conditions that are often genetic. Genetic sequencing is typically second-tier in terms of NBS, being used chiefly to identify genes involved in a condition such as cystic fibrosis.

Neuronal ceroid lipofuscinosis type 2 (CLN2) is an autosomal recessive neurodegenerative disorder with enzyme replacement therapy available. We present two siblings with a clinical diagnosis of CLN2 disease, but no identifiable TPP1 variants after standard clinical testing. Long-read sequencing identified a homozygous deep intronic variant predicted to affect splicing, confirmed by clinical DNA and RNA sequencing. This case demonstrates how traditional laboratory assays can complement emerging molecular technologies to provide a precise molecular diagnosis.

The serotonin transporter (5-HTTLPR) and brain-derived neurotrophic factor (BDNF) gene polymorphisms have been associated with risk for affective disorders and functional variability of the amygdala. We examined whether the two genotypes interactively influence intrinsic functional connectivity (FC) of the amygdala and whether FC mediates the genetic association with anxiety. Eighty genotyped healthy adults underwent resting state fMRI and completed the self-reported State-Trait Anxiety Inventory. Interactive genetic association with anxiety was observed such that effects of 5-HTTLPR depended on the BDNF Val66Met polymorphism (rs6265 variant), with higher anxiety scores in short and Met carriers compared to the other allelic groups. Voxel-wise FC with left and right amygdala seeds identified regions that were sensitive to variability in anxiety scores. A significant moderated mediation model demonstrated that the effect of 5-HTTLPR genotype on anxiety, moderated by BDNF Val66Met genotype, was fully mediated by FC between the left amygdala and the right dorsolateral prefrontal cortex, a cognitive control-related region, during a task-free state. FC was highest in carriers of the 5-HTTLPR short allele and BDNF Met allele. These findings establish intrinsic amygdala-prefrontal functional connectivity as a potential intermediate phenotype for anxiety, an important step toward identification of causal pathways for vulnerability to affective disorders.

BackgroundInterleukin-15 (IL-15) is a myokine associated with muscle strength, possibly by attenuating protein breakdown. A variant in the alpha-receptor (IL-15R 1775 A>C, rs2228059) partially modulates the muscle strength and size response to resistance training. We examined if this polymorphism associated with habitual physical activity among European-American adults. MethodsMen (n=240, 23.70.3year, body mass index [BMI] 25.30.3 kg/m(2)) and women (n=292, 23.2 +/- 0.3year, 24.0 +/- 0.3kg/m(2)) were genotyped. Physical activity phenotypes were derived from the Paffenbarger Physical Activity Questionnaire. Analysis of covariance (ancova) tested log-transformed differences between the IL-15R genotype and physical activity phenotypes by gender with age and BMI as covariates. ResultsMen with the IL-15R 1775AA genotype spent more time in light intensity physical activity (39.4 +/- 2.4hr/week) than men with the CC genotype (28.6 +/- 2.3hr/week, (p=.009). ConclusionFurther research is needed to confirm our finding and determine the possible mechanisms by which the IL-15R variant modulates light intensity physical activity.

Amygdala dysfunction has been implicated in numerous neurodevelopmental disorders, including autism spectrum disorder (ASD). Previous studies in mice and humans, respectively, have linked Pac1r/PAC1R function to social behavior and PTSD‐susceptibility. Based on this connection to social and emotional processing and the central role played by the amygdala in ASD, we examined a putative role for PAC1R in social deficits in ASD and determined the pattern of gene expression in the developing mouse and human amygdala. We reveal that Pac1r/PAC1R is expressed in both mouse and human amygdala from mid‐neurogenesis through early postnatal stages, critical time points when altered brain trajectories are hypothesized to unfold in ASD. We further find that parents of autistic children carrying a previously identified PTSD‐risk genotype (CC) report greater reciprocal social deficits compared to those carrying the non‐risk GC genotype. Additionally, by exploring resting‐state functional connectivity differences in a subsample of the larger behavioral sample, we find higher functional connectivity between the amygdala and right middle temporal gyrus in individuals with the CC risk genotype. Thus, using multimodal approaches, our data reveal that the amygdala‐expressed PAC1R gene may be linked to severity of ASD social phenotype and possible alterations in brain connectivity, therefore potentially acting as a modifier of amygdala‐related phenotypes. Autism Res 2019, 12: 200–211 © 2018 International Society for Autism Research, Wiley Periodicals, Inc.Lay SummaryIn this multimodal study across mouse and human, we examined expression patterns of Pac1r/PAC1R, a gene implicated in social behavior, and further explored whether a previously identified human PTSD‐linked mutation in PAC1R can predict brain connectivity and social deficits in ASD. We find that PAC1R is highly expressed in the both the mouse and human amygdala. Furthermore, our human data suggest that PAC1R genotype is linked to severity of social deficits and functional amygdala connectivity in ASD.

Introduction: Tumor necrosis factor-alpha (TNF-alpha) is a potent pro-inflammatory cytokine involved in the acute phase stress response. The genetic variant, rs1800629, is located in the promoter region of the TNF-alpha gene and has been shown to affect the production of TNF-alpha. The purpose of this study was to determine whether the TNF-alpha pro-inflammatory response induced by an acute bout of exercise is affected by Marine Corps training and/or the rs1800629 variant and whether the rs1800629 variant is predictive of physical performance in male U.S. Marine Corps infantrymen. Methods: Plasma samples were collected before and after a 5 km (Day 12 of training) and 20 km (Day 40 of training) march to measure TNF-alpha concentration. DNA was extracted from whole blood, and genotyping was performed in 122 Marines. Relationships between physical fitness test measures (run, sit-ups, and pull-ups) and genotype were determined. Results: TNF-alpha concentrations before and after the 5-km march on Day 12 of training were significantly higher than levels observed before and after the 20-km march on day 40 of training (3.4 +/- 0.2 vs. 3.0 +/- 0.2 pg.mL(-1); p < 0.05). There was a main effect of time, with lower pre-march TNF-alpha concentrations than post-march concentrations (2.7 +/- 0.2 vs. 3.7 +/- 0.2 pg.mL(-1); p < 0.05). There were no interaction effects between rs1800629 genotypes and march distance (p > 0.05), between genotype and march time point (p > 0.05), or between genotype, march distance, and march time point (p > 0.05). There was no difference for any of the physical fitness test scores between the genotype groups (p > 0.05); nor were there any differences between the absolute runtime, number of pull-ups, or number of sit-ups (p > 0.05). Conclusion: U.S. Marine Corps infantry training reduces the TNF-alpha stress response induced by an acute bout of exercise. The rs1800629 variant does not influence performance or the TNF-alpha stress response in Marine Corps students undergoing infantry training.

PURPOSE: A decision to participate in physical activity is heavily influenced by one’s self-efficacy related to exercise capacity, but it is not clear if muscle size and strength influence one’s decision to engage in sports and recreation. We examined this relationship and hypothesized that those with stronger and larger muscle would engage in more sports and recreation. METHODS: Subjects were young (23.4 ± 5.6yr), normal weight (24.4 ± 4.6 kg/m2) European-American women (n=227) and men (n=192). The Paffenbarger Physical Activity Questionnaire assessed self-reported weekly Kcal expended in sport and recreational physical activity. We obtained muscle size and strength on the dominant and non-dominant arms. Muscle strength was measured with the maximum voluntary contraction (MVC) and one repetition maximum (1RM), and muscle size by cross sectional area (CSA) using magnetic resonance imaging. Weekly sport and recreation participation was categorized by the median for purposes of statistical analysis. Logistic regression tested the associations among muscle size and strength and sport and recreation participation by gender adjusting for age and body mass index (BMI). Akaike Information Criterion was used to identify the most parsimonious model. RESULTS: On average, men spent about 1568.7±2397.5 kcal/wk and women spent 1732.2±2184.8kcal/wk in sports and recreation. Among men, a one-unit increase in dominant arm 1RM and MVC was associated with 16.9% (95%CI: 5.0-31.1%) and 2.3% (95%CI: 0.6-4.2%) higher odds of engaging in sports and recreation, respectively. Among women, a one-unit increase in non-dominant arm MVC was associated with 5.3% (95%CI = 2.2-8.7%) higher odds of engaging in sports and recreation, while a one- unit increase in non-dominant arm CSA was associated with 19.8 % (95%CI = 8.9-30.0%) lower odds of engaging in sports and recreation. CONCLUSIONS: As hypothesized, greater MVC predicted engaging in more sport and recreation for both men and women, but greater 1RM predicted engaging in more sport and recreation among men only. Contrary to our hypothesis, greater CSA (i.e., muscle size) predicted engaging in less sports and recreation among women only. The interactions among putative psychosocial mediators, muscle capacity, and sport and recreation participation warrants future investigation.

BACKGROUND:The angiotensin-converting enzyme (ACE) insertion/deletion (I/D) polymorphism (rs4340) (ACE DIP) accounts for half of the variability in plasma ACE concentrations. ACE has been widely studied for its influence on sports performance; however, research on its influence in physical activity is limited and inconsistent. We examined the influence of the ACE DIP on physical activity among 461 European Americans. METHODS:Subjects completed the Paffenbarger Physical Activity Questionnaire for weekly walking distance. Multivariate analysis of covariance (MANCOVA) tested log-transformed differences in weekly walking distance among ACE DIP genotypes (II, ID, DD) with gender as a fixed factor, and age and body mass index (BMI) as covariates. Because we found a significant ACE DIPxBMI interaction (P = 0.03), we categorized the sample by normal weight (NW: BMI<25.0 kg/m2) and overweight (OW: BMI ≥25.0 kg/m2) and repeated the MANCOVA with multiple comparison adjustments. RESULTS:NW adults with ACE II walked 15.8 ± 11.1 km/week, ID 13.2 ± 10.6 km/week, and DD 17.9 ± 13.0 km/week, with ID walking less than II (P = 0.03) and DD (P = 0.01). OW adults with ACE II walked 16.7 ± 12.6 km/week, ID 13.8 ± 11.6 km/week, and DD 9.7 ± 9.0 km/week, with DD walking less than II (P = 0.02). Weekly walking distance was 8.2 ± 2.4 km/week less among OW adults with ACE DD than NW (P = 0.02). CONCLUSION:BMI interacted with ACE DD such that OW walked ~8.2 km/week less than NW, potentially equating to a body weight differential of ~3.5 kg annually.

Studies of physical activity behaviours have increasingly shown the importance of heritable factors such as genetic variation. Nonsynonymous polymorphisms of alpha-actinin 3 (ACTN3) and the β-adrenergic receptors 1 and 3 (ADRB1 and ADRB3) have been previously associated with exercise capacity and cardiometabolic health. We thus hypothesized that these polymorphisms are also related to physical activity behaviours in young adults. To test this hypothesis we examined relationships between ACTN3 (R577X), ARDB1 (Arg389Gly), ADRB3 (Trp64Arg), and physical activity behaviours in university students. We stratified for student enrollment in kinesiology degree programs compared with nonmajors as we previously found this to be a predictor of physical activity. We did not identify novel associations between physical activity and ACTN3. However, the minor alleles of ADRB1 and ADRB3 were significantly underrepresented in kinesiology students compared with nonmajors. Furthermore, carriers of the ADRB1 minor allele reported reduced participation in moderate physical activity and increased afternoon fatigue compared with ancestral allele homozygotes. Together, these findings suggest that the heritability of physical activity behaviours in young adults may be linked to nonsynonymous polymorphisms within β-adrenergic receptors.

Here we report whole exome sequencing (WES) on a cohort of 71 patients with persistently unresolved white matter abnormalities with a suspected diagnosis of leukodystrophy or genetic leukoencephalopathy. WES analyses were performed on trio, or greater, family groups. Diagnostic pathogenic variants were identified in 35% (25 of 71) of patients. Potentially pathogenic variants were identified in clinically relevant genes in a further 7% (5 of 71) of cases, giving a total yield of clinical diagnoses in 42% of individuals. These findings provide evidence that WES can substantially decrease the number of unresolved white matter cases. Ann Neurol 2016;79:1031-1037.

Glucocorticoid receptor (NR3C1) polymorphisms associate with obesity, muscle strength, and cortisol sensitivity. We examined associations among four NR3C1 polymorphisms and the muscle response to resistance training (RT). European-American adults (n = 602, 23.8±0.4yr) completed a 12 week unilateral arm RT program. Maximum voluntary contraction (MVC) assessed isometric strength (kg) and MRI assessed biceps size (cm2) pre- and post-resistance training. Subjects were genotyped for NR3C1 -2722G>A, -1887G>A, -1017T>C, and +363A>G. Men carrying the -2722G allele gained less relative MVC (17.3±1.2vs33.5±6.1%) (p = 0.010) than AA homozygotes; men with -1887GG gained greater relative MVC than A allele carriers (19.6±1.4vs13.2±2.3%) (p = 0.016). Women carrying the -1017T allele gained greater relative size (18.7±0.5vs16.1±0.9%) (p = 0.016) than CC homozygotes. We found sex-specific NR3C1 associations with the muscle strength and size response to RT. Future studies should investigate whether these associations are partially explained by cortisol’s actions in muscle tissue as they interact with sex differences in cortisol production.

We describe a patient with failure to thrive, hepatomegaly, liver dysfunction, and elevation of multiple plasma lysosomal enzyme activities mimicking mucolipidosis II or III, in whom a diagnosis of hereditary fructose intolerance (HFI) was ultimately obtained. She presented before introduction of solid foods, given her consumption of a fructose-containing infant formula. We present the most extensive panel of lysosomal enzyme activities reported to date in a patient with HFI, and propose that multiple enzyme elevations in plasma, especially when in conjunction with a normal plasma α-mannosidase activity, should elicit a differential diagnosis of HFI. We also performed a review of the literature on the different etiologies of elevated lysosomal enzyme activities in serum or plasma. © 2016 Wiley Periodicals, Inc.