Genomic Medicine-Progress, Pitfalls, and Promise.

In the wake of the Human Genome Project (HGP), strong expectations were set for the timeline and impact of genomics on medicine-an anticipated transformation in the diagnosis, treatment, and prevention of disease. In this Perspective, we take stock of the nascent field of genomic medicine. In what areas, if any, is genomics delivering on this promise, or is the path to success clear? Where are we falling short, and why? What have been the unanticipated developments? Overall, we argue that the optimism surrounding the transformational potential of genomics on medicine remains justified, albeit with a considerably different form and timescale than originally projected. We also argue that the field needs to pivot back to basics, as understanding the entirety of the genotype-to-phenotype equation is a likely prerequisite for delivering on the full potential of the human genome to advance the human condition.

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.

Nucleosome positioning varies between cell types. By deep sequencing cell-free DNA (cfDNA), isolated from circulating blood plasma, we generated maps of genome-wide in vivo nucleosome occupancy and found that short cfDNA fragments harbor footprints of transcription factors. The cfDNA nucleosome occupancies correlate well with the nuclear architecture, gene structure, and expression observed in cells, suggesting that they could inform the cell type of origin. Nucleosome spacing inferred from cfDNA in healthy individuals correlates most strongly with epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how nucleosome footprints can be used to infer cell types contributing to cfDNA in pathological states such as cancer. Since this strategy does not rely on genetic differences to distinguish between contributing tissues, it may enable the noninvasive monitoring of a much broader set of clinical conditions than currently possible.

Heteroplasmic pathogenic m.12315G>A variant in MT-TL2 presenting with MELAS syndrome and depletion of nitric oxide donors.

The MT-TL2 m.12315G>A pathogenic variant has previously been reported in five individuals with mild clinical phenotypes. Herein we report the case of a 5-year-old child with heteroplasmy for this variant who developed neurological regression and stroke-like episodes similar to those observed in mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS). Biochemical evaluation revealed depletion of arginine on plasma amino acid analysis and low z-scores for citrulline on untargeted plasma metabolomics analysis. These findings suggested that decreased availability of nitric oxide may have contributed to the stroke-like episodes. The use of intravenous arginine during stroke-like episodes and daily enteral L-citrulline supplementation normalized her biochemical values of arginine and citrulline. Untargeted plasma metabolomics showed the absence of nicotinamide and 1-methylnicotinamide, and plasma total glutathione levels were low; thus, nicotinamide riboside and N-acetylcysteine therapies were initiated. This report expands the phenotype associated with the rare mitochondrial variant MT-TL2 m.12315G>A to include neurological regression and a MELAS-like phenotype. Individuals with this variant should undergo in-depth biochemical analysis to include untargeted plasma metabolomics, plasma amino acids, and glutathione levels to help guide a targeted approach to treatment.

Observation of Gapped Topological Surface States and Isolated Surface Resonances in PdTe2 Ultrathin Films.

The superconductor PdTe2 is known to host bulk Dirac bands and topological surface states. The coexistence of superconductivity and topological surface states makes PdTe2 a promising platform for exploring topological superconductivity and Majorana bound states. In this work, we report the spectroscopic characterization of ultrathin PdTe2 films with thickness down to three monolayers (ML). In the 3 ML PdTe2 film, we observed spin-polarized surface resonance states, which are isolated from the bulk bands due to the quantum size effects. In addition, the hybridization of surface states on opposite faces leads to a thickness-dependent gap in the topological surface Dirac bands. Our photoemission results show clearly that the size of the hybridization gap increases as the film thickness is reduced. The observation of isolated surface resonances and gapped topological surface states sheds light on the applications of PdTe2 quantum films in spintronics and topological quantum computation.

Clinical genome sequencing: Three years' experience at a tertiary children's hospital.

PURPOSE: Genome sequencing (GS) may shorten the diagnostic odyssey for patients, but clinical experience with this assay in nonresearch settings remains limited. Texas Children's Hospital began offering GS as a clinical test to admitted patients in 2020, providing an opportunity to study GS utilization, possibilities for test optimization, and testing outcomes. METHODS: We retrospectively reviewed GS orders for admitted patients for a nearly 3-year period from March 2020 through December 2022. We gathered anonymized clinical data from the electronic health record to answer the study questions. RESULTS: The diagnostic yield over 97 admitted patients was 35%. The majority of GS clinical indications were neurologic or metabolic (61%) and most patients were in intensive care (58%). Tests were often characterized as candidates for intervention/improvement (56%), frequently because of redundancy with prior testing. Patients receiving GS without prior exome sequencing (ES) had higher diagnostic rates (45%) than the cohort as a whole. In 2 cases, GS revealed a molecular diagnosis that is unlikely to be detected by ES. CONCLUSION: The performance of GS in clinical settings likely justifies its use as a first-line diagnostic test, but the incremental benefit for patients with prior ES may be limited.

Postdischarge thromboembolic outcomes and mortality of hospitalized patients with COVID-19: the CORE-19 registry.

Thromboembolic events, including venous thromboembolism (VTE) and arterial thromboembolism (ATE), and mortality from subclinical thrombotic events occur frequently in coronavirus disease 2019 (COVID-19) inpatients. Whether the risk extends postdischarge has been controversial. Our prospective registry included consecutive patients with COVID-19 hospitalized within our multihospital system from 1 March to 31 May 2020. We captured demographics, comorbidities, laboratory parameters, medications, postdischarge thromboprophylaxis, and 90-day outcomes. Data from electronic health records, health informatics exchange, radiology database, and telephonic follow-up were merged. Primary outcome was a composite of adjudicated VTE, ATE, and all-cause mortality (ACM). Principal safety outcome was major bleeding (MB). Among 4906 patients (53.7% male), mean age was 61.7 years. Comorbidities included hypertension (38.6%), diabetes (25.1%), obesity (18.9%), and cancer history (13.1%). Postdischarge thromboprophylaxis was prescribed in 13.2%. VTE rate was 1.55%; ATE, 1.71%; ΑCM, 4.83%; and MB, 1.73%. Composite primary outcome rate was 7.13% and significantly associated with advanced age (odds ratio [OR], 3.66; 95% CI, 2.84-4.71), prior VTE (OR, 2.99; 95% CI, 2.00-4.47), intensive care unit (ICU) stay (OR, 2.22; 95% CI, 1.78-2.93), chronic kidney disease (CKD; OR, 2.10; 95% CI, 1.47-3.0), peripheral arterial disease (OR, 2.04; 95% CI, 1.10-3.80), carotid occlusive disease (OR, 2.02; 95% CI, 1.30-3.14), IMPROVE-DD VTE score ≥4 (OR, 1.51; 95% CI, 1.06-2.14), and coronary artery disease (OR, 1.50; 95% CI, 1.04-2.17). Postdischarge anticoagulation was significantly associated with reduction in primary outcome (OR, 0.54; 95% CI, 0.47-0.81). Postdischarge VTE, ATE, and ACM occurred frequently after COVID-19 hospitalization. Advanced age, cardiovascular risk factors, CKD, IMPROVE-DD VTE score ≥4, and ICU stay increased risk. Postdischarge anticoagulation reduced risk by 46%.

Arthropod Bites and Stings.

Arthropods, including insects and arachnids, significantly affect humans as vectors for infectious diseases. Arthropod bites and stings commonly cause minor, usually self-limited reactions; however, some species are associated with more severe complications. Spider bites are rarely life-threatening. There are two medically relevant spiders in the United States. Widow spider (Latrodectus) envenomation can cause muscle spasm and severe pain that should be treated with analgesics and benzodiazepines. Antivenom is not widely available in the United States but may be considered for severe, refractory cases. Recluse spider (Loxosceles) bites are often overdiagnosed, should be treated supportively, and only rarely cause skin necrosis. Centruroides scorpions are the only medically relevant genus in the United States. Envenomation causes neuromuscular and autonomic dysfunction, which should be treated with analgesics, benzodiazepines, supportive care, and, in severe cases, antivenom. Hymenoptera, specifically bees, wasps, hornets, and fire ants, account for the most arthropod-related deaths in humans, most commonly by severe allergic reactions to envenomation. In severe cases, patients are treated with analgesia, local wound care, and systemic glucocorticoids. Diptera include flies and mosquitoes. The direct effects of their bites are usually minor and treated symptomatically; however, they are vectors for numerous infectious diseases. Arthropod bite and sting prevention strategies include avoiding high-risk areas, covering exposed skin, and wearing permethrin-impregnated clothing. N,N-diethyl- m-toluamide (DEET) 20% to 50% is the most studied and widely recommended insect repellant.

Risk Stratification and Pain Outcomes Following Revision Total Hip Arthroplasty for Adverse Local Tissue Reactions.

BACKGROUND: Revision total hip arthroplasty (THA) for adverse local tissue reactions (ALTRs) secondary to head-neck taper corrosion is associated with a high complication rate. Diagnosis of ALTR is based on risk stratification using the patient's history and examination, implant risk, serum metal ion levels, and imaging. The purpose of this study was to determine if stratification using similar risk factors is predictive of outcomes following revision THA for metal-on-polyethylene (MoP) ALTR. METHODS: We performed a retrospective review on 141 patients revised for ALTR due to head-neck taper corrosion. Pain outcomes following surgery were analyzed using a generalized linear mixed model. Complications were defined as instability/dislocation, infection, fracture, nerve palsy, leg-length discrepancy, or reoperation. RESULTS: The overall complication rate was 17.7%. The odds of having pain decreased by 44% after revision surgery (Odds Ratio = 0.56, 95% Confidence Interval: 0.324 to 0.952). There was no significant difference in instability/dislocation based on either increased or decreased head-neck offset (P = .67) or magnetic resonance imaging findings of abductor loss, effusion size, and degree of ALTR (P = .73). Increased serum cobalt (P = .31) and chromium (P = .08) levels did not predict complications; however, a decreased cobalt-chromium ratio was associated with postoperative complications (2.8 versus 3.5; P = .002). CONCLUSION: These findings are the first to suggest that patients who have ALTR after MoP THA undergoing revision surgery demonstrated major pain relief. Increasing femoral head offset did not change rates of instability/dislocation. In clinical scenarios where preoperative cobalt-chromium femoral head offsets were greater than available ceramic head offsets, a mandatory decrease in femoral head offset did not increase rates of instability/dislocation.

Evaluating Initial Empiric Therapy for Neutropenic Fever in Vancomycin-Resistant Enterococcus-Colonized Patients.

OBJECTIVES: Vancomycin-resistant enterococcus infections impact mortality in oncology patients. Given the low rate of vancomycin-resistant enterococcus bacteremia, low virulence of vancomycin-resistant enterococcus, and advent of rapid diagnostic systems, vancomycin-resistant enterococcus-directed empiric therapy in vancomycin-resistant enterococcus-colonized patients with neutropenic fever may be unnecessary, promoting increased antimicrobial resistance, drug-related toxicity, and cost. METHODS: Vancomycin-resistant enterococcus-colonized adults admitted for hematopoietic stem cell transplantation or induction therapy for acute leukemia/myeloid sarcoma with neutropenic fever were stratified by vancomycin-resistant enterococcus bacteremia development and empiric vancomycin-resistant enterococcus-directed antimicrobial strategy for first neutropenic fever (Empiric Therapy vs. non-Empiric Therapy). Primary endpoints included vancomycin-resistant enterococcus-related, in-hospital, and 100-day mortality rates. Secondary outcomes included vancomycin-resistant enterococcus bacteremia incidence for first neutropenic fever and the entire hospitalization, length of stay, Clostridioides difficile infection rate, and duration and cost of vancomycin-resistant enterococcus-directed therapy. RESULTS: During first neutropenic fever, 3 of 70 eligible patients (4%) developed vancomycin-resistant enterococcus bacteremia. Although all 3 (100%) were non-Empiric Therapy, no mortality (0%) occurred. Of 67 patients not developing vancomycin-resistant enterococcus bacteremia, 42 (63%) received Empiric Therapy and 25 (37%) non-Empiric Therapy. Empiric Therapy had significantly greater median duration (3 days vs. 0 days; P<.001) and cost ($1604 vs. $0; P<.001) of vancomycin-resistant enterococcus-directed therapy but demonstrated no significant differences in clinical outcomes. CONCLUSION: Available data suggest Empiric Therapy may offer no clinical benefit to this population, regardless of whether vancomycin-resistant enterococcus is identified in blood culture or no pathogen is found. Such an approach may only expose the majority of patients to unnecessary vancomycin-resistant enterococcus-directed therapy and drug-related toxicities while increasing institutional drug and monitoring costs. Even in the few patients developing vancomycin-resistant enterococcus bacteremia, waiting until the organism is identified in culture to start directed therapy likely makes no difference in mortality. This lack of benefit warrants consideration to potentially omit empiric vancomycin-resistant enterococcus-directed therapy in first neutropenic fever in many of these patients.

Haplotype-resolved genome sequencing: experimental methods and applications.

Human genomes are diploid and, for their complete description and interpretation, it is necessary not only to discover the variation they contain but also to arrange it onto chromosomal haplotypes. Although whole-genome sequencing is becoming increasingly routine, nearly all such individual genomes are mostly unresolved with respect to haplotype, particularly for rare alleles, which remain poorly resolved by inferential methods. Here, we review emerging technologies for experimentally resolving (that is, 'phasing') haplotypes across individual whole-genome sequences. We also discuss computational methods relevant to their implementation, metrics for assessing their accuracy and completeness, and the relevance of haplotype information to applications of genome sequencing in research and clinical medicine.

Antimony oxide nanostructures in the monolayer limit: self-assembly of van der Waals-bonded molecular building blocks.

Antimony oxide nanostructures have been identified as candidates for a range of electronic and optoelectronic applications. Here we demonstrate the growth of 2-dimensional antimony oxide nanostructures on various substrates, including highly oriented pyrolytic graphite (HOPG), MoS2 and α-Bi(110) nanoislands. Using scanning tunneling microscopy (STM) we show that the nanostructures formed are exclusively highly crystalline α-Sb2O3(111) monolayers with a lattice constant of 796 pm ± 7 pm. The nanostructures are triangular with lateral dimensions of up to ∼30 nm. Even though elemental antimony nanostructures are grown simultaneously mixed phases are not observed and both materials exhibit their own distinct growth modes. Moiré patterns are also observed and simulated, allowing confirmation of the atomic unit cell and an understanding of the orientation of the Sb2O3 structures with respect to the supporting materials. As in the bulk, the Sb2O3 nanostructures are formed from Sb4O6 molecules that are weakly interacting through van der Waals forces. This allows physical modification of the nanostructures with the STM tip. Scanning tunnelling spectroscopy reveals a wide band gap of at least 3.5 eV. Finally, we show that possible alternative structures that have unit cells comparable to those observed can be excluded based on our DFT calculations. The considered structures are a 2 × 2 reconstruction of ß-Sb with one vacancy per unit cell and a van der Waals solid composed of Sb4 clusters. Previous reports have predominantly demonstrated Sb2O3 structures with much larger thicknesses.

Comparison of Asymptomatic and Symptomatic Adverse Local Tissue Reaction in Patients With Head-Neck Taper Corrosion.

BACKGROUND: Diagnosis of adverse local tissue reaction (ALTR) in metal-on-polyethylene (MoP) total hip arthroplasty (THA) secondary to head-neck taper corrosion is challenging. The purpose of this study is to compare differences between asymptomatic and symptomatic ALTR in an observational cohort, including presentation, metal ion differences, and metal artifact reduction sequence (MARS) magnetic resonance imaging (MRI) findings. METHODS: We performed a retrospective review of an observational cohort of 492 MoP THA patients at increased risk of developing ALTR. Ninety-four patients underwent revision arthroplasty for ALTR. Patients were stratified into symptomatic and asymptomatic ALTR groups. Presentation, metal ion levels, and imaging findings were compared. RESULTS: For patients with confirmed ALTR, 41% were asymptomatic. There was a statistically significant difference in the serum chromium levels between symptomatic and asymptomatic ALTR patients (2.2 µg/L vs 3.1 µg/L, P = .05). There was no statistically significant difference between the serum cobalt levels or MRI findings in these 2 groups. We observed that extracapsular disease associated with ALTR could be misinterpreted as trochanteric bursitis. CONCLUSION: Almost half of the MoP THA ALTR cases identified were asymptomatic. Cobalt levels could not differentiate between symptomatic and asymptomatic pseudotumor formation. Symptomatic and asymptomatic MoP ALTRs have similar MARS MRI characteristics. Our findings suggest that it is essential to risk stratify patients who could potentially have ALTR based on implant type, symptoms, ion levels, and MARS MRI.

Copy-number variation and false positive prenatal aneuploidy screening results.

Investigations of noninvasive prenatal screening for aneuploidy by analysis of circulating cell-free DNA (cfDNA) have shown high sensitivity and specificity in both high-risk and low-risk cohorts. However, the overall low incidence of aneuploidy limits the positive predictive value of these tests. Currently, the causes of false positive results are poorly understood. We investigated four pregnancies with discordant prenatal test results and found in two cases that maternal duplications on chromosome 18 were the likely cause of the discordant results. Modeling based on population-level copy-number variation supports the possibility that some false positive results of noninvasive prenatal screening may be attributable to large maternal copy-number variants. (Funded by the National Institutes of Health and others.).

Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains.

Large-scale bacterial genome sequencing efforts to date have provided limited information on the most prevalent category of disease: sporadically acquired infections caused by common pathogenic bacteria. Here, we performed whole-genome sequencing and de novo assembly of 312 blood- or urine-derived isolates of extraintestinal pathogenic (ExPEC) Escherichia coli, a common agent of sepsis and community-acquired urinary tract infections, obtained during the course of routine clinical care at a single institution. We find that ExPEC E. coli are highly genomically heterogeneous, consistent with pan-genome analyses encompassing the larger species. Investigation of differential virulence factor content and antibiotic resistance phenotypes reveals markedly different profiles among lineages and among strains infecting different body sites. We use high-resolution molecular epidemiology to explore the dynamics of infections at the level of individual patients, including identification of possible person-to-person transmission. Notably, a limited number of discrete lineages caused the majority of bloodstream infections, including one subclone (ST131-H30) responsible for 28% of bacteremic E. coli infections over a 3-yr period. We additionally use a microbial genome-wide-association study (GWAS) approach to identify individual genes responsible for antibiotic resistance, successfully recovering known genes but notably not identifying any novel factors. We anticipate that in the near future, whole-genome sequencing of microorganisms associated with clinical disease will become routine. Our study reveals what kind of information can be obtained from sequencing clinical isolates on a large scale, even well-characterized organisms such as E. coli, and provides insight into how this information might be utilized in a healthcare setting.

Acute Appendicitis: Efficient Diagnosis and Management.

Appendicitis is one of the most common causes of acute abdominal pain in adults and children, with a lifetime risk of 8.6% in males and 6.7% in females. It is the most common nonobstetric surgical emergency during pregnancy. Findings from the history, physical examination, and laboratory studies aid in the diagnosis of acute appendicitis. Right lower quadrant pain, abdominal rigidity, and periumbilical pain radiating to the right lower quadrant are the best signs for ruling in acute appendicitis in adults. Absent or decreased bowel sounds, a positive psoas sign, a positive obturator sign, and a positive Rovsing sign are most reliable for ruling in acute appendicitis in children. The Alvarado score, Pediatric Appendicitis Score, and Appendicitis Inflammatory Response score incorporate common clinical and laboratory findings to stratify patients as low, moderate, or high risk and can help in making a timely diagnosis. Recommended first-line imaging consists of point-of-care or formal ultrasonography. Appendectomy via open laparotomy or laparoscopy is the standard treatment for acute appendicitis. However, intravenous antibiotics may be considered first-line therapy in selected patients. Pain control with opioids, nonsteroidal anti-inflammatory drugs, and acetaminophen should be a priority and does not result in delayed or unnecessary intervention. Perforation can lead to sepsis and occurs in 17% to 32% of patients with acute appendicitis. Prolonged duration of symptoms before surgical intervention raises the risk. In moderate- to high-risk patients, surgical consultation should be accomplished quickly to reduce morbidity and mortality resulting from perforation.

Genetic patterns across an invasion's history: a test of change versus stasis for the Eurasian round goby in North America.

Biological invasions comprise accidental evolutionary experiments, whose genetic compositions underlie relative success, spread and persistence in new habitats. However, little is known about whether, or how, their population genetic patterns change temporally and/or spatially across the invasion's history. Theory predicts that most would undergo founder effect, exhibit low genetic divergence across the new range and gain variation over time via new arriving propagules. To test these predictions, we analyse population genetic diversity and divergence patterns of the Eurasian round goby Neogobius melanostomus across the two decades of its North American invasion in the Laurentian Great Lakes, comparing results from 13 nuclear DNA microsatellite loci and mitochondrial DNA cytochrome b sequences. We test whether 'genetic stasis', 'genetic replacement' and/or 'genetic supplement' scenarios have occurred at the invasion's core and expansion sites, in comparison with its primary native source population in the Dnieper River, Black Sea. Results reveal pronounced genetic divergence across the exotic range, with population areas remaining genetically distinct and statistically consistent across two decades, supporting 'genetic stasis' and 'founder takes most'. The original genotypes continue to predominate, whose high population growth likely outpaced the relative success of later arrivals. The original invasion core has stayed the most similar to the native source. Secondary expansion sites indicate slight allelic composition convergence towards the core population over time, attributable to some early 'genetic supplementation'. The geographic and temporal coverage of this investigation offers a rare opportunity to discern population dynamics over time and space in context of invasion genetic theory vs. reality.

Serotonin Syndrome Complicating Treatment of Ifosfamide Neurotoxicity With Methylene Blue.

Methylene blue is a widely used treatment for ifosfamide neurotoxicity. We present a case of severe encephalopathy complicating ifosfamide-based therapy for recurrent retroperitoneal leiomyosarcoma. After treatment with methylene blue, the patient experienced clinical decompensation and was diagnosed with serotonin syndrome based on a constellation of clinical findings. Withdrawal of methylene blue and other serotonergic medications led to clinical stabilization and ultimately neurological recovery. Our case highlights the challenge of diagnosing serotonin syndrome in the face of preexisting ifosfamide neurotoxicity, as there is significant clinical overlap between these 2 syndromes. Practitioners must remain vigilant of this potential life-threatening complication in this vulnerable population.

Successful management of Mycobacterium haemophilum lower extremity cutaneous infection in a matched-unrelated donor stem cell transplant recipient.

Nontuberculous mycobacterial infections can often occur in individuals with adequate immune function. Such infections typically have cutaneous involvement and are caused by rapidly growing mycobacterium. Other nontuberculous mycobacteria species, like Mycobacterium haemophilum, almost always present as opportunistic infections occurring in severely immunocompromised hosts. Here, we present a complicated and protracted course of diagnosing M. haemophilum lower extremity cutaneous infection in a matched-unrelated donor stem cell transplant recipient.

Vancomycin Infiltrate-Induced Dermatitis Mimicking Bullous Cellulitis.

Extravasation of medications can manifest as tenderness, pain, tissue necrosis, and thrombophlebitis and lead to infection and severe long-term complications. Risk factors for leakage of medications include mechanical and pharmacologic mechanisms such as cannulation technique, vasoconstriction, and cytotoxicity. Well-known vesicants like anthracyclines, vinca alkaloids, and vasopressors are usually administered with proper caution. Often overlooked are many antimicrobial agents, which typically act via differences in osmolality and pH. Vancomycin harms the vascular wall by the latter (pH 2.5-4.5). Although similar in appearance to vancomycin hypersensitivity reactions (eg, linear immunoglobulin A bullous dermatosis), we present a patient whose dermatitis and subsequent cellulitis likely originated due to extravasation of the drug from the peripheral intravenous catheter. The visible dermatitis mimicked bullous cellulitis from toxin-producing Staphylococcus aureus, Group A Streptococcus, and gram-negative rods or anaerobes in the setting of neutropenia. Our case illustrates the importance of getting an appropriate history and recognizing non-infectious causes of rashes that mimic chronic infections.