High-fidelity, large-scale targeted profiling of microsatellites.

Microsatellites are highly mutable sequences that can serve as markers for relationships among individuals or cells within a population. The accuracy and resolution of reconstructing these relationships depends on the fidelity of microsatellite profiling and the number of microsatellites profiled. However, current methods for targeted profiling of microsatellites incur significant "stutter" artifacts that interfere with accurate genotyping, and sequencing costs preclude whole-genome microsatellite profiling of a large number of samples. We developed a novel method for accurate and cost-effective targeted profiling of a panel of more than 150,000 microsatellites per sample, along with a computational tool for designing large-scale microsatellite panels. Our method addresses the greatest challenge for microsatellite profiling-"stutter" artifacts-with a low-temperature hybridization capture that significantly reduces these artifacts. We also developed a computational tool for accurate genotyping of the resulting microsatellite sequencing data that uses an ensemble approach integrating three microsatellite genotyping tools, which we optimize by analysis of de novo microsatellite mutations in human trios. Altogether, our suite of experimental and computational tools enables high-fidelity, large-scale profiling of microsatellites, which may find utility in diverse applications such as lineage tracing, population genetics, ecology, and forensics.

Peer education as a strategy to promote vaccine acceptance: A randomized controlled trial within New York community healthcare practices.

BACKGROUND: Effective strategies are needed to improve vaccine acceptance. This study sought to determine if a peer-led vaccine education intervention embedded within community medical practices increases parental acceptance of pediatric pneumococcal conjugate vaccination. METHODS: From March 2022-July 2023, we conducted a randomized trial at three pediatric health practices in predominantly Hasidic Jewish neighborhoods in New York, where vaccine deferral is common. Parents of children up to 18 months due/overdue for routine pneumococcal vaccination were randomized (1:1) to receive routine care alone or routine care plus a peer educational intervention. Peer educators trained in motivational interviewing and vaccine science provided counseling at enrollment and follow-up telephone engagement in the intervention arm at day 30 and 60. Primary outcome was child's pneumococcal immunization status by allocation arm expressed as at least one dose received between enrollment and 90 days post-enrollment. RESULTS: 144 parent-child dyads were eligible for outcome analysis. Participants in the group receiving routine care along with peer-led vaccine counseling were significantly more likely to have their child receive at least 1 vaccine dose between enrollment and 90 days compared to the group who received routine care alone (28.4 % vs 12.9 %, risk ratio [RR] 2.21, confidence interval [CI] 1.09-4.49, p = 0.022). The effect of peer education was greatest in dyads with children less than 1 year old at enrollment (34 % vs 12.7 %, RR 2.67, CI (1.22-5.86), p = 0.009). CONCLUSIONS: Peer vaccine education can increase vaccine acceptance compared to routine care alone and may be particularly valuable in decreasing vaccination delays for younger infants. (Funded by EGL Charitable Foundation, ClinicalTrials.gov NCT05875779).

Demographic reporting and language exclusion in gynecologic oncology clinical trials.

BACKGROUND: Participation in clinical trials may help mitigate disparate cancer outcomes. Thus, ensuring equitable access to clinical trials is a major priority for national cancer organizations. OBJECTIVE: This study aimed to examine clinical trial eligibility criteria that may adversely affect the enrollment of underrepresented groups and assess the availability of demographic information in published gynecologic oncology studies. STUDY DESIGN: ClinicalTrials.gov was searched for gynecologic oncology studies conducted between 1997 and 2021. Each study's inclusion and exclusion criteria were reviewed to determine whether demographic factors were used for enrollment screening. For published studies, demographic variables that were reported were identified. The expected clinical trial enrollment based on disease incidence and mortality was compared with the observed trial enrollment based on race. RESULTS: There were 1597 gynecologic oncology studies: 883 (55%) from ovarian cancer studies, 336 (21%) from cervical cancer studies, 262 (17%) from uterine cancer studies, and 116 (7%) from multisite gynecologic oncology studies. Of the 581 published studies, 554 (95%) reported age, 363 (63%) reported race, and 171 (29%) reported ethnicities. Cervical cancer studies were most likely to report demographic information, including race (P=.026) and ethnicity (P<.001). During the study period, 189 studies (12%) excluded patients based on the language spoken. Industry-sponsored trials (odds ratio, 0.07; 95% confidence interval, 0.02-0.30) and organization-sponsored trials (odds ratio, 0.40; 95% confidence interval, 0.22-0.73) were less likely to exclude patients because of language than investigator-initiated trials. A minority of patients (37%) in cervical cancer trials were of White race, compared with 85% of patients in uterine cancer trials and 82% of patients in ovarian cancer trials. CONCLUSION: Over the last 3 decades, 1 in 10 gynecologic oncology trials excluded patients because of language. Race and ethnicity were reported in more than half of the available studies. Initiatives to increase transparency in recruiting underrepresented patients and reporting demographic data are urgently needed.

Serial enrichment of heteroduplex DNA using a MutS-magnetic bead system.

Numerous applications in molecular biology and genomics require characterization of mutant DNA molecules present at low levels within a larger sample of non-mutant DNA. This is often achieved either by selectively amplifying mutant DNA, or by sequencing all the DNA followed by computational identification of the mutant DNA. However, selective amplification is challenging for insertions and deletions (indels). Additionally, sequencing all the DNA in a sample may not be cost effective when only the presence of a mutation needs to be ascertained rather than its allelic fraction. The MutS protein evolved to detect DNA heteroduplexes in which the two DNA strands are mismatched. Prior methods have utilized MutS to enrich mutant DNA by hybridizing mutant to non-mutant DNA to create heteroduplexes. However, the purity of heteroduplex DNA these methods achieve is limited because they can only feasibly perform one or two enrichment cycles. We developed a MutS-magnetic bead system that enables rapid serial enrichment cycles. With six cycles, we achieve complete purification of heteroduplex indel DNA originally present at a 5% fraction and over 40-fold enrichment of heteroduplex DNA originally present at a 1% fraction. This system may enable novel approaches for enriching mutant DNA for targeted sequencing.

Stability of N18C6H6: triangular versus hexagonal structure.

Large nitrogen cage molecules Nx have been previously shown to prefer elongated, cylindrical structures with triangular caps versus more spherical structures composed entirely of pentagons and hexagons. It was argued that this preference derived from the electronic properties of the nitrogen atoms, including the lone pairs. In the current study, the same structural comparison is carried out, with the substitution of C-H-bonding groups for six of the nitrogens. Various substitution patterns on the cylindrical (triangular) and spherical (hexagonal) frameworks are examined. Isomers of N18C6H6 are studied by theoretical calculations to determine the relative stability of triangular versus hexagonal structures, as well as the stability effects of the substitution patterns on each framework. Hartree-Fock theory, density functional theory (PBE1PBE), and perturbation theory (MP2) are employed, in conjunction with the correlation-consistent basis sets of Dunning. Stability trends within each class of molecules and between the two classes of molecules are calculated and discussed.

Stability of N10C10H10 and N12C12H12 Cages and the Effects of Endohedral Atoms and Ions.

Cages of carbon and nitrogen have been studied by theoretical calculations to determine the potential of these molecules as high-energy density materials. Following previous theoretical studies of high-energy N6C6H6 and N8C8H8 cages, a series of calculations on several isomers of the larger N10C10H10 and N12C12H12 is carried out to determine relative stability among a variety of three-coordinate cage isomers with four-membered, five-membered, and/or six-membered rings. Additionally, calculations are carried out on the same molecules with atoms or ions inside the cage. Calculations are carried out with the B3LYP and PBE1PBE density functional (DFT) methods, with MP2 and MP4 calculations carried out to evaluate the accuracy of the DFT results. Trends in stability with respect to cage geometry and arrangements of atoms are calculated and discussed. Stability effects caused by the endohedral atoms and ions are also calculated and discussed.

Isomer stability and bond-breaking energies of N8C8H8 cages.

Molecules consisting entirely or predominantly of nitrogen have been extensively investigated for their potential as high-energy density materials (HEDM). Such molecules react to produce N2 and large amounts of energy, but many such molecules are too unstable for practical applications. In the present study, cage isomers of N8C8H8 are studied using theoretical calculations to determine the structural features that lead to the most stable cages and determine the energetics of dissociation for the various isomers. The isomers are evaluated for thermodynamic (isomer vs isomer) stability and kinetic (with respect to dissociation) stability. Density functional theory (B3LYP), perturbation theory (MP2), and coupled-cluster theory [CCSD(T)] are employed, in conjunction with the cc-pVDZ basis set of Dunning. Trends in isomer stability and dissociation energies are calculated and discussed.

Stability of high-energy N14H4(2+) ion and the effects of carbon and halogen substitution.

Previous studies of oxygen addition into an N12 cage framework revealed the possibility of stable high-energy density materials (HEDM) resulting from such additions. In the current study, nitrogen addition into N12 is studied as a means of generating stable HEDM. Nitrogen addition into N12 is shown to yield an N14H4(2+) ion, which is examined by theoretical calculations to determine its stability with respect to dissociation. Other variations on this ion are generated by substituting carbon for nitrogen and/or halogens for hydrogen. The cage structures will be compared with respect to stability, and factors that enhance stability will be discussed.