Reporting off-target effects of recombinant engineering using the pORTMAGE system.

pORTMAGE recombineering is a simple technique for incorporation of novel point mutations into bacterial genomes that eliminates off-target effects. Here we inserted point mutations into the cusS gene from Escherichia coli, then, using Illumina sequencing, report genetic variants in all mutant strains. Several off-site mutations were found at high frequency. Low frequency mutations also show high heterogeneity. This means that it is essential for studies to report all off-target effects and acknowledge the effect that this may have on resultant phenotypes.

Single-nuclei transcriptomics enable detection of somatic variants in patient brain tissue.

Somatic variants are a major cause of human disease, including neurological disorders like focal epilepsies, but can be challenging to study due to their mosaicism in bulk tissue biopsies. Coupling single-cell genotype and transcriptomic data has potential to provide insight into the role somatic variants play in disease etiology, such as by determining what cell types are affected or how the mutations affect gene expression. Here, we asked whether commonly used single-nucleus 3'- or 5'-RNA-sequencing assays can be used to derive single-nucleus genotype data for a priori known variants that are located near to either end of a transcript. To that end, we compared performance of commercially available single-nuclei 3'- and 5'- gene expression kits using resected brain samples from three pediatric patients with focal epilepsy. We quantified the ability to detect genetic variants in single-nucleus datasets depending on distance from the transcript end. Finally, we demonstrated the ability to identify affected cell types in a patient with a RHEB somatic variant causing an epilepsy-associated cortical malformation. Our results demonstrate that single-nuclei 3' or 5'-RNA-sequencing data can be used to identify known somatic variants in single-nuclei when they are expressed within proximity to a transcript end.

Impact of Remote Symptom Monitoring With Electronic Patient-Reported Outcomes on Hospitalization, Survival, and Cost in Community Oncology Practice: The Texas Two-Step Study.

PURPOSE: There is raising interest to implement electronic patient-reported outcomes (ePROs) for symptom monitoring to enhance the quality of cancer care. Step 1 of the Texas Two-Step Study demonstrated successful implementation of an ePRO system in >200 sites of service of a large community oncology practice. We now report step 2 of this study which evaluates the impact of ePROs on outcomes among patients enrolled in the Centers for Medicare & Medicaid Services' Oncology Care Model (OCM) program. METHODS: This observational study focused on patients with metastatic cancer enrolled in OCM at large community oncology practice located in Texas between July 2020 and December 2020. Patients who completed ≥1 survey via the ePRO tool were included in the study group and were propensity score matched with patients in a control group. Adverse events (AEs; hospitalizations, emergency department visits, deaths) and total cost of care were a priori study outcomes. Mann-Whitney U and chi-square tests compared continuous and categorical variables, respectively, with multivariable logistic regression for adjustment of covariates. RESULTS: Of 831 patients with metastatic cancer, 458 matched patients (229/group) were identified, with 52% male and a mean age of 74 years. Mean total AEs were lower in the study group compared with control (0.98 v 1.41; P = .007), with decreased hospitalizations (20% v 32.5%; P = .002), emergency visits (38.4% v 42.3%; P > .05), and deaths (11.8% v 16.6%; P > .05). Average number of hospitalizations was lower (0.28 v 0.52; P = .003) with reduced mean duration of hospitalizations (1.9 vs 3.2 d; P = .03). The total cost of care was reduced by an average of $1,146 per member per month. CONCLUSION: Symptom monitoring with ePROs improved quality and value of cancer care delivery by reducing hospitalizations, emergency visits, and deaths while lowering cost of care in a large oncology practice.

HIV-1 subtypes and drug resistance mutations among female sex workers varied in different cities and regions of the Democratic Republic of Congo.

BACKGROUND: Complex mosaic structures of HIV-1 were found in the Democratic Republic of Congo (DRC). Currently, there is limited information on the circulating HIV-1 strains, the distribution of these strains and antiretroviral (ART) resistant viruses in different regions of the country, and the HIV-1 strains harbored by the high-risk groups like female sex workers (FSW) reported to be the source of recombinant and ART resistant viruses. METHODS: Dried Blood Spots (DBS), collected from 325 infected FSWs in ten cities from 2012 DRC HIV/STI Integrated Biological and Behavioral Surveillance Survey, were tested for HIV-1 genotypes and antiretroviral resistance mutations. Regional segregation of HIV-1 clades was detected using phylogenetics. The significance for differences in HIV-1 subtype and drug resistance mutations were evaluated using Chi-square tests. RESULTS: There were 145 (env) and 93 (pol) sequences analyzed. Based on env sequences, the predominant subtype was A1 (44%), and recombinants as defined pol sequences comprised 35% of the total sample. Paired sequences of pol and env from DRC FSW revealed mosaic recombinant in 54% of the sequences. Distinct geographic distributions of different HIV-1 subtypes and recombinants were observed. Subtype A1 was prevalent (40%) in Goma located in the East and significantly higher than in Mbuji-Mayi (p<0.05) in the South-central region, or in Lubumbashi in the South. Antiretroviral resistance was detected in 21.5% of 93 pol sequences analyzed, with the M184I/V and K103N mutations that confer high-level resistance to NRTI and NNRTI, respectively, being the most frequent mutations. However, the K103N mutant viruses were found only in the East. CONCLUSION: HIV-1 variants found in DRC FSW reflect those reported to circulate in the general population from the corresponding geographical locations. HIV-1 mosaic genetics were readily detected in FSW. Importantly, ART resistance mutations to NNRTI and NRTI were common in the DRC sex workers.