De novo mutation rates at the single-mutation resolution in a human HBB gene-region associated with adaptation and genetic disease

While it is known that the mutation rate varies across the genome, previous estimates were based on averaging across various numbers of positions. Here we describe a method to measure the origination rates of target mutations at target base positions and apply it to a 6-bp region in the human hemoglobin subunit beta (HBB) gene and to the identical, paralogous hemoglobin subunit delta (HBD) region in sperm cells from both African and European donors. The HBB region of interest (ROI) includes the site of the hemoglobin S (HbS) mutation, which protects against malaria, is common in Africa and has served as a classic example of adaptation by random mutation and natural selection. We found a significant correspondence between de novo mutation rates and past observations of alleles in carriers, showing that mutation rates vary substantially in a mutation-specific manner that contributes to the site frequency spectrum. We also found that the overall point mutation rate is significantly higher in Africans than in Europeans in the HBB region studied. Finally, the rate of the 20A→T mutation, called the 'HbS mutation' when it appears in HBB, is significantly higher than expected from the genome-wide average for this mutation type. Nine instances were observed in the African HBB ROI, where it is of adaptive significance, representing at least three independent originations; no instances were observed elsewhere. Further studies will be needed to examine mutation rates at the single-mutation resolution across these and other loci and organisms and to uncover the molecular mechanisms responsible.

Clinical Features and Surgical Treatment of Synchronous Multiple Primary Lung Adenocarcinomas With Different EGFR Mutations

BackgroundWith the popularity of lung cancer screening and advances in imaging technology, more and more synchronous multiple primary lung adenocarcinomas (SMPLA) are being diagnosed clinically, however, the clinical characteristics and prognosis of SMPLA with different EGFR mutations remains unclear. We aimed to explore clinical features and surgical outcomes of these patients to aid in the diagnosis and treatment of SMPLA.MethodsMedical records of patients with different EGFR mutations who have been diagnosed as SMPLA and underwent surgical resection from March 2015 to December 2019 were retrospectively analyzed. Clinical characteristics, surgical outcomes, recurrence-free survival (RFS) and overall survival (OS) were investigated.ResultsA total of 70 patients (68.6% female and 77.1% non-somkers) were included. Total of 161 lesions in all patients, 84.4% were ground-glass opacity (GGO) lesions. EGFR mutations were detected in 108 lesions, most of which were L858R (35.4%) and 19Del (20.5%). The mutation rate of mixed GGO is significantly higher than that of pure GGO and solid nodules (SN); the mutation rate of invasive adenocarcinoma is significantly higher than that of other histology subtypes; the mutation rate of lesions >20 mm was significantly higher than that of ≤20 mm. However, there is no significant difference in the mutation rate of specific driver gene between different radiological features, pathological characteristics and sizes. After a median follow-up time of 29 months, the 3-year OS and RFS were 94.4% and 86.0%, respectively.ConclusionsA high discordance of EGFR mutations were identified between tumors in patients with SMPLA. Synchronous multiple lung adenocarcinomas with predominantly multiple GGO should be considered as SMPLA, and surgery may be aggressively performed for these patients due to a good prognosis.

The mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates

In the past decade, several studies have estimated the human per-generation germline mutation rate using large pedigrees. More recently, estimates for various non-human species have been published. However, methodological differences among studies in detecting germline mutations and estimating mutation rates make direct comparisons difficult. Here, we describe the many different steps involved in estimating pedigree-based mutation rates, including sampling, sequencing, mapping, variant calling, filtering, and how to appropriately account for false-positive and false-negative rates. For each step, we review the different methods and parameter choices that have been used in the recent literature. Additionally, we present the results from a 'Mutationathon', a competition organized among five research labs to compare germline mutation rate estimates for a single pedigree of rhesus macaques. We report almost a two-fold variation in the final estimated rate among groups using different post-alignment processing, calling, and filtering criteria and provide details into the sources of variation across studies. Though the difference among estimates is not statistically significant, this discrepancy emphasizes the need for standardized methods in mutation rate estimations and the difficulty in comparing rates from different studies. Finally, this work aims to provide guidelines for computational and statistical benchmarks for future studies interested in identifying germline mutations from pedigrees.

Efficacy of current treatments against hepatitis C virus

It is estimated that currently, in the world, approximately 3% of the population has chronic hepatitis, the hepatitis C virus is the etiological agent most related to the development of this pathology. The diversity of genotypes (7) and quasi-species of HCV, due to its high mutation rate, interferes with an effective humoral immunity. The aim of this work is precisely to evoke those usual drugs used in HCV therapy, as well as cutting-edge drugs. The goal of treatment is the eradication of HCV infection. One strategy offered by the WHO is to eradicate the virus in at-risk populations. Alternatives to the previously used treatment with interferon and ribavirin are shown in this paper; protease inhibitors and other targets have now been developed to make eradication of the virus more effective.

Spontaneous mutation rate estimates for the principal malaria vectors Anopheles coluzzii and Anopheles stephensi

Using high-depth whole genome sequencing of F0 mating pairs and multiple individual F1 offspring, we estimated the nuclear mutation rate per generation in the malaria vectors Anopheles coluzzii and Anopheles stephensi by detecting de novo genetic mutations. A purpose-built computer program was employed to filter actual mutations from a deep background of superficially similar artifacts resulting from read misalignment. Performance of filtering parameters was determined using software-simulated mutations, and the resulting estimate of false negative rate was used to correct final mutation rate estimates. Spontaneous mutation rates by base substitution were estimated at 1.00 × 10−9 (95% confidence interval, 2.06 × 10−10—2.91 × 10−9) and 1.36 × 10−9 (95% confidence interval, 4.42 × 10−10—3.18 × 10−9) per site per generation in A. coluzzii and A. stephensi respectively. Although similar studies have been performed on other insect species including dipterans, this is the first study to empirically measure mutation rates in the important genus Anopheles, and thus provides an estimate of µ that will be of utility for comparative evolutionary genomics, as well as for population genetic analysis of malaria vector mosquito species.

Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility

Due to genome segmentation, rotaviruses must co-package a set of eleven distinct genomic RNAs. The packaging is mediated by virus-encoded RNA chaperones, such as the rotavirus (RV) NSP2 protein. While the activities of distinct viral RNA chaperones are well studied on synthetic RNA substrates, little is known about their global effect on the entire viral transcriptome. Here we used Selective 2′-hydroxyl Acylation Analyzed by Primer Extension and Mutational Profiling (SHAPE-MaP) to systematically examine the secondary structure of the RV transcriptome composed of eleven distinct transcripts in the absence and presence of increasing concentrations of RV NSP2. Surprisingly, SHAPE-MaP data reveals that despite the well-documented helix-unwinding activity of NSP2 in vitro, its incubation with cognate RV transcripts does not induce a significant change in the SHAPE reactivities. However, a quantitative analysis of the per nucleotide mutation rate measured by mutational profiling, from which SHAPE reactivities are derived, reveals a global five-fold rate increase in the presence of molar excess of NSP2. We demonstrate that the standard normalization procedure used in deriving SHAPE reactivities from mutation rates can mask an important global effect of an RNA chaperone activity. Further analysis of the mutation rate in the context of structural classification reveals a larger effect on stems rather than loop elements. Together, these data provide the first experimentally derived secondary structure model of the RV transcriptome and reveal that NSP2 acts by globally increasing RNA backbone flexibility in a concentration-dependent manner, consistent with its promiscuous RNA-binding nature.

Identification of Breast Cancer Immune Subtypes by Analyzing Bulk Tumor and Single Cell Transcriptomes

Background: The histological and molecular classification of breast cancer (BC) is being used in the clinical management of this disease. However, subtyping of BC based on the tumor immune microenvironment (TIME) remains insufficiently explored, although such investigation may provide new insights into intratumor heterogeneity in BC and potential clinical implications for BC immunotherapy.Methods: Based on the enrichment scores of 28 immune cell types, we performed clustering analysis of transcriptomic data to identify immune-specific subtypes of BC using six different datasets, including five bulk tumor datasets and one single-cell dataset. We further analyzed the molecular and clinical features of these subtypes.Results: Consistently in the six datasets, we identified three BC subtypes: BC-ImH, BC-ImM, and BC-ImL, which had high, medium, and low immune signature scores, respectively. BC-ImH displayed a significantly better survival prognosis than BC-ImL. Triple-negative BC (TNBC) and human epidermal growth factor receptor-2-positive (HER2+) BC were likely to have the highest proportion in BC-ImH and the lowest proportion in BC-ImL. In contrast, hormone receptor-positive (HR+) BC had the highest proportion in BC-ImL and the lowest proportion in BC-ImH. Furthermore, BC-ImH had the highest tumor mutation burden (TMB) and predicted neoantigens, while BC-ImL had the highest somatic copy number alteration (SCNA) scores. It is consistent with that TMB and SCNA correlate positively and negatively with anti-tumor immune response, respectively. TP53 had the highest mutation rate in BC-ImH and the lowest mutation rate in BC-ImL, supporting that TP53 mutations promote anti-tumor immune response in BC. In contrast, PIK3CA displayed the highest mutation rate in BC-ImM, while GATA3 had the highest mutation rate in BC-ImL. Besides immune pathways, many oncogenic pathways were upregulated in BC-ImH, including ErbB, MAPK, VEGF, and Wnt signaling pathways; the activities of these pathways correlated positively with immune signature scores in BC.Conclusions: The tumors with the strong immune response (“hot” tumors) have better clinical outcomes than the tumors with the weak immune response (“cold” tumors) in BC. TNBC and HER2+ BC are more immunogenic, while HR + BC is less immunogenic. Certain HER2+ or HR + BC patients could be propitious to immunotherapy in addition to TNBC.

Genetic optimization for engine combustion system calibration: A case study of optimization performance sensitivity to algorithm search parameters

The use of genetic optimization algorithms (GOA) has been shown to significantly reduce the resource intensity of engine calibration, motivating investigation into the development of these methods. The objective of this work was to quantify the sensitivity of GOA performance to the algorithm search parameter values, in a case study of engine calibration. A GOA was used to calibrate four combustion system control parameters for a direct-injection gasoline engine at a single operating condition, with an optimization goal to minimize brake specific fuel consumption (BSFC) for a specified engine-out NOx concentration limit. The calibration process was repeated for two NOx limit values and a wide range of values for five GOA search parameters, including the number of genes, mutation rate, and convergence criteria. Results indicated GOA performance is very sensitive to algorithm search parameter values, with converged calibrations yielding BSFC values from 1 to 14% higher than the global minimum value, and the number of iterations required to converge ranging from 10 to 3,000. Broadly, GOA performance sensitivity was found to increase as the NOx limit was decreased from 4,500 to 1,000 ppm. GOA performance was the most sensitive to the number of genes and the gene mutation rate, whereas sensitivity to convergence criteria values was minimal. Identification of one set of algorithm search parameter values which universally maximized GOA performance was not possible as ideal values depended strongly on engine behavior, NOx limit, and the maximum level of error acceptable to the user.