Frequency Of Deleterious Mutations Research Articles

Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding.

Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little is known about the prevalence of such mutations and their effects on phenotypic traits in the context of modern crop breeding. To address this, we examined the number and frequency of deleterious mutations in 350 elite maize inbred lines developed over the past few decades in China and the United States. Our findings reveal an accumulation of weakly deleterious mutations and a decrease in strongly deleterious mutations, indicating the dominant effects of genetic drift and purifying selection for the two types of mutations, respectively. We also discovered that slightly deleterious mutations, when at lower frequencies, were more likely to be heterozygous in the developed hybrids. This is consistent with complementation as a potential explanation for heterosis. Subsequently, we found that deleterious mutations accounted for more of the variation in phenotypic traits than nondeleterious mutations with matched minor allele frequencies, especially for traits related to leaf angle and flowering time. Moreover, we detected fewer deleterious mutations in the promoter and gene body regions of differentially expressed genes across breeding eras than in nondifferentially expressed genes. Overall, our results provide a comprehensive assessment of the prevalence and impact of deleterious mutations in modern maize breeding and establish a useful baseline for future maize improvement efforts.

Molecular predictors and immunomodulatory role of dual checkpoint inhibitor blockade using ipilimumab/nivolumab in patients with extensive stage small cell lung cancer.

8597 Background: Small cell lung cancer (SCLC) is an aggressive neuroendocrine carcinoma with poor prognosis. In extensive stage patients, frontline treatment with chemoimmunotherapy shows modest clinical benefit. However, the biological impact of immunotherapy in SCLC is poorly understood with no clear predictive biomarkers to guide patient selection in this setting. Methods: We collected paired baseline (pre-treatment), on-treatment (week 4), and progression biopsies from patients with relapsed advanced-stage SCLC treated with combination nivolumab (nivo) and ipilimumab (ipi) in a single-arm, phase 2 clinical trial (NCT03670056). Nivo 1 mg/kg and ipi 3 mg/kg were administered every 3 weeks for 4 cycles, followed by nivo maintenance until progressive disease (PD) by RECIST 1.1 or treatment-limiting toxicity. Paired pre/on-treatment samples were available from 16/22 patients, as well as 3 biopsies at progression. The tumor samples were studied using whole exome DNA sequencing (including germline DNA) and RNA-sequencing coupled to Ocean Genomics TxomeAI data analysis pipeline. Results: 6/11 evaluable patients had PD; 5 patients showed clinical activity of treatment (3 with stable disease, 2 with partial response). The frequency of deleterious mutations in TP53 and RB1 was 91% and 64%, respectively. Mutations in HLA-A were more common in baseline samples from patients with PD than those with clinical activity. New TP53 and PLEC mutations were found 4 of 6 patients with PD in week 4 samples vs baseline. The baseline tumor mutational burden was not associated with treatment sensitivity and prominently increased in week 4 biopsies of PD patients. All four molecular SCLC transcriptomic subtypes based on the expression of ASCL1, NEUROD1, and POU2F3 were present in the trial with SCLC-A being the most common (9/16 cases). All patients with clinical activity to ipi/nivo were of SCLC-A subtype. 2/16 of cases showed a different molecular subtype after 4 weeks of treatment: one case with SCLC-N switched to SCLC-A and another case converted from SCLC-A to SCLC-N. Comparison of baseline and on-treatment samples showed upregulation of transcripts associated with T-cell activation and PD-1 signaling. In the 3 biopsies at progression, transcriptomic changes included reduction of neutrophil degranulation, type 1/2 interferon and signatures, as well as down-regulation of β-2 microglobulin, while cell cycle and mitotic prophase pathways were overexpressed. Conclusions: Dual checkpoint blockade using nivo/ipi has a prominent immunomodulatory role in extensive stage SCLC characterized by increased local adaptive immune responses, reduced HLA class-I antigen presentation and change in the molecular subtype in a subset of cases. We identified genomic features associated with treatment sensitivity/resistance. Clinical trial information: NCT03670056 .

Genomic and environmental influences on resilience in a cold-water fish near the edge of its range.

Small, isolated populations present a challenge for conservation. The dueling effects of selection and drift in a limited pool of genetic diversity make the responses of small populations to environmental perturbations erratic and difficult to predict. This is particularly true at the edge of a species range, where populations often persist at the limits of their environmental tolerances. Populations of cisco, Coregonus artedi, in inland lakes have experienced numerous extirpations along the southern edge of their range in recent decades, which are thought to result from environmental degradation and loss of cold, well‐oxygenated habitat as lakes warm. Yet, cisco extirpations do not show a clear latitudinal pattern, suggesting that local environmental factors and potentially local adaptation may influence resilience. Here, we used genomic tools to investigate the nature of this pattern of resilience. We used restriction site‐associated DNA capture (Rapture) sequencing to survey genomic diversity and differentiation in southern inland lake cisco populations and compared the frequency of deleterious mutations that potentially influence fitness across lakes. We also examined haplotype diversity in a region of the major histocompatibility complex involved in stress and immune system response. We correlated these metrics to spatial and environmental factors including latitude, lake size, and measures of oxythermal habitat and found significant relationships between genetic metrics and broad and local factors. High levels of genetic differentiation among populations were punctuated by a phylogeographic break and residual patterns of isolation‐by‐distance. Although the prevalence of deleterious mutations and inbreeding coefficients was significantly correlated with latitude, neutral and non‐neutral genetic diversity were most strongly correlated with lake surface area. Notably, differences among lakes in the availability of estimated oxythermal habitat left no clear population genomic signature. Our results shed light on the complex dynamics influencing these isolated populations and provide valuable information for their conservation.

Why are deleterious mutations maintained in selfing populations? An analysis of the effects of early- and late-acting mutations by a two-locus two-allele model

Frequencies of deleterious mutations are higher than expected in many plants. Here, by developing a two-locus two-allele model, I examine the effects of differential timing of the expression of deleterious mutations (two-stage effects) on the maintenance of mutations. I assume early- and late-acting loci to distinguish whether maintenance of mutations in populations with high selfing rates is explained better by two-stage effects of single mutations, or by separate mutations in both early- and late-acting loci. I found that, when ovules are overproduced, the stable frequency of early-acting mutations is higher if mutations also occur in a late-acting locus than if a late-acting mutation is lacking. The stable frequency of late-acting mutations is higher if mutations also occur in an early-acting locus than if an early-acting mutation is lacking. Selective interference does not account for these results because analyses in which the number of loci subject to mutations is equalized are included. Overproduction of ovules has little effect on maintenance if either early- or late-acting mutations are lacking, whereas when ovules are not overproduced, the two-stage effect does not enhance the maintenance of mutations. Hence, mutations occurring in both loci coupled with overproduction of ovules enhances the maintenance of mutations in populations with high selfing rates. The detailed mechanisms underlying the two-stage effect were also analyzed.

Revisiting the notion of deleterious sweeps.

It has previously been shown that, conditional on its fixation, the time to fixation of a semi-dominant deleterious autosomal mutation in a randomly mating population is the same as that of an advantageous mutation. This result implies that deleterious mutations could generate selective sweep-like effects. Although their fixation probabilities greatly differ, the much larger input of deleterious relative to beneficial mutations suggests that this phenomenon could be important. We here examine how the fixation of mildly deleterious mutations affects levels and patterns of polymorphism at linked sites-both in the presence and absence of interference amongst deleterious mutations-and how this class of sites may contribute to divergence between-populations and species. We find that, while deleterious fixations are unlikely to represent a significant proportion of outliers in polymorphism-based genomic scans within populations, minor shifts in the frequencies of deleterious mutations can influence the proportions of private variants and the value of FST after a recent population split. As sites subject to deleterious mutations are necessarily found in functional genomic regions, interpretations in terms of recurrent positive selection may require reconsideration.

Abstract PS19-19: Whole exome sequencing and BRCAness estimation in TNBCs and their correlation with response to platinum

Abstract Background: Triple-Negative Breast Cancer (TNBC) comprises approximately 30% of all breast cancers in Indian women. The hallmark of TNBC is genomic instability with very high rates of TP53 mutation. BRCAness has been defined by Ashworth et al (2004 &2014), as the phenocopying of BRCA1&2 mutation by alternate genetic or Epigenetic mechanisms. The consequence of this is DNA damage repair (DDR) deficiency. Though PARP inhibitors have been of utility in treating this subset of TNBC, trials have in general not found an unequivocal support for the use of platinum. We have developed an assay for BRCAness, the BRCA1 deficiency score (BDS) (Korlimarla et al 2016). In this study, we have applied BDS assay in tandem with whole exome sequencing to a small retrospective series of TNBC patients more than half of whom were treated with Platinum. Methods: 40 TNBC primary specimens along with complete clinical data from a retrospective series at the SSCHRC were obtained under all IERB approvals and informed patient consent for BDS assay and mutational analysis. BDS assay is a multianalyte assay involving measurement of BRCA1 (Transcript and protein) as well as additional epigenetic regulators of BRCA1, mir182 and ID4. Whole Exome Sequenced (WES) using the Agilent Sureselect V6 kit on Illumina HiSeq platform. Variant calling analysis was performed using GATK Mutect2 with Hg38 reference genome following the best practice workflow. Variants annotated as protein affecting based on their functional impact prediction and mapped to known cancer related genes (from COSMIC), were selected. Results: Clinical details: Mean age of patient in the series was 49. 37/40 qualified for BDS assay. 21/37 (57%) patients were treated with Carboplatin in combination with Docetaxel in an adjuvant setting. Remaining patients were treated with Cyclophosphamide Adriamycin with or without Docetaxel. 15/37 (45%) were BRCA1 deficient and10/15 were treated with Platinum and 8 (80%) were responders. 39 passed QC and considered for analysis. Spectrum of variants were missense mutations (86.5%), followed by stop gained (5.91%) and frame shift (3.76%). Results were compared to TCGA TNBC set (n=123). The most frequently mutated gene was TP53 (62%) as reported in TCGA. We also report higher frequency of deleterious mutations on DNA damage repair (DDR) genes like ATM and BRCA2 (15%). Response to Platinum therapy in this subset, correlated with Mutations in DNA damage repair genes (p ≤ 0.003). 4/6 samples mutated were also In the BDS deficient group. BRCAness score for predicting Platinum response also correlated significantly (p ≤ 0.05). Other genes which showed significant alterations were KMT2A and KMT2D (15% and 13%) which encode the histone methyl transferase and are responsible in altering the chromatin structure and RECQL4 (10%) which is a helicase involved in DDR Conclusion: Both BRCAness and mutation profile identified a DDR deficient group within TNBC patients. In addition to TP53 which is the most frequently mutated gene, our small sample set has shown higher frequencies of mutations in DDR genes like ATM and BRCA2. This group of patients showed favourable response to platinum therapy. Since very little is known about the molecular heterogeneity of TNBCs in Indian patients, our analysis aids in identification of actionable mutations in TNBCs and may be of use in selection of patients for platinum therapy. CHARACTERSn%Platinum Treatment - ( n )Treatment response%BDS3721Deficient154513BRCA1 deficient response861Proficient19518BRCA1 Proficient response450Undet34 Citation Format: Aruna Korlimarla, Sabarinathan Radhakrishnan, Snijesh VP, Jyothi S Prabhu, Naveen Luke Demonte, Savitha Rajarajan, Yatish Patil, Ravi Diwakar, Sandhya Apachu, BS Srinath, Sridhar TS, Anguraj Sadanandam. Whole exome sequencing and BRCAness estimation in TNBCs and their correlation with response to platinum [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS19-19.

The prevalence of CDK12 alterations in Chinese cancer patients and the association with tumor mutation burden(TMB) and survival.

e13663 Background: Cyclin-dependent kinase 12 (CDK12) is a cyclin-dependent kinase that regulates transcription and RNA splicing, thereby modulating multiple cellular processes. It has been suggested that CDK12 loss-of-function mutations lead to a higher neoantigen burden and favorable responses to PD-1 inhibitors in advanced prostate cancer. Given this potentially actionable molecular subtype, we sought to determine the prevalence of CDK12 alterations in Chinese cancer patients and the association with TMB and overall survival(OS). Methods: The prevalence of CDK12 alterations were queried in 3D Medicines database with 15,745 Chinese cancer patients involved. Whole-exome sequencing data of 464 patients with prostate adenocarcinoma(PRAD) from the Cancer Genome Altas (TCGA) were downloaded to explore the association between CDK12 gene alteration and OS. And the association with TMB were analyzed in a cohort of 731 patients with various cancer types published by Memorial Sloan Kettering (MSKCC) (Samstein et al., Nature Genetics, 2019). Results: Any CDK12 and known or likely deleterious CDK12 mutations were identified in 598(3.8%) and 98(0.62%) patients, respectively. Across all cancer types, prostate adenocarcinoma(PRAD) was found to have the highest frequency of deleterious mutations(8.75%, 23/263), followed by breast cancer (4.97%, 25/503). Mutations were also detected in multiple cancer types including bladder cancer, ovarian cancer, lung cancer, colorectal cancer and so on with a frequency of less than 1%. CDK12 mutations were associated with shorter OS (HR = 15.25; 95% CI, 2.88-80.73; p < 0.001) in TCGA PRAD and cholangiocarcinoma datasets, which was not seen in other cancer types. Patients harboring CDK12 mutation had a significant higher TMB(p < 0.001) in the pan-cancer study of publicly-available cohort from MSKCC. Conclusions: CDK12 alterations existed across tumor types in Chinese patients with relatively high frequencies detected in PRAD and breast cancer and represent extremely rare events in multiple cancers. CDK12 mutation was a poor prognostic factor in PRAD and cholangiocarcinoma. In a pan cancer analysis patients with CDK12 mutation tended to have a significant higher TMB and may benefit from PD-1/L1 blockade immunotherapy.

Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato.

SummaryGenome‐wide mutations induced by ethyl methanesulfonate (EMS) and gamma irradiation in the tomato Micro‐Tom genome were identified by a whole‐genome shotgun sequencing analysis to estimate the spectrum and distribution of whole‐genome DNA mutations and the frequency of deleterious mutations. A total of ~370 Gb of paired‐end reads for four EMS‐induced mutants and three gamma‐ray‐irradiated lines as well as a wild‐type line were obtained by next‐generation sequencing technology. Using bioinformatics analyses, we identified 5920 induced single nucleotide variations and insertion/deletion (indel) mutations. The predominant mutations in the EMS mutants were C/G to T/A transitions, while in the gamma‐ray mutants, C/G to T/A transitions, A/T to T/A transversions, A/T to G/C transitions and deletion mutations were equally common. Biases in the base composition flanking mutations differed between the mutagenesis types. Regarding the effects of the mutations on gene function, >90% of the mutations were located in intergenic regions, and only 0.2% were deleterious. In addition, we detected 1 140 687 spontaneous single nucleotide polymorphisms and indel polymorphisms in wild‐type Micro‐Tom lines. We also found copy number variation, deletions and insertions of chromosomal segments in both the mutant and wild‐type lines. The results provide helpful information not only for mutation research, but also for mutant screening methodology with reverse‐genetic approaches.

Distinguishing neutral from deleterious mutations in growing populations

Distinguishing neutral from deleterious mutations in growing populations

A Theory of Age-Dependent Mutation and Senescence

Laboratory experiments show us that the deleterious character of accumulated novel age-specific mutations is reduced and made less variable with increased age. While theories of aging predict that the frequency of deleterious mutations at mutation-selection equilibrium will increase with the mutation's age of effect, they do not account for these age-related changes in the distribution of de novo mutational effects. Furthermore, no model predicts why this dependence of mutational effects upon age exists. Because the nature of mutational distributions plays a critical role in shaping patterns of senescence, we need to develop aging theory that explains and incorporates these effects. Here we propose a model that explains the age dependency of mutational effects by extending Fisher's geometrical model of adaptation to include a temporal dimension. Using a combination of simple analytical arguments and simulations, we show that our model predicts age-specific mutational distributions that are consistent with observations from mutation-accumulation experiments. Simulations show us that these age-specific mutational effects may generate patterns of senescence at mutation-selection equilibrium that are consistent with observed demographic patterns that are otherwise difficult to explain.

Limited dispersal, deleterious mutations and the evolution of sex.

This study presents a mathematical model that allows for some offspring to be dispersed at random, while others stay close to their mothers. A single genetic locus is assumed to control fertility, and this locus is subject to the occurrence of deleterious mutations. It is shown that, at equilibrium, the frequency of deleterious mutations in the population is inversely related to the rate of dispersal. This is because dispersal of offspring leads to enhanced competition among adults. The results also show that sexual reproduction can lead to a decrease in the equilibrium frequency of deleterious mutations. The reason for this relationship is that sex involves the dispersal of genetic material, and thus, like the dispersal of offspring, sex enhances competition among adults. The model is described using the example of a hermaphroditic plant population. However, the results should apply to animal populations as well.