Biology subjects

Stolyarova, A.

Publications and source records attributed to Stolyarova, A..

6 recordsLinked to original sources

bioRxiv2026

A sibling study of variation in parental mutation rates

People are born with variable numbers of de novo germline mutations (DNMs), depending primarily on the ages of their parents. To explore additional causes, we developed an approach to call DNMs from nucleotide differences between siblings in genomic regions inherited identical by descent from both parents. Applying it to whole genome sequences from 28,985 sibling pairs of diverse genetic ancestries present in the UK Biobank and All of Us datasets, as well as 2,330 trios, we identified >800K autosomal DNMs and characterized mutation phenotypes in 27,645 sets of parents. We found subtle shifts in the mutation spectrum but no differences in total DNM rates among genetic ancestry groups, or between smokers and non-smokers. Testing for associations between parental mutation phenotypes and their burden of loss-of-function and deleterious missense variants in a set of 180 DNA repair and maintenance genes, we discovered that disruptions in REV1 and LIG1 increase germline mutation rates, and thus that rare mutator alleles segregate in population cohorts.

genomics↗

bioRxiv2025

What sets the mutation rate of a cell type in an animal species?

Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of lifespan are comparable across mammals. These observations point to a key role for natural selection in shaping mutation rates. In this essay, we summarize the patterns identified to date and outline existing theories for how selection pressures might shape mutation rates in animal germline and soma. We argue that an understanding of what sets the mutation rate of a given cell type in a species requires better integration of genetics and development with population processes of selection and genetic drift.

evolutionary biology↗

bioRxiv2025

Mutation bias in driver genes reveals the distribution of effects of oncogenic mutations

Although many cancer driver genes have been identified, the full set of mutations within these genes that can promote tumorigenesis remains unknown. The contribution of a mutation depends on both its probability of occurrence and the selective advantage it confers. Here, we introduce a metric that quantifies how selection biases the spectrum of observed mutations in driver genes, and use it to develop a method estimating the number of driver mutations and their effect distribution at individual genes. Applying this framework to large cancer cohorts, we find that in most oncogenes, nearly all driver mutations have already been observed, whereas in most tumor-suppressor genes, the majority remain undiscovered. These results reveal fundamental differences in how mutation and selection shape mutational patterns across gene classes and provide a framework for interpreting newly detected variants.

genetics↗

bioRxiv2025

The distribution of highly deleterious variants across human ancestry groups

A major focus of human genetics is to map severe disease mutations. Increasingly that goal is understood as requiring huge numbers of people to be sequenced from every broadly-defined genetic ancestry group, so as not to miss "ancestry-specific variants." Here, we argue that this focus is unwarranted. We start with first principles considerations, based on models of mutation-drift-selection balance, which suggest highly pathogenic mutations should be at similarly low frequencies across ancestry groups. Severe disease mutations tend to be strongly deleterious, and thus evolutionarily young, and are kept at relatively constant frequency through recurrent mutation. Therefore, highly pathogenic alleles are shared identical by descent within extended families, not broad ancestry groups, and sequencing more people should yield similar numbers regardless of ancestry. We illustrate these points using gnomAD genetic ancestry groupings, and show that the classes of variants most likely to be highly pathogenic, notably sets of loss of function alleles at strongly constrained genes, conform well to these predictions. While there are many important reasons to diversify genomic research, strongly deleterious alleles will be found at comparable rates in people of all ancestries, and the information they provide about human biology is shared across ancestries.

genetics↗

bioRxiv2020

Sex-dependent effects of chronic intermittent voluntary alcohol consumption on attentional, not motivational, measures during probabilistic learning and reversal

BackgroundForced alcohol (ethanol, EtOH) exposure has been shown to cause significant impairments on reversal learning, a widely-used assay of cognitive flexibility, specifically on fully-predictive, deterministic versions of this task. However, previous studies have not adequately considered voluntary EtOH consumption and sex effects on probabilistic reversal learning. The present study aimed to fill this gap in the literature. MethodsMale and female Long-Evans rats underwent either 10 weeks of voluntary intermittent 20% EtOH access or water only (H2O) access. Rats were then pretrained to initiate trials and learn stimulus-reward associations via touchscreen response, and subsequently required to select between two visual stimuli, rewarded with probability 0.70 or 0.30. In the final phase, reinforcement contingencies were reversed. ResultsWe found significant sex differences on several EtOH-drinking variables, with females reaching a higher maximum EtOH consumption, exhibiting more high-drinking days, and escalating their EtOH at a quicker rate compared to males. During early abstinence, EtOH drinkers made more initiation omissions and were slower to initiate trials than H2O drinking controls, particularly during pretraining. EtOH drinking females were most affected. A similar pattern in trial initiations was also observed in discrimination, but not in reversal learning. EtOH drinking rats were unaffected in their reward collection and stimulus response times, indicating intact motivation and motor responding. Although there were sex differences in discrimination and reversal phases, performance improved over time. We also observed sex-independent drinking group differences in win-stay and lose-shift strategies specific to the reversal phase. ConclusionsFemales exhibit increased vulnerability to EtOH effects in early learning: there were sex-dependent EtOH effects on attentional measures during pretraining and discrimination phases. We also found sexindependent EtOH effects on exploration strategies during reversal. Future studies should aim to uncover the neural mechanisms for changes in attention and exploration in both acute and prolonged EtOH withdrawal.

pharmacology and toxicology↗

bioRxiv2019

Dissociable roles for Anterior Cingulate Cortex and Basolateral Amygdala in Decision Confidence and Learning under Uncertainty

It has been suggested the subjective sense of certainty, or confidence, in ambiguous sensory cues can alter the interpretation of reward feedback and facilitate learning. We trained rats to report the orientation of ambiguous visual stimuli according to a spatial stimulus-response rule. Following choice, rats could wait a self-timed delay for reward or initiate a new trial. Waiting times increased with discrimination accuracy, demonstrating that this measure could be used as a proxy for confidence. Chemogenetic silencing of BLA shortened waiting times overall whereas ACC inhibition rendered waiting times insensitive to confidence-modulating attributes of visual stimuli, suggesting contribution of ACC but not BLA to confidence computations. Subsequent reversal learning was enhanced by confidence. Both ACC and BLA inhibition blocked this enhancement but via differential modulation of learning strategies and consistency in using learned rules. Altogether, we demonstrate dissociable roles for ACC and BLA in transmitting confidence and learning under uncertainty.

neuroscience↗