Prioritization of Genetic Variants Predisposing to Alzheimer's Disease in Young Healthy Bulgarian Individuals Using Centenarian Exomes

The present study aims to identify pathogenic/risky variants in the exomes of healthy young individuals predisposing to Alzheimer's disease (AD) by their validation in centenarian's exomes. The group of Bulgarian centenarians included 32 individuals (mean age 102.4) without AD diagnosis and the matched control group of 61 young healthy individuals (mean age 21.9). Two DNA pools were constructed with equimolar amounts of DNA from each participant and whole exome sequencing analysis (WES) was performed. We examined the WES data for pathogenic or risky SNPs predisposing to AD. Of altogether 1929 variants selected from DisGeNet database for association with AD, only 174 (9.02%) were detected in our WES data. One hundred and fifty-two (152) SNPs were present in both studied groups, 8 in centenarians and 14 in controls only. Seven variants have significantly higher frequency in young individuals or absence in centenarians. Based on sufficiently unambiguous literature data, we nominated rs63750264 in APP, rs429358 in APOE, rs1800562 in HFE variants for predisposition to AD in young individuals. To a lesser extent, the carriership of rs2070045 in SORL1, rs6265 in BDNF, rs769449 in APOE, rs4988514 in SST can increase the risk to AD development. These variants could find implication in the Alzheimer's disease estimation in young individuals before the onset of clinical symptoms.

Spatio-temporal dynamics of pathogenic variants associated with monogenic disorders reconstructed with ancient DNA

Genetic disease burden in ancient communities has barely been evaluated despite an ever expanding body of ancient genomes becoming available. In this study, we inspect 2729 publicly available ancient genomes (100 BP—52000 BP) for the presence of pathogenic variants in 32643 disease-associated loci. We base our subsequent analyses on 19 variants in seven genes—PAH, EDAR, F11, HBB, LRRK2, SLC12A6 and MAOA, associated with monogenic diseases and with well-established pathogenic impact in contemporary populations. We determine 230 homozygote genotypes of these variants in the screened 2729 ancient DNA samples. Eleven of these are in the PAH gene (126 ancient samples in total), a gene associated with the condition phenylketonuria in modern populations. The variants examined seem to show varying dynamics over the last 10000 years, some exhibiting a single upsurge in frequency and subsequently disappearing, while others maintain high frequency levels (compared to contemporary population frequencies) over long time periods. The geographic distribution and age of the ancient DNA samples with established pathogenic variants suggests multiple independent origin of these variants. Comparison of estimates of the geographic prevalence of these variants from ancient and contemporary data show discontinuity in their prevalence and supports their recurrent emergence. The oldest samples in which a variant is established might give an indication of their age and place origin, and an EDAR gene pathogenic variant was established in a sample estimated to be 33210–32480 calBCE. Knowledge about the historical prevalence of variants causing monogenic disorders provides insight on their emergence, dynamics and spread.

Clinical impact of copy number variation changes in bladder cancer samples

The aim of the present study was to detect copy number variations (CNVs) related to tumour progression and metastasis of urothelial carcinoma through whole-genome scanning. A total of 30 bladder cancer samples staged from pTa to pT4 were included in the study. DNA was extracted from freshly frozen tissue via standard phenol-chloroform extraction and CNV analysis was performed on two alternative platforms (CytoChip Oligo aCGH, 4x44K and Infinium OncoArray-500K BeadChip; Illumina, Inc.). Data were analysed with BlueFuse Multi software and Karyostudio, respectively. The results highlight the role of genomic imbalances in regions containing genes with metastatic and proliferative potential for tumour invasion. A high level of genomic instability in uroepithelial tumours was observed and a total of 524 aberrations, including 175 losses and 349 gains, were identified. The most prevalent genetic imbalances affected the following regions: 1p, 1q, 2q, 4p, 4q, 5p, 5q, 6p, 6q, 7q, 8q, 9p, 9q, 10p, 10q, 11q, 13q and 17q. High-grade tumours more frequently harboured genomic imbalances (n=227) than low-grade tumours (n=103). A total of 36 CNVs in high-grade bladder tumours were detected in chromosomes 1-5, 8-11, 14, 17, 19 and 20. Furthermore, five loss of heterozygosity variants containing 176 genes were observed in high-grade bladder cancer and may be used as potential targets for precision therapy. Revealing specific chromosomal regions related to the metastatic potential of uroepithelial tumours may lay a foundation for implementing molecular CNV profiling of bladder tumours as part of a routine progression risk estimation strategy, thus expanding the personalized therapeutic approach.

Centenarian Exomes as a Tool for Evaluating the Clinical Relevance of Germline Tumor Suppressor Mutations

Objectives:

The aim of the present study was to evaluate the clinical relevance of mutations in tumor suppressor genes using whole-exome sequencing data from centenarians and young healthy individuals.

Methods:

Two pools, one of centenarians and one of young individuals, were constructed and whole-exome sequencing was performed. We examined the whole-exome sequencing data of Bulgarian individuals for carriership of tumor suppressor gene variants.

Results:

Of all variants annotated in both pools, 5080 (0.06%) are variants in tumor suppressor genes but only 46 show significant difference in allele frequencies between the two studied groups. Four variants (0.004%) are pathogenic/risk factors according to single nucleotide polymorphism database: rs1566734 in PTPRJ, rs861539 in XRCC3, rs203462 in AKAP10, and rs486907 in RNASEL.

Discussion:

Based on their high minor allele frequencies and presence in the centenarian group, we could reclassify them from pathogenic/risk factors to benign. Our study shows that centenarian exomes can be used for re-evaluating the clinically uncertain variants.

Ancient mitochondrial DNA pathogenic variants putatively associated with mitochondrial disease

Mitochondrial DNA variants associated with diseases are widely studied in contemporary populations, but their prevalence has not yet been investigated in ancient populations. The publicly available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different periods. The objective of this study was to use this data to establish the presence of pathogenic mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants were determined using online platforms. The analyzed ancient mtDNAs contain six variants designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C in the MT-TS1 gene, was found in a sample from the Neolithic period, dated 5800-5400 BCE. All six have well established clinical association, and their pathogenic effect is corroborated by very low population frequencies in contemporary populations. Analysis of the geographic location of the ancient samples, contemporary epidemiological trends and probable haplogroup association indicate diverse spatiotemporal dynamics of these variants. The dynamics in the prevalence and distribution is conceivably result of de novo mutations or human migrations and subsequent evolutionary processes. In addition, ten variants designated as possibly or likely pathogenic were found, but the clinical effect of these is not yet well established and further research is warranted. All detected mutations putatively associated with mitochondrial disease in ancient mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 2) that is characterized by loss of D-loop/T-loop interaction. Exposing pathogenic variants in ancient human populations expands our understanding of their origin and prevalence dynamics.

Genetic parentage analysis confirms a polygynandrous breeding system in the European grayling (Thymallus thymallus)

Knowing the breeding system of a species is important in order to understand individual variation in reproductive success. Large variation in reproductive success and thus reproductive skew strongly impacts on the effective number of breeders and thus the long-term effective population size (Ne). Fishes, in particular species belonging to the salmonid family, exhibit a wide diversity of breeding systems. In general, however, breeding systems are rarely studied in detail in the wild. Here we examine the breeding system of the spring-spawning European grayling Thymallus thymallus from a small Norwegian stream using parentage assignment based on the genotyping of 19 polymorphic microsatellite loci. In total 895 individual grayling fry and 154 mature grayling (57 females and 97 males) were genotyped. A total of 466 offspring were assigned a father, a mother, or a parent pair with a confidence of 90% or higher. Successfully reproducing males had on average 11.9 ± 13.3 (SD) offspring with on average 2.1 ± 1.2 partners, whereas successful females had on average 9.5 ± 12.8 offspring and 2.3 ± 1.5 partners. Parents with more partners also produced more offspring. Thus the grayling breeding system within this small stream revealed a polygynandrous breeding system, similar to what has been observed for many other salmonid fish species. The present study thus unambiguously corroborates a polygynadrous breeding system in the European grayling. This knowledge is critical for managing populations of this species, which has suffered significant local population declines throughout its range over the last several decades.

Probabilistic maturation reaction norms assessed from mark-recaptures of wild fish in their natural habitat

Reaction norms are a valuable tool in evolutionary biology. Lately, the probabilistic maturation reaction norm approach, describing probabilities of maturing at combinations of age and body size, has been much applied for testing whether phenotypic changes in exploited populations of fish are mainly plastic or involving an evolutionary component. However, due to typical field data limitations, with imperfect knowledge about individual life histories, this demographic method still needs to be assessed. Using 13 years of direct mark-recapture observations on individual growth and maturation in an intensively sampled population of brown trout (Salmo trutta), we show that the probabilistic maturation reaction norm approach may perform well even if the assumption of equal survival of juvenile and maturing fish does not hold. Earlier studies have pointed out that growth effects may confound the interpretation of shifts in maturation reaction norms, because this method in its basic form deals with body size rather than growth. In our case, however, we found that juvenile body size, rather than annual growth, was more strongly associated with maturation. Viewed against earlier studies, our results also underscore the challenges of generalizing life-history patterns among species and populations.

NGS nominated CELA1, HSPG2, and KCNK5 as candidate genes for predisposition to Balkan endemic nephropathy

Balkan endemic nephropathy (BEN) is a familial chronic tubulointerstitial disease with insidious onset and slow progression leading to terminal renal failure. The results of molecular biological investigations propose that BEN is a multifactorial disease with genetic predisposition to environmental risk agents. Exome sequencing of 22 000 genes with Illumina Nextera Exome Enrichment Kit was performed on 22 DNA samples (11 Bulgarian patients and 11 Serbian patients). Software analysis was performed via NextGene, Provean, and PolyPhen. The frequency of all annotated genetic variants with deleterious/damaging effect was compared with those of European populations. Then we focused on nonannotated variants (with no data available about them and not found in healthy Bulgarian controls). There is no statistically significant difference between annotated variants in BEN patients and European populations. From nonannotated variants with more than 40% frequency in both patients' groups, we nominated 3 genes with possible deleterious/damaging variants--CELA1, HSPG2, and KCNK5. Mutant genes (CELA1, HSPG2, and KCNK5) in BEN patients encode proteins involved in basement membrane/extracellular matrix and vascular tone, tightly connected to process of angiogenesis. We suggest that an abnormal process of angiogenesis plays a key role in the molecular pathogenesis of BEN.

Fractional parentage analysis and a scale-free reproductive network of brown trout

In this study, we developed a method of fractional parentage analysis using microsatellite markers. We propose a method for calculating parentage probability, which considers missing data and genotyping errors due to null alleles and other causes, by regarding observed alleles as realizations of random variables which take values in the set of alleles at the locus and developing a method for simultaneously estimating the true and null allele frequencies of all alleles at each locus. We then applied our proposed method to a large sample collected from a wild population of brown trout (Salmo trutta). On analyzing the data using our method, we found that the reproductive success of brown trout obeyed a power law, indicating that when the parent-offspring relationship is regarded as a link, the reproductive system of brown trout is a scale-free network. Characteristics of the reproductive network of brown trout include individuals with large bodies as hubs in the network and different power exponents of degree distributions between males and females.

Life history and demographic determinants of effective/census size ratios as exemplified by brown trout (Salmo trutta)

A number of demographic factors, many of which related to human-driven encroachments, are predicted to decrease the effective population size (N(e)) relative to the census population size (N), but these have been little investigated. Yet, it is necessary to know which factors most strongly impact N(e), and how to mitigate these effects through sound management actions. In this study, we use parentage analysis of a stream-living brown trout (Salmo trutta) population to quantify the effect of between-individual variance in reproductive success on the effective number of breeders (N(b)) relative to the census number of breeders (N(i)). Comprehensive estimates of the N(b)/N ratio were reduced to 0.16-0.28, almost entirely due to larger than binomial variance in family size. We used computer simulations, based on empirical estimates of age-specific survival and fecundity rates, to assess the effect of repeat spawning (iteroparity) on N(e) and found that the variance in lifetime reproductive success was substantially higher for repeat spawners. Random family-specific survival, on the other hand, acts to buffer these effects. We discuss the implications of these findings for the management of small populations, where maintaining high and stable levels of N(e) is crucial to extenuate inbreeding and protect genetic variability.

Mating patterns and determinants of individual reproductive success in brown trout (Salmo trutta) revealed by parentage analysis of an entire stream living population

Reproductive success and its determinants are difficult to infer for wild populations of species with no parental care where behavioural observations are difficult or impossible. In this study, we characterized the breeding system and provide estimates of individual reproductive success under natural conditions for an exhaustively sampled stream-resident brown trout (Salmo trutta) population. We inferred parentage using a full probability Bayesian model that combines genetic (microsatellite) with phenotypic data. By augmenting the potential parents file with inferred parental genotypes from sib-ship analysis in cases where large families had unsampled parents, we could make more precise inference on variance of family size. We observed both polygamous and monogamous matings and large reproductive skew for both sexes, particularly in males. Correspondingly, we found evidence for sexual selection on body size for both sexes. We show that the mating system of brown trout has the potential to be very flexible and we conjecture that environmental uncertainty could be driving the evolution and perhaps select for the maintenance of plasticity of the mating system in this species.

Quantitative genetic parameters for wild stream-living brown trout: heritability and parental effects

Adaptability depends on the presence of additive genetic variance for important traits. Yet few estimates of additive genetic variance and heritability are available for wild populations, particularly so for fishes. Here, we estimate heritability of length-at-age for wild-living brown trout (Salmo trutta), based on long-term mark-recapture data and pedigree reconstruction based on large-scale genotyping at 15 microsatellite loci. We also tested for the presence of maternal and paternal effects using a Bayesian version of the Animal model. Heritability varied between 0.16 and 0.31, with reasonable narrow confidence bands, and the total phenotypic variance increased with age. When introducing dam as an additional random effect (accounting for c. 7% of total phenotypic variance), the level of additive genetic variance and heritability decreased (0.12-0.21). Parental size (both for sires and for dams) positively influenced length-at-age for juvenile trout--either through direct parental effects or through genotype-environment correlations. Length-at-age is a complex trait reflecting the effects of a number of physiological, behavioural and ecological processes. Our data show that fitness-related traits such as length-at-age can retain high levels of additive genetic variance even when total phenotypic variance is high.