Complex Genotypes Research Articles

Synthetic Engineering of Microbes for Production of Terpenoid Food Ingredients.

Terpenoids are a class of chemicals comprising many food ingredient chemicals. Synthetic biology and metabolic engineering have been performed to produce microbial cell factories for their production. For improved production of various terpenoid ingredients, heterologous synthetic pathways can be optimized at multiple dimensions. Optimizing chassis precursor supply and overcoming the host's inherent metabolic rigidity are crucial for enhancing overall efficiency of heterologous terpenoid production. Integrating synthetic regulatory circuits can facilitate the staged programming and precise optimization of heterologous and endogenous metabolism. Engineering long-term genetic and metabolic stability is essential for the successful scale-up of commercial production. Maximizing efficiency in food terpenoid production will rely on interdisciplinary synthetic and engineering biology tools to advance state-of-the-art capabilities for the streamlined design and construction of complex genotypes in microbial chassis.

Development of a Nomogram for Predicting Tuberous Sclerosis Complex Genotypes in Children Using Advanced Diffusion MRI and Clinical Data

Development of a Nomogram for Predicting Tuberous Sclerosis Complex Genotypes in Children Using Advanced Diffusion MRI and Clinical Data

Highly replicated experiments studying complex genotypes using nested DNA barcodes.

Many biological experiments involve studying the differences caused by genetic modifications, including genotypes composed of modifications at more than one locus. However, as the number and complexity of the genotypes increases, independently generating and tracking the necessary number of biological replicate samples becomes a major challenge. We developed a barcode-based method to track large numbers of independent replicates of combinatorial genotypes in a pooled format, enabling robust detection of subtle phenotypic differences. To construct a plasmid library of combinatorial genotypes, we utilized a nested serial cloning process to combine gene variants of interest that have associated DNA barcodes. The final plasmids each contain variants of multiple genes of interest, and a combined barcode that specifies the genotype of all the genes while also encoding a random sequence for tracking individual replicates. Sequencing of the pool of barcodes by next-generation sequencing allows the whole population to be studied in a single flask, enabling a high degree of replication even for complex genotypes. Using this approach, we tested the functionality of combinations of yeast, human, and null orthologs of the nucleotide excision repair factor I (NEF-1) complex and found that cells expressing all three yeast NEF-1 subunits had superior growth in DNA-damaging conditions. We also assessed the sensitivity of our method by simulating downsampling of barcodes across different degrees of phenotypic differentiation. Our results demonstrate the utility of NICR barcodes for high-throughput combinatorial genetic screens and provide a scalable framework for exploring complex genotype-phenotype relationships.

ГЕНЫ БЕЛКОВОГО ОБМЕНА И ПОКАЗАТЕЛИ КАЧЕСТВА МОЛОКА КОРОВ ДЖЕРСЕЙСКОЙ ПОРОДЫ, ПРИНАДЛЕЖАЩИХ ООО «ПМК» САБИНСКОГО РАЙОНА РЕСПУБЛИКИ ТАТАРСТАН

The genetic potential of animals is determined by a complex of hereditary genes, and, based on this, DNA assessment is important in the selection of animals for breeding. One of the methods of early assessment is the prediction of the breeding value of animals using DNA technologies. Research has shown that the factors of productivity of farm animals include not only the conditions of maintenance and the quality of feeding, but also the genetic potential of individuals. The genotype plays an important role in the formation of breeding qualities of animals, and these qualities depend on inherited genetic complexes. During the analysis of the productivity of Jersey cows in the "PMK" of the Sabinsky district of the Republic of Tatarstan, it was found that animals with the complex genotype CSN3BBBLGBB had the highest protein milk yield - 3.79 %, the mass fraction of protein - 255.76 kg. Such cows are 18.1 %. The accumulation of animals with the complex genotype CSN3BBBLGBB in herds will lead to an increase in not only the milk productivity of animals, but also to an increase in the production of high-quality protein milk products. In the future, this will increase the level of profitability of milk production, improve the competitiveness of products in the domestic and global food markets, increase the efficiency of industry development, and help in the formation of the country's national food security system.

Initial growth response of twelve Saccharum Complex genotypes to inoculation using Nitrospirillum viridazoti

ABSTRACT Sugar and alcohol production in Brazil comes from planting hybrids from the crossing of species belonging to the Saccharum Complex. However, little is known about the growth response of these genera to inoculation using a diazotrophic bacteria Nitrospirillum viridazoti strain BR11145, currently recommended in Brazil as an inoculant for sugarcane growth promotion. This study aimed to evaluate the initial growth of 12 sugarcane genotypes inoculated or not with the strain BR11145. After 109 days, plant growth, biomass and macronutrient accumulation were evaluated. Fresh and dry mass at the end of the trial showed a positive response to inoculation for the genotypes US72-1319, CPDAU 849678, and NG77-122 of S. spontaneum and for Fiji 10 of Miscanthus. A negative response was observed for Q45416 of Saccharum sp. The growth of S. spontaneum US72-1319 is significantly improved by the inoculation with BR11145, which leads to a high accumulation of nutrients, especially N, standing out among the genotypes tested.

Limiting Hearing Loss in Transgenic Mouse Models.

Transgenic mice provide unprecedented access to manipulate and visualize neural circuits; however, those on a C57BL/6 background develop progressive hearing loss, significantly confounding systems-level and behavioral analysis. While outbreeding can limit hearing loss, it introduces strain variability and complicates the generation of complex genotypes. Here, we propose an approach to preserve hearing by crossing transgenic mice with congenic B6.CAST-Cdh23Ahl + mice, which maintain low-threshold hearing into adulthood. Widefield and two-photon imaging of the auditory cortex revealed that 2.5-month-old C57BL/6 mice exhibit elevated thresholds to high-frequency tones and widespread cortical reorganization, with most neurons responding best to lower frequencies. In contrast, Ahl+ C57BL/6 mice exhibited robust neural responses across tested frequencies and sound levels (4-64 kHz, 30-90 dB SPL) and retained low thresholds into adulthood. Our approach offers a cost-effective solution for generating complex genotypes and facilitates more interpretable systems neuroscience research by eliminating confounding effects from hearing loss.

Milk productivity of simmental cattle by combined kappacasein and somatotropin genes

The economically important productive traits of cattle that contribute to the development of the dairy industry are considered to be abundant milk yield, protein and fat content in milk. In recent years, breeders have focused their attention on cattle breeding programmes based on molecular genetic research methods. The potential of animal productivity largely depends on genetic variants of marker genes present in the genotype of an individual. The genes of kappa-casein and somatotropin are considered to be promising DNA markers, as they are responsible for qualitative and quantitative traits of cattle productivity. In this work we studied milk productivity of 84 cows of Simmental breed from the breeding plant in the Urals by kappa-casein and somatotropin genes, as well as by complex genes. On the gene kappa-casein on milk yield in advantage are individuals with genotypes CSN3AB 6937,6 kg. The higher content of protein in milk, milk fat and protein yield, as well as the sum of nutrients were recorded in cows with CSN3BB genotypes 3.40%, 282.5 kg, 234.2 kg and 516.7 kg, respectively. In terms of somatotropin gene, cows with GHVV genotypes had the most abundant milk production 7160.0 kg. In terms of protein-milk yield, coevals with GHLL genotypes are more productive 3.4 %. The sum of nutrients, milk fat and protein yield is more established in milk of cows with GHVV genotypes 522.7 kg, 293.6 kg and 229.1 kg, respectively. All nine possible variants of complex genotypes for kappa-casein and somatotropin genes occur in this Simmental herd: AA/LV 26 cows; AA/LL 14; AA/VV 12; AB/LL 13; AB/LV 10; AB/VV 2; BB/LL 4; BB/ VV 2; BB/LV 1. Data processing on the effect of complex genotypes on milk productivity included a number of 10 cows or more. Higher milk yield, milk protein content, milk fat and protein yield, and nutrient sum were found in AB/LL complex genotypes: 6756.0 kg, 3.4 %, 277.0 kg and 229.7 kg, 506.7 kg, respectively. Significant differences were found between cow groups in the content of mass fraction of protein.

Long-read sequencing revealed complex biallelic pentanucleotide repeat expansions in RFC1-related Parkinson’s disease

Biallelic intronic pentanucleotide repeat expansions, mainly (AAGGG)exp and/or (ACAGG)exp in RFC1, are detected in cerebellar ataxia, neuropathy and vestibular areflexia syndrome, late-onset ataxia, and in a wide disease spectrum including Charcot-Marie-Tooth disease, multiple system atrophy, and Parkinson’s disease (PD). However, the genotype-phenotype correlation and underlying mechanism are mostly unknown. We screened RFC1-repeat expansions in 1445 patients with parkinsonism. Comprehensive genetic and clinical, and pathological assessments were performed. We report two early-onset patients with PD carrying complex biallelic pentanucleotide repeat expansions in RFC1. Long-read sequencing revealed a novel repeat configuration of (AGGGG)exp(AAGGG)14 and a possible somatic variant of (AAGGG)exp(AATGG)exp(AAGGG)exp in the (AAGGG)exp alleles in two RFC1-related PD patients. RNA foci were detected in the (AGGGG)exp-expressed HEK293T cell line as well as (AAGGG)exp and (ACAGG)exp, supporting (AGGGG)exp as a novel pathogenic repeat motif. This work revealed complex genotypes with novel repeat configuration of (AGGGG)exp and possible somatic (AATGG)exp insertion in RFC1-related PD.

Germination of Saccharum complex genotypes in response to inoculation using selected diazotrophic bacteria before and after a heat treatment

ABSTRACT Breeding of new cultivars of sugarcane uses several species belonging to the Saccharum complex genus. In this study, a set of 20 genotypes from the Saccharum complex was assessed for their growth promotion during germination using a mixed inoculant containing five selected diazotrophs and their resistance to short heat treatment (52°C / 30 min). The percentage of germination was evaluated, leading to the identification of three response groups. Saccharum officinarum (group I) showed the highest germination percentage, succeeded by Erianthus arundinaceus genotypes (group II) and the other genotypes (group III). The mean germination time (MGT) varied among the genotypes and segregated the growth response into two groups. Saccharum officinarum only required less than 15 days to reach the MGT, whereas the other genera required more than two or three days during the initial growth process. Bacterial counting also differed between the groups, being effective for S. officinarum and other genotypes, improving the colonization of the plants 100–1,000 times higher than the control and heat treatments. Further comparison was made among eight genotypes, including one Saccharum spontaneum(US72-1319), one S. officinarum (IN845), and six E. arundinaceus. This comparison measured biomass accumulation and root parameters. The E. arundinaceus group demonstrated less susceptibility to the heat treatment, resulting in stimulation of the root dry mass of IJ76-381 and root parameters of this genotype, as well as IJ76-364, although not associated to the inoculation treatment. Inoculation applied to US72-1319 and IN845 enhanced only the Shoot/Root ratio.

Transcriptomic and genetic profiling in a spontaneous non-human primate model of hypertrophic cardiomyopathy and sudden cardiac death

Hypertrophic cardiomyopathy (HCM) afflicts humans, cats, pigs, and rhesus macaques. Disease sequelae include congestive heart failure, thromboembolism, and sudden cardiac death (SCD). Sarcomeric mutations explain some human and cat cases, however, the molecular basis in rhesus macaques remains unknown. RNA-Seq of the LV tissues of five HCM-affected and seven healthy control rhesus macaques was employed for differential transcriptomic analyses. DNA from 15 severely HCM-affected and 21 healthy geriatric rhesus macaques were selected for whole-genome sequencing. A genome-wide association study (GWAS) of disease status and SCD outcome was performed. 614 down- and 1,065 upregulated differentially expressed genes (DEGs) were identified between groups. The top DEG (MAFF) was overexpressed in affected animals (log2FoldChange = 4.71; PAdjusted-value = 1.14E-133). Channelopathy-associated enriched terms were identified in ~ 57% of downregulated DEGs providing transcriptomic evidence of hypertrophic and arrhythmic disease processes. For GWAS, no putative variant withstood segregation. Polygenic modeling analysis resulted in poor prediction power and burden testing could not explain HCM by an association of multiple variants in any gene. Neither single nor compound genetic variant(s), or identified polygenic profile, suggest complex genotype–phenotype interactions in rhesus macaques. Brought forth is an established dataset of robustly phenotyped rhesus macaques as an open-access resource for future cardiovascular disease genetic studies.

Phenotypic and genotypic characterization of Candida species from the oral cavity of healthy individuals in Lublin province, Poland

ABSTRACT Background Candida spp., particularly C. albicans, are commonly isolated fungi in the oral cavity. However, their prevalence in healthy participants and their genotype–phenotype relation remains elusive. Aim This study aimed to update the information on Candida species colonizing the oral cavity of healthy population, identify the most common species, and characterize the intraspecific diversity to determine the genotype-phenotype relationship. Methods Oral swabs of healthy participants who declared an absence of oral infection were analyzed. Microbiological methods: chromogenic media, sugar assimilation tests, drug susceptibility, filamentation tests, temperature tolerance analysis, and assessment of biofilm formation ability. Genotyping methods: PCR amplification of the internal transcribed spacer (ITS) region with MspI restriction enzyme digestion and 25S rDNA region. Results Of the 500 individuals tested, 130 harbored C. albicans in 77%, C. dubliniensis in 12%, Pichia kudriavzevii (previously C. krusei) in 8%, and Nakaseomyces glabrata (previously C. glabrata) in 3%. The microbiological tests yielded conflicting results. Analysis of the 25S rDNA transposable intron region contributed to the identification of individual Candida spp. and intraspecific identification of C. albicans genotypes. Genotype A accounted for 70% (n = 100) of C. albicans isolates, whereas genotypes B, C, and D (C. dubliniensis) accounted for 17%, 9%, and 4% of the isolates, respectively. Conclusion The results indicate a complex genotype–phenotype relationship in Candida spp. and recommends combining microbiological and molecular methods for the efficient typing of Candida spp.

DeepAT: A Deep Learning Wheat Phenotype Prediction Model Based on Genotype Data

Genomic selection serves as an effective way for crop genetic breeding, capable of significantly shortening the breeding cycle and improving the accuracy of breeding. Phenotype prediction can help identify genetic variants associated with specific phenotypes. This provides a data-driven selection criterion for genomic selection, making the selection process more efficient and targeted. Deep learning has become an important tool for phenotype prediction due to its abilities in automatic feature learning, nonlinear modeling, and high-dimensional data processing. Current deep learning models have improvements in various aspects, such as predictive performance and computation time, but they still have limitations in capturing the complex relationships between genotype and phenotype, indicating that there is still room for improvement in the accuracy of phenotype prediction. This study innovatively proposes a new method called DeepAT, which mainly includes an input layer, a data feature extraction layer, a feature relationship capture layer, and an output layer. This method can predict wheat yield based on genotype data and has innovations in the following four aspects: (1) The data feature extraction layer of DeepAT can extract representative feature vectors from high-dimensional SNP data. By introducing the ReLU activation function, it enhances the model’s ability to express nonlinear features and accelerates the model’s convergence speed; (2) DeepAT can handle high-dimensional and complex genotype data while retaining as much useful information as possible; (3) The feature relationship capture layer of DeepAT effectively captures the complex relationships between features from low-dimensional features through a self-attention mechanism; (4) Compared to traditional RNN structures, the model training process is more efficient and stable. Using a public wheat dataset from AGT, comparative experiments with three machine learning and six deep learning methods found that DeepAT exhibited better predictive performance than other methods, achieving a prediction accuracy of 99.98%, a mean squared error (MSE) of only 28.93 tones, and a Pearson correlation coefficient close to 1, with yield predicted values closely matching observed values. This method provides a new perspective for deep learning-assisted phenotype prediction and has great potential in smart breeding.

Efficient DNA-free co-targeting of nuclear genes in Chlamydomonas reinhardtii

Chlamydomonas reinhardtii, a model organism for unicellular green microalgae, is widely used in basic and applied research. Nonetheless, proceeding towards synthetic biology requires a full set of manipulation techniques for inserting, removing, or editing genes. Despite recent advancements in CRISPR/Cas9, still significant limitations in producing gene knock-outs are standing, including (i) unsatisfactory genome editing (GE) efficiency and (ii) uncontrolled DNA random insertion of antibiotic resistance markers. Thus, obtaining efficient gene targeting without using marker genes is instrumental in developing a pipeline for efficient engineering of strains for biotechnological applications. We developed an efficient DNA-free gene disruption strategy, relying on phenotypical identification of mutants, to (i) precisely determine its efficiency compared to marker-relying approaches and (ii) establish a new DNA-free editing tool. This study found that classical CRISPR Cas9-based GE for gene disruption in Chlamydomonas reinhardtii is mainly limited by DNA integration. With respect to previous results achieved on synchronized cell populations, we succeeded in increasing the GE efficiency of single gene targeting by about 200 times and up to 270 times by applying phosphate starvation. Moreover, we determined the efficiency of multiplex simultaneous gene disruption by using an additional gene target whose knock-out did not lead to a visible phenotype, achieving a co-targeting efficiency of 22%. These results expand the toolset of GE techniques and, additionally, lead the way to future strategies to generate complex genotypes or to functionally investigate gene families. Furthermore, the approach provides new perspectives on how GE can be applied to (non-) model microalgae species, targeting groups of candidate genes of high interest for basic research and biotechnological applications.

Chromosomal analysis of progenies between Lilium intersectional hybrids and wild species using ND-FISH and GISH.

Intersectional hybrids in lilies possess significant breeding value, but the lack of complete lily genomes and complex genotypes pose challenges for early identification of lily hybrids. This study aimed to use intersectional hybrid cultivars as female parents and wild lilies as male parents to facilitate early identification of hybrid offsprings and enhance the efficiency and convenience of the process. We investigated the nature of cross combinations using Non-denaturing Fluorescence In Situ Hybridization (ND-FISH) and Genomic In Situ Hybridization (GISH) techniques. Three novel oligonucleotide probes-Oligo-pTa794, Oligo-pITS and Oligo-telo-were developed for lily chromosome research. Our results demonstrated successful hybridization between wild lilies and intersectional hybrid cultivars, producing a total of 130 hybrid progenies. The combination of ND-FISH and GISH analyses effectively revealed the genomic composition of the hybrid progeny and determined the parental origin of specific chromosomes. This research provides significant guidance for lily breeding practices and offers a valuable reference for the application of ND-FISH and GISH techniques in interspecific hybridization breeding and molecular cytogenetic research across various plant species. The methods developed enable more precise, efficient, and convenient identification of hybrid offsprings.

Comprehensive Next Generation Sequencing Reveals that Purported Primary Squamous Cell Carcinomas of the Parotid Gland are Genetically Heterogeneous.

Squamous cell carcinoma (SCC) is one of the most common malignancies involving the parotid gland, but it has been recognized that the vast majority of parotid SCC represents metastases, especially from the ipsilateral facial skin. Bona fide primary SCC of the parotid is so rare that it is unclear whether it truly exists at all. We sought to molecularly characterize cases diagnosed as primary parotid gland SCC to see if they possess a unique genetic makeup.We identified cases in our archives which had been diagnosed as primary SCC of the parotid gland. In all cases, metastatic disease was excluded by a thorough history and physical examination. Cases with histologic evidence of a precursor neoplasm (e.g., carcinoma ex-pleomorphic adenoma) were also excluded. Targeted next-generation sequencing (NGS) was attempted on all cases.Six cases diagnosed as primary parotid SCC were identified, arising in 4 males and 2 females ranging from 8 to 73 years (mean, 51.8 years). All cases exhibited keratinization and unequivocal invasion. Four of 6 appeared to be arising from cystically dilated ducts. Five of 6 exhibited well-developed cellular atypia; the remaining case, while cytologically bland, demonstrated perineural invasion. Targeted NGS was successful in 5 of 6 cases. Two SCC harbored several mutations in a mutational profile reminiscent of SCCs seen in other organs. One case harbored YAP1::MAML2, a fusion previously reported in porocarcinoma and other neoplasms. One case harbored IRF2BP2::RUNX2, and presumably represents keratocystoma or SCC ex-keratocystoma. Finally, one case an increase of C > T mutations consistent with ultraviolet damage, suggesting that this case represented a cryptic metastasis from cutaneous SCC.Our analysis did not confirm a unifying genetic signature for purported primary parotid SCC. Indeed, our findings suggest that true primary parotid gland SCC is even rarer than already believed. In our 5 cases with results, NGS findings demonstrated that one was likely a keratocystoma, one a cryptic metastasis from a cutaneous SCC, and one a porocarcinoma, either metastatic or primary. The two remaining cases had complex genotypes reminiscent of SCCs from other sites. This may be the signature of genuine parotid primary SCC, but metastasis from an SCC from another organ cannot be excluded. Accordingly, a diagnosis of primary parotid gland SCC should be viewed with skepticism.

Deciphering the Complexity of FSHD: A Multimodal Approach as a Model for Rare Disorders

Rare diseases are heterogeneous diseases characterized by various symptoms and signs. Due to the low prevalence of such conditions (less than 1 in 2000 people), medical expertise is limited, knowledge is poor and patients’ care provided by medical centers is inadequate. An accurate diagnosis is frequently challenging and ongoing research is also insufficient, thus complicating the understanding of the natural progression of the rarest disorders. This review aims at presenting the multimodal approach supported by the integration of multiple analyses and disciplines as a valuable solution to clarify complex genotype–phenotype correlations and promote an in-depth examination of rare disorders. Taking into account the literature from large-scale population studies and ongoing technological advancement, this review described some examples to show how a multi-skilled team can improve the complex diagnosis of rare diseases. In this regard, Facio-Scapulo-Humeral muscular Dystrophy (FSHD) represents a valuable example where a multimodal approach is essential for a more accurate and precise diagnosis, as well as for enhancing the management of patients and their families. Given their heterogeneity and complexity, rare diseases call for a distinctive multidisciplinary approach to enable diagnosis and clinical follow-up.

Sigmodontinae rodents as potential reservoirs for Borrelia burgdorferi sensu lato in the Delta and Paraná Islands ecoregion, Argentina.

The Borrelia burgdorferi sensu lato (s.l.) complex includes a group of spirochete bacteria that are involved in transmission cycles with vertebrates and the ticks associated with them. Rodents play an essential role in the ecoepidemiology of Borrelia, acting as reservoirs for the bacteria and hosts for ticks. To identify potential reservoir vertebrate hosts of Borrelia spirochetes in Argentina, we conducted molecular analyses on tissues obtained from a population of Sigmodontinae rodents inhabiting the Delta and Parana Islands ecoregion. We report the presence of B. burgdorferi s.l. complex genotypes infecting Akodon azarae and Oxymycterus rufus in this ecoregion. Phylogenetic analysis revealed at least three flaB haplotypes related to 'Candidatus Borrelia paulista' and Borrelia sp. strain Pampa from Brazil and to several Borrelia haplotypes from Uruguay. Additionally, we identified different alleles of the plasmid-borne gene ospC in B. burgdorferi s.l. infecting A. azarae and Ox. rufus. The ospC allele present in Borrelia from Ox. rufus was also detected in Borrelia from Oligoryzomys mattogrossae, indicating the ability of Borrelia harbouring this ospC allele to infect multiple Sigmodontinae species, whereas the ospC allele from Borrelia infecting A. azarae represents a novel variant. Further research is needed to determine host specificity of ospC alleles present in South America.

Atypical ADPKD Due to Complex Genotypes of Both PKD1 and HNF1B Pathogenic Variants: An Educational Case Report

Atypical ADPKD Due to Complex Genotypes of Both PKD1 and HNF1B Pathogenic Variants: An Educational Case Report

ОЦЕНКА КОРОВ-ПЕРВОТЁЛОК ЧЁРНО-ПЁСТРОЙ ПОРОДЫ ПО ДНК-МАРКЕРАМ, АССОЦИИРОВАННЫХ С ХОЗЯЙСТВЕННО-ПОЛЕЗНЫМИ ПРИЗНАКАМИ

At present time are widely used genetic markers as means in the selection of highly productive animals. Since the genes: CSN3 (kappa-casein), PIT-1 (pituitary-specific transcription factor), PRL (prolactin), GH (somatotropin) are polymorphic and encode various proteins, the study of their influence on the productive traits of cattle is relevant. In this regard, the goal of the work is to determine the influence of complex genotypes of the studied genes on the milk productivity of first-calf cows of the Black-and-White breed bred in the collective farm-breeding plant «Kazminsky» in the Kochubeevsky district of the Stavropol Territory. The place of research is the Department of Genetics and Biotechnology, VNIIOK, a branch of the North Caucasian Federal National Research Center. This article presents the results of DNA genotyping of allelic polymorphism for the CSN3, PIT-1, PRL, GH genes using PCR-RFLP methods in first-calf cows of the Black-and-White breed. It was established that these genes in the studied sample are polymorphic. The frequency of occurrence of the desired CSN3B allele in the studied sample was 0.23. The presence of alleles PIT-1A and PIT-1B of the pituitary-specific transcription factor gene was noted with a frequency of occurrence of 0.52 and 0.48. A feature of the PRL gene polymorphism was the fairly high frequency of occurrence of the PRLA allele (0.60). In this study sample of dairy cattle, the frequency of occurrence of the desired GHL allele of the somatotropin gene was 0.62. All variants of complex genotypes were also identified and their relationship with milk productivity in black-and-white cows was noted. The study sample was dominated by animals carrying complex desirable genotypes, consisting of four and three marker alleles of three and two genes (CSN3AB/PIT-1BB/GHLV; CSN3AB/PIT1AB/GHLL or PIT-1AB/PRLAB/GHLV; PIT-1AA/GHLL ) - 46.7 %. Milk yield per lactation between groups of black-and-white first-calf cows with different complex genotypes ranged from 5839.14 to 8611.33 kg. The mass fraction of fat in milk ranged from 3.93 to 4.04 %, and protein from 2.99 to 3.14 %.

Long-read sequencing of CYP2D6 may improve psychotropic prescribing and treatment outcomes: A systematic review and meta-analysis.

The enzyme expression (i.e. phenotype) of the Cytochrome P450 2D6 (CYP2D6) gene is highly relevant to the metabolism of psychotropic medications, and therefore to precision medicine (i.e. personalised prescribing). This review aims to assess the improvement in CYP2D6 phenotyping sensitivity (IPS) and accuracy (IPA) offered by long-read sequencing (LRS), a new genetic testing technology. Human DNA samples that underwent LRS genotyping of CYP2D6 in published, peer-reviewed clinical research were eligible for inclusion. A systematic literature search was conducted until 30 September 2023. CYP2D6 genotypes were translated into phenotypes using the international consensus method. IPS was the percentage of non-normal LRS CYP2D6 phenotypes undetectable with FDA-approved testing (AmpliChip). IPA was the percentage of LRS CYP2D6 phenotypes mischaracterised by non-LRS genetic tests (for samples with LRS and non-LRS data). Six studies and 1411 samples were included. In a meta-analysis of four studies, IPS was 10% overall (95% CI = (2, 18); n = 1385), 20% amongst Oceanians (95% CI = (17, 23); n = 582) and 2% amongst Europeans (95% CI = (1, 4); n = 803). IPA was 4% in a large European cohort (95% CI = (2, 7); n = 567). When LRS was used selectively (e.g. for novel or complex CYP2D6 genotypes), very high figures were observed for IPS (e.g. 88%; 95% CI = (72, 100); n = 17; country = Japan) and IPA (e.g. 76%; 95% CI = (55, 98); n = 17; country = Japan). LRS improves CYP2D6 phenotyping compared to established genetic tests, particularly amongst Oceanian and Japanese individuals, and those with novel or complex genotypes. LRS may therefore assist in optimising personalised prescribing of psychotropic medications. Further research is needed to determine associated clinical benefits, such as increased medication safety and efficacy.