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Preterm birth (PTB), or birth that occurs earlier than 37 weeks of gestational age, is a major contributor to infant mortality and neonatal hospitalization. Mutations in the mitochondrial genome (mtDNA) have been linked to various rare mitochondrial disorders and may be a contributing factor in PTB given that maternal genetic factors have been strongly linked to PTB. However, to date, no study has found a conclusive connection between a particular mtDNA variant and PTB. Given the high mtDNA copy number per cell, an automated pipeline was developed for detecting mtDNA variants using low-coverage whole-genome sequencing (lcWGS) data. The pipeline was first validated against samples of known heteroplasmy, and then applied to 929 samples from a PTB cohort from diverse ethnic backgrounds with an average gestational age of 27.18 weeks (range: 21-30). Our new pipeline successfully identified haplogroups and a large number of mtDNA variants in this large PTB cohort, including 8 samples carrying known pathogenic variants and 47 samples carrying rare mtDNA variants. These results confirm that lcWGS can be utilized to reliably identify mtDNA variants. These mtDNA variants may make a contribution toward preterm birth in a small proportion of live births.

This document is an editorial published in the journal Frontiers in Genetics. It discusses the current progress in genomic and genetic research on human viral diseases. The editorial emphasizes the importance of understanding the interplay between viruses and their human hosts, particularly in light of the COVID-19 pandemic. The integration of both host and virus perspectives through genetic and genomic studies can enhance our understanding of viral infections and contribute to the development of effective strategies against human viral diseases. The editorial also highlights several research articles published in the journal that address topics such as COVID-19, HIV-1, and the application of next-generation sequencing in detecting infectious agents. [Extracted from the article]

This article discusses the use of 'omics' data, such as genomics, proteomics, and metabolomics, in cardiovascular biology research. The article highlights the shift towards a human-forward approach, where large-scale data is generated from human samples to gain mechanistic insights, identify disease risk, and discover new therapeutic targets. However, the translation of these costly experiments into biomarkers or therapeutics for patient care has been limited. The article emphasizes the need for interdisciplinary team science, better bioinformatics, and time to bridge the gap between 'omics' discovery and clinical application. [Extracted from the article]

In this issue of Neuron , Chemparathy et al. 1 provide human genetics data suggesting that APOE loss-of-function mutations may confer resistance to Alzheimer's disease (AD) without compromising longevity. These data strongly support the APOE toxic gain-of-function hypothesis for AD. In this issue of Neuron , Chemparathy et al. provide human genetics data suggesting that APOE loss-of-function mutations may confer resistance to Alzheimer's disease (AD) without compromising longevity. These data strongly support the APOE toxic gain-of-function hypothesis for AD. [ABSTRACT FROM AUTHOR]

This article discusses chromatinopathies, a group of genetic conditions caused by disruptions to the structure or function of chromatin. Chromatinopathies were first proposed in 2011 and include disorders such as Rubinstein-Taybi syndrome, Fragile X syndrome, and Rett syndrome. Recent advancements in genomics and other techniques have expanded the understanding of chromatinopathies to include 179 disorders, some of which are not associated with neurological manifestations. The article also explores the role of histones, the regulation of transcriptional programs, nuclear speckleopathies, variant interpretation challenges, and the potential use of DNA methylation as a diagnostic tool. The authors emphasize the importance of patient participation and clinician observations in advancing the understanding of chromatinopathies. Overall, this comprehensive exploration of chromatinopathies contributes to our understanding of these complex conditions and has the potential to improve patient outcomes. [Extracted from the article]

This article reports on the first case of fibrochondrogenesis type I (FBCG1) in Korea. FBCG1 is a rare autosomal recessive skeletal dysplasia caused by a mutation in the COL11A1 gene. The patient, a 5-year-old boy, exhibited short stature, skeletal anomalies, facial dysmorphism, and other characteristic features of FBCG1. Whole exome sequencing revealed compound heterozygous variants in the COL11A1 gene. This case provides insight into the phenotypic spectrum of FBCG1 and highlights the importance of genetic testing for early diagnosis and management. [Extracted from the article]

This article analyzes the genetic variants in protein-coding genes of the Aoluguya reindeer, a subspecies of reindeer facing the threat of extinction. The study collected blood samples from healthy and unrelated male adult individuals and sequenced their DNA. The analysis revealed a significant number of single nucleotide polymorphisms (SNPs) and indels in the reindeer population. The findings provide valuable insights into the genetic variation and adaptation of the Aoluguya reindeer and the entire reindeer species. [Extracted from the article]

The article discusses the use of preclinical murine models to study atherosclerosis and their limited success in translating findings to human disease. The authors propose a method called PRESCIANT that integrates and contextualizes preclinical data to improve translation. They analyzed data from studies using ApoE and LDLR knockout mouse models and identified biologic pathways associated with atherosclerosis. They also evaluated the association between these pathways and human atherosclerotic cardiovascular disease. The results showed that increasing biological contextualization improved the significance of enrichment for associations with human disease. The study highlights the importance of lipid handling, fibrosis, and inflammation pathways in atherosclerosis and suggests the need for further research to define clinical associations specific to vascular bed and disease acuity. [Extracted from the article]

This article is based on the address given by the author at the 2023 meeting of The American Society of Human Genetics (ASHG) in Washington, D.C. A video of the original address can be found at the ASHG website. [ABSTRACT FROM AUTHOR]

This article is based on the address given by the author at the 2023 meeting of The American Society of Human Genetics (ASHG). A video of the original address can be found at the ASHG website. [ABSTRACT FROM AUTHOR]

This article discusses the implications of blood type in personalized microbiome therapy. The study conducted a genome-wide association study between human genetics and gut microbial structural variations, specifically focusing on the ABO gene and the gut microbe Faecalibacterium prausnitzii. The study found a significant association between the ABO gene and a specific SV region in F. prausnitzii, indicating that blood type A sugar can fuel gut microbes and promote human health. The findings suggest that personalized microbiome-based medicine may be necessary, and further research is needed to understand the causal relationship between blood type, F. prausnitzii, and host health outcomes. [Extracted from the article]

The greater muscle fiber cross-sectional area (CSA) is associated with greater skeletal muscle mass and strength, whereas muscle fiber atrophy is considered a major feature of sarcopenia. Muscle fiber size is a polygenic trait influenced by both environmental and genetic factors. However, the genetic variants underlying inter-individual differences in muscle fiber size remain largely unknown. The aim of our study was to determine whether 1535 genetic variants previously identified in a genome-wide association study of appendicular lean mass are associated with the CSA of fast-twitch muscle fibers (which better predict muscle strength) in the m. vastus lateralis of 148 physically active individuals (19 power-trained and 28 endurance-trained females, age 28.0 ± 1.1; 28 power-trained and 73 endurance-trained males, age 31.1 ± 0.8). Fifty-seven single-nucleotide polymorphisms (SNPs) were identified as having an association with muscle fiber size (p < 0.05). Of these 57 SNPs, 31 variants were also associated with handgrip strength in the UK Biobank cohort (n = 359,729). Furthermore, using East Asian and East European athletic (n = 731) and non-athletic (n = 515) cohorts, we identified 16 SNPs associated with athlete statuses (sprinter, wrestler, strength, and speed–strength athlete) and weightlifting performance. All SNPs had the same direction of association, i.e., the lean mass-increasing allele was positively associated with the CSA of muscle fibers, handgrip strength, weightlifting performance, and power athlete status. In conclusion, we identified 57 genetic variants associated with both appendicular lean mass and fast-twitch muscle fiber size of m. vastus lateralis that may, in part, contribute to a greater predisposition to power sports.

We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward.

The growing prevalence of opioid use disorder (OUD) constitutes an urgent health crisis. Ample evidence indicates that risk for OUD is heritable. As a surrogate (or proxy) for OUD, we explored the genetic basis of using prescription opioids 'not as prescribed'. We hypothesized that misuse of opiates might be a heritable risk factor for OUD. To test this hypothesis, we performed a genome-wide association study (GWAS) of problematic opioid use (POU) in 23andMe research participants of European ancestry (N = 132,113; 21% cases). We identified two genome-wide significant loci (rs3791033, an intronic variant of KDM4A; rs640561, an intergenic variant near LRRIQ3). POU showed positive genetic correlations with the two largest available GWAS of OUD and opioid dependence (rg = 0.64, 0.80, respectively). We also identified numerous additional genetic correlations with POU, including alcohol dependence (rg = 0.74), smoking initiation (rg = 0.63), pain relief medication intake (rg = 0.49), major depressive disorder (rg = 0.44), chronic pain (rg = 0.42), insomnia (rg = 0.39), and loneliness (rg = 0.28). Although POU was positively genetically correlated with risk-taking (rg = 0.38), conditioning POU on risk-taking did not substantially alter the magnitude or direction of these genetic correlations, suggesting that POU does not simply reflect a genetic tendency towards risky behavior. Lastly, we performed phenome- and lab-wide association analyses, which uncovered additional phenotypes that were associated with POU, including respiratory failure, insomnia, ischemic heart disease, and metabolic and blood-related biomarkers. We conclude that opioid misuse can be measured in population-based cohorts and provides a cost-effective complementary strategy for understanding the genetic basis of OUD.

PurposeWe examined the demographic and clinicopathological parameters associated with the time to convert from active surveillance to treatment among men with prostate cancer.Materials and methodsA multi-institutional cohort of 7,279 patients managed with active surveillance had data and biospecimens collected for germline genetic analyses.ResultsOf 6,775 men included in the analysis, 2,260 (33.4%) converted to treatment at a median followup of 6.7 years. Earlier conversion was associated with higher Gleason grade groups (GG2 vs GG1 adjusted hazard ratio [aHR] 1.57, 95% CI 1.36-1.82; ≥GG3 vs GG1 aHR 1.77, 95% CI 1.29-2.43), serum prostate specific antigen concentrations (aHR per 5 ng/ml increment 1.18, 95% CI 1.11-1.25), tumor stages (cT2 vs cT1 aHR 1.58, 95% CI 1.41-1.77; ≥cT3 vs cT1 aHR 4.36, 95% CI 3.19-5.96) and number of cancerous biopsy cores (3 vs 1-2 cores aHR 1.59, 95% CI 1.37-1.84; ≥4 vs 1-2 cores aHR 3.29, 95% CI 2.94-3.69), and younger age (age continuous per 5-year increase aHR 0.96, 95% CI 0.93-0.99). Patients with high-volume GG1 tumors had a shorter interval to conversion than those with low-volume GG1 tumors and behaved like the higher-risk patients. We found no significant association between the time to conversion and self-reported race or genetic ancestry.ConclusionsA shorter time to conversion from active surveillance to treatment was associated with higher-risk clinicopathological tumor features. Furthermore, patients with high-volume GG1 tumors behaved similarly to those with intermediate and high-risk tumors. An exploratory analysis of self-reported race and genetic ancestry revealed no association with the time to conversion.

Summary: Molecular quantitative trait loci (QTLs) allow us to understand the biology captured in genome-wide association studies (GWASs). The placenta regulates fetal development and shows sex differences in DNA methylation. We therefore hypothesized that placental methylation QTL (mQTL) explain variation in genetic risk for childhood onset traits, and that effects differ by sex. We analyzed 411 term placentas from two studies and found 49,252 methylation (CpG) sites with mQTL and 2,489 CpG sites with sex-dependent mQTL. All mQTL were enriched in regions that typically affect gene expression in prenatal tissues. All mQTL were also enriched in GWAS results for growth- and immune-related traits, but male- and female-specific mQTL were more enriched than cross-sex mQTL. mQTL colocalized with trait loci at 777 CpG sites, with 216 (28%) specific to males or females. Overall, mQTL specific to male and female placenta capture otherwise overlooked variation in childhood traits.

Summary: A long CGG-repeat tract in the FMR1 gene induces the epigenetic silencing that causes fragile X syndrome (FXS). Epigenetic changes include H4K20 trimethylation, a heterochromatic modification frequently implicated in transcriptional silencing. Here, we report that treatment with A-196, an inhibitor of SUV420H1/H2, the enzymes responsible for H4K20 di-/trimethylation, does not affect FMR1 transcription, but does result in increased chromosomal duplications. Increased duplications were also seen in FXS cells treated with SCR7, an inhibitor of Lig4, a ligase essential for NHEJ. Our study suggests that the fragile X (FX) locus is prone to spontaneous DNA damage that is normally repaired by NHEJ. We suggest that heterochromatinization of the FX allele may be triggered, at least in part, in response to this DNA damage.

Summary: Successful genome editing in primary human islets could reveal features of the genetic regulatory landscape underlying β cell function and diabetes risk. Here, we describe a CRISPR-based strategy to interrogate functions of predicted regulatory DNA elements using electroporation of a complex of Cas9 ribonucleoprotein (Cas9 RNP) and guide RNAs into primary human islet cells. We successfully targeted coding regions including the PDX1 exon 1, and non-coding DNA linked to diabetes susceptibility. CRISPR-Cas9 RNP approaches revealed genetic targets of regulation by DNA elements containing candidate diabetes risk SNPs, including an in vivo enhancer of the MPHOSPH9 gene. CRISPR-Cas9 RNP multiplexed targeting of two cis-regulatory elements linked to diabetes risk in PCSK1, which encodes an endoprotease crucial for Insulin processing, also demonstrated efficient simultaneous editing of PCSK1 regulatory elements, resulting in impaired β cell PCSK1 regulation and Insulin secretion. Multiplex CRISPR-Cas9 RNP provides powerful approaches to investigate and elucidate human islet cell gene regulation in health and diabetes.

ABSTRACTBackground In recent times, stem cell therapy has recently gained popularity, and is used for regenerating oral and maxillofacial structures. This study aimed to review stem cell applications in the reconstructive treatment of cleft lip and palate and other craniofacial anomalies.Methods A search on the PubMed database, Dental and Oral Science and CINAHL was conducted to identify relevant studies on stem cells and their implications in the reconstructive treatment of cleft lip and palate.Results Studies included in this review reported stem cell usage in the reconstruction of defects in cleft lip and palate cases, hemifacial microsomia, Treacher-Collins syndrome, Parry-Romberg syndrome and craniosynostosis. Stem cell knowledge is being utilized for several different tissues and organs. Preclinical data has displayed the potential of stem cells for craniofacial surgery.Conclusions Fortunately, stem cell-based oral and maxillofacial regeneration has shown promising results. Understanding stem cell practice will open a new era of research and proposed advancement in treating various diseases.

Studies of genetic factors associated with severe COVID-19 in young adults have been limited in non-Caucasian populations. Here, we clinically characterize a case series of patients with COVID-19, who were otherwise healthy, young adults (N = 55; mean age 34.1 ± SD 5.0 years) from 16 Asian, Middle Eastern, and North African countries. Using whole exome sequencing, we identify rare, likely deleterious variants affecting 16 immune-related genes in 17 out of 55 patients (31%), including 7 patients (41% of all carriers or 12.7% of all patients) who harbored multiple such variants mainly in interferon and toll-like receptor genes. Protein network analysis as well as transcriptomic analysis of nasopharyngeal swabs from an independent COVID-19 cohort (N = 50; 42% Asians and 22% Arabs) revealed that most of the altered genes, as identified by whole exome sequencing, and the associated molecular pathways were significantly altered in COVID-19 patients. Genetic variants tended to be associated with mortality, intensive care admission, and ventilation support. Our clinical cases series, genomic and transcriptomic findings suggest a possible role for interferon pathway genes in severe COVID-19 and highlight the importance of extending genetic studies to diverse populations to better understand the human genetics of disease. [ABSTRACT FROM AUTHOR]

Human genetic variants that introduce an AG into the intronic region between the branchpoint (BP) and the canonical splice acceptor site (ACC) of protein-coding genes can disrupt pre-mRNA splicing. Using our genome-wide BP database, we delineated the BP-ACC segments of all human introns and found extreme depletion of AG/YAG in the [BP+8, ACC-4] high-risk region. We developed AGAIN as a genome-wide computational approach to systematically and precisely pinpoint intronic AG-gain variants within the BP-ACC regions. AGAIN identified 350 AG-gain variants from the Human Gene Mutation Database, all of which alter splicing and cause disease. Among them, 74% created new acceptor sites, whereas 31% resulted in complete exon skipping. AGAIN also predicts the protein-level products resulting from these two consequences. We performed AGAIN on our exome/genomes database of patients with severe infectious diseases but without known genetic etiology and identified a private homozygous intronic AG-gain variant in the antimycobacterial gene SPPL2A in a patient with mycobacterial disease. AGAIN also predicts a retention of six intronic nucleotides that encode an in-frame stop codon, turning AG-gain into stop-gain. This allele was then confirmed experimentally to lead to loss of function by disrupting splicing. We further showed that AG-gain variants inside the high-risk region led to misspliced products, while those outside the region did not, by two case studies in genes STAT1 and IRF7. We finally evaluated AGAIN on our 14 paired exome-RNAseq samples and found that 82% of AG-gain variants in high-risk regions showed evidence of missplicing. [ABSTRACT FROM AUTHOR]

Quantitative traits are often complex because of the contribution of many loci, with further complexity added by environmental factors. In medical research, systems genetics is a powerful approach for the study of complex traits, as it integrates intermediate phenotypes, such as RNA, protein, and metabolite levels, to understand molecular and physiological phenotypes linking discrete DNA sequence variation to complex clinical and physiological traits. The primary purpose of this review is to describe some of the resources and tools of systems genetics in humans and rodent models, so that researchers in many areas of biology and medicine can make use of the data. [ABSTRACT FROM AUTHOR]

Background: Biorepositories archive and distribute well-characterized biospecimens for research to support the development of medical diagnostics and therapeutics. Knowledge of biobanking and associated practices is incomplete in low- and middle-income countries where disease burden is disproportionately high. In 2011, the African Society of Human Genetics (AfSHG), the National Institutes of Health (NIH), and the Wellcome Trust founded the Human Heredity and Health in Africa (H3Africa) consortium to promote genomic research in Africa and established a network of three biorepositories regionally located in East, West, and Southern Africa to support biomedical research. This manuscript describes the processes established by H3Africa biorepositories to prepare research sites to collect high-quality biospecimens for deposit at H3Africa biorepositories. Methods: The biorepositories harmonized practices between the biorepositories and the research sites. The biorepositories developed guidelines to establish best practices and define biospecimen requirements; standard operating procedures (SOPs) for common processes such as biospecimen collection, processing, storage, transportation, and documentation as references; requirements for minimal associated datasets and formats; and a template material transfer agreements (MTA) to govern biospecimen exchange. The biorepositories also trained and mentored collection sites in relevant biobanking processes and procedures and verified biospecimen deposit processes. Throughout these procedures, the biorepositories followed ethical and legal requirements. Results: The 20 research projects deposited 107,982 biospecimens (76% DNA, 81,067), in accordance with the ethical and legal requirements and established best practices. The biorepositories developed and customized resources and human capacity building to support the projects. [The biorepositories developed 34 guidelines, SOPs, and documents; trained 176 clinicians and scientists in over 30 topics; sensitized ethical bodies; established MTAs and reviewed consent forms for all projects; attained import permits; and evaluated pilot exercises and provided feedback. Conclusions: Biobanking in low- and middle-income countries by local skilled staff is critical to advance biobanking and genomic research and requires human capacity and resources for global partnerships. Biorepositories can help build human capacity and resources to support biobanking by partnering with researchers. Partnerships can be structured and customized to incorporate document development, ethics, training, mentorship, and pilots to prepare sites to collect, process, store, and transport biospecimens of high quality for future research. [ABSTRACT FROM AUTHOR]

Advances in long-read sequencing and assembly now mean that individual labs can generate phased genomes that are more accurate and more contiguous than the original human reference genome. With declining costs and increasing democratization of technology, we suggest that complete genome assemblies, where both parental haplotypes are phased telomere to telomere, will become standard in human genetics. Soon, even in clinical settings where rigorous sample-handling standards must be met, affected individuals could have reference-grade genomes fully sequenced and assembled in just a few hours given advances in technology, computational processing, and annotation. Complete genetic variant discovery will transform how we map, catalog, and associate variation with human disease and fundamentally change our understanding of the genetic diversity of all humans. In the next decade, advancements in long-read sequencing technologies will facilitate widespread access to complete, haplotype-phased genome assemblies. This will significantly enhance variant discovery, understanding of genetic diversity, and epigenetic characterization, transforming the field of human genetics and our approach to associating genetic variations with diseases. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA (mtDNA) is an indispensable genetic marker in forensic genetics. The emergence and development of massively parallel sequencing (MPS) makes it possible to obtain complete mitochondrial genome sequences more quickly and accurately. The study evaluated the advantages and limitations of the ForenSeq mtDNA Whole Genome Kit in the practical application of forensic genetics by detecting human genomic DNA standards and thirty-three case samples. We used control DNA with different amount to determine sensitivity of the assay. Even when the input DNA is as low as 2.5 pg, most of the mitochondrial genome sequences could still be covered. For the detection of buccal swabs and aged case samples (bloodstains, bones, teeth), most samples could achieve complete coverage of mitochondrial genome. However, when ancient samples and hair samples without hair follicles were sequenced by the kit, it failed to obtain sequence information. In general, the ForenSeq mtDNA Whole Genome Kit has certain applicability to forensic low template and degradation samples, and these results provide the data basis for subsequent forensic applications of the assay. The overall detection process and subsequent analysis are easy to standardize, and it has certain application potential in forensic cases. [ABSTRACT FROM AUTHOR]

To accelerate the impact of African genomics on human health, data science skills and awareness of Africa's rich genetic diversity must be strengthened globally. We describe the first African genomics data science workshop, implemented by the African Society of Human Genetics (AfSHG) and international partners, providing a framework for future workshops. [ABSTRACT FROM AUTHOR]

This article provides an overview of the use of viruses in gene therapy to treat human diseases. It explains that viruses can be modified to carry healthy genes into cells and replace faulty genes, offering potential treatments for genetic disorders. The article acknowledges that gene therapy has shown promise but also highlights challenges, such as improving delivery methods and addressing previous tissue damage. It also raises ethical concerns about the permanent changes made to human DNA and the potential for unintended consequences. The article concludes by noting that while gene therapy is currently expensive and not widely available, scientists are working to improve its effectiveness and accessibility. [Extracted from the article]

Understanding how human infrastructure and other landscape attributes affect genetic differentiation in animals is an important step for identifying and maintaining dispersal corridors for these species. We built upon recent advances in the field of landscape genetics by using an individual‐based and multiscale approach to predict landscape‐level genetic connectivity for grizzly bears (Ursus arctos) across ~100,000 km2 in Canada's southern Rocky Mountains. We used a genetic dataset with 1156 unique individuals genotyped at nine microsatellite loci to identify landscape characteristics that influence grizzly bear gene flow at multiple spatial scales and map predicted genetic connectivity through a matrix of rugged terrain, large protected areas, highways and a growing human footprint. Our corridor‐based modelling approach used a machine learning algorithm that objectively parameterized landscape resistance, incorporated spatial cross validation and variable selection and explicitly accounted for isolation by distance. This approach avoided overfitting, discarded variables that did not improve model performance across withheld test datasets and spatial predictive capacity compared to random cross‐validation. We found that across all spatial scales, geographic distance explained more variation in genetic differentiation in grizzly bears than landscape variables. Human footprint inhibited connectivity across all spatial scales, while open canopies inhibited connectivity at the broadest spatial scale. Our results highlight the negative effect of human footprint on genetic connectivity, provide strong evidence for using spatial cross‐validation in landscape genetics analyses and show that multiscale analyses provide additional information on how landscape variables affect genetic differentiation. [ABSTRACT FROM AUTHOR]

Background: Turner syndrome (TS) is the most common chromosomal abnormality in females. The diagnosis of TS is based on karyotyping of 30 blood lymphocytes. This technique does not rule out tissue mosaicism or low-grade mosaicism in the blood. Because of the associated risk of gonadoblastoma, mosaicism is especially important in case this involves a Y chromosome. Aims: This study was set to determine the value of additional genetic studies such as fluorescent in situ hybridisation and the inclusion of buccal cells in search for mosaicism in TS patients. Settings and Design: This cross-sectional, descriptive study was performed in Human Genetics Department, Medical Research Institute, Alexandria University. Materials and Methods: Fluorescence in situ hybridisation technique was applied to lymphocyte cultures as well as buccal smears using centromeric probes for X and Y chromosomes. Genotype phenotype correlation was also evaluated. Statistical Analysis Used: Descriptive study where categorical variables were described using number and percentage and continuous variables were described using mean and standard deviation. Results: Fluorescence in situ hybridisation technique study detected hidden mosaicism in 60% of studied patients; 20% of patients had a cell line containing Y material, while 40% had variable degrees of X, XX mosaicism, and in the remaining 40% no second cell line was detected. Fluorescence in situ hybridisation study helped identify the origin of the marker to be Y in all patients. The introduction of an additional cell line helped in identifying mosaicism in patients with monosomy X. Virilisation signs were only observed among TS patients with Y cell line mosaicism. The clinical manifestations were more severe in patients with monosomy X than other mosaic cases. Conclusions: Molecular cytogenetic investigation for all suspected cases of TS should be considered for appropriate treatment plan and genetic counselling. [ABSTRACT FROM AUTHOR]

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The need for knowledge of one's own biological nature was a crucial impetus for scientific-technological progress in the fields of molecular biology, chemistry, and genetic engineering, which soon turned into a way to control human genetic material and its evolution. Although the procedure for reconstructing the personality genome is designed to protect humanity from hereditary or oncological diseases, there is still a huge risk of using this technology to modify intellectual abilities or physical characteristics. The purpose of this study is to describe and characterize the moral, ethical, and legal factors that arise in using technology to correct a person's genetic code for non-medical reasons. Through systematic analysis and dialectical method, the current state of the legislative framework in the field of editing the biological material of the individual was investigated, while the generalisation method allowed identifying the main bioethical dilemmas associated with a certain problem. Exploring the possibility of changing the human genome through the prism of its interdependence with globalising metamorphoses in society, the key threats of the use of technology, its impact on the formation of the latest ethical standards, and compliance with the fundamental rights and freedoms of the patient were identified. Therewith, focusing on identifying gaps in the regulatory regulation of the human genome correction procedure, recommendations were made to improve the international legal foundation in this area of legal relations. In general, the chosen subject contains a considerable number of still unexplored aspects, so this study is designed to draw the scientific community's attention to the problem of editing a person's biological identity for non-medical purposes. [ABSTRACT FROM AUTHOR]

Population-scale biobanks linked to electronic health record data provide vast opportunities to extend our knowledge of human genetics and discover new phenotype-genotype associations. Given their dense phenotype data, biobanks can also facilitate replication studies on a phenome-wide scale. Here, we introduce the phenotype-genotype reference map (PGRM), a set of 5,879 genetic associations from 523 GWAS publications that can be used for high-throughput replication experiments. PGRM phenotypes are standardized as phecodes, ensuring interoperability between biobanks. We applied the PGRM to five ancestry-specific cohorts from four independent biobanks and found evidence of robust replications across a wide array of phenotypes. We show how the PGRM can be used to detect data corruption and to empirically assess parameters for phenome-wide studies. Finally, we use the PGRM to explore factors associated with replicability of GWAS results. The phenotype-genotype reference map (PGRM) is a curated set of GWAS associations that facilitates efficient phenome-wide replication studies with biobank data. The PGRM can be used to detect data corruption, assess model parameters, and explore factors that affect replicability of findings. [ABSTRACT FROM AUTHOR]

The recent development of high-throughput sequencing platforms provided impressive insights into the field of human genetics and contributed to considering structural variants (SVs) as the hallmark of genome instability, leading to the establishment of several pathologic conditions, including neoplasia and neurodegenerative and cognitive disorders. While SV detection is addressed by next-generation sequencing (NGS) technologies, the introduction of more recent long-read sequencing technologies have already been proven to be invaluable in overcoming the inaccuracy and limitations of NGS technologies when applied to resolve wide and structurally complex SVs due to the short length (100-500 bp) of the sequencing read utilized. Among the long-read sequencing technologies, Oxford Nanopore Technologies developed a sequencing platform based on a protein nanopore that allows the sequencing of "native" long DNA molecules of virtually unlimited length (typical range 1-100 Kb). In this review, we focus on the bioinformatics methods that improve the identification and genotyping of known and novel SVs to investigate human pathological conditions, discussing the possibility of introducing nanopore sequencing technology into routine diagnostics. [ABSTRACT FROM AUTHOR]

Background Congenital anomalies of the kidney and urinary tract (CAKUT) are the leading cause of kidney failure in children with phenotypic and genotypic heterogeneity. Our objective was to describe the genetic spectrum and identify the risk factors for kidney failure in children with CAKUT. Methods Clinical and genetic data were derived from a multicentre network [Chinese Children Genetic Kidney Disease Database (CCGKDD)] and the Chigene database. A total of 925 children with CAKUT who underwent genetic testing from 2014 to 2020 across China were studied. Data for a total of 584 children were obtained from the CCGKDD, including longitudinal data regarding kidney function. The risk factors for kidney failure were determined by the Kaplan–Meier method and Cox proportional hazards models. Results A genetic diagnosis was established in 96 of 925 (10.3%) children, including 72 (8%) with monogenic variants, 20 (2%) with copy number variants (CNVs) and 4 (0.4%) with major chromosomal anomalies. Patients with skeletal abnormalities were more likely to have large CNVs or abnormal karyotypes than monogenic variants. Eighty-two patients from the CCGKDD progressed to kidney failure at a median age of 13.0 years (95% confidence interval 12.4–13.6) and 24 were genetically diagnosed with variants of PAX2, TNXB, EYA1, HNF1B and GATA3 or the 48,XXYY karyotype. The multivariate analysis indicated that solitary kidney, posterior urethral valves, bilateral hypodysplasia, the presence of certain variants and premature birth were independent prognostic factors. Conclusions The genetic spectrum of CAKUT varies among different subphenotypes. The identified factors indicate areas that require special attention. [ABSTRACT FROM AUTHOR]

Large-effect loci--those statistically significant loci discovered by genome-wide association studies or linkage mapping--associated with key traits segregate amidst a background of minor, often undetectable, genetic effects in wild and domesticated plants and animals. Accurately attributing mean differences and variance explained to the correct components in the linear mixed model analysis is vital for selecting superior progeny and parents in plant and animal breeding, gene therapy, and medical genetics in humans. Marker-assisted prediction and its successor, genomic prediction, have many advantages for selecting superior individuals and understanding disease risk. However, these two approaches are less often integrated to study complex traits with different genetic architectures. This simulation study demonstrates that the average semivariance can be applied to models incorporating Mendelian, oligogenic, and polygenic terms simultaneously and yields accurate estimates of the variance explained for all relevant variables. Our previous research focused on largeeffect loci and polygenic variance separately. This work aims to synthesize and expand the average semivariance framework to various genetic architectures and the corresponding mixed models. This framework independently accounts for the effects of large-effect loci and the polygenic genetic background and is universally applicable to genetics studies in humans, plants, animals, and microbes. [ABSTRACT FROM AUTHOR]

In this paper I argue that the extent to which a human trait is genetically caused can causally depend upon whether the trait is categorized within human genetics as genetically caused. This makes the kind genetically caused trait an interactive kind. I demonstrate that this thesis is both conceptually coherent and empirically plausible. I outline the core rationale of this thesis and demonstrate its conceptual coherence by drawing upon Waters' (2007) analysis of genetic causation. I add empirical plausibility to the thesis by describing a hypothetical but empirically plausible mechanism by which the fact that obesity is categorized as genetically caused within human genetics increases the extent to which obesity is in fact genetically caused. [ABSTRACT FROM AUTHOR]

ObjectivesOur aim in this study was to understand how genetics ideas are appropriated and mobilized online toward the political projects of White nationalism and the alt right. Studying three different online venues, we investigated how genetics is used to support racial realism, hereditarianism, and racial hierarchy. We analyzed how these ideas are connected to political and metapolitical projects. In addition, we examined the strategies used to build authority for these interpretations.MethodsWe analyze three online venues in which genetics has been mobilized to advance racial realism and hereditarian explanations of racial differences. These were (a) the use of genetic ancestry tests in online nationalist discussions, (b) blogs and other venues in which the human biodiversity ideas are articulated, (c) activities surrounding the OpenPsych collection of online journals. Ethnographic and interpretive methods were applied to investigate scientific and political meanings of efforts to mobilize genetic ideas.ResultsWe found that White nationalists use genetic ancestry tests to align White identity with ideas of racial purity and diversity, educating each other about genetics, and debating the boundaries of Whiteness. "Human biodiversity" has been mobilized as a movement to catalog and create hereditarian ideas about racial differences and to distribute them as "red pills" to transform online discourse. The OpenPsych journals have allowed amateur hereditarian psychologists to publish papers, coordinate activity, and legitimate their project at the academic margins.ConclusionsThese various appropriations of genetics aim to further racial realism and hereditarian explanations of racial social and behavioral differences. Beyond these substantive aims, on a "metapolitical" level, they serve to reframe concepts and standards for political and scientific discussion of race, challenge structures of academic legitimacy and expertise, and build a cadre of ideological foot soldiers armed with an argumentative toolkit. As professional anthropologists and geneticists aim to accurately communicate their science and its implications for understanding human differences to the public, they must contend with these substantive claims and metapolitical contexts.

Abstract Background Malakoplakia is a rare condition characterized by inflammatory masses with specific histological characteristics. These soft tissue masses can mimic tumors and tend to develop in association with chronic or recurrent infections, typically of the urinary tract. A specific defect in innate immunity has been described. In the absence of randomized controlled trials, management is based on an understanding of the biology and on case reports. Case presentation Here we describe a case of presacral malakoplakia in a British Indian woman in her late 30s, presenting with complex unilateral foot drop. Four years earlier, she had suffered a protracted episode of intrapelvic sepsis following a caesarean delivery. Resection of her presacral soft tissue mass was not possible. She received empiric antibiotics, a cholinergic agonist, and ascorbic acid. She responded well to medical management both when first treated and following a recurrence of symptoms after completing an initial 8 months of therapy. Whole exome sequencing of the patient and her parents was undertaken but no clear causal variant was identified. Conclusions Malakoplakia is uncommon but the diagnosis should be considered where soft tissue masses develop at the site of chronic or recurrent infections. Obtaining tissue for histological examination is key to making the diagnosis. This case suggests that surgical resection is not always needed to achieve a good clinical and radiological outcome.

Abstract Introduction The KMT2 family of genes is essential epigenetic regulators promoting gene expression. The gene family contains three subgroups, each with two paralogues: KMT2A and KMT2B; KMT2C and KMT2D; KMT2F and KMT2G. KMT2A‐D are among the most frequent somatically altered genes in several different cancer types. Somatic KMT2A rearrangements are well‐characterized in infant leukemia (IL), and growing evidence supports the role of additional family members (KMT2B, KMT2C, and KMT2D) in leukemogenesis. Enrichment of rare heterozygous frameshift variants in KMT2A and C has been reported in acute myeloid leukemia (AML), IL, and solid tumors. Currently, the non‐synonymous variation, prevalence, and penetrance of these four genes are unknown. Methods This study determined the prevalence of pathogenic/likely pathogenic (P/LP) germline KMT2A‐D variants in a cancer‐free adult population from the Genome Aggregation Database (gnomAD). Two methods of variant interpretation were utilized: a manual genomic variant interpretation and an automated ACMG pipeline. Results The ACMG pipeline identified considerably fewer P/LP variants (n = 89) compared to the manual method (n = 660) in all 4 genes. Consequently, the total P/LP prevalence and allele frequency (AF) were higher in the manual method (1:112, AF = 4.46E‐03) than in ACMG (1:832, AF = 6.01E‐04). Multiple ancestry‐exclusive P/LP variants were identified along with an increased frequency in males compared to females. Many of these variants identified in this population database are also associated with severe juvenile conditions. Conclusion These data demonstrate that putatively functional germline variation in these developmentally important genes is more common than previously appreciated and identification in cancer‐free adults may indicate incomplete penetrance for many of these variants. Future research should examine a genetic predisposing role in IL and other pediatric cancers.

Prof. Alberto Piazza, a renowned human population geneticist, passed away at the age of 82. He faced challenges in his early life due to persecution by the Italian fascist regime, but went on to have a successful career in genetics. Piazza made significant contributions to the study of the human histocompatibility system, known as HLA, and collaborated with other prominent scientists in the field. He also held important administrative positions and promoted an ethical approach to genetic research. Piazza's work helped to clarify human genetic variation and the worldwide distribution of certain diseases. He will be remembered as a generous and respected figure in the scientific community. [Extracted from the article]

Dr. Holger Prokisch, a researcher at the Institute of Human Genetics in Germany, has been awarded the GfH Medal of Honour by the German Society of Human Genetics. He is being recognized for his work in identifying the molecular basis of mitochondrial dysfunction and exploring personalized treatment options for mitochondrial disorders. Dr. Prokisch has published over 350 papers in his 30-year career, with a focus on mitochondrial function and disorders. He has also been involved in coordinating national and international research networks and has contributed to the dissemination of his research through conferences and workshops. Despite his scientific successes, Dr. Prokisch has chosen to remain in his current position to focus on his research and prioritize his family. [Extracted from the article]

The human genome contains vast genetic diversity as naturally occurring coding variants, yet the impact of these variants on protein function and physiology is poorly understood. RGS14 is a multifunctional signaling protein that suppresses synaptic plasticity in dendritic spines of hippocampal neurons. RGS14 also is a nucleocytoplasmic shuttling protein, suggesting that balanced nuclear import/export and dendritic spine localization are essential for RGS14 functions. We identified genetic variants L505R (LR) and R507Q (RQ) located within the nuclear export sequence (NES) of human RGS14. Here we report that RGS14 encoding LR or RQ profoundly impacts protein functions in hippocampal neurons. RGS14 membrane localization is regulated by binding Gαi-GDP, whereas RGS14 nuclear export is regulated by Exportin 1 (XPO1). Remarkably, LR and RQ variants disrupt RGS14 binding to Gαi1-GDP and XPO1, nucleocytoplasmic equilibrium, and capacity to inhibit long-term potentiation (LTP). Variant LR accumulates irreversibly in the nucleus, preventing RGS14 binding to Gαi1, localization to dendritic spines, and inhibitory actions on LTP induction, while variant RQ exhibits a mixed phenotype. When introduced into mice by CRISPR/Cas9, RGS14-LR protein expression was detected predominantly in the nuclei of neurons within hippocampus, central amygdala, piriform cortex, and striatum, brain regions associated with learning and synaptic plasticity. Whereas mice completely lacking RGS14 exhibit enhanced spatial learning, mice carrying variant LR exhibit normal spatial learning, suggesting that RGS14 may have distinct functions in the nucleus independent from those in dendrites and spines. These findings show that naturally occurring genetic variants can profoundly alter normal protein function, impacting physiology in unexpected ways.