jMorp: Japanese Multi-Omics Reference Panel update report 2023.

Modern medicine is increasingly focused on personalized medicine, and multi-omics data is crucial in understanding biological phenomena and disease mechanisms. Each ethnic group has its unique genetic background with specific genomic variations influencing disease risk and drug response. Therefore, multi-omics data from specific ethnic populations are essential for the effective implementation of personalized medicine. Various prospective cohort studies, such as the UK Biobank, All of Us and Lifelines, have been conducted worldwide. The Tohoku Medical Megabank project was initiated after the Great East Japan Earthquake in 2011. It collects biological specimens and conducts genome and omics analyses to build a basis for personalized medicine. Summary statistical data from these analyses are available in the jMorp web database (https://jmorp.megabank.tohoku.ac.jp), which provides a multidimensional approach to the diversity of the Japanese population. jMorp was launched in 2015 as a public database for plasma metabolome and proteome analyses and has been continuously updated. The current update will significantly expand the scale of the data (metabolome, genome, transcriptome, and metagenome). In addition, the user interface and backend server implementations were rewritten to improve the connectivity between the items stored in jMorp. This paper provides an overview of the new version of the jMorp.

On the genes, genealogies, and geographies of Quebec.

Population genetic models only provide coarse representations of real-world ancestry. We used a pedigree compiled from 4 million parish records and genotype data from 2276 French and 20,451 French Canadian individuals to finely model and trace French Canadian ancestry through space and time. The loss of ancestral French population structure and the appearance of spatial and regional structure highlights a wide range of population expansion models. Geographic features shaped migrations, and we find enrichments for migration, genetic, and genealogical relatedness patterns within river networks across regions of Quebec. Finally, we provide a freely accessible simulated whole-genome sequence dataset with spatiotemporal metadata for 1,426,749 individuals reflecting intricate French Canadian population structure. Such realistic population-scale simulations provide opportunities to investigate population genetics at an unprecedented resolution.

Meeting the ancestors.

DNA from a medieval German cemetery opens a window on the history of today's largest Jewish population.

Substitution mutational signatures in whole-genome-sequenced cancers in the UK population.

Whole-genome sequencing (WGS) permits comprehensive cancer genome analyses, revealing mutational signatures, imprints of DNA damage and repair processes that have arisen in each patient's cancer. We performed mutational signature analyses on 12,222 WGS tumor-normal matched pairs, from patients recruited via the UK National Health Service. We contrasted our results to two independent cancer WGS datasets, the International Cancer Genome Consortium (ICGC) and Hartwig Foundation, involving 18,640 WGS cancers in total. Our analyses add 40 single and 18 double substitution signatures to the current mutational signature tally. Critically, we show for each organ, that cancers have a limited number of 'common' signatures and a long tail of 'rare' signatures. We provide a practical solution for utilizing this concept of common versus rare signatures in future analyses.

A genetic probe into the ancient and medieval history of Southern Europe and West Asia.

Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom's northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.

Revealing the recent demographic history of Europe via haplotype sharing in the UK Biobank.

Haplotype-based analyses have recently been leveraged to interrogate the fine-scale structure in specific geographic regions, notably in Europe, although an equivalent haplotype-based understanding across the whole of Europe with these tools is lacking. Furthermore, study of identity-by-descent (IBD) sharing in a large sample of haplotypes across Europe would allow a direct comparison between different demographic histories of different regions. The UK Biobank (UKBB) is a population-scale dataset of genotype and phenotype data collected from the United Kingdom, with established sampling of worldwide ancestries. The exact content of these non-UK ancestries is largely uncharacterized, where study could highlight valuable intracontinental ancestry references with deep phenotyping within the UKBB. In this context, we sought to investigate the sample of European ancestry captured in the UKBB. We studied the haplotypes of 5,500 UKBB individuals with a European birthplace; investigated the population structure and demographic history in Europe, showing in parallel the variety of footprints of demographic history in different genetic regions around Europe; and expand knowledge of the genetic landscape of the east and southeast of Europe. Providing an updated map of European genetics, we leverage IBD-segment sharing to explore the extent of population isolation and size across the continent. In addition to building and expanding upon previous knowledge in Europe, our results show the UKBB as a source of diverse ancestries beyond Britain. These worldwide ancestries sampled in the UKBB may complement and inform researchers interested in specific communities or regions not limited to Britain.

Identification of recurrent pathogenic alleles using exome sequencing data: Proof-of-concept study of Russian subjects.

Whole exome sequencing (WES) is a powerful tool for the cataloguing of population-specific genetic diseases. Within this proof-of-concept study we evaluated whether analysis of a small number of individual exomes is capable of identifying recurrent pathogenic alleles. We considered 106 exomes of subjects of Russian origin and revealed 13 genetic variants, which occurred more than twice and fulfilled the criteria for pathogenicity. All these alleles turned out to be indeed recurrent, as revealed by the analysis of 1045 healthy Russian donors. Eight of these variants (NAGA c.973G>A, ACADM c.985A>C, MPO c.2031-2A>C, SLC3A1 c.1400T>C, LRP2 c.6160G>A, BCHE c.293A>G, MPO c.752T>C, FCN3 c.349delC) are non-Russian-specific, as their high prevalence was previously demonstrated in other European populations. The remaining five disease-associated alleles appear to be characteristic for subjects of Russian origin and include CLCN1 c.2680C>T (myotonia congenita), DHCR7 c.453G>A (Smith-Lemli-Opitz syndrome), NUP93 c.1162C>T (steroid-resistant nephrotic syndrome, type 12), SLC26A2 c.1957T>A (multiple epiphyseal dysplasia) and EIF3F c.694T>G (mental retardation). These recessive disease conditions may be of particular relevance for the Russian Federation and other countries with a significant Slavic population.

Free acquisition of psychotropic drugs by the Brazilian adult population and presence on the National List of Essential Medicines

Abstract The aims of the present study were to estimate the free-of-charge acquisition of psychotropic drugs among Brazilian adults; analyze the distribution of psychotropics according to their presence on the Relação Nacional de Medicamentos Essenciais (RENAME [National List of Essential Medicines]) and acquisition according to the source of funding (free of charge or direct payment); and estimate the proportion of free-of-charge psychotropic drugs according to therapeutic class and presence on the RENAME. This study involved the analysis of data from the 2014 National Survey on the Accessibility, Use and Promotion of the Rational Use of Medicines considering psychotropic drugs used by the adult population (≥20 years; n = 32,348). The prevalence of the acquisition of free-of-charge psychotropic drugs was 53.3% and 64.6% of these drugs were on the RENAME. Among the psychotropic drugs acquired by direct payment, 70.8% were not on the national list. Regarding free-of-charge acquisition according to the therapeutic class and presence on the RENAME, differences were found for antidepressants, anxiolytics and antipsychotics (p <0.05). In conclusion, the most used psychotropic medicines were listed in the RENAME, but free-of-charge acquisition was not provided for all of them

Fatores associados ao nível de segurança alimentar e nutricional no município e estado de São Paulo e no Brasil: uma análise dos resultados obtidos pela escala brasileira de insegurança alimentar / Food and nutritional security level associated factors in the city and state of São Paulo and in Brazil: an analysis of obtained results from the Brazilian food insecurity scale

A falta de segurança alimentar e nutricional (SAN) consiste em um fenômeno multifatorial, que pode afetar o estado nutricional do indivíduo por ela acometido de diversas maneiras e em qualquer faixa etária. A falta de SAN pode desencadear tanto desnutrição, como obesidade e assim favorecer o aumento da prevalência de doenças crônicas não transmissíveis, o que diminui a qualidade de vida e se constitui um importante problema de saúde pública. Objetivo: Analisar e comparar a força da associação dos fatores socioeconômicos e demográficos à segurança alimentar e nutricional (SAN) no Brasil e áreas geográficas selecionadas. Metodologia: Trata-se de um estudo ecológico, transversal e analítico, que utilizou como base os microdados da Pesquisa de Orçamento Familiar (POF/IBGE), realizada nos anos de 2017-2018, envolvendo 757 famílias residentes no município de São Paulo (MSP), 3.406 famílias do estado de São Paulo (ESP) e 49.365 famílias do Brasil. Utilizou-se a técnica de regressão logística multinomial, do tipo ordinal, para o processamento do modelo de associação entre o nível de SAN (nSAN) e as variáveis demográficas, socioeconômicas e clínicas, utilizando o módulo survey do Stata versão 14. Adotouse o nível de significância estatística de 5% e o odds ratio proporcional para descrever as associações. Resultados: A grande maioria dos indivíduos de referência dos domicílios componentes da amostra é do sexo masculino, adulta, com obesidade, sem seguro saúde e que não fazem nenhum tipo de dieta, variando as características de raça/cor e escolaridade entre as três localidades analisadas. Para as três localidades estudadas, encontrou-se proporções elevadas da população com segurança alimentar e nutricional garantida (acima de 59%). As associações encontradas demonstraram que as famílias com pessoas de referência do sexo feminino apresentam maior chance de piora do nSAN, bem como aquelas com menores níveis de saneamento básico e estratos de renda mais pobres, para os quais a chance de piora do nSAN em relação aos estratos de renda mais ricos se eleva em até 12 vezes. Ser de raça branca foi fator protetor à IAN, bem como ter idade mais avançada e mais anos de escolaridade. Conclusão: As características sociodemográficas sexo, raçacor, idade e escolaridade, e socioeconômicas, renda e presença de saneamento básico, apresentam importante associação ao nível de SAN das famílias, quando este é analisado por meio da Escala Brasileira de Insegurança Alimentar (EBIA). Entretanto, faz-se necessária a construção de um instrumento que avalie todas as dimensões da SAN

Lack of food and nutrition security (FNS) is a multifactorial phenomenon, which can impact the nutritional status of individual affected by it in different ways and in any age group. The lack of FNS can trigger both malnutrition and obesity and thus favor the prevalence increase of chronic non-communicable diseases, which reduces lifes quality and constitutes an important public health problem. Objective: To analyze and compare the strength of association of socioeconomic and demographic factors with FNS in Brazil and selected geographical areas. Methodology: Ecological, crosssectional, and analytical study, which used the microdata of the Research as a basis Family Budget (POF / IBGE), carried out in 2017-2018, involving 757 families residing in São Paulo city (SPC), 3,406 families from São Paulo state (SPS) and 49,365 families from Brazil. Multinomial logistic regression technique, of the ordinal type, was used to process the association model between the FNS level (FNSl) and the demographic, socioeconomic and clinical variables, using the survey module of Stata version 14. It was adopted statistical significance of 5% and proportional odds ratio to describe the associations. Results: Most reference individuals in the sample's households are male, adult, obese, without health insurance and who do not follow any type of diet, varying the characteristics of race / color and education between the three locations analyzed. For the three locations studied, high proportions of the population were found with guaranteed FNS (above 59%). Associations found showed that families headed by female individuals are more likely to worsen FNSl, as well as those with lower levels of basic sanitation and poorer income strata, for which the chance of worsening FNSl in relation to strata wealthier income rises to 12 times. Being white was a protective factor for food insecurity, as well as being older and with more years of schooling. Conclusion: Sociodemographic characteristics of sex, race-color, age and education, and socioeconomic, income and presence of basic sanitation, present important association at the FNSl of families, when this is analyzed through the Brazilian Food Insecurity Scale (EBIA). However, it is necessary to build an instrument that assesses all dimensions of the FNS

Use of medication and associated factors in adults living in Rio Branco, Acre. Use of medication in adults

Abstract We analyzed use of medication and associated factors in adults aged 18-59 years living in Rio Branco, Acre. This is a cross-sectional and population-based study that used a probabilistic sample of the population from rural and urban areas of the city of Rio Branco, Acre. The Prevalence Ratio (PR) was calculated with 95% confidence intervals and associations were estimated by Poisson regression. This study found a 29.4% prevalence ratio of use of medication among individuals aged from 18 to 59 years (685 adults: 473 women and 212 men; producing estimates for 211,902 adults: 110,769 women and 101,133 men). After adjusted analysis, their use was associated with: age (50-59 years, PR: 2.36; 95%CI: 2.29-2.43); women (PR: 1.25; 95%CI: 1.23-1.27); up to elementary school (PR: 1.13; 95%CI: 1.11-1.15); and poor or very poor self-rated health (PR: 1.47; 95%CI: 1.43-1.51). The health conditions associated with use of medication were: number of comorbidities, hypertension, diabetes, insomnia, depression, number of health complaints and use of health services. The most frequently used drugs were those belonging to the following ATC categories: alimentary tract and metabolism, cardiovascular system, nervous system, and the musculoskeletal system.

The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture.

Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.

Spectrum of Genetic Diseases in Tunisia: Current Situation and Main Milestones Achieved.

Genetic diseases in Tunisia are a real public health problem given their chronicity and the lack of knowledge concerning their prevalence and etiology, and the high rates of consanguinity. Hence, we performed systematic reviews of the literature in order to provide a more recent spectrum of these disorders and to expose the challenges that still exist to tackle these kinds of diseases. A manual textual data mining was conducted using MeSH and PubMed databases. Collected data were classified according to the CIM-10 classification and the transmission mode. The spectrum of these diseases is estimated to be 589 entities. This suggests remarkable progress through the development of biomedical health research activities and building capacities. Sixty percent of the reported disorders are autosomal recessive, which could be explained by the high prevalence of endogamous mating. Congenital malformations (29.54%) are the major disease group, followed by metabolic diseases (22%). Sixty percent of the genetic diseases have a known molecular etiology. We also reported additional cases of comorbidity that seem to be a common phenomenon in our population. We also noticed that epidemiological data are scarce. Newborn and carrier screening was only limited to pilot projects for a few genetic diseases. Collected data are being integrated into a database under construction that will be a valuable decision-making tool. This study provides the current situation of genetic diseases in Tunisia and highlights their particularities. Early detection of the disease is important to initiate critical intervention and to reduce morbidity and mortality.

Sequence variants in malignant hyperthermia genes in Iceland: classification and actionable findings in a population database.

Malignant hyperthermia (MH) susceptibility is a rare life-threatening disorder that occurs upon exposure to a triggering agent. MH is commonly due to protein-altering variants in RYR1 and CACNA1S. The American College of Medical Genetics and Genomics recommends that when pathogenic and likely pathogenic variants in RYR1 and CACNA1S are incidentally found, they should be reported to the carriers. The detection of actionable variants allows the avoidance of exposure to triggering agents during anesthesia. First, we report a 10-year-old Icelandic proband with a suspected MH event, harboring a heterozygous missense variant NM_000540.2:c.6710G>A r.(6710g>a) p.(Cys2237Tyr) in the RYR1 gene that is likely pathogenic. The variant is private to four individuals within a three-generation family and absent from 62,240 whole-genome sequenced (WGS) Icelanders. Haplotype sharing and WGS revealed that the variant occurred as a somatic mosaicism also present in germline of the proband's paternal grandmother. Second, using a set of 62,240 Icelanders with WGS, we assessed the carrier frequency of actionable pathogenic and likely pathogenic variants in RYR1 and CACNA1S. We observed 13 actionable variants in RYR1, based on ClinVar classifications, carried by 43 Icelanders, and no actionable variant in CACNA1S. One in 1450 Icelanders carries an actionable variant for MH. Extensive sequencing allows for better classification and precise dating of variants, and WGS of a large fraction of the population has led to incidental findings of actionable MH genotypes.

A study of elective genome sequencing and pharmacogenetic testing in an unselected population.

BACKGROUND: Genome sequencing (GS) of individuals without a medical indication, known as elective GS, is now available at a number of centers around the United States. Here we report the results of elective GS and pharmacogenetic panel testing in 52 individuals at a private genomics clinic in Alabama. METHODS: Individuals seeking elective genomic testing and pharmacogenetic testing were recruited through a private genomics clinic in Huntsville, AL. Individuals underwent clinical genome sequencing with a separate pharmacogenetic testing panel. RESULTS: Six participants (11.5%) had pathogenic or likely pathogenic variants that may explain one or more aspects of their medical history. Ten participants (19%) had variants that altered the risk of disease in the future, including two individuals with clonal hematopoiesis of indeterminate potential. Forty-four participants (85%) were carriers of a recessive or X-linked disorder. All individuals with pharmacogenetic testing had variants that affected current and/or future medications. CONCLUSION: Our study highlights the importance of collecting detailed phenotype information to interpret results in elective GS.

Population dynamics of GC-changing mutations in humans and great apes.

The nucleotide composition of the genome is a balance between the origin and fixation rates of different mutations. For example, it is well-known that transitions occur more frequently than transversions, particularly at CpG sites. Differences in fixation rates of mutation types are less explored. Specifically, recombination-associated GC-biased gene conversion (gBGC) may differentially impact GC-changing mutations, due to differences in their genomic distributions and efficiency of mismatch repair mechanisms. Given that recombination evolves rapidly across species, we explore gBGC of different mutation types across human populations and great ape species. We report a stronger correlation between segregating GC frequency and recombination for transitions than for transversions. Notably, CpG transitions are most strongly affected by gBGC in humans and chimpanzees. We show that the overall strength of gBGC is generally correlated with effective population sizes in humans, with some notable exceptions, such as a stronger effect of gBGC on non-CpG transitions in populations of European descent. Furthermore, species of the Gorilla and Pongo genus have a greatly reduced gBGC effect on CpG sites. We also study the dependence of gBGC dynamics on flanking nucleotides and show that some mutation types evolve in opposition to the gBGC expectation, likely due to the hypermutability of specific nucleotide contexts. Our results highlight the importance of different gBGC dynamics experienced by GC-changing mutations and their impact on nucleotide composition evolution.

The genetic structure of Norway.

The aim of the present study was to describe the genetic structure of the Norwegian population using genotypes from 6369 unrelated individuals with detailed information about places of residence. Using standard single marker- and haplotype-based approaches, we report evidence of two regions with distinctive patterns of genetic variation, one in the far northeast, and another in the south of Norway, as indicated by fixation indices, haplotype sharing, homozygosity, and effective population size. We detect and quantify a component of Uralic Sami ancestry that is enriched in the North. On a finer scale, we find that rates of migration have been affected by topography like mountain ridges. In the broader Scandinavian context, we detect elevated relatedness between the mid- and northern border areas towards Sweden. The main finding of this study is that despite Norway's long maritime history and as a former Danish territory, the region closest to mainland Europe in the south appears to have been an isolated region in Norway, highlighting the open sea as a barrier to gene flow into Norway.

Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments.

Bones and teeth are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites. Mitochondrial DNA (mtDNA) has been retrieved from cave sediments but provides limited value for studying population relationships. We therefore developed methods for the enrichment and analysis of nuclear DNA from sediments and applied them to cave deposits in western Europe and southern Siberia dated to between 200,000 and 50,000 years ago. We detected a population replacement in northern Spain about 100,000 years ago, which was accompanied by a turnover of mtDNA. We also identified two radiation events in Neanderthal history during the early part of the Late Pleistocene. Our work lays the ground for studying the population history of ancient hominins from trace amounts of nuclear DNA in sediments.

Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease.

Long non-coding RNA (lncRNA) genes have well-established and important impacts on molecular and cellular functions. However, among the thousands of lncRNA genes, it is still a major challenge to identify the subset with disease or trait relevance. To systematically characterize these lncRNA genes, we used Genotype Tissue Expression (GTEx) project v8 genetic and multi-tissue transcriptomic data to profile the expression, genetic regulation, cellular contexts, and trait associations of 14,100 lncRNA genes across 49 tissues for 101 distinct complex genetic traits. Using these approaches, we identified 1,432 lncRNA gene-trait associations, 800 of which were not explained by stronger effects of neighboring protein-coding genes. This included associations between lncRNA quantitative trait loci and inflammatory bowel disease, type 1 and type 2 diabetes, and coronary artery disease, as well as rare variant associations to body mass index.

Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences.

Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35 638 VNTR loci and classified 5676 as commonly polymorphic (i.e. with non-reference alleles occurring in >5% of the population). Commonly polymorphic VNTR loci were found to be enriched in genomic regions with regulatory function, i.e. transcription start sites and enhancers. Investigation of the commonly polymorphic VNTRs in the context of population ancestry revealed that 1096 loci contained population-specific alleles and that those could be used to classify individuals into super-populations with near-perfect accuracy. Search for quantitative trait loci (eQTLs), among the VNTRs proximal to genes, indicated that in 187 genes expression differences correlated with VNTR genotype. We validated our predictions in several ways, including experimentally, through the identification of predicted alleles in long reads, and by comparisons showing consistency between sequencing platforms. This study is the most comprehensive analysis of minisatellite VNTRs in the human population to date.