Genome Project Research Articles

Genetic Variants of GBP4: Reduced Risks for Drug-Induced Acute Liver Failure in Non-Finnish European Population.

Acute liver failure (ALF) is a serious condition, typically in individuals without prior liver disease. Drug-induced ALF (DIALF) constitutes a major portion of ALF cases. Our research aimed to identify potential genetic predispositions to DIALF. We analysed the potential genetic variants associated with DIALF using the whole exome sequencing data from 75 cases, including 40 non-Finnish European cases in the pilot study. Chi-square tests were performed for case-control analysis against the 1000 genomes project as the control. A replication study of 44 DIALF cases that included 24 non-Finnish Europeans was conducted to validate candidate variants. The association between clinical phenotype and genotypes was analysed using one-way analysis of variance. Eight variants (rs561037, rs561042, rs608339, rs655260, rs1142886, rs1142888, rs1142889 and rs1142890) in the guanylate binding protein 4 (GBP4) were significantly associated with DIALF in non-Finnish Europeans in the pilot study and confirmed in the replication study. Rs561037 and rs561042 were highly significant with the lowest allele frequencies in both pilot and replication studies. An association was also found between these variants and milder clinical outcomes, indicated by lower peak levels of ALT, AST and higher Karnofsky performance scores. Our study identified eight GBP4 missense variants linked to a lower risk of DIALF in the non-Finnish European population. The GBP4 protein, activated by interferon-gamma, plays a critical role in innate immunity. These findings suggest that GBP4 variants might influence immune and inflammatory responses in DIALF, though further studies are needed to elucidate the underlying mechanisms.

TMEM160 Promotes Tumor Growth in Lung Adenocarcinoma and Cervical Adenocarcinoma Cell Lines

The Chromosome-Centric Human Proteome Project (C-HPP) is an international initiative. It aims to create a protein list expressed in human cells by each chromosomal and mitochondrial DNA to enhance our understanding of disease mechanisms, akin to the gene list generated by the Human Genome Project. Transmembrane protein 160 (TMEM160) is a member of the transmembrane proteins (TMEM) family. TMEM proteins have been implicated in cancer-related processes, including cell proliferation, migration, epithelial-mesenchymal transition, metastasis, and resistance to chemotherapy and radiotherapy. This study aimed to investigate the role of TMEM160 in non-small cell lung cancer and cervical cancer using cell lines, clinical samples, and xenograft studies. Our findings demonstrated that TMEM160 knockdown decreased the proliferation of lung and cervical cancer cell lines. We observed that TMEM160 is localized in the nucleus and cytoplasm and dynamic localization during mitosis of cancer cells and discovered a novel interaction between TMEM160 and nuclear proteins such as NUP50. Furthermore, the TMEM160 interactome was enriched in processes associated with apical junctions, xenobiotic metabolism, glycolysis, epithelial-mesenchymal transition, reactive oxygen species, UV response DNA, the P53 pathway, and the mitotic spindle. This study provides an initial understanding of the function of TMEM160 in lung and cervical cancer progression and clarifies the need to continue investigating the participation of TMEM160 in these cancers.

Personalising dietary advice for disease prevention: concepts and experiences.

Personalised nutrition (PN) as a new endeavour emerged in the background of the human genome project with the ease to analyse genetic heterogeneity. First commercial offers with recommendations for diet and lifestyle changes, usually based on a few polymorphisms, entered markets soon after the presentation of the human genome blueprint. Although PN has seen many attempts, meanwhile, with the inclusion of other biomedical measures such as microbiome and/or continuous glucose monitoring, scientific assessments of such approaches in various settings revealed limited success. Although personalisation improved general compliance over generic advice, particular benefits in referring to biomedical measures and individual risks did, in most cases, not provide any significant advantage. Moreover, scholars criticised such approaches as of limited impact from a public health perspective by attracting mainly technology-open individuals of high social status and proper financial capabilities. Based on these experiences, new avenues for personalising dietary advice are developed, and those are going beyond pure biomedical data by assessing the entire food environment of the individual with its capabilities and constraints in the given life setting. Embedded into digital environments for data collection but also for bidirectional communication, new possibilities emerge. Artificial intelligence methods allow for the multitude of input data and highly complex decision trees to be derived to customize advice. And that can be delivered on the spot and in time in any language whenever decisions are made on what to buy or what to eat. But systems can also be employed to increase physical activity levels and for the adoption of a more healthy lifestyle in general.

Genomic analysis of three medieval parchments from German monasteries

In the last two decades there has been growing interest in the analysis of ancient DNA obtained from the parchment used in historic documents. The genetic insight that this data provides makes collections of historic documents an invaluable source for studying the development and spread of historical livestock populations. Additionally, the biological data may provide new information for the historical analysis that could be used to determine the provenance as well as the authenticity of these documents. In this study, we extracted DNA from three medieval parchments that were written in German monasteries in the twelfth century. The source animal of the parchments could be identified as cattle and we compared their genome sequences with those of modern populations that are part of the 1000 Bull Genomes Project. The three animals were found to carry mtDNA haplogroup T3 and show a closer genetic relationship to other historic animals than to modern breeds. We further identified 39 haplotypes and 132 SNPs variants, which are rare (<0.1) or even non-existent in modern breeds. Finally, the genetic distances between the parchment samples show a putative association with the dates when the documents were written, indicating the usefulness of genetic analysis for provenance research.

Secrets of the Goo: the Genome assembly of the Pacific Banana Slug, Ariolimax columbianus.

The Pacific banana slug, Ariolimax columbianus, is endemic to the forests of the Pacific Northern West. Found throughout coastal foothills and mountains of California, the hermaphroditic molluscs Ariolimax spp. are niche-constrained, hyper-localized, and phenotypically diverse. The evolutionary history and more recent population history and environmental conditions leading to their phenotypic and genetic variation are not understood. To facilitate such research, we present the first high-quality de novo genome assembly of A. columbianus as part of the California Conservation Genomics Project (CCGP). Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technologies were used to produce a de novo genome assembly, consistent with the standard CCGP genome assembly protocol. This assembly comprises 401 scaffolds spanning 2.29 Gb, represented by a scaffold N50 of 94.9Mb, a contig N50 of 3.7Mb, and a benchmarking universal single-copy ortholog (BUSCO) completeness score of 93.9%. Future work will use the A. columbianus genome to study the population structure of Ariolimax spp. across California to understand patterns of population structure, genetic diversity and the broader ecological connections with their habitat. This data will contribute to the CCGP, expanding the knowledge about the partitioning of genomic variation across the different ecoregions of California.

Dissecting the Genetic Basis of Preharvest Sprouting in Rice Using a Genome-Wide Association Study.

Preharvest sprouting (PHS) is an unfavorable trait in cereal crops that significantly reduces grain yield and quality. However, the regulatory mechanisms underlying this complex trait are still largely unknown. Here, 276 rice accessions from the 3000 Rice Genomes Project were used to perform a genome-wide association study. In total, seven PHS-associated quantitative trait loci (QTLs) were identified, including two novel QTLs and five previously reported QTLs. Among them, four QTLs were identified in 2020 and 2021, and rice accessions carrying at least two favorable alleles exhibited significantly improved PHS resistance. Within these four stable QTLs, five candidate genes were identified based on haplotype and gene expression analyses, including two genes in qPhs-1.1, one gene in qPhs-3, one gene in qPhs-6, and one gene in qPhs-7. Notably, the novel QTL qPhs-6 was found to contain the candidate gene Pi starvation-induced transcription factor 1 (OsPTF1). We discovered that OsPTF1 plays a novel role in negatively regulating PHS in rice and identified two elite haplotypes of OsPTF1 associated with low PHS. Our results provide future insight into the genetic basis of PHS and will prove useful in the future studies on the role of OsPTF1 in PHS in rice.

Pilot work of the 10K Chinese People Genomic Diversity Project along the Silk Road suggests a complex east-west admixture landscape and biological adaptations.

Genomic sources from China are underrepresented in the population-specific reference database. We performed whole-genome sequencing or genome-wide genotyping on 1,207 individuals from four linguistically diverse groups (1,081 Sinitic, 56 Mongolic, 40 Turkic, and 30 Tibeto-Burman people) living in North China included in the 10K Chinese People Genomic Diversity Project (10K_CPGDP) to characterize the genetic architecture and adaptative history of ethnic groups in the Silk Road Region of China. We observed a population split between Northwest Chinese minorities (NWCMs) and Han Chinese since the Upper Paleolithic and later Neolithic genetic differentiation within NWCMs. The observed population substructures among ethnically/linguistically diverse NWCMs suggested that differentiated admixture events contributed to the differences in their genomic and phenotypic diversity. We estimated that the Dongxiang, Tibetan, and Yugur people inherited more than 10% of the Western Eurasian ancestry, which is much greater than that of the Salar and Tu people (<7%), while Han neighbors showed less West Eurasian ancestry (∼1%-3%). Male-biased admixture introduced Western Eurasian ancestry in the Dongxiang, Tibetan, and Yugur populations. We found that the eastern-western admixture in NWCMs occurred ∼800-1,100 years ago, coinciding with intensive economic and cultural exchanges during the Tang and Song dynasties. Additionally, we identified the signatures of natural selection associated with cardiovascular system diseases or lipid metabolism and developmental/neurogenetic disorders. Moreover, the EPAS1 gene showed relatively high population branch statistic values in NWCMs. The well-fitted demographical models presented the vast landscape of complex admixture processes of the Silk Road people, and the newly reported functionally important variations suggested the importance of including ethnolinguistically diverse populations in Chinese genetic studies for uncovering the genetic basis of complex traits/diseases.

Overcoming challenges associated with broad sharing of human genomic data.

Since the Human Genome Project, the consensus position in genomics has been that data should be shared widely to achieve the greatest societal benefit. This position relies on imprecise definitions of the concept of 'broad data sharing'. Accordingly, the implementation of data sharing varies among landmark genomic studies. In this Perspective, we identify definitions of broad that have been used interchangeably, despite their distinct implications. We further offer a framework with clarified concepts for genomic data sharing and probe six examples in genomics that produced public data. Finally, we articulate three challenges. First, we explore the need to reinterpret the limits of general research use data. Second, we consider the governance of public data deposition from extant samples. Third, we ask whether, in light of changing concepts of broad, participants should be encouraged to share their status as participants publicly or not. Each of these challenges is followed with recommendations.

New insights into interspecies relationships, chromosomal evolution, and hybrid identification in the Lycoris Herb.

BackgroundFrequent interspecific hybridization, unclear genetic backgrounds, and ambiguous evolutionary relationships within the genus Lycoris pose significant challenges to the identification and classification of hybrids, thereby impacting the application and development of Lycoris. This study utilizes karyotype structure, genome size, and fluorescent in situ hybridization (FISH) technology to explore the chromosomal evolution and hybrid identification of Lycoris employing three approaches at the cytogenetic level.ResultsThe findings indicate that species with a smaller basic chromosome number exhibit less asymmetry than those with a larger basic chromosome number, suggesting that species with different basic chromosome numbers may have followed different evolutionary pathways. Lycoris aurea has a more symmetrical karyotype, which may be the plesiomorphic state, reflecting an evolutionary transition from symmetry to asymmetry in Lycoris chromosomes. Systematic clustering of 18 Lycoris species is consistent with chromosomal karyotype classification, primarily dividing into two groups: species with M + T + A type an M + T type as one group, and A type as another group. The average nuclear genome size (C-value) of the Lycoris genus is 22.99 Gb, with the smallest genome being that of L. wulingensis (17.10 Gb) and the largest being L. squamigera (33.06 Gb). Chromosome length is positively correlated with the C-value, and the haploid genome size (Cx-value) decreases with an increase in basic chromosome number (x). The FISH technique can quickly identify and authenticate artificial hybrids, thus inferring the parentage of natural hybrids.ConclusionThe study reveals the genetic background and interspecific relationships of 18 Lycoris species, identifies the authenticity of artificial Lycoris hybrids, and infers the possible parentage of natural hybrids, offering technical insights for the identification, classification, and genomic projects of Lycoris.

Comprehensive phylogenetic analysis of newly detected rodent adenoviruses sheds light on ancient host-switches.

Here we provide a comprehensive update on the diversity and genetic relatedness of adenoviruses occurring in rodents. Extensive PCR screenings revealed the presence of adenoviral DNA in samples originating from representatives of 17 rodent species from four different suborders of Rodentia. Distinct sequences of 28 different adenoviruses were obtained from the positive samples. Out of these, 20 were from hitherto unknown, putative novel adenoviruses, whereas 6 were variants of previously published murine adenoviruses. Additionally, two known viruses, guinea pig adenovirus 1 and squirrel adenovirus 1 were also detected. By PCR and primer walking, we determined the sequence of a considerable part of the genomic DNA of squirrel adenovirus 1, detected in red squirrel (Sciurus vulgaris) samples from Germany previously. We annotated the almost complete genome sequence of a novel mastadenovirus found by data mining in the bulk data of the Ord's kangaroo rat (Dipodomys ordii) genome project. We revisited the sequence of the gene of E1B 19 K protein of mouse adenovirus 3. In contrast to the prototype strain, where a truncated version of this gene has been found, in our sample of mouse adenovirus 3, it seemed to be intact. Based on phylogeny reconstructions, all rodent adenoviruses clustered in the genus Mastadenovirus. Interestingly, however, there wasn't a common monophyletic clade encompassing every adenovirus of rodent origin. Instead, three major lineages were observed. Because two lineages contained viral sequences deduced from samples of three suborders, and one consisted almost exclusively of adenoviruses from the family Muridae, we hypothesize there has been a long-term coevolution with the rodent hosts, as a result of possible ancient host-switch events. Several putative viruses appeared in distinct branches further away from the three clades. Thus, the evolutionary past of the adenoviruses of rodents remains to be studied further.

Locuszoomr: an R package for visualising publication-ready regional gene locus plots

Abstract Summary Locuszoomr is an R package for visualising and creating publication-ready regional gene locus plots similar to those produced by the original web interface ‘LocusZoom’, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics or ‘ggplot2’, allowing flexibility and easy customisation. Modular plotting functions enable layering of multiple GWAS plots such as for PheWAS, comparing GWAS with eQTL signals, and aligning multiple locus plots on the same page. Interactive plots can be visualised using ‘plotly’ enabling quick identification of data points for labelling. The ‘LDlink’ API (https://ldlink.nih.gov/) can be programmatically queried to obtain linkage disequilibrium (LD) data from the 1000 Genomes Project which is overlaid on plots. The package allows users to query Ensembl databases from Bioconductor or AnnotationHub for genomic information, so it can be used to show gene track information for any species available in Ensembl. Helper functions enable recombination rate data from UCSC to be overlaid on plots. The package has a detailed vignette and includes embedded example GWAS data to allow users to try out different features. Locuszoomr is also fast: identifying 50 peaks in a GWAS of around 8 million SNPs takes around 0.6 seconds. Exporting 50 locus plots with 1Mbp window with recombination rate takes around 30 seconds on Intel 9th gen CPU or 14 seconds on Apple ARM M3. Availability and implementation The R package locuszoomr is open-source and available from CRAN: https://cran.r-project.org/package=locuszoomr and GitHub: https://github.com/myles-lewis/locuszoomr

Genome sequence data of Bacillus spizizenii GM2: a lipopeptide producer.

We present the findings from the genome-sequencing project of Bacillus spizizenii GM2, sourced from rhizospheric soil and renowned for its lipopeptide production. The genome spans 4,216,713 base pairs with an average G + C content of 43,6%.

Subcontinental Genetic Diversity in the All of Us Research Program: Implications for Biomedical Research.

The All of Us Research Program ( All of Us ) seeks to accelerate biomedical research and address the underrepresentation of minorities by recruiting over one million ethnically diverse participants across the United States. A key question is how self-identification with discrete, predefined race and ethnicity categories compares to genetic diversity at continental and subcontinental levels. To contextualize the genetic diversity in All of Us , we analyzed ∼2 million common variants from 230,016 unrelated whole genomes using classical population genetics methods, alongside reference panels such as the 1000 Genomes Project, Human Genome Diversity Project, and Simons Genome Diversity Project. Our analysis reveals that participants within self-identified race and ethnicity groups exhibit a gradient of genetic diversity rather than discrete clusters. The distributions of continental and subcontinental ancestries show considerable variation within race and ethnicity, both nationally and across states, reflecting the historical impacts of U.S. colonization, the transatlantic slave trade, and recent migrations. All of Us samples filled most gaps along the top five principal components of genetic diversity in current global reference panels. Notably, "Hispanic or Latino" participants spanned much of the three-way (African, Native American, and European) admixture spectrum. Ancestry was significantly associated with body mass index (BMI) and height, even after adjusting for socio-environmental covariates. In particular, West-Central and East African ancestries showed opposite associations with BMI. This study emphasizes the importance of assessing subcontinental ancestries, as the continental approach is insufficient to control for confounding in genetic association studies.

Modeling Biases from Low-Pass Genome Sequencing to Enable Accurate Population Genetic Inferences.

Low-pass genome sequencing is cost-effective and enables analysis of large cohorts. However, it introduces biases by reducing heterozygous genotypes and low-frequency alleles, impacting subsequent analyses such as model-based demographic history inference. Several approaches exist for inferring an unbiased allele frequency spectrum (AFS) from low-pass data, but they can introduce spurious noise into the AFS. Rather than correcting the AFS, here, we developed an approach that incorporates low-pass biases into the demographic modeling and directly analyzes the AFS from low-pass data. Our probabilistic model captures biases from the Genome Analysis Toolkit multisample calling pipeline, and we implemented it in the population genomic inference software dadi. We evaluated the model using simulated low-pass datasets and found that it alleviated low-pass biases in inferred demographic parameters. We further validated the model by downsampling 1000 Genomes Project data, demonstrating its effectiveness on real data. Our model is widely applicable and substantially improves model-based inferences from low-pass population genomic data.

Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs.

The formation of animal breeds usually begins with a small subsample from their ancestral population. Deleterious mutations accumulate in the population under genetic drift, inbreeding, and artificial selection during the development and maintenance of traits desired by humans. White raccoon dogs are among the most popular breeds of farmed raccoon dogs, but white raccoon dogs are more susceptible to disease and have a lower reproductive ability. However, the accumulation of deleterious mutations in this white breed is largely unknown. By analyzing and comparing whole-genome sequencing data from 20 white raccoon dogs and 38 normal raccoon dogs, we detected an increased occurrence of loss-of-function (LoF) mutations in white raccoon dogs compared with normal raccoon dogs. With the finding of a significantly higher dosage of homozygous missense mutations in the white raccoon dog genome, we detected a greater fitness cost in white raccoon dogs. Although a much higher FROH level for ROH fragments longer than 1 Mb has been reported in white raccoon dogs, we did not detect a genetic signal of genetic purging in white raccoon dogs. This study provides valuable genomic resources and new insights into the accumulation of mutation loads in farmed raccoon dogs.

Integrating Genomic Medicine into Public Health: A Comprehensive Review of Advancements, Challenges, and Ethical Considerations

This review explores the integration of genomic medicine into public health, with a focus on advancements, challenges, and ethical considerations. The objectives included understanding disease predisposition, enhancing diagnostics, and optimizing treatment plans to improve population health outcomes. This review evaluates current literature, case studies, and ongoing public health genomics initiatives, such as the Genomic England 100,000 Genomes Project, to assess successful integration strategies and identify barriers to implementation. Genomic advancements, such as precision medicine, demonstrate considerable potential in personalised healthcare. However, challenges remain, particularly concerning accessibility, high costs, and ethical issues like privacy, informed consent, and genetic discrimination. Addressing these issues requires the development of comprehensive governance frameworks. The successful integration of genomics into public health will depend on interdisciplinary collaboration, investments in education, equitable access, and ongoing research. Ethical governance frameworks and active community engagement are essential for ensuring responsible genomic integration and achieving positive health outcomes.

Genome Annotation.

The hallmark of genome sequencing projects is to provide genetic information on a species with functional annotations of genes and proteins. This process heavily relies on genome annotation based on homology detections from previously known genomic data. The rapid advancement of genome sequencing technologies has made genome sequencing affordable and effective in terms of the time frame for the generation of genomic data. Hence, genome sequencing has become a common practice. The annotation and characterization of newly sequenced genomes are crucial factors for the success of any biological experiment based on genomic data. The proteogenomic sector requires annotated genome further characterization of proteomic-based studies, and these are coupled with genomic and RNA-seq data. This chapter describes the genome annotation process from scratch genome sequencing to general genome annotation and specialized genome annotation using BLAST, BLAT2GO (now OMICSBOX), PANNZER, gene ontology (GO), and KEGG. It also covers different processes like repeat identification and masking, gene prediction, genome-wide annotation process, and RNA-seq protocol. It also focuses on genes of interest such as genes associated with BGCs (biosynthetic gene clusters), carbohydrate-active enzymes (CAZymes), serpins (serine protease inhibitors), membrane transporters, and toxins. Manual annotation is also a critical step for at least some groups of genes, which are often critical for the species in consideration. This chapter also briefly describes the phylogenetic and phylogenomic processes required during genome annotation.

A brief history of the cortical thick ascending limb: a systems-biology perspective.

Here, we review key events in the accrual of knowledge about the cortical thick ascending limb (CTAL) of the kidney, starting with its initial characterization by Maurice Burg in 1973. Burg's work showed that the CTAL actively reabsorbs NaCl and that, because its water permeability is virtually zero, it can lower the luminal NaCl concentration to a "static head" level well below blood levels. This process is central to the kidney's ability to excrete dilute urine in states of high water intake. Following Burg's original observations, Greger and Schlatter, working in the 1980s, identified the membrane transport processes responsible for transepithelial NaCl transport in the CTAL. In the 1990s, several investigators identified the key transporter genes and proteins at a molecular level by cDNA cloning. The successful completion of human and mouse genome sequencing projects at the turn of the century led to the development of transcriptomic and proteomic methodologies that allowed the identification of complete transcriptomes and proteomes of CTAL cells. Knowledge accrual was enhanced by the development of differential equation-based models of transport in the CTAL in the 2010s. Here, we used a simplified mathematical model of NaCl ("salt"), urea, and water transport in the CTAL to address three key questions about CTAL function: 1) What is the mechanism of Burg's "static head" phenomenon? 2) How does the kidney compensate for the very short length of the CTALs of juxtamedullary nephrons? 3) Which of the three isoforms of the apical Na-K-2Cl cotransporter (NKCC2) dominates functionally in the CTAL?NEW & NOTEWORTHY Here, we review key events in the accrual of knowledge about the cortical thick ascending limb (CTAL) of the kidney, starting with its initial characterization by Maurice Burg in 1973, and culminating with the application of systems biology techniques including mathematical modeling.

The Genomics Revolution Drives a New Era in Entomology.

Thanks to the fast development of sequencing techniques and bioinformatics tools, sequencing the genome of an insect species for specific research purposes has become an increasingly popular practice. Insect genomes not only provide sets of gene sequences but also represent a change in focus from reductionism to systemic biology in the field of entomology. Using insect genomes, researchers are able to identify and study the functions of all members of a gene family, pathway, or gene network associated with a trait of interest. Comparative genomics studies provide new insights into insect evolution, addressing long-lasting controversies in taxonomy. It is also now feasible to uncover the genetic basis of important traits by identifying variants using genome resequencing data of individual insects, followed by genome-wide association analysis. Here, we review the current progress in insect genome sequencing projects and the application of insect genomes in uncovering the phylogenetic relationships between insects and unraveling the mechanisms of important life-history traits. We also summarize the challenges in genome data sharing and possible solutions. Finally, we provide guidance for fully and deeply mining insect genome data.

Trajectory of human migration: insights from autosomal and non-autosomal variant clustering patterns

Genetic variations present in the Y chromosomal and mitochondrial DNA provide the mole-cular basis to support the archeological and anthropological evidence that formulates the theories for describing the trajectory of human migration, which started almost 200,000 years ago out of Africa. These genetic variations have long been used as ancestry informative markers (AIMs) in forensics and evolutionary studies, primarily because of their uniparental inheritance and lack of recombination, despite the fact that gender-specific gene flow and socio-cultural practices may cause discrepancies. Moreover, the genetic markers on the Y chromosome constitute only a minor fraction of the entire human genome. Here, we analyzed over 75 million genetic variants (single nucleotide variants (SNVs) and short insertion-deletion (InDels)) within consecutive 2500000 base pair windows in the autosomal as well as non-autosomal chromosomes of 22 populations in four major geographic regions that are cataloged in the 1000 Genomes Project to understand the clustering patterns of the autosomal and non-autosomal variants. While autosomal and X-chromosomal variants cluster the populations of similar geographic regions together, Y-chromosomal variants constantly place the East Asian Japanese and the European Finnish populations in a single clade in hierarchical clusters. This comprehensive genome-wide analysis essentially introduces new insights into mapping the path of human migration based on the Y-chromosomal and other chromosomal variants.