Human Y-chromosome variation in the genome-sequencing era

Picuris Pueblo oral history and genomics reveal continuity in US Southwest

Indigenous groups often encounter significant challenges when asserting ancestral claims and cultural affiliations based on oral histories, particularly in the USA where such narratives have historically been undervalued. Although ancient DNA offers a tool to complement traditional knowledge and address gaps in oral history, longstanding disregard for Indigenous sovereignty and beliefs has understandably led many Indigenous communities to distrust DNA studies1-4. Earlier research often focused on repatriation claims5-7, whereas more recent work has increasingly moved towards enhancing Tribal histories8,9. Here we present a collaborative study initiated by a federally recognized Native American tribe, the sovereign nation of Picuris Pueblo in the Northern Rio Grande region of New Mexico, USA, to address gaps in traditional knowledge and further their understanding of their population history and ancestry. We generated genomes from 16 ancient Picuris individuals and 13 present-day members of Picuris Pueblo, providing genomic data spanning the last millennium. We show genetic continuity between ancient and present-day Picuris, and more broadly with Ancestral Puebloans from Pueblo Bonito in Chaco Canyon10, 275 km to the west. This suggests a firm spatiotemporal link among these Puebloan populations of the North American Southwest. Furthermore, we see no evidence of population decline before European arrival11-13, and no Athabascan ancestry in individuals predating 1500 CE, challenging earlier migration hypotheses14-16. This work prioritizes Indigenous control of genetic data and brings together oral tradition, archaeology, ethnography and genetics.

Exploring genome-transcriptome correlations in cancer

We examine the complex relationship between genomic copy number variation (CNV) and gene expression, highlighting the relevance to cancer biology and other biological contexts. By tracing the history of genometranscriptome correlations, we emphasize the complexity and challenges in understanding these interactions, particularly within the heterogeneous landscape of human cancers. Recent advances in computational algorithms and high-throughput single-cell multi-omic sequencing technologies are discussed, demonstrating their potential to refine our understanding of cancer biology and their limitations. The integration of genomic and transcriptomic analyses, which offers novel insights into tumor evolution and heterogeneity as well as therapeutic strategies, is presented as a crucial approach for advancing cancer research.

Perspectives and opportunities in forensic human, animal, and plant integrative genomics in the Pangenome era

The Human Pangenome Reference Consortium, the Chinese Pangenome Consortium, and other plant and animal pangenome projects have announced the completion of pilot work aimed at constructing high-quality, haplotype-resolved reference graph genomes representative of global ethno-linguistically different populations or different plant and animal species. These graph-based, gapless pangenome references, which are enriched in terms of genomic diversity, completeness, and contiguity, have the potential for enhancing long-read sequencing (LRS)-based genomic research, as well as improving mappability and variant genotyping on traditional short-read sequencing platforms. We comprehensively discuss the advancements in pangenome-based genomic integrative genomic discoveries across forensic-related species (humans, animals, and plants) and summarize their applications in variant identification and forensic genomics, epigenetics, transcriptomics, and microbiome research. Recent developments in multiplexed array sequencing have introduced a highly efficient and programmable technique to overcome the limitations of short forensic marker lengths in LRS platforms. This technique enables the concatenation of short RNA transcripts and DNA fragments into LRS-optimal molecules for sequencing, assembly, and genotyping. The integration of new pangenome reference coordinates and corresponding computational algorithms will benefit forensic integrative genomics by facilitating new marker identification, accurate genotyping, high-resolution panel development, and the updating of statistical algorithms. This review highlights the necessity of integrating LRS-based platforms, pangenome-based study designs, and graph-based pangenome references in short-read mapping and LRS-based innovations to achieve precision forensic science.

YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database

BACKGROUND

The advancements in second-/third-generation sequencing technologies, alongside computational innovations, have significantly enhanced our understanding of the genomic structure of Y-chromosomes and their unique phylogenetic characteristics. These researches, despite the challenges posed by the lack of population-scale genomic databases, have the potential to revolutionize our approach to high-resolution, population-specific Y-chromosome panels and databases for anthropological and forensic applications.

OBJECTIVES

This study aimed to develop the highest-resolution Y-targeted sequencing panel, utilizing time-stamped, core phylogenetic informative mutations identified from high-coverage sequences in the YanHuang cohort. This panel is intended to provide a new tool for forensic complex pedigree search and paternal biogeographical ancestry inference, as well as explore the general patterns of the fine-scale paternal evolutionary history of ethnolinguistically diverse Chinese populations.

RESULTS

The sequencing performance of the East Asian-specific Y-chromosomal panel, including 2999-core SNP variants, was found to be robust and reliable. The YHSeqY3000 panel was designed to capture the genetic diversity of Chinese paternal lineages from 3500 years ago, identifying 408 terminal lineages in 2097 individuals across 41 genetically and geographically distinct populations. We identified a fine-scale paternal substructure that was correlating with ancient population migrations and expansions. New evidence was provided for extensive gene flow events between minority ethnic groups and Han Chinese people, based on the integrative Chinese Paternal Genomic Diversity Database.

CONCLUSIONS

This work successfully integrated Y-chromosome-related basic genomic science with forensic and anthropological translational applications, emphasizing the necessity of comprehensively characterizing Y-chromosome genomic diversity from genomically under-representative populations. This is particularly important in the second phase of our population-specific medical or anthropological genomic cohorts, where dense sampling strategies are employed.

Advancing precision and personalized breast cancer treatment through multi-omics technologies

Breast cancer is the most common malignant tumour in women, with more than 685,000 women dying of breast cancer each year. The heterogeneity of breast cancer complicates both treatment and diagnosis. Traditional methods based on histopathology and hormone receptor status are now no longer sufficient. Recently, advances in multi-omics techniques, including genomic, proteomic, and transcriptomic analyses, have deepened our understanding of breast cancer. Combining these approaches allows for precise molecular subtyping, which is essential for the detection of key mutations, protein interactions and gene expression patterns that are highly relevant to different therapeutic strategies. Genomic analyses have been effectively identifying key mutations in cancer. Meanwhile, proteomics and transcriptomics complement by identifying new therapeutic targets and elucidating gene expression dynamics. Integrating multi-omics and conventional diagnostics improves tumour characterisation and enables prognostic accuracy comparable to established standards and treatment response. Existing and emerging technologies enable real-time enhanced tumour follow-up and data analysis through liquid biopsy and artificial intelligence, respectively. Despite these clinical implementation challenges, multi-omics including clinical phenotyping offers significant potential for precision breast cancer treatment. This article describes recent advances in molecular subtyping and multi-omics technologies that are driving key innovations to optimise patient outcomes and further develop personalised medicine in the context of breast cancer care.

Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages

The Indo-European languages are among the most widely spoken in the world, yet their early diversification remains contentious1-5. It is widely accepted that the spread of this language family across Europe from the 5th millennium BP correlates with the expansion and diversification of steppe-related genetic ancestry from the onset of the Bronze Age6,7. However, multiple steppe-derived populations co-existed in Europe during this period, and it remains unclear how these populations diverged and which provided the demographic channels for the ancestral forms of the Italic, Celtic, Greek, and Armenian languages8,9. To investigate the ancestral histories of Indo-European-speaking groups in Southern Europe, we sequenced genomes from 314 ancient individuals from the Mediterranean and surrounding regions, spanning from 5,200 BP to 2,100 BP, and co-analysed these with published genome data. We additionally conducted strontium isotope analyses on 224 of these individuals. We find a deep east-west divide of steppe ancestry in Southern Europe during the Bronze Age. Specifically, we show that the arrival of steppe ancestry in Spain, France, and Italy was mediated by Bell Beaker (BB) populations of Western Europe, likely contributing to the emergence of the Italic and Celtic languages. In contrast, Armenian and Greek populations acquired steppe ancestry directly from Yamnaya groups of Eastern Europe. These results are consistent with the linguistic Italo-Celtic10,11 and Graeco-Armenian1,12,13 hypotheses accounting for the origins of most Mediterranean Indo-European languages of Classical Antiquity. Our findings thus align with specific linguistic divergence models for the Indo-European language family while contradicting others. This underlines the power of ancient DNA in uncovering prehistoric diversifications of human populations and language communities.

Genetic Polymorphism of Y-Chromosome in Turkmen Population from Turkmenistan

This study investigates the Y-chromosome genetic diversity of the Turkmen population in Turkmenistan, analyzing 23 Y-STR loci for the first time in a sample of 100 individuals. Combined with comparative data from Turkmen populations in Afghanistan, Iran, Iraq, Russia, and Uzbekistan, this analysis offers insights into the genetic structure and relationships among Turkmen populations across regions across Central Asia and the Near East. High haplotype diversity in the Turkmen of Turkmenistan is shaped by founder effects (lineage expansions) from distinct haplogroups, with haplogroups Q and R1a predominating. Subhaplogroups Q1a and Q1b identified in Turkmenistan trace back to ancient Y-chromosome lineages from the Bronze Age. Comparative analyses, including genetic distance (RST), median-joining network, and multidimensional scaling (MDS), highlight the genetic proximity of the Turkmen in Turkmenistan to those in Afghanistan and Iran, while Iraqi Turkmen display unique characteristics, aligning with Near Eastern populations. This study underscores the Central Asian genetic affinity across most Turkmen populations. It demonstrates the value of deep-sequencing Y-chromosome data in tracing the patrilineal history of Central Asia for future studies. These findings contribute to a more comprehensive understanding of Turkmen genetic ancestry and add new data to the ongoing study of Central Asian population genetics.

The impact of mosaic loss of the Y chromosome (mLOY) in men of advanced age

The Y chromosome has long been considered to be a "genetic wasteland" harboring only few genes essentially involved in male sex development and spermatogenesis. However, the discovery of mosaic loss of the Y chromosome (mLOY) in older men has led to revisiting of the potential impact of the Y chromosome on health and the pathophysiological processes of multiple diseases such as cancer, Alzheimer's disease and cardiovascular disease. Hence, developing more sensitive techniques for the detection of mLOY has become an emergent concern. In this article, we present a comprehensive review of the literature regarding mLOY. Additionally, we discuss the emerging discoveries concerning mLOY as well as the underlying mechanisms promoting disease in men of advanced age.

Y-Chromosomal insights into the paternal genealogy of the Kerey tribe have called into question their descent from the Stepfather of Genghis Khan

The Kerey is one of the prominent Kazakh tribes and has long been a subject of ethnographic scrutiny, with a lack of consensus on its origin and traditional genealogy. Their historical significance, intertwined with the emergence of the empire established by Genghis Khan, necessitates a comprehensive understanding of their genetic history. This study focuses on unraveling the genetic heritage of the Kerey tribe. We conducted a comprehensive analysis of Y-chromosome data from genetic genealogy as citizen science and genetic screening of 23 Y-STRs and 37 Y-SNPs on 207 males from the Kerey tribe within academic science. Our results reveal two prevalent phylogenetic lineages within the C2a1a3a-F3796 haplogroup, also known as the C2*-Star Cluster (C2*-ST), which is one of the founding paternal lineages of the ancient Niru'un clan of the Mongols: C2-FT411734 and C2-FT224144, corresponding to the Abak and Ashamaily clans. While indicating a common male ancestry for them, our findings challenge the notion that they are full siblings. Additionally, genetic diversity analysis of the Y-chromosomes in the Kerey tribe and Kazakhs confirms their kinship with the Uissun tribe but refutes the claim of the Abak clan's progenitor originating from this tribe. Furthermore, genetic evidence fails to support popular historical and ethnographic hypotheses regarding the Kerey tribe's kinship with the Uak, Sirgeli, Adai, Törtkara, Karakerey, and Kereyit Kazakh tribes. The absence of a genetic paternal connection with the Kereyt tribe raises doubts about the genealogical link between the Kerey tribe and the stepfather of Genghis Khan.

Y-chromosome analysis recapitulates key events of Mediterranean populations

The remarkable geographical situation of the Mediterranean region, located between Europe, Africa, and Asia, with numerous migratory routes, has made this area a crucible of cultures. Studying the Y-chromosome variability is a very performant tool to explore the genetic ancestry and evaluate scenarios that may explain the current Mediterranean gene pool. Here, six Mediterranean populations, including three Balearic Islands (Ibiza, Majorca, and Minorca) and three Southern Italian regions (Catanzaro, Cosenza, and Reggio di Calabria) were typed using 23 Y-STR loci and up to 39 Y-SNPs and compared to geographically targeted key reference populations to explore their genetic relationship and provide an overview of Y-chromosome variation across the Mediterranean basin. Pairwise RST genetic distances calculated with STRs markers and Y-haplogroups mirror the West to East geographic distribution of European and Asian Mediterranean populations, highlighting the North-South division of Italy, with a higher Eastern Mediterranean component in Southern Italian populations. In contrast, the African populations from the Southern coast of the Mediterranean clustered separately. Overall, these results support the notion that migrations from Magna Graecia or the Byzantine Empire, which followed similar Neolithic and post-Neolithic routes into Southern Italy, may have contributed to maintaining and/or reinforcing the Eastern Mediterranean genetic component in Southern Italian populations.

Estimating Haplotype Structure and Frequencies: A Bayesian Approach to Unknown Design in Pooled Genomic Data

The estimation of haplotype structure and frequencies provides crucial information about the composition of genomes. Techniques, such as single-individual haplotyping, aim to reconstruct individual haplotypes from diploid genome sequencing data. However, our focus is distinct. We address the challenge of reconstructing haplotype structure and frequencies from pooled sequencing samples where multiple individuals are sequenced simultaneously. A frequentist method to address this issue has recently been proposed. In contrast to this and other methods that compute point estimates, our proposed Bayesian hierarchical model delivers a posterior that permits us to also quantify uncertainty. Since matching permutations in both haplotype structure and corresponding frequency matrix lead to the same reconstruction of their product, we introduce an order-preserving shrinkage prior that ensures identifiability with respect to permutations. For inference, we introduce a blocked Gibbs sampler that enforces the required constraints. In a simulation study, we assessed the performance of our method. Furthermore, by using our approach on two distinct sets of real data, we demonstrate that our Bayesian approach can reconstruct the dominant haplotypes in a challenging, high-dimensional set-up.

Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis

Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.

Mitochondrial DNA and Y chromosome reveal the genetic structure of the native Polish Konik horse population

Polish Konik remains one of the most important horse breeds in Poland. The primitive, native horses with a stocky body and mouse-like coat color are protected by a conservation program, while their Polish population consists of about 3,480 individuals, representing 16 dam and six sire lines. To define the population's genetic structure, mitochondrial DNA and Y chromosome sequence variables were identified. The mtDNA whole hypervariable region analysis was carried out using the Sanger sequencing method on 233 Polish Koniks belonging to all dam lines, while the Y chromosome analysis was performed with the competitive allele-specific PCR genotyping method on 36 horses belonging to all sire lines. The analysis of the mtDNA hypervariable region detected 47 SNPs, which assigned all tested horses to 43 haplotypes. Most dam lines presented more than one haplotype; however, five dam lines were represented by only one haplotype. The haplotypes were classified into six (A, B, E, J, G, R) recognized mtDNA haplogroups, with most horses belonging to haplogroup A, common among Asian horse populations. Y chromosome analysis allocated Polish Koniks in the Crown group, condensing all modern horse breeds, and divided them into three haplotypes clustering with coldblood breeds (28 horses), warmblood breeds (two horses), and Duelmener Pony (six horses). The clustering of all Wicek sire line stallions with Duelmener horses may suggest a historical relationship between the breeds. Additionally, both mtDNA and Y chromosome sequence variability results indicate crossbreeding before the studbooks closure or irregularities in the pedigrees occurred before the DNA testing introduction.

Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies

Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species (Rangifer tarandus). It has survived the Holocene thanks to its immense adaptability and successful coexistence with humans in different forms of hunting and herding cultures. Here, we examine the paternal and maternal history of Rangifer based on robust Y-chromosomal and mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest reindeer, Svalbard reindeer, Alaska tundra caribou, and woodland caribou. We first assembled Y-chromosomal contigs, representing 1.3 Mb of single-copy Y regions. Based on 545 Y-chromosomal and 458 mtDNA SNPs defined in 55 males, maximum parsimony trees were created. We observed two well separated clades in both phylogenies: the "EuroBeringian clade" formed by animals from Arctic Islands, Eurasia, and a few from North America and the "North American clade" formed only by caribou from North America. The time calibrated Y tree revealed an expansion and dispersal of lineages across continents after the Last Glacial Maximum. We show for the first time unique paternal lineages in Svalbard reindeer and Finnish forest reindeer and reveal a circumscribed Y haplogroup in Fennoscandian tundra reindeer. The Y chromosome in domesticated reindeer is markedly diverse indicating that several male lineages have undergone domestication and less intensive selection on males. This study places R. tarandus onto the list of species with resolved Y and mtDNA phylogenies and builds the basis for studies of the distribution and origin of paternal and maternal lineages in the future.

Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives

Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.

Loss of the Y Chromosome: A Review of Molecular Mechanisms, Age Inference, and Implications for Men's Health

Until a few years ago, it was believed that the gradual mosaic loss of the Y chromosome (mLOY) was a normal age-related process. However, it is now known that mLOY is associated with a wide variety of pathologies in men, such as cardiovascular diseases, neurodegenerative disorders, and many types of cancer. Nevertheless, the mechanisms that generate mLOY in men have not been studied so far. This task is of great importance because it will allow focusing on possible methods of prophylaxis or therapy for diseases associated with mLOY. On the other hand, it would allow better understanding of mLOY as a possible marker for inferring the age of male samples in cases of human identification. Due to the above, in this work, a comprehensive review of the literature was conducted, presenting the most relevant information on the possible molecular mechanisms by which mLOY is generated, as well as its implications for men's health and its possible use as a marker to infer age.

Assessment of Y chromosome copy number alterations in non-neoplastic and neoplastic leukocytes of male dogs

The loss of the Y chromosome (ChrY), also known as LOY, is a common genetic alteration observed in men. It occurs in non-neoplastic cells as an age-related change as well as in neoplastic cells of various cancer types. While well-documented in humans, LOY has not been extensively studied in non-human mammals. In this study, we developed simple digital PCR-based assays to assess the copy number of ChrY relative to the X chromosome (ChrX) and chromosome 8 (Chr8) to evaluate ChrY numerical alterations in male canine DNA specimens. Using these assays, we analyzed non-neoplastic leukocytes from 162 male dogs without hematopoietic neoplasia to investigate the occurrence of age-related LOY in non-neoplastic leukocytes. Additionally, we examined 101 tumor DNA specimens obtained from male dogs diagnosed with various types of lymphoma and leukemia to determine whether copy number alterations of the ChrY occur in canine hematopoietic cancers. Analysis of the 162 non-neoplastic leukocyte DNA specimens from male dogs of varying ages revealed a consistent ∼1:1 ChrY:ChrX ratio. This suggests that age-related LOY in non-neoplastic leukocytes is rare or absent in dogs. Conversely, a decreased or increased ChrY:ChrX ratio was detected in canine neoplastic leukocytes at varying frequencies across different canine hematopoietic malignancies (P = 0.01, Fisher's exact test). Notably, a higher incidence of LOY was observed in more aggressive cancer types. To determine if this relative LOY to ChrX was caused by changes in ChrY or ChrX, we further analyzed their relative copy numbers using Chr8 as a reference. Loss of ChrX relative to Chr8 was found in 21% (9/41) of B-cell lymphomas and 6% (1/18) of non-T-zone/high-grade T-cell lymphomas. In contrast, a subset (29%, 4/14) of T-cell chronic lymphocytic leukemia showed gain of ChrX relative to Chr8. Notably, no relative LOY to Chr8 was detected indolent hematopoietic cancers such as T-zone lymphoma (0/9) and chronic lymphocytic leukemia of B-cell (0/11) and T-cell origins (0/14). However, relative LOY to Chr8 was present in more aggressive canine hematopoietic cancers, with incidences of 24% (10/41) in B-cell lymphoma, 44% (8/18) in non-T-zone/high-grade T-cell lymphoma, and 75% (6/8) in acute leukemia. This study highlights both similarities and differences in LOY between human and canine non-neoplastic and neoplastic leukocytes. It underscores the need for further research into the role of ChrY in canine health and disease, as well as the significance of LOY across various species.

Sequenced-based Rwanda population provides insights into demographic history

Rwanda is known as the heart of Africa, reflecting the history of the world. Colonization and genocide have led to Rwanda's existing genetic structure. Herein, we used massively parallel sequencing to analyze 296 loci in 185 Rwandans and constructed a database for Rwandan forensic data for the first time. We found the following results: First, forensic parameters demonstrated that all loci were highly informative and could be used for forensic identification and paternity tests in Rwandans. Second, we found that the differences in genetic background between Rwandans and other African populations were similar but slight, as indicated by the massively parallel sequencing panel. Rwandans belonged to the African population and were inseparable from populations from neighboring countries. Also, Rwandans were closer to the European and American populations because of colonization, war, and other reasons. There was no scientific basis for racial classification established by colonization. Further research still needs to be carried out on more loci and larger Rwandan samples.

Single Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting (SNACS): A tool for demultiplexing single-cell DNA sequencing data

Motivation

Recently, single-cell DNA sequencing (scDNA-seq) and multi-modal profiling with the addition of cell-surface antibodies (scDAb-seq) have provided key insights into cancer heterogeneity. Scaling these technologies across large patient cohorts, however, is cost and time prohibitive. Multiplexing, in which cells from unique patients are pooled into a single experiment, offers a possible solution. While multiplexing methods exist for scRNAseq, accurate demultiplexing in scDNAseq remains an unmet need.

Results

Here, we introduce SNACS: Single-Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting. SNACS relies on a combination of patient-level cell-surface identifiers and natural variation in genetic polymorphisms to demultiplex scDNAseq data. We demonstrated the performance of SNACS on a dataset consisting of multi-sample experiments from patients with leukemia where we knew truth from single-sample experiments from the same patients. Using SNACS, accuracy ranged from 0.948 - 0.991 vs 0.552 - 0.934 using demultiplexing methods from the single-cell literature.

Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Central Kazakhstan

BACKGROUND

The haplotypes from Northern, Southern, Eastern, and Western Kazakhstan, analysed for 27 Y-STR loci, have been contributed to the Y-Chromosome STR Haplotype Reference Database, while the genetic profile of Central Kazakhstan remains inadequately explored.

AIM

To investigate the genetic diversity of 27 Y-STR loci in the Kazakh populations from Central Kazakhstan.

SUBJECTS AND METHODS

A total of 112 unrelated Central Kazakh males were genotyped via the Yfiler Plus kit. Data analysis yielded haplotype and allele frequencies, and forensic parameters. Genetic distances were graphically represented by a multidimensional scaling plot, with genetic linkages further elucidated through Nei's distance dendrograms and Median-joining networks.

RESULTS

A total of 102 haplotypes were detected, of which 96 were unique. The haplotype diversity and discrimination capacity were 0.997 and 0.91, respectively. Central Kazakhstan displays a unique cluster in analyses, underscoring its distinct Y-chromosome diversity compared to other Kazakh regions. The analysis of the Naiman tribe, predominantly residing in Central, Southern and Eastern Kazakhstan, revealed three genetic clusters of distinct haplogroups associated with their clans.

CONCLUSIONS

The identified haplotypes will enhance the existing reference database for Y-chromosomal studies in Kazakhstan, offering a robust tool for future research in population genetics, forensic science and genetic genealogy.

Impact of age and sex on myelopoiesis and inflammation during myocardial infarction

Of all the different risk factors known to cause cardiovascular disease (CVD), age and sex are considered to play a crucial role. Aging follows a continuum from birth to death, and therefore it inevitably acts as a risk for CVD. Along with age, sex differences have also been shown to demonstrate variations in immune system responses to pathological insults. It has been widely perceived that females are protected against myocardial infarction (MI) and the protection is quite apparent in young vs. old women. Acute MI leads to changes in the population of myeloid and lymphoid cells at the injury site with myeloid bias being observed in the initial inflammation and the lymphoid in the late-resolution phases of the pathology. Multiple evidence demonstrates that aging enhances damage to various cellular processes through inflamm-aging, an inflammatory process identified to increase pro-inflammatory markers in circulation and tissues. Following MI, marked changes were observed in different sub-sets of major myeloid cell types viz., neutrophils, monocytes, and macrophages. There is a paucity of information regarding the tissue and site-specific functions of these sub-sets. In this review, we highlight the importance of age and sex as crucial risk factors by discussing their role during MI-induced myelopoiesis while emphasizing the current status of myeloid cell sub-sets. We further put forth the need for designing and executing age and sex interaction studies aimed to determine the appropriate age and sex to develop personalized therapeutic strategies post-MI.

A novel regulatory sex-skewing method that inhibits testicular DPY30 expression to increase female rate of dairy goat offspring

The demand for goat milk products has increased exponentially with the growth of the global population. The shortage of dairy products will be addressed extraordinarily by manipulating the female rate of goat offspring to expand the goat population and goat milk yield. No studies have reported bioinformatic analyses of X- and Y-bearing sperm of dairy goats, although this will contribute to exploring novel and applied sex-skewing technologies. Regulatory subunit of the histone methyltransferase complex (DPY30) was determined to be the key differentially expressed protein (DEP) among 15 DEPs identified in the present study. The spatiotemporal expression of DPY30 strongly suggested a functional involvement of the protein in spermatogenesis. DPY30 promoted meiosis via upregulating SYCP3, which played a crucial role in mediating sex ratio skewing in goats. Although DPY30 suppressed the self-renewal of spermatogonia stem cells through AKT/PLZF, DPY30 inhibition in the testis did not induce testicular dysgenesis. Based on the biosafety assessment in mice testes, lentivirus-mediated DPY30 knockdown in bucks' testes increased X-bearing sperm proportion and female kids' rate (22.8 percentage points) without affecting sperm quality, pregnancy rate, and kidding rate. This study provides the first evidence of the DEGs in the sexed sperm of dairy goats. DPY30 inhibition in the testes of bucks increased the female kids' rate without influencing reproductive performance. The present study provides evidence for expanding the female dairy goat population to address the concern of dairy product shortage.

Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan

BACKGROUND

The Kazakhs are one of the biggest Turkic-speaking ethnic groups, controlling vast swaths of land from the Altai to the Caspian Sea. In terms of area, Kazakhstan is ranked ninth in the world. Northern, Eastern, and Western Kazakhstan have already been studied in relation to genetic polymorphism 27 Y-STR. However, current information on the genetic polymorphism of the Y-chromosome of Southern Kazakhstan is limited only by 17 Y-STR and no geographical study of other regions has been studied at this variation.

RESULTS

The Kazakhstan Y-chromosome Haplotype Reference Database was expanded with 468 Kazakh males from the Zhambyl and Turkestan regions of South Kazakhstan by having their 27 Y-STR loci and 23 Y-SNP markers analyzed. Discrimination capacity (DC = 91.23%), haplotype match probability (HPM = 0.0029) and haplotype diversity (HD = 0.9992) are defined. Most of this Y-chromosome variability is attributed to haplogroups C2a1a1b1-F1756 (2.1%), C2a1a2-M48 (7.3%), C2a1a3-F1918 (33.3%) and C2b1a1a1a-M407 (6%). Median-joining network analysis was applied to understand the relationship between the haplotypes of the three regions. In three genetic layer can be described the position of the populations of the Southern region of Kazakhstan-the geographic Kazakh populations of Kazakhstan, the Kazakh tribal groups, and the people of bordering Asia.

CONCLUSION

The Kazakhstan Y-chromosome Haplotype Reference Database was formed for 27 Y-STR loci with a total sample of 1796 samples of Kazakhs from 16 regions of Kazakhstan. The variability of the Y-chromosome of the Kazakhs in a geographical context can be divided into four main clusters-south, north, east, west. At the same time, in the genetic space of tribal groups, the population of southern Kazakhs clusters with tribes from the same region, and genetic proximity is determined with the populations of the Hazaras of Afghanistan and the Mongols of China.

Parallel signatures of Mycobacterium tuberculosis and human Y-chromosome phylogeography support the Two Layer model of East Asian population history

The Two Layer hypothesis is fast becoming the favoured narrative describing East Asian population history. Under this model, hunter-gatherer groups who initially peopled East Asia via a route south of the Himalayas were assimilated by agriculturalist migrants who arrived via a northern route across Eurasia. A lack of ancient samples from tropical East Asia limits the resolution of this model. We consider insight afforded by patterns of variation within the human pathogen Mycobacterium tuberculosis (Mtb) by analysing its phylogeographic signatures jointly with the human Y-chromosome. We demonstrate the Y-chromosome lineages enriched in the traditionally hunter-gatherer groups associated with East Asia's first layer of peopling to display deep roots, low long-term effective population size, and diversity patterns consistent with a southern entry route. These characteristics mirror those of the evolutionarily ancient Mtb lineage 1. The remaining East Asian Y-chromosome lineage is almost entirely absent from traditionally hunter-gatherer groups and displays spatial and temporal characteristics which are incompatible with a southern entry route, and which link it to the development of agriculture in modern-day China. These characteristics mirror those of the evolutionarily modern Mtb lineage 2. This model paves the way for novel host-pathogen coevolutionary research hypotheses in East Asia.

MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes

Microsatellites are short tandem DNA repeats, ubiquitous in genomes. They are believed to be under selection pressure, considering their high distribution and abundance beyond chance or random accumulation. However, limited analysis of microsatellites in single taxonomic groups makes it challenging to understand their evolutionary significance across taxonomic boundaries. Despite abundant genomic information, microsatellites have been studied in limited contexts and within a few species, warranting an unbiased examination of their genome-wide distribution in distinct versus closely related-clades. Large-scale comparisons have revealed relevant trends, especially in vertebrates. Here, "MicrosatNavigator", a new tool that allows quick and reliable investigation of perfect microsatellites in DNA sequences, was developed. This tool can identify microsatellites across the entire genome sequences. Using this tool, microsatellite repeat motifs were identified in the genome sequences of 186 vertebrates. A significant positive correlation was noted between the abundance, density, length, and GC bias of microsatellites and specific lineages. The (AC)n motif is the most prevalent in vertebrate genomes, showing distinct patterns in closely related species. Longer microsatellites were observed on sex chromosomes in birds and mammals but not on autosomes. Microsatellites on sex chromosomes of non-fish vertebrates have the lowest GC content, whereas high-GC microsatellites (≥ 50 M% GC) are preferred in bony and cartilaginous fishes. Thus, similar selective forces and mutational processes may constrain GC-rich microsatellites to different clades. These findings should facilitate investigations into the roles of microsatellites in sex chromosome differentiation and provide candidate microsatellites for functional analysis across the vertebrate evolutionary spectrum.

Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data

In anthropological, medical, and forensic studies, the nonrecombinant region of the human Y chromosome (NRY) enables accurate reconstruction of pedigree relationships and retrieval of ancestral information. Using high-throughput sequencing (HTS) data, we present a benchmarking analysis of command-line tools for NRY haplogroup classification. The evaluation was performed using paired Illumina data from whole-genome sequencing (WGS) and whole-exome sequencing (WES) experiments from 50 unrelated donors. Additionally, as a validation, we also used paired WGS/WES datasets of 54 individuals from the 1000 Genomes Project. Finally, we evaluated the tools on data from third-generation HTS obtained from a subset of donors and one reference sample. Our results show that WES, despite typically offering less genealogical resolution than WGS, is an effective method for determining the NRY haplogroup. Y-LineageTracker and Yleaf showed the highest accuracy for WGS data, classifying precisely 98% and 96% of the samples, respectively. Yleaf outperforms all benchmarked tools in the WES data, classifying approximately 90% of the samples. Yleaf, Y-LineageTracker, and pathPhynder can correctly classify most samples (88%) sequenced with third-generation HTS. As a result, Yleaf provides the best performance for applications that use WGS and WES. Overall, our study offers researchers with a guide that allows them to select the most appropriate tool to analyze the NRY region using both second- and third-generation HTS data.

Mosaic loss of the Y chromosome in human neurodegenerative and oncological diseases

The development of new biomarkers for prediction and early detection of human diseases, as well as for monitoring the response to therapy is one of the most relevant areas of modern human genetics and genomics. Until recently, it was believed that the function of human Y chromosome genes was limited to determining sex and controlling spermatogenesis. Thanks to occurance of large databases of the genome-wide association study (GWAS), there has been a transition to the use of large samples for analyzing genetic changes in both normal and pathological conditions. This has made it possible to assess the association of mosaic aneuploidy of the Y chromosome in somatic cells with a shorter lifespan in men compared to women. Based on data from the UK Biobank, an association was found between mosaic loss of the Y chromosome (mLOY) in peripheral blood leukocytes and the age of men over 70, as well as a number of oncological, cardiac, metabolic, neurodegenerative, and psychiatric diseases. As a result, mLOY in peripheral blood cells has been considered a potential marker of biological age in men and as a marker of certain age-related diseases. Currently, numerous associations have been identified between mLOY and genes based on GWAS and transcriptomes in affected tissues. However, the exact cause of mLOY and the impact and consequences of this phenomenon at the whole organism level have not been established. In particular, it is unclear whether aneuploidy of the Y chromosome in blood cells may affect the development of pathologies that manifest in other organs, such as the brain in Alzheimer's disease, or whether it is a neutral biomarker of general genomic instability. This review examines the main pathologies and genetic factors associated with mLOY, as well as the hypotheses regarding their interplay. Special attention is given to recent studies on mLOY in brain cells in Alzheimer's disease.

Comprehensive insights into the genetic background of Chinese populations using Y chromosome markers

China is located in East Asia. With a high genetic and cultural diversity, human migration in China has always been a hot topic of genetics research. To explore the origins and migration routes of Chinese males, 3333 Chinese individuals (Han, Hui, Mongolia, Yi and Kyrgyz) with 27 Y-STRs and 143 Y-SNPs from published literature were analysed. Our data showed that there are five dominant haplogroups (O2-M122, O1-F265, C-M130, N-M231, R-M207) in China. Combining analysis of haplogroup frequencies, geographical positions and time with the most recent common ancestor (TMRCA), we found that haplogroups C-M130, N-M231 and R1-M173 and O1a-M175 probably migrated into China via the northern route. Interestingly, we found that haplogroup C*-M130 in China may originate in South Asia, whereas the major subbranches C2a-L1373 and C2b-F1067 migrated from northern China. The results of BATWING showed that the common ancestry of Y haplogroup in China can be traced back to 17 000 years ago, which was concurrent with global temperature increases after the Last Glacial Maximum.

Y Chromosome Genomic Variations and Biological Significance in Human Diseases and Health

The Y chromosome is a haploid genome unique to males with no genes essential for life. It is easily transmitted to the next generation without being repaired by recombination, even if a major genomic structural alteration occurs. On the other hand, the Y chromosome genome is basically a region transmitted only from father to son, reflecting a male-specific inheritance between generations. The Y chromosome exhibits genomic structural differences among different ethnic groups and individuals. The Y chromosome was previously thought to affect only male-specific phenotypes, but recent studies have revealed associations between the Y chromosomes and phenotypes common to both males and females, such as certain types of cancer and neuropsychiatric disorders. This evidence was discovered with the finding of the mosaic loss of the Y chromosome in somatic cells. This phenomenon is also affected by environmental factors, such as smoking and aging. In the past, functional analysis of the Y chromosome has been elucidated by assessing the function of Y chromosome-specific genes and the association between Y chromosome haplogroups and human phenotypes. These studies are currently being conducted intensively. Additionally, the recent advance of large-scale genome cohort studies has increased the amount of Y chromosome genomic information available for analysis, making it possible to conduct more precise studies of the relationship between genome structures and phenotypes. In this review, we will introduce recent analyses using large-scale genome cohort data and previously reported association studies between Y chromosome haplogroups and human phenotypes, such as male infertility, cancer, cardiovascular system traits, and neuropsychiatric disorders. The function and biological role of the Y chromosome in human phenotypes will also be discussed.

Insights into Sex and Gender Differences in Brain and Psychopathologies Using Big Data

The societal implication of sex and gender (SG) differences in brain are profound, as they influence brain development, behavior, and importantly, the presentation, prevalence, and therapeutic response to diseases. Technological advances have enabled speed up identification and characterization of SG differences during development and in psychopathologies. The main aim of this review is to elaborate on new technological advancements, such as genomics, imaging, and emerging biobanks, coupled with bioinformatics analyses of data generated from these technologies have facilitated the identification and characterization of SG differences in the human brain through development and psychopathologies. First, a brief explanation of SG concepts is provided, along with a developmental and evolutionary context. We then describe physiological SG differences in brain activity and function, and in psychopathologies identified through imaging techniques. We further provide an overview of insights into SG differences using genomics, specifically taking advantage of large cohorts and biobanks. We finally emphasize how bioinformatics analyses of big data generated by emerging technologies provides new opportunities to reduce SG disparities in health outcomes, including major challenges.

Y chromosome toxicity does not contribute to sex-specific differences in longevity

While sex chromosomes carry sex-determining genes, they also often differ from autosomes in size and composition, consisting mainly of silenced heterochromatic repetitive DNA. Even though Y chromosomes show structural heteromorphism, the functional significance of such differences remains elusive. Correlative studies suggest that the amount of Y chromosome heterochromatin might be responsible for several male-specific traits, including sex-specific differences in longevity observed across a wide spectrum of species, including humans. However, experimental models to test this hypothesis have been lacking. Here we use the Drosophila melanogaster Y chromosome to investigate the relevance of sex chromosome heterochromatin in somatic organs in vivo. Using CRISPR-Cas9, we generated a library of Y chromosomes with variable levels of heterochromatin. We show that these different Y chromosomes can disrupt gene silencing in trans, on other chromosomes, by sequestering core components of the heterochromatin machinery. This effect is positively correlated to the level of Y heterochromatin. However, we also find that the ability of the Y chromosome to affect genome-wide heterochromatin does not generate physiological sex differences, including sexual dimorphism in longevity. Instead, we discovered that it is the phenotypic sex, female or male, that controls sex-specific differences in lifespan, rather than the presence of a Y chromosome. Altogether, our findings dismiss the 'toxic Y' hypothesis that postulates that the Y chromosome leads to reduced lifespan in XY individuals.

Circulating macrophages as the mechanistic link between mosaic loss of Y-chromosome and cardiac disease

BACKGROUND

Genetics evidences have long linked mosaic loss of Y-chromosome (mLOY) in peripheral leukocytes with a wide range of male age-associated diseases. However, a lack of cellular and molecular mechanistic explanations for this link has limited further investigation into the relationship between mLOY and male age-related disease. Excitingly, Sano et al. have provided the first piece of evidence directly linking mLOY to cardiac fibrosis through mLOY enriched profibrotic transforming growth factor β1 (TGF-β1) regulons in hematopoietic macrophages along with suppressed interleukin-1β (IL-1β) proinflammatory regulons. The results of this novel finding can be extrapolated to other disease related to mLOY, such as cancer, cardiac disease, and age-related macular degeneration.

RESULTS

Sano et al. used a CRISPR-Cas9 gRNAs gene editing induced Y-chromosome ablation mouse model to assess results of a UK biobank prospective analysis implicating the Y-chromosome in male age-related disease. Using this in vivo model, Sano et al. showed that hematopoietic mLOY accelerated cardiac fibrosis and heart failure in male mice through profibrotic pathways. This process was linked to monocyte-macrophage differentiation during hematopoietic development. Mice confirmed to have mLOY in leukocytes, by loss of Y-chromosome genes Kdm5d, Uty, Eif2s3y, and Ddx3y, at similar percentages to the human population were shown to have accelerated rates of interstitial and perivascular fibrosis and abnormal echocardiograms. These mice also recovered poorly from the transverse aortic constriction (TAC) model of heart failure and developed left ventricular dysfunction at higher rates. This was attributed to aberrant proliferation of cardiac MEF-SK4 + fibroblasts promoted by mLOY macrophages enriched in profibrotic regulons and lacking in proinflammatory regulons. These pro-fibrotic macrophages localized to heart and eventually resulted in cardiac fibrosis via enhanced TGF-β1 and suppressed IL-1β signaling. Furthermore, treatment of mLOY mice with TGFβ1 neutralizing antibody was able to improve their cardiac function. This study by Sano et al. was able to provide a causative link between the known association between mLOY and male cardiac disease morbidity and mortality for the first time, and thereby provide a new target for improving human health.

CONCLUSIONS

Using a CRISPR-Cas9 induced Y-chromosome ablation mouse model, Sano et al. has proven mosaic loss of Y-chromosome in peripheral myeloid cells to have a causative effect on male mobility and mortality due to male age-related cardiac disease. They traced the mechanism of this effect to hyper-expression of the profibrotic TGF-β1 and reduced pro-inflammatory IL-1β signaling, attenuation of which could provide another potential strategy in improving outcomes against age-related diseases in men.

Characterizing the evolution and phenotypic impact of ampliconic Y chromosome regions

A major part of the human Y chromosome consists of palindromes with multiple copies of genes primarily expressed in testis, many of which have been claimed to affect male fertility. Here we examine copy number variation in these palindromes based on whole genome sequence data from 11,527 Icelandic men. Using a subset of 7947 men grouped into 1449 patrilineal genealogies, we infer 57 large scale de novo copy number mutations affecting palindrome 1. This corresponds to a mutation rate of 2.34 × 10-3 mutations per meiosis, which is 4.1 times larger than our phylogenetic estimate of the mutation rate (5.72 × 10-4), suggesting that de novo mutations on the Y are lost faster than expected under neutral evolution. Although simulations indicate a selection coefficient of 1.8% against non-reference copy number carriers, we do not observe differences in fertility among sequenced men associated with their copy number genotype, but we lack statistical power to detect differences resulting from weak negative selection. We also perform association testing of a diverse set of 341 traits to palindromic copy number without any significant associations. We conclude that large-scale palindrome copy number variation on the Y chromosome has little impact on human phenotype diversity.

Y chromosome sequence and epigenomic reconstruction across human populations

Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). Native DNA was sequenced on a MinION Oxford Nanopore Technologies sequencing device to generate genome assemblies for seven major chrY human haplogroups. We analyzed and compared the chrY enrichment of sequencing data obtained using two different selective sequencing approaches: adaptive sampling and flow cytometry chromosome sorting. We show that adaptive sampling can produce data to create assemblies comparable to chromosome sorting while being a less expensive and time-consuming technique. We also assessed haplogroup-specific structural variants, which would be otherwise difficult to study using short-read sequencing data only. Finally, we took advantage of this technology to detect and profile epigenetic modifications among the considered haplogroups. Altogether, we provide a framework to study complex genomic regions with a simple, fast, and affordable methodology that could be applied to larger population genomics datasets.

Refining the evolutionary tree of the horse Y chromosome

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.

Clonal hematopoiesis: the nonhereditary genetics of age-associated cardiovascular disease

PURPOSE OF REVIEW

Somatic mutations, described as noninherited changes in DNA that arise and are passed on to descendant cells, are well known to cause cancers; however, it is increasingly appreciated that the propagation of somatic mutations within a tissue may have a role in causing nonneoplastic disorders and abnormalities in elderly individuals. The nonmalignant clonal expansion of somatic mutations in the hematopoietic system is termed clonal hematopoiesis. This review will briefly discuss how this condition has been linked to various age-related diseases outside the hematopoietic system.

RECENT FINDINGS

Clonal hematopoiesis, resulting from leukemic driver gene mutations or mosaic loss of the Y chromosome in leukocytes, is associated with the development of various forms of cardiovascular disease, including atherosclerosis and heart failure, in a mutation-dependent manner.

SUMMARY

Accumulating evidence shows that clonal hematopoiesis represents a new mechanism for cardiovascular disease and a new risk factor that is as prevalent and consequential as the traditional risk factors that have been studied for decades.

Multiple founding paternal lineages inferred from the newly-developed 639-plex Y-SNP panel suggested the complex admixture and migration history of Chinese people

BACKGROUND

Non-recombining regions of the Y-chromosome recorded the evolutionary traces of male human populations and are inherited haplotype-dependently and male-specifically. Recent whole Y-chromosome sequencing studies have identified previously unrecognized population divergence, expansion and admixture processes, which promotes a better understanding and application of the observed patterns of Y-chromosome genetic diversity.

RESULTS

Here, we developed one highest-resolution Y-chromosome single nucleotide polymorphism (Y-SNP) panel targeted for uniparental genealogy reconstruction and paternal biogeographical ancestry inference, which included 639 phylogenetically informative SNPs. We genotyped these loci in 1033 Chinese male individuals from 33 ethnolinguistically diverse populations and identified 256 terminal Y-chromosomal lineages with frequency ranging from 0.0010 (singleton) to 0.0687. We identified six dominant common founding lineages associated with different ethnolinguistic backgrounds, which included O2a2b1a1a1a1a1a1a1-M6539, O2a1b1a1a1a1a1a1-F17, O2a2b1a1a1a1a1b1a1b-MF15397, O2a2b2a1b1-A16609, O1b1a1a1a1b2a1a1-F2517, and O2a2b1a1a1a1a1a1-F155. The AMOVA and nucleotide diversity estimates revealed considerable differences and high genetic diversity among ethnolinguistically different populations. We constructed one representative phylogenetic tree among 33 studied populations based on the haplogroup frequency spectrum and sequence variations. Clustering patterns in principal component analysis and multidimensional scaling results showed a genetic differentiation between Tai-Kadai-speaking Li, Mongolic-speaking Mongolian, and other Sinitic-speaking Han Chinese populations. Phylogenetic topology inferred from the BEAST and Network relationships reconstructed from the popART further showed the founding lineages from culturally/linguistically diverse populations, such as C2a/C2b was dominant in Mongolian people and O1a/O1b was dominant in island Li people. We also identified many lineages shared by more than two ethnolinguistically different populations with a high proportion, suggesting their extensive admixture and migration history.

CONCLUSIONS

Our findings indicated that our developed high-resolution Y-SNP panel included major dominant Y-lineages of Chinese populations from different ethnic groups and geographical regions, which can be used as the primary and powerful tool for forensic practice. We should emphasize the necessity and importance of whole sequencing of more ethnolinguistically different populations, which can help identify more unrecognized population-specific variations for the promotion of Y-chromosome-based forensic applications.

Internal validation of an improved system for forensic application: a 41-plex Y-STR panel

Y-chromosome short tandem repeats (Y-STRs) have a unique role in forensic investigation. However, low-medium mutating Y-STRs cannot meet the requirements for male lineage differentiation in inbred populations, whereas rapidly mutating (RM) high-resolution Y-STRs might cause unexpected exclusion of paternal lineages. Thus, combining Y-STRs with low and high mutation rates helps to distinguish male individuals and lineages in family screening and analysis of genetic relationships. In this study, a novel 6-dye, 41-plex Y-STR panel was developed and validated, which included 17 loci from the Yfiler kit, nine RM Y-STR loci, 15 low-medium mutating Y-STR loci, and three Y-InDels. Developmental validation was performed for this panel, including size precision testing, stutter analysis, species specificity analysis, male specificity testing, sensitivity testing, concordance evaluation, polymerase chain reaction inhibitors analysis, and DNA mixture examination. The results demonstrated that the novel 41-plex Y-STR panel, developed in-house, was time efficient, accurate, and reliable. It showed good adaptability to directly amplify a variety of case-type samples. Furthermore, adding multiple Y-STR loci significantly improved the system's ability to distinguish related males, making it highly informative for forensic applications. In addition, the data obtained were compatible with the widely used Y-STR kits, facilitating the search and construction of population databases. Moreover, the addition of Y-Indels with short amplicons improves the analyses of degraded samples.

Key Points

A novel multiplex comprising 41 Y-STR and 3 Y-InDel was developed for forensic application.The multiplex included rapidly mutating Y-STRs and low-medium mutating Y-STRs, which is compatible with many commonly used Y-STR kits.The multiplex is a powerful tool for distinguishing related males, familial searching, and constructing DNA databases.

Genetic polymorphisms and phylogenetic characteristics of Tibeto-Burman-speaking Lahu population from southwest China based on 41 Y-STR loci

BACKGROUND

Male sex-linked Y-chromosome short tandem repeats (Y-STRs) have been widely used in forensic cases and population genetics research. At present, the forensic-related Y-STR data in the Chinese Lahu population are still poorly understood.

AIM

To enrich the available Y-STR data of this Chinese minority population and investigate its phylogenetic relationships with other reported populations.

SUBJECTS AND METHODS

The genetic polymorphisms of 41 Y-STR loci were analysed in 299 unrelated healthy Lahu male individuals from Southwest China. Phylogenetic analyses were performed by multidimensional scaling analysis and neighbor-joining phylogenetic tree construction.

RESULTS

A total of 379 alleles were observed at the 41 Y-STR loci. The allele frequencies ranged from 0.0033 to 0.9666. The genetic diversity values ranged from 0.0653 to 0.9072. A total of 254 different haplotypes of the 41 Y-STR loci were observed in 299 individuals. The values of haplotype diversity, haplotype match probability, and discrimination capacity were 0.9987, 0.0047, and 0.8495, respectively. The phylogenetic analysis indicated that the Tibeto-Burman-speaking Lahu population showed a close genetic relationship with the Yunnan Yi population.

CONCLUSIONS

The haplotype data of the present study can enrich the forensic databases of this Chinese minority population and will be useful for population genetics and forensic DNA application.

Development and validation of a new multiplex for upgrading Y-STRs population databases from 12 to 23 markers and its forensic casework application

Y chromosomal short tandem repeats (Y-STRs) are used in forensic investigations as a useful complementary tool to autosomal markers. The ongoing development of new kits with an increasing number of markers makes it necessary to update populations typed in the Y-STR Haplotype Reference Database to reach at least 23 Y-STRs. A novel Y-STR multiplex panel was developed to offer a cost-efficient alternative to update Y-STR haplotypes from 12 to 23 loci. This panel includes the eleven markers, DYS448, DYS456, DYS458, DYS635, Y-GATA H4, DYS576, DYS481, DYS549, DYS533, DYS570 and DYS643, as well as DYS385a/b for traceability purpose. Developmental validation of this panel was conducted following the recommendations of the Scientific Working Group on DNA Analysis Methods (SWGDAM), showing high sensitivity, tolerance to common inhibitors as well as high species specificity. It was efficient for degraded DNA samples and for detection of male mixtures. When applying it for extending the current data of the Ibiza population, both the discrimination capacity and the haplotype diversity increased from 0.5952 to 0.9048 and from 0.9808 to 0.9977, respectively. Together, the study demonstrates the suitability of this panel in forensic casework.

Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups

Structural rearrangements like copy number variations in the male-specific Y chromosome have been associated with male fertility phenotypes in human and mouse but have been sparsely studied in other mammalian species. Here, we designed digital droplet PCR assays for 7 horse male-specific Y chromosome multicopy genes and SRY and evaluated their absolute copy numbers in 209 normal male horses of 22 breeds, 73 XY horses with disorders of sex development and/or infertility, 5 Przewalski's horses and 2 kulans. This established baseline copy number for these genes in horses. The TSPY gene showed the highest copy number and was the most copy number variable between individuals and breeds. SRY was a single-copy gene in most horses but had 2-3 copies in some indigenous breeds. Since SRY is flanked by 2 copies of RBMY, their copy number variations were interrelated and may lead to SRY-negative XY disorders of sex development. The Przewalski's horse and kulan had 1 copy of SRY and RBMY. TSPY and ETSTY2 showed significant copy number variations between cryptorchid and normal males (P < 0.05). No significant copy number variations were observed in subfertile/infertile males. Notably, copy number of TSPY and ETSTY5 differed between successive male generations and between cloned horses, indicating germline and somatic mechanisms for copy number variations. We observed no correlation between male-specific Y chromosome gene copy number variations and male-specific Y chromosome haplotypes. We conclude that the ampliconic male-specific Y chromosome reference assembly has deficiencies and further studies with an improved male-specific Y chromosome assembly are needed to determine selective constraints over horse male-specific Y chromosome gene copy number and their relation to stallion reproduction and male biology.

Y Chromosome Haplotypes Enlighten Origin, Influence, and Breeding History of North African Barb Horses

In horses, demographic patterns are complex due to historical migrations and eventful breeding histories. Particularly puzzling is the ancestry of the North African horse, a founding horse breed, shaped by numerous influences throughout history. A genetic marker particularly suitable to investigate the paternal demographic history of populations is the non-recombining male-specific region of the Y chromosome (MSY). Using a recently established horse MSY haplotype (HT) topology and KASP™ genotyping, we illustrate MSY HT spectra of 119 Barb and Arab-Barb males, collected from the Maghreb region and European subpopulations. All detected HTs belonged to the Crown haplogroup, and the broad MSY spectrum reflects the wide variety of influential stallions throughout the breed’s history. Distinct HTs and regional disparities were characterized and a remarkable number of early introduced lineages were observed. The data indicate recent refinement with Thoroughbred and Arabian patrilines, while 57% of the dataset supports historical migrations between North Africa and the Iberian Peninsula. In the Barb horse, we detected the HT linked to Godolphin Arabian, one of the Thoroughbred founders. Hence, we shed new light on the question of the ancestry of one Thoroughbred patriline. We show the strength of the horse Y chromosome as a genealogical tool, enlighten recent paternal history of North African horses, and set the foundation for future studies on the breed and the formation of conservation breeding programs.

Limited Effect of Y Chromosome Variation on Coronary Artery Disease and Mortality in UK Biobank-Brief Report

BACKGROUND

The effect of genetic variation in the male-specific region of the Y chromosome (MSY) on coronary artery disease and cardiovascular risk factors has been disputed. In this study, we systematically assessed the association of MSY genetic variation on these traits using a kin-cohort analysis of family disease history in the largest sample to date.

METHODS

We tested 90 MSY haplogroups against coronary artery disease, hypertension, blood pressure, classical lipid levels, and all-cause mortality in up to 152 186 unrelated, genomically British individuals from UK Biobank. Unlike previous studies, we did not adjust for heritable lifestyle factors (to avoid collider bias) and instead adjusted for geographic variables and socioeconomic deprivation, given the link between MSY haplogroups and geography. For family history traits, subject MSY haplogroups were tested against father and mother disease as validation and negative control, respectively.

RESULTS

Our models find little evidence for an effect of any MSY haplogroup on cardiovascular risk in participants. Parental models confirm these findings.

CONCLUSIONS

Kin-cohort analysis of the Y chromosome uniquely allows for discoveries in subjects to be validated using family history data. Despite our large sample size, improved models, and parental validation, there is little evidence to suggest cardiovascular risk in UK Biobank is influenced by genetic variation in MSY.

Human Y chromosome sequences from Q Haplogroup reveal a South American settlement pre-18,000 years ago and a profound genomic impact during the Younger Dryas

The settlement of the Americas has been the focus of incessant debate for more than 100 years, and open questions regarding the timing and spatial patterns of colonization still remain today. Phylogenetic studies with complete human Y chromosome sequences are used as a highly informative tool to investigate the history of human populations in a given time frame. To study the phylogenetic relationships of Native American lineages and infer the settlement history of the Americas, we analyzed Y chromosome Q Haplogroup, which is a Pan-American haplogroup and represents practically all Native American lineages in Mesoamerica and South America. We built a phylogenetic tree for Q Haplogroup based on 102 whole Y chromosome sequences, of which 13 new Argentine sequences were provided by our group. Moreover, 1,072 new single nucleotide polymorphisms (SNPs) that contribute to its resolution and diversity were identified. Q-M848 is known to be the most frequent autochthonous sub-haplogroup of the Americas. The present is the first genomic study of Q Haplogroup in which current knowledge on Q-M848 sub-lineages is contrasted with the historical, archaeological and linguistic data available. The divergence times, spatial structure and the SNPs found here as novel for Q-Z780, a less frequent sub-haplogroup autochthonous of the Americas, provide genetic support for a South American settlement before 18,000 years ago. We analyzed how environmental events that occurred during the Younger Dryas period may have affected Native American lineages, and found that this event may have caused a substantial loss of lineages. This could explain the current low frequency of Q-Z780 (also perhaps of Q-F4674, a third possible sub-haplogroup autochthonous of the Americas). These environmental events could have acted as a driving force for expansion and diversification of the Q-M848 sub-lineages, which show a spatial structure that developed during the Younger Dryas period.

Establishment of New Genetic Markers and Methods for Sex Determination of Mouse and Human Cells using Polymerase Chain Reactions and Crude DNA Samples

Background: The currently available methods for sexing human or mouse cells have weaknesses. Therefore, it is necessary to establish new methods. Methods: We used bioinformatics approach to identify genes that have alleles on both the X and Y chromosomes of mouse and human genomes and have a region showing a significant difference between the X and Y alleles. We then used polymerase chain reactions (PCR) followed by visualization of the PCR amplicons in agarose gels to establish these genomic regions as genetic sex markers. Results: Our bioinformatics analyses identified eight mouse sex markers and 56 human sex markers that are new, i.e. are previously unreported. Six of the eight mouse markers and 14 of the 56 human markers were verified using PCR and ensuing visualization of the PCR amplicons in agarose gels. Most of the tested and untested sex markers possess significant differences in the molecular weight between the X- and Y-derived PCR amplicons and are thus much better than most, if not all, previously-reported genetic sex markers. We also established several simple and essentially cost-free methods for extraction of crude genomic DNA from cultured cells, blood samples, and tissues that could be used as template for PCR amplification. Conclusion: We have established new sex genetic markers and methods for extracting genomic DNA and for sexing human and mouse cells. Our work may also lend some methodological strategies to the identification of new genetic sex markers for other organismal species.

Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs

Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) are genetic markers on the male Y chromosome for individual identification, forensic applications, and paternal genetic history analysis. In this study we successfully genotyped 38 Y-STR loci and 24 Y-SNP loci of Pudong Han (n = 689) and Chongming Han (n = 530) in Shanghai. The haplotype diversity of the Y filer platinum genotyping system was the highest in the Han population in the Pudong area of Shanghai (0.99996) and Chongming Island (0.99997). The proportion of unique haplotypes was 97.10% (Pudong) and 98.49% (Chongming), respectively. The multidimensional scaling analysis and phylogenetic analysis were performed according to the genetic distance Rst, which was calculated based on the Y-STR gene frequency data. Moreover, we made a comparison on the frequency distribution analysis and principal component analysis of haplogroups in both populations. As a result, Shanghai Pudong Han, Chongming Island Han, and Jiangsu Han were determined to have a strong genetic affinity. The haplogroup distribution characteristics of the Pudong Han and Chongming Han populations were similar to those of the southern Han population. The results of haplotype network analysis showed that Jiangsu Wujiang Han and Jiangsu Changshu Han had more paternal genetic contributions to the formation of Shanghai Pudong Han and Chongming Island Han. Through the joint analysis of SNPs and STRs, this study deeply analyzed the paternal genetic structure of the Pudong Han and Chongming Han populations. The addition of Y-SNP haplogroups to forensic applications can provide information for pedigree investigation.

Hematopoietic loss of Y chromosome leads to cardiac fibrosis and heart failure mortality

Hematopoietic mosaic loss of Y chromosome (mLOY) is associated with increased risk of mortality and age-related diseases in men, but the causal and mechanistic relationships have yet to be established. Here, we show that male mice reconstituted with bone marrow cells lacking the Y chromosome display increased mortality and age-related profibrotic pathologies including reduced cardiac function. Cardiac macrophages lacking the Y chromosome exhibited polarization toward a more fibrotic phenotype, and treatment with a transforming growth factor β1-neutralizing antibody ameliorated cardiac dysfunction in mLOY mice. A prospective study revealed that mLOY in blood is associated with an increased risk for cardiovascular disease and heart failure-associated mortality. Together, these results indicate that hematopoietic mLOY causally contributes to fibrosis, cardiac dysfunction, and mortality in men.