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.

CCMN: A General Framework for Learning With Class-Conditional Multi-Label Noise.

Class-conditional noise commonly exists in machine learning tasks, where the class label is corrupted with a probability depending on its ground-truth. Many research efforts have been made to improve the model robustness against the class-conditional noise. However, they typically focus on the single label case by assuming that only one label is corrupted. In real applications, an instance is usually associated with multiple labels, which could be corrupted simultaneously with their respective conditional probabilities. In this paper, we formalize this problem as a general framework of learning with Class-Conditional Multi-label Noise (CCMN for short). We establish two unbiased estimators with error bounds for solving the CCMN problems, and further prove that they are consistent with commonly used multi-label loss functions. Finally, a new method for partial multi-label learning is implemented with the unbiased estimator under the CCMN framework. Empirical studies on multiple datasets and various evaluation metrics validate the effectiveness of the proposed method.

Population genetics and forensic efficiency of 30 InDel markers in four Chinese ethnic groups residing in Sichuan.

Sichuan Province is located at the transitional junction regions of the Qinghai-Tibet Plateau and the low-altitude plains. It also serves as the corridor of Sino-Tibetan-speaking population migration and expansion since neolithic expansion of Proto-Tibeto-Burman populations from Middle/Upper Yellow River during Majiayao period (3300-2000 BC). However, the population structure and the corresponding genetic diversity of forensic-related markers in this region remain unclear. Thus, we genotyped 30 insertion-deletion (InDel) markers in 444 samples from four ethnic groups (Han, Tibetan, Hui and Yi) from Sichuan Province using the Investigator® DIPplex kit to explore the characteristics of population genetics and forensic genetic focuses. All the loci were found to be in Hardy-Weinberg Equilibrium (HWE) after applying a Bonferroni correction and no pairwise loci showed prominent linkage disequilibrium. The combined matching probability (CMP) and the combined power of discrimination (CPD) are larger than 1.8089 × 10-11 and 0.99999999995, respectively. Principal component analysis, multi-dimensional scaling plots and Neighbour-Joining tree among 65 worldwide populations indicated that Sichuan Hui and Han are genetically close to Hmong-Mien and Tai-Kadai-speaking populations, and Sichuan Tibetan and Yi bear a strong genetic affinity with Tibeto-Burman-speaking populations. The model-based genetic structure further supports the genetic affinity between the studied populations and linguistically close populations.Key PointsForensic parameters of 30 insertion-deletions (InDels) in 444 individuals from four populations are reported, which showed abundant genetic affinity and diversity among populations and high value in personal identification.Genetic similarities existed between the studied populations and ethnically, linguistically close populations.Sichuan Hui and Han are genetically close to Hmong-Mien and Tai-Kadai-speaking populations.Sichuan Tibetan and Yi bear a strong genetic affinity with Tibeto-Burman-speaking populations.

Development and validation of a novel 26-plex system for prenatal diagnosis with forensic markers.

Short tandem repeat (STR) loci are commonly used in forensic casework, such as personal identification and paternity testing. In recent years, STR has also been widely used for rapid, accurate and automated prenatal diagnosis, known as quantitative fluorescent PCR (QF-PCR). Despite their usefulness, the current systems often lack the power to detect mosaicism for Turner syndrome. In this study, we developed a novel 26-plex system that combined the 22 STRs in chromosome 21/18/13/X, 3 sex loci and 1 quality control marker (TAF9L). The system was generated to achieve greater diagnostic power of trisomy 21/18/13 and sex chromosome abnormalities. Studies of the sensitivity, specificity, stability and accuracy were performed according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. Compared with the results of the chromosomal microarray analysis (CMA)/copy number variation sequencing (CNV-seq), the detection ratio of non-mosaic chromosome abnormalities of this system in the identification of chromosome 21/18/13/X/Y aneuploidies reached 100%, and the rate of negative results was consistently 100% based on 203 prenatal diagnosis sample analyses. In addition, our results suggested that this panel was a useful tool for mosaicism for Turner syndrome cases. Interestingly, we found one case with large segment loss of chromosome X, which indicated that we should be alert to this situation when the STR genotype of the parent-child is inconsistent in forensic genetics. In summary, this study demonstrated that our system is an accurate, cost-effective and rapid approach for the detection of chromosome numerical abnormalities in prenatal diagnosis.

Partial Multi-Label Learning With Noisy Label Identification.

Partial multi-label learning (PML) deals with problems where each instance is assigned with a candidate label set, which contains multiple relevant labels and some noisy labels. Recent studies usually solve PML problems with the disambiguation strategy, which recovers ground-truth labels from the candidate label set by simply assuming that the noisy labels are generated randomly. In real applications, however, noisy labels are usually caused by some ambiguous contents of the example. Based on this observation, we propose a partial multi-label learning approach to simultaneously recover the ground-truth information and identify the noisy labels. The two objectives are formalized in a unified framework with trace norm and l1 norm regularizers. Under the supervision of the observed noise-corrupted label matrix, the multi-label classifier and noisy label identifier are jointly optimized by incorporating the label correlation exploitation and feature-induced noise model. Furthermore, by mapping each bag to a feature vector, we extend PML-NI method into multi-instance multi-label learning by identifying noisy labels based on ambiguous instances. A theoretical analysis of generalization bound and extensive experiments on multiple data sets from various real-world tasks demonstrate the effectiveness of the proposed approach.

Genetic structure and forensic characteristics of the Kyrgyz population from Kizilsu Kirghiz autonomous prefecture based on autosomal DIPs.

Living in the heart of Eurasia, the Kyrgyz ethnic minority have a complex human evolutionary and migration history. However, the genetic architecture of the Kyrgyz population has not been fully explored. We studied 526 Kyrgyz samples from Kizilsu Kirghiz Autonomous Prefecture in Xinjiang using the Investigator® DIPplex kit. All loci followed Hardy-Weinberg equilibrium (HWE). The combined power of discrimination (CPD) and combined power of paternity exclusion (CPE) was 0.9999999999988 and 0.9936, respectively. Compared with 90 reference populations, five InDels (HLD99, HLD81, HLD64, HLD118, and HLD111) have the potential to distinguish the Kyrgyz/Uyghur/Kazak population from other East Asian populations. Our results suggested a close genetic relationship between the Kyrgyz population and the Uyghur/Kazak populations, followed by South Asian populations. This was in accordance with the inland migration hypothesis or modern human migration influenced by warfare. Overall, this system can be used as a powerful tool in forensic individual identification and as a complementary tool in paternity cases and biogeographic ancestry analyses.

Deciphering the Intercellular Communication Network of Peripartum Decidua that Orchestrates Delivery.

Intercellular communication in the decidua plays important roles in relaying information between the maternal and fetal systems in the maintenance of pregnancy and the transition to labor. To date, several studies have explored cell-cell communications in the decidua during different periods of pregnancy, but studies systematically decoding the intercellular communication network, its internal cascades, and their involvement in labor are still lacking. In this study, we reconstructed a decidual cell-cell communication network based on scRNA-seq of peripartum decidua via the CellCall method. The results showed that endometrial cells (EECs) and extravillous trophoblasts relayed most of the common intercellular signals in the decidua both before delivery (DBD) and after delivery (DAD). Endothelial cells and EECs controlled many WNT-signaling-related intercellular communication factors that differed between DBD and DAD, some of which could be candidate biomarkers for the diagnosis of labor. Analysis of intercellular communications related to T cells identified abundant maternal-fetal immune-tolerance-related communication, such as TNFSF14-TNFRSF14/LTBR and FASLG-FAS signalings. We further explored the characteristics of the B cell receptor (BCR) and T cell receptor (TCR) repertoires by single-cell BCR/TCR sequencing. The results showed no significant differences in clonal expansion of B/T cells between DAD and DBD, indicating there was no significant change to adaptive immunity at the maternal-fetal interface during delivery. In summary, the findings provide a comprehensive view of the intercellular communication landscape in the peripartum decidua and identified some key intercellular communications involved in labor and maternal-fetal immune tolerance. We believe that our study provides valuable clues for understanding the mechanisms of pregnancy and provides possible diagnostic strategies for the onset of labor.

Paternal genetic structure of Kyrgyz ethnic group in China revealed by high-resolution Y-chromosome STRs and SNPs.

Kyrgyz ethnic group is one of the nomads in China, with the majority in Xinjiang and a small part of them living in Heilongjiang province. Historically, they have went through five migrations westward due to the wars. The name "Kyrgyz" means 40 tribes, originating from the primary groups of Kyrgyz. However, it is a largely understudied population, especially from the Y chromosome. In this study, we used a previously validated high-resolution Y-chromosome single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) system to study Kyrgyz ethnic group. A total of 314 male samples of Kyrgyz ethnic group were genotyped by 173 Y-SNPs and 27 Y-STRs. After data analysis, the results unveiled that Kyrgyz ethnic group was a population with high percentage of both haplogroup C2a1a3a1d∼-F10091 (91/134) and R1a1a1b2a2-Z2124 (109/134), which has never been reported. This implied that Kyrgyz ethnic group might have gone through bottleneck effects twice, with these two main lineages left. Mismatch analysis indicated that the biggest mismatch number in haplogroup C2a1a3a1d∼-F10091 was 10, while that of haplogroup R1a1a1b2a2-Z2124 was 20. This huge difference reflected the different substructure in two lineages, suggesting that haplogroup C2a1a3a1d∼-F10091 might have the least admixture compared to the other two lineages. After admixture modelling with other datasets, the conclusion could be drawn that Kyrgyz ethnic group had great genetic affinity with Punjabi from Lahore, Pakistan, which supported that Kyrgyz ethnic group in China was close to central Asian.

Evaluation of the AGCU Expressmarker 30 Kit composed of 31 loci for forensic application.

With the widespread use of STR in identification of individuals, paternity testing, as well as population genetics, many commercially robust and validated STR multiplex kits were developed. The AGCU Expressmarker 30 Kit is a new autosomal STR system that contains 29 autosomal STR loci (D3S1358, vWA, D1S1656, CSF1PO, D8S1132, D19S253, D3S3045, D8S1179, D21S11, D16S539, TPOX, D6S477, Penta D, D2S441, D5S818, TH01, FGA, D15S659, D22S1045, D19S433, D13S317, D7S820, D6S1043, D10S1435, D10S1248, D2S1338, D18S51, D12S391, and Penta E), one insertion/deletion polymorphic marker on the Y chromosome (Y indel), and the amelogenin locus. A series of validation studies were performed in this context according to the guidelines of "Validation Guidelines for Forensic DNA Analysis Methods". The sensitivity study showed that a full profile was observed with template DNA as low as 40 pg. In the stability study, all STR profiles were obtained at concentrations of humic acid up to 800 ng/µL, hematin up to 250 µM, and tannic acid up to 200 ng/µL. The mixture study demonstrated that all of the minor alleles could be called at ratios from 1:1-29:1 when the total DNA was 2 ng. In the population study, the total discrimination power for three population (Sichuan-Han, Gansu-Hui, and Guangxi-Zhuang) were above 0.9999999999999999999999999999999992, 0.999999999999999999999999999999998 and 0.999999999999999999999999999999994 as well as the cumulative probability of paternity exclusion were 0.999999999999953, 0.999999999999178, and 0.999999999999611 respectively. These results demonstrated that the AGCU Expressmarker 30 Kit is a useful tool for analyzing both forensic casework and database samples.

A Biallelic Frameshift Mutation in Nephronectin Causes Bilateral Renal Agenesis in Humans.

BACKGROUND: Bilateral renal agenesis (BRA) is a lethal con genital anomaly caused by the failure of normal development of both kidneys early in embryonic development. Oligohydramnios on fetal ultrasonography reveals BRA. Although the exact causes are not clear, BRA is associated with mutations in many renal development genes. However, molecular diagnostics do not pick up many clinical patients. Nephronectin (NPNT) may be a candidate protein for widening diagnosis. It is essential in kidney development, and knockout of Npnt in mice frequently leads to kidney agenesis or hypoplasia. METHODS: A consanguineous Han family experienced three cases of induced abortion in the second trimester of pregnancy, due to suspected BRA. Whole-exome sequencing (WES)-based homozygosity mapping detected underlying genetic factors, and a knock-in mouse model confirmed the renal agenesis phenotype. RESULTS: WES and evaluation of homozygous regions in II:3 and II:4 revealed a pathologic homozygous frameshift variant in NPNT (NM_001184690:exon8:c.777dup/p.Lys260*), which leads to a premature stop in the next codon. The truncated NPNT protein exhibited decreased expression, as confirmed in vivo by the overexpression of WT and mutated NPNT. A knock-in mouse model homozygous for the detected Npnt mutation replicated the BRA phenotype. CONCLUSIONS: A biallelic loss-of-function NPNT mutation causing an autosomal recessive form of BRA in humans was confirmed by the corresponding phenotype of knock-in mice. Our results identify a novel genetic cause of BRA, revealing a new target for genetic diagnosis, prenatal diagnosis, and preimplantation diagnosis for families with BRA.

Genetic reconstruction and phylogenetic analysis by 193 Y-SNPs and 27 Y-STRs in a Chinese Yi ethnic group.

Yi is the seventh-largest ethnic group in China and features mountainous regional characteristics. The Liangshan Yi Autonomous Prefecture is the largest Yi agglomeration with isolated geographical conditions, profoundly impeding genetic communication. Here, we investigated 427 unrelated males of Liangshan from 193 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 27 Y-chromosome short tandem repeats (Y-STRs) to reveal the genetic structure and paternal phylogeny of the group. The haplogroup diversity reached 0.9169 with 46 different subhaplogroups by 193 Y-SNPs, and the haplotype diversity reached 0.9999 by 27 Y-STR loci. Multidimensional scaling (MDS), N-J tree, and Network were constructed to decipher and visualize the genetic relations between Yi and worldwide groups. Our results revealed: (1) the Network by Y-STRs and Y-SNPs showed the haplogroup D1a1a-M15 in the Liangshan Yi population was a ramification of Tibetan groups' expansion from west to east on the plateau; (2) the haplogroup distribution and the mismatch mutation analysis indicated the haplogroup O2a2b1a1a1a4a2-Z25929 of Liangshan Yi derived from manifold Southeast Asian immigrants; (3) a high-resolution Y-SNPs panel is vital to depict accurate paternal derivations and build an integrated and refining genetic structure of ethnic groups.

Evaluation of a six-dye multiplex composed of 27 markers for forensic analysis and databasing.

BACKGROUND: Short tandem repeat (STR) markers play a significant role in genetic applications and have proved to be effective for the personal identification in forensic medicine. In this study, a six-dye multiplex composed of 23 autosomal STR loci (TH01, D3S1358, Penta D, D6S1043, D21S11, TPOX, D1S1656, D12S391, Penta E, D10S1248, D22S1045, D19S433, D8S1179, D2S1338, D2S441, D18S51, vWA, FGA, D16S539, CSF1PO, D13S317, D5S818, D7S820), one Y chromosome STR (DYS391), two internal quality control markers (Quality Sensor QS1 and QS2), and Amelogenin was evaluated. METHODS: Evaluation studies, including PCR-based studies, sensitivity studies, species specificity studies, stability studies, DNA mixture studies, concordance studies, and precision evaluations were performed according to the guidelines of "Validation Guidelines for Forensic DNA Analysis Methods (2016)" by the Scientific Working Group on DNA Analysis Methods (SWGDAM). In addition, the forensic characteristics of 357 unrelated male samples from Han and Hui populations in China were investigated using 27 markers. RESULTS: Full STR profiles were obtained from different reaction volumes (5 ~ 25 µl), cycle numbers (28 ~ 34 cycles) and annealing temperatures (58 ~ 62°C). All STR profiles were obtained at humic acid concentration of up to 200 ng/µl and hematin concentration of up to 500 µM. No peaks were observed in most common animal samples except two innovative internal PCR controls (Quality Sensor QS1 and QS2). The six-dye multiplex showed a notably high value for the combined probability of exclusion (CPE), exhibiting values of with 0.99999999977688 in the Han population and 0.999999999583875 in the Hui population. The values of combined probability of discrimination (CPD) were 0.999999999999999999999999999997453 in the Han population and 0. 999999999999999999999999999994398 in the Hui population. In addition, concordance studies showed that there was no difference with the AGCU Express Marker 22 Kit. CONCLUSION: The results indicated that the Investigator® 26plex QS Kit is a robust, reliable, and suitable tool for forensic analysis and databasing.

Genetic diversity and phylogenetic analysis of 29 Y-STR loci in the Tibetan population from Sichuan Province, Southwest China.

Y-Chromosomal short tandem repeat polymorphisms (Y-STRs) are widely applied in human forensic cases and population genetic studies. There is a lack of information about the Sichuan Tibetan population in the Y-STR Haplotype Reference Database (YHRD, https://yhrd.org, release 59). In this study, 502 unrelated male individuals residing in the Sichuan Province were recruited and genotyped at 29 Y-STR loci. A total of 479 haplotypes were observed, 460 (96.03%) of which were unique. The haplotype diversity (HD) and discrimination capacity (DC) for the Sichuan Tibetan population were 0.9998 and 0.9542, respectively. To reveal the genetic diversities and relationships between the Chinese Sichuan Tibetan and 29 other previously reported populations, forensic parameter analysis, multi-dimensional scaling, and phylogenetic reconstruction were performed. The results showed that the Sichuan Tibetan population was relatively isolated from other populations, suggesting that genetic proximity is in line with geographical boundaries.

Validation of the AGCU Expressmarker 16 + 22Y Kit: a new multiplex for forensic application.

Genotyping by targeting short tandem repeats (STRs) has been widely used in forensic applications. However, most commercial kits detect autosomal STRs or Y-STRs alone, which waste both time and opportunity. The AGCU Expressmarker 16 + 22Y Kit includes 16 autosomal and 22 Y-chromosomal STR loci and is designed for the forensic science field and obtaining quicker results. Here, we conducted the validation study according to Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. Validation of PCR-based studies, species specificity, sensitivity, DNA mixture studies, inhibitors, precision, and sizing accuracy were performed. Furthermore, this system was also tested in 346 random male samples from Han, Hui, Tibetan, and Zhuang populations in China, showing its high power for forensic discrimination in the Chinese population. In addition, this system was able to deal with AMELY deletion cases, which can correctly identify sex in forensic criminal investigations. Our results suggested that the AGCU Expressmarker 16 + 22Y Kit is a useful tool for rapid criminal investigation.

Expression profile analysis of piwi-interacting RNA in forensically relevant biological fluids.

During the last decade, RNA profiling has emerged as one of the fastest developed methods for discriminating forensically relevant biological samples. As a category of small non-coding RNA, piwi-interacting RNA (piRNA) has recently been proposed to be differentially expressed in different types of body fluids, which indicates that its potential in forensic science is worth exploring. In this study, small RNA from 6 types of biological samples (venous blood, menstrual blood, saliva, semen, vaginal secretions and skin) was prepared and sequenced in order to characterize the expression pattern of piRNA using Ion S5 XL platform. Multiple bioinformatic methods were applied to make interpretation of the massively parallel sequencing data and identify representative biomarkers. A total of 376 piRNAs were initially identified after normalization and filtering. Hierarchical clustering and partial least squares-discriminant analysis (PLS-DA) revealed that their expression profiles exhibited an acceptable discriminating ability for most biological samples. Besides, a panel consists of 37 piRNA candidates was subsequently established for further analysis. The results suggested that with the optimal number of PLS components, the marker-reduced panel was sufficient to construct a PLS-DA model with the same performance as that can be achieved by the entire 376 piRNAs (classification error rate = 0.04). In addition, 5 targeted candidates were further selected for validation. TaqMan RT-qPCR assay results verified the potential of 3 piRNAs (piR-hsa-27622, piR-hsa-1207 and piR-hsa-27493) in distinguishing venous blood and menstrual blood, as well as 2 piRNA (piR-hsa-27493 and piR-hsa-26591) for the discrimination of saliva and vaginal secretions, which emphasized the feasibility of our biomarker selection approach. In brief, our study expanded the amount of potential piRNA biomarkers and demonstrated that the expression features of piRNA could provide valuable information for discriminating forensically relevant biological samples.

Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population.

Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) frequency distributions provide resources for assessment of male population stratification among world-wide populations. Currently, the Y-STR Haplotype Reference Database (YHRD) contains numerous Y-chromosome haplotype profiles from various populations and countries around the world. However, for many of the recently discovered and already phylogenetically mapped Y-SNPs, the population data are scarce. Herein, the typing of 27 Y-STRs (Yfiler Plus) and 143 Y-SNPs (self-designed Y-SNP panel) was performed on 1269 unrelated males from 11 Han Chinese populations. Haplogroup O-M175 was the most predominant haplogroup in our Han Chinese data, ranging from 67.34% (Henan Han) to 93.16% (Guangdong Han). The highest haplogroup diversity (0.967056) was observed in Heilongjiang Han, with a discrimination capacity (DC) value of 0.3723. The number of alleles at single-copy loci varied from 2 for DYS391 (Guangdong Han) to 16 for DYS518 (Henan Han). For the majority of the populations (8/11), both the haplotype diversity and DC values are 1.0000. Furthermore, genetic differentiations were observed between Northern and Southern Han Chinese. These genetic differences were mainly reflected in haplogroup distribution and frequency, and they were confirmed by statistical analysis.

Genetic substructure and forensic characteristics of Chinese Hui populations using 157 Y-SNPs and 27 Y-STRs.

The Hui group is the second largest ethnic minority and one of the most widespread ethnic groups in China. However, the genetic architecture of the Hui population remains largely unexplored, particularly with respect to the male-specific region of the Y chromosome. Here, we studied nine Hui populations (Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, Henan, Shandong, Sichuan, Yunnan) using 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 27 short tandem repeats (Y-STRs) to unravel their genetic substructure and forensic characteristics. A total of 650 unrelated male samples from the Hui populations were genotyped by SNaPshot®, a single base extension (SBE) assay. Finally, 95 terminal haplogroups and high haplotype diversity (0.9999) were observed in Hui populations. Frequency heat map matrices, genetic distance (FST) and network analysis within Hui populations indicated that these nine Hui populations can be divided into three groups: Hui populations from the northwest (NWH), Hui populations from Sichuan and Shandong (SSH), and Hui populations from Yunnan (YNH). Our results suggested that we should use different databases for different Hui samples in forensic cases. Comparison with other populations that used different population genetic analysis revealed that the Hui populations had close relationships with East Asian populations, especially Chinese Han population. Overall, the high-resolution panel with Y-SNPs and Y-STRs gives new and complete insight into Hui populations, which can be used to interpret the genetic substructure of Hui populations and affect the utility of forensic databases.