Advanced Ensemble Staking Model Employing cfDNA Fragmentation for Early Detection of Esophageal and Gastric Cancer.

Esophageal and gastric cancers are aggressive malignancies with poor prognoses due to late-stage diagnosis. Our study recruited 275 healthy participants, 201 gastric cancer patients, 74 esophageal patients and 103 patients with precancerous conditions. The participants were assigned into training and validation cohorts.

Prehistoric genomes from Yunnan reveal ancestry related to Tibetans and Austroasiatic speakers.

The human landscape in East and Southeast Asia is vastly complex, and successful retrieval of genome-wide data from prehistoric humans of southern East Asia is sparse. We successfully sampled 127 ancient human genomes from southwestern China. A 7100-year-old female individual from central Yunnan shows a previously unsampled Basal Asian ancestry related to a ghost population that contributed to Tibetan Plateau populations.

Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Gray Wolves (Canis lupus).

The gray wolf (Canis lupus) is the only wild ancestor of dogs (Canis lupus familiaris) and serves a crucial role in understanding the highly controversial issue of dog origins. Recently, ancient DNA studies on gray wolves from different regions of the Eurasian continent have achieved significant breakthroughs, providing important clues about the dog origins. As one of the potential origin areas for dogs, East Asia has seen some research on ancient dogs; however, reports related to gray wolves remain limited.

Early detection of multiple cancer types using multidimensional cell-free DNA fragmentomics.

The multicancer early detection (MCED) test has the potential to enhance current cancer-screening methods. We evaluated a new MCED test that analyzes plasma cell-free DNA using genetic- and fragmentomics-based features from whole-genome sequencing. The present study included an internal validation cohort of 3,021 patients with cancer and 3,370 noncancer controls, and an independent cohort of 677 patients with cancer and 687 noncancer individuals.

Development and Validation of a Cell-Free DNA Fragmentomics-Based Model for Early Detection of Pancreatic Cancer.

Purpose: Pancreatic ductal adenocarcinoma (PDAC), known for its high fatality rate, is often diagnosed in its advanced stages where surgical options are not viable. This highlights the critical need for innovative and effective early detection techniques. This study focuses on the potential of cell-free DNA (cfDNA) fragmentomics integrating advanced machine learning to identify early-stage PDAC with high accuracy.

Genome-wide Identification and Functional Analysis of Genes in Soybean Resistance to Cyst Nematodes.

The genes maintain endogenous hormone homeostasis by conjugating excess hormones with amino acids. Herein, we identified the members of the GH3 family in soybeans and analyzed their phylogeny, gene duplication, structure, domains, conserved motifs, cis-elements in promoter regions for stress responses, and functional characteristics. We found that genes are induced by pathogens in Group-II.

East Asian Gene flow bridged by northern coastal populations over past 6000 years.

Coastal areas of northern East Asia in the ShanDong region, which show complex cultural transitions in the last 10,000 years, have helped to facilitate population interactions between more inland regions of mainland East Asia and islands such as those in the Japanese archipelago. To examine how ShanDong populations changed over time and interacted with island and inland East Asian populations, we sequenced 85 individuals from 11 ancient sites in the ShanDong region dating to ~6000-1500 BP. We found that ancestry related to ShanDong populations likely explains the mainland East Asian ancestry observed in post-Yayoi populations from the Japanese archipelago, particularly recent populations who lived in the Ryukyu Islands after ~2800 BP.

Leveraging cfDNA fragmentomic features in a stacked ensemble model for early detection of esophageal squamous cell carcinoma.

In this study, we develop a stacked ensemble model that utilizes cell-free DNA (cfDNA) fragmentomics for the early detection of esophageal squamous cell carcinoma (ESCC). This model incorporates four distinct fragmentomics features derived from whole-genome sequencing (WGS) and advanced machine learning algorithms for robust analysis. It is validated across both an independent validation cohort and an external cohort to ensure its generalizability and effectiveness.

Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs.

Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia).

Overexpression of Genes Enhances Soybean Resistance Against .

Soybean cyst nematode (, soybean cyst nematode [SCN]) disease adversely affects the yield of soybean and leads to billions of dollars in losses every year. To control the disease, it is necessary to study the resistance genes of the plant and their mechanisms. Isoflavonoids are secondary metabolites of the phenylalanine pathway, and they are synthesized in soybean.

Maternal genetic history of ancient Tibetans over the past 4000 years.

The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstruct a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show that ancient Tibetans share the most recent common ancestor with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene.

Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China.

Shimao City is considered an important political and religious center during the Late Neolithic Longshan period of the Middle Yellow River basin. The genetic history and population dynamics among the Shimao and other ancient populations, especially the Taosi-related populations, remain unknown. Here, we sequenced 172 complete mitochondrial genomes, ranging from the Yangshao to Longshan period, from individuals related to the Shimao culture in northern Shaanxi Province and Taosi culture in southern Shanxi Province, Middle Yellow River basin.

Bronze and Iron Age population movements underlie Xinjiang population history.

The Xinjiang region in northwest China is a historically important geographical passage between East and West Eurasia. By sequencing 201 ancient genomes from 39 archaeological sites, we clarify the complex demographic history of this region. Bronze Age Xinjiang populations are characterized by four major ancestries related to Early Bronze Age cultures from the central and eastern Steppe, Central Asian, and Tarim Basin regions.

Fluorescent Soybean Hairy Root Construction and Its Application in the Soybean-Nematode Interaction: An Investigation.

Background: The yield of soybean is limited by the soybean cyst nematode (SCN, ). Soybean transformation plays a key role in gene function research but the stable genetic transformation of soybean usually takes half a year.

Methods: Here, we constructed a vector, pNI-GmUbi, in an -mediated soybean hypocotyl transformation to induce fluorescent hairy roots (FHRs).

Ancient DNA reveals the maternal genetic history of East Asian domestic pigs.

Zoo-archaeological and genetic evidence suggest that pigs were domesticated independently in Central China and Eastern Anatolia along with the development of agricultural communities and civilizations. However, the genetic history of domestic pigs, especially in China, has not been fully explored. In this study, we generate 42 complete mitochondrial DNA sequences from ∼7500- to 2750-year-old individuals from the Yellow River basin.

Evaluation of Scopoletin from Snef1650 for the Control of in Soybean.

Soybean cyst nematode (SCN) ( Ichinohe) is responsible for causing a major soybean disease globally. The fungal strain Snef1650 was evaluated against . However, the effective determinants of the strain are unknown.