Genome-wide analyses based on a novel donkey 40K liquid chip reveal the gene responsible for coat color diversity in Chinese Dezhou donkey

Dezhou donkey is one of the representative local breeds in China, which is mainly divided into two strains: Sanfen and Wutou. There are obvious differences in coat color between the two strains. The former shows light points around the eyes, around the muzzle and under the belly, while the latter is completely solid black. In this study, genome-wide association analysis was performed for the differences in coat color traits between the Sanfen (n = 97) and Wutou (n = 108) strains using a novel donkey 40K liquid chip developed based on GenoBaits technology, to identify genomic regions and causal genes that could explain this variation. We also used FST and The cross-population composite likelihood ratio test (XPCLR) analyses to explore selected regions related to coat color differences. We identified one significant region on chromosome 15, with the most significant SNP located within the agouti signaling protein (ASIP) gene. At the same time, both FST and XPCLR methods detected the same selected region on chromosome 15, and ASIP was the gene with the strongest signal. ASIP and melanocortin 1 receptor (MC1R) control the ratio of eumelanin to pheomelanin through their protein activity. They are deeply involved in the process of melanosome organation and melanogenesis, thus affecting mammals' coat color variation. We used a range of genome-wide approach to identify the genetic basis of coat color variation in Dezhou donkeys. The results provide a supplement to the color variation study in Chinese donkeys at the genome-wide level, and preliminarily verified the reliability of the Molbreeding Donkey No. 1 40K liquid chip.

A tumor-associated autoantibody panel for the detection of non-small cell lung cancer

Lung cancer is the second most frequent malignancy and the leading cause of cancer-associated death worldwide. Compared with patients diagnosed at advanced disease stages, early detection of lung cancer significantly improved the 5-year survival rate from 3.3% to 48.8%, which highlights the importance of early detection. Although multiple technologies have been applied to the screening and early diagnosis of lung cancer so far, some limitations still exist so they could not fully suit the needs for clinical application. Evidence show that autoantibodies targeting tumor-associated antigens(TAAs) could be found in the sera of early-stage patients, and they are of great value in diagnosis. Methods, we identified and screened TAAs in early-stage non-small cell lung cancer(NSCLC) samples using the serological analysis of recombinant cDNA expression libraries(SEREX). We measured the levels of the 36 autoantibodies targeting TAAs obtained by preliminary screening via liquid chip technique in the training set(332 serum samples from early-stage NSCLC patients, 167 samples from patients with benign lung lesions, and 208 samples from patients with no obvious abnormalities in lungs), and established a binary logistic regression model based on the levels of 8 autoantibodies to distinguish NSCLC samples. Results, We validated the diagnostic efficacy of this model in an independent test set(163 serum samples from early-stage NSCLC patients, and 183 samples from patients with benign lung lesions), the model performed well in distinguishing NSCLC samples with an AUC of 0.8194. After joining the levels of 4 serum tumor markers into its independent variables, the final model reached an AUC of 0.8568, this was better than just using the 8 autoantibodies (AUC:0.8194) or the 4 serum tumor markers alone(AUC: 0.6948). In conclusion, we screened and identified a set of autoantibodies in the sera of early-stage NSCLC patients through SEREX and liquid chip technique. Based on the levels of 8 autoantibodies, we established a binary logistic regression model that could diagnose early-stage NSCLC with high sensitivity and specificity, and the 4 conventional serum tumor markers were also suggested to be effective supplements for the 8 autoantibodies in the early diagnosis of NSCLC.

New insights into the novel sequences of the chicken pan-genome by liquid chip

Increasing evidence indicates that the missing sequences and genes in the chicken reference genome are involved in many crucial biological pathways, including metabolism and immunity. The low detection rate of novel sequences by resequencing hindered the acquisition of these sequences and the exploration of the relationship between new genes and economic traits. To improve the capture ratio of novel sequences, a 48K liquid chip including 25K from the reference sequence and 23K from the novel sequence was designed. The assay was tested on a panel of 218 animals from 5 chicken breeds. The average capture ratio of the reference sequence was 99.55%, and the average sequencing depth of the target sites was approximately 187X, indicating a good performance and successful application of liquid chips in farm animals. For the target region in the novel sequence, the average capture ratio was 33.15% and the average sequencing depth of target sites was approximately 60X, both of which were higher than that of resequencing. However, the different capture ratios and capture regions among varieties and individuals proved the difficulty of capturing these regions with complex structures. After genotyping, GWAS showed variations in novel sequences potentially relevant to immune-related traits. For example, a SNP close to the differentiation of lymphocyte-related gene IGHV3-23-like was associated with the H/L ratio. These results suggest that targeted capture sequencing is a preferred method to capture these sequences with complex structures and genes potentially associated with immune-related traits.

Identification of six serum antigens and autoantibodies for the detection of early stage epithelial ovarian carcinoma by bioinformatics analysis and liquid chip analysis

The early detection of ovarian cancer is critical for improving the prognosis of patients, but there are currently insufficient tumor biomarkers for early detection owing to their low diagnostic sensitivity and specificity. The aim of the present study was to investigate the use of the serum antigens C-C motif chemokine ligand 18 and C-X-C motif chemokine ligand 1, and autoantibodies C1D, transmembrane 4 L six family member 1, zinc finger protein 675 and fragile X mental retardation 1 autosomal homolog 1, for the early screening of epithelial ovarian cancer (EOC). The expression of these sex genes/proteins in ovarian cancer and normal ovarian tissue was examined, and the potential functions of the six genes/proteins in ovarian cancer were analyzed by bioinformatics. Finally, these data were verified in clinical samples, and the multi-analyte suspension array method was compared with the ELISA method. Taken together, these data indicated that these six genes/proteins may serve as potential biomarkers for the early detection of EOC.

Alu methylation serves as a biomarker for non-invasive diagnosis of glioma

Current techniques for diagnosing glioma are invasive and do not accurately predict prognosis. We developed a novel, non-invasive liquid chip assay to diagnose glioma and predict prognosis. Using this method, we determined the methylation state of the Alu element in cell-free DNA extracted from the serum of 109 glioma patients. Controls included 56 patients with benign intracranial tumors and 50 healthy subjects. Matched tumor tissues were processed for 36 patients. The cfDNA from glioma patients showed lower levels of Alu methylation than the controls (P<0.01). Alu methylation was also lower in high-grade than low-grade gliomas (P<0.01), indicating that Alu methylation correlates negatively with disease severity. Moreover, Alu methylation correlated positively with survival (P<0.01). These findings suggest high-throughput liquid chip could serve as a non-invasive diagnostic assay for glioma.