[Results analysis of mNGS applied to infectious diseases].

The application of metagenomic second-generation sequencing (mNGS) is shifting from research to clinical laboratories due to rapid technological advances and significant cost reductions. Although many studies and case reports have confirmed that the success of mNGS in improving the prevention, diagnosis, treatment and tracking of infectious diseases, there are still some obstacles that must be overcome. The results of mNGS show all the possible pathogens in the sample, however, in the face of thousands of microbes that can infect humans, it remains challenging to accurately identify the key pathogens. So far, there is no unified interpretation standard for mNGS in clinical practice. This article reviews the interpretation of mNGS results for pathogen infection in different systems, the clinical interpretation and application regulations of mNGS results, and the challenges of mNGS interpretation in pathogen diagnosis.

Verification and evaluation of grain QTLs using RILs from TD70 x Kasalath in rice.

Grain size is an important trait that directly influences the yield of rice. Validation and evaluation of grain genes is important in rice genetic studies and for breeding. In a population of 240 recombinant inbred lines (RILs) derived from a cross between an extra-large grain japonica variety TD70 and a small grain indica variety Kasalath, we mapped 19 QTLs controlling grain traits. These QTLs included six cloned grain genes, namely, GW2, GS3, qSW5, qGL3, GS5, and GW8. All of the alleles with the optimal effects on grain size came from TD70, the variety with extra-large grains. To verify these gene loci, we cloned and sequenced GW2, GS3, GW5 (qSW5), qGL3, GS5, GW8, and TGW6 in TD70 and Kasalath, and found several functional polymorphisms in the sequences of the genes. New functional markers for the cloned genes were designed to identify parents and RILs. The contributions of these polymorphisms to the improvement in rice grain size traits were evaluated. Our results indicate that at least six functional polymorphisms have additive effects on grain shape and that one non-functional polymorphism in TGW6 affects grain shape in TD70. The newly designed markers will be useful in further studies to identify functional grain genes. Our findings provide insight into the control of grain size in rice, and they will be of value for improving rice grain yield.

Expanding the phenotypic and genetic spectrum of Chinese patients with congenital absence of vas deferens bearing CFTR and ADGRG2 alleles.

BACKGROUND: Congenital absence of vas deferens (CAVD) is a major cause of obstructive azoospermia. Mutations in CFTR and ADGRG2 are responsible for this disease. However, until now the genetic spectrum of the CFTR and ADGRG2 genes in Chinese population and the reasons of the differences from Caucasian cohorts were not clear. OBJECTIVES: (i) To study the characteristic and functional consequences of CFTR and ADGRG2 mutations in Chinese CAVD patients. (ii) To describe the genetic spectrum of Chinese CAVD patients and explain the reasons of the differences from Caucasian cohorts and Chinese cystic fibrosis (CF) patients. MATERIALS AND METHODS: Patients were screened for mutations in CFTR by Sanger sequencing. Patients with only one or no mutations were further investigated by multiplex ligation-dependent probe amplification analysis and direct sequencing of ADGRG2 gene. Bioinformatic analysis and structural modeling of proteins were performed. RESULTS: A total of 28 mutations in CFTR were identified in 72 patients, of which five mutations were novel. Fifty-five patients (76.39%) had CFTR mutations but no indels, among which 80.00% CBAVD patients have at least one CFTR mutation and 66.67% CUAVD have at least one CFTR mutation. Two novel mutations (p.Lys818* and p.Arg1008Gln) in ADGRG2 were detected. These novel mutations were predicted to be damaging by bioinformatics and were absent or extremely low frequency among our controls and databases. The genetic spectrum of Chinese CAVD patients revealed that the most common mutations were c.1210-12T[5], p.Ile556Val and p.Gln1352His, the last two of which were predicted to reduce the domains' contacts and weaken adenosine triphosphate binding. DISCUSSION AND CONCLUSION: This study illustrates the significance of all exon sequencing in CFTR and ADGRG2. A picture of the genetic spectrum of Chinese CAVD patients and the most common mutations can be described, which are different from Caucasian cohorts and Chinese CF patients.