The feasibility study of non-invasive fetal trisomy 18 and 21 detection with semiconductor sequencing platform

Objective: Recent non-invasive prenatal testing (NIPT) technologies are based on next-generation sequencing (NGS). NGS allows rapid and effective clinical diagnoses to be determined with two common sequencing systems: Illumina and Ion Torrent platforms. The majority of NIPT technology is associated with Illumina platform. We investigated whether fetal trisomy 18 and 21 were sensitively and specifically detectable by semiconductor sequencer: Ion Proton. Methods: From March 2012 to October 2013, we enrolled 155 pregnant women with fetuses who were diagnosed as high risk of fetal defects at Xiamen Maternal & Child Health Care Hospital (Xiamen, Fujian, China). Adapter-ligated DNA libraries were analyzed by the Ion Proton??? System (Life Technologies, Grand Island, NY, USA) with an average 0.3 ?? sequencing coverage per nucleotide. Average total raw reads per sample was 6.5 million and mean rate of uniquely mapped reads was 59.0%. The results of this study were derived from BWA mapping. Z-score was used for fetal trisomy 18 and 21 detection. Results: Interactive dot diagrams showed the minimal z-score values to discriminate negative versus positive cases of fetal trisomy 18 and 21. For fetal trisomy 18, the minimal z-score value of 2.459 showed 100% positive predictive and negative predictive values. The minimal z-score of 2.566 was used to classify negative versus positive cases of fetal trisomy 21. Conclusion: These results provide the evidence that fetal trisomy 18 and 21 detection can be performed with semiconductor sequencer. Our data also suggest that a prospective study should be performed with a larger cohort of clinically diverse obstetrics patients.open2

Clinicopathological features and prognosis of gastroenteropancreatic neuroendocrine neoplasms in a Chinese population: a large, retrospective single-centre study

Abstract Background Gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) are the most common type of neuroendocrine tumors, accounting for more than half of neuroendocrine neoplasms (NENs). We performed a retrospective study in our center to investigate the clinicopathological features, risk factors of metastasis, and prognosis of GEP-NENs in a Chinese population. Methods Four hundred forty patients with GEP-NENs treated at the First Affiliated Hospital of Zhengzhou University between January 2011 and March 2016 were analyzed retrospectively. Multivariate logistic regression was performed to identify independent risk factors for metastasis of the tumors. The Kaplan-Meier method was used for survival analysis, and log-rank tests for comparisons among groups. Results Primary sites were the stomach (24.3%), rectum (24.1%), pancreas (20.5%), esophagus (12.3%), unknown primary origin (UPO-NEN) (8.0%), duodenum (6.1%). Three hundred eighty-nine of the 440 GEP-NENs cases (88.4%) were non-functional tumors, and patients had non-specific symptoms, which could have led to delay in diagnosis and treatment. Neuroendocrine tumor, neuroendocrine carcinoma, and mixed adenoendocrine carcinoma were 56.8%, 33.2% and 3.2%, respectively, of the cases. One hundred thirty (29.5%) of the tumors were G1, 120 (27.3%) G2, and 190 (43.2%) G3. The immunohistochemical positive rate of synaptophysin was 97.7% and of chromogranin 48.7%. Logistic regression analysis revealed that the diameter and pathological classification of tumors were the most important predictors for metastasis. The median survival time was 34 months for patients with well-differentiated neuroendocrine tumors grade G3 and 11 months for poorly differentiated neuroendocrine carcinoma. The median survival time of patients with localized disease, regional disease, and distant disease was 36 months, 15 month, and 6 months, respectively. Conclusions This study constitutes a comprehensive analysis of the clinicopathological features of GEP-NENs in a Chinese population. GEP-NENs may occur at any part of the digestive system. The diameter and pathological classification of tumor are the most important predictors for metastasis. The prognosis is poor for patients with poorly differentiated neuroendocrine cancers and distant metastases

Genome-Wide Dissection of Quan 9311A Breeding Process and Application Advantages

Germplasm resource innovation is a crucial factor for cultivar development, particularly within the context of hybrid rice breeding based on the three-line system. Quan 9311A, a cytoplasmic male sterile (CMS) line, has been successfully cultivated using rice restoration materials and extensively employed as a female parent in hybrid breeding program in China. This line was developed by crossing the CMS line Zhong 9A with a two-line restorer line 93-11, with the intention of eliminating the restoring ability of 93-11 while retaining the sterility gene WA352c from Zhong 9A. Quan 9311A effectively amalgamates the most favorable agronomic traits from both parental lines. In this study, the relationship between phenotypic characteristics and the known functional genes of Quan 9311A were analyzed using the rice genome navigation technology based on whole-genome sequencing. The findings revealed that Quan 9311A harbors multiple superior alleles from both 93-11 and Zhong 9A, providing exceptional agronomic traits that are unavailable in earlier CMS lines. Despite the removal of the fertility restorer gene Rf3 from 93-11, numerous chromosomal segments from 93-11 persist in the Quan 9311A genome. Furthermore, the hybrid rice Quanyousimiao (QYSM) and the restorer line Wushansimiao (WSSM) were used as examples to illustrate the important role of Quan 9311A as the female parent in heterosis. It was found that QYSM carries a great number of superior alleles, which accounts for its high grain yield and wide adaptability. These insights not only advanced the utilization of hybrid rice pairing groups but also provided guidance for future breeding endeavors. The study introduced innovative concepts to further integrate genomics with traditional breeding techniques. Ultimately, Quan 9311A signified a significant milestone in rice breeding technology, opening up novel avenues for hybrid rice development

Demographic characteristics of study subjects.

<p>T18, Trisomy 18; T21, Trisomy 21; SD, standard deviation; NIPT, non-invasive prenatal testing.</p><p>Demographic characteristics of study subjects.</p

Positive predictive and negative predictive values in this study.

<p>T18, trisomy 18; T21, trisomy 21.</p><p>Positive predictive and negative predictive values in this study.</p

Interactive dot diagrams of trisomy 18 and 21.

<p>(A) Interactive dot diagram of trisomy 18. (B) Interactive dot diagram of trisomy 21.</p