Semiconductor Sequencing Analysis of Chromosomal Copy Number Variations in Spontaneous Miscarriage.

BACKGROUND Array CGH is the criterion standard for identifying copy number variations (CNV), but the restrictive requirement of DNA quality and relatively high cost prevent the use of this method as a general assay in hospitals in developing countries. Our principal objective was to determine whether the semiconductor sequencing platform (SSP) could be an alternative method in CNV detection for spontaneous miscarriage. MATERIAL AND METHODS A total of 443 spontaneous miscarriage samples were collected and subjected to low-coverage (0.1X) whole-genome analysis by SSP. These samples were verified by array CGH and 8 low-quality DNA samples were analyzed by SSP and validated by MLPA. RESULTS SSP detected 195 chromosomal numerical abnormalities, 74 CNVs, and 9 mosaicisms among the 435 samples. Among 74 CNV abnormalities, SSP detected an equal number (56) of CNVs 56 >1 Mb with array CGH. However, SSP missed more 6 cases CNVs <1 Mb than array CGH (12 vs. 18). SSP detected more mosaicisms than array CGH (9 vs. 7, p=0.5). Interestingly, SSP detected the mosaicism which had only 8% X monosomy, which was much lower than the minimal percentage of monosomy that was detected by array CGH. CONCLUSIONS SSP is of equivalent efficacy as array CGH in detecting CNVs >1 Mb, and performs better in identifying mosaicism. With the merits of low cost and less demand of input DNA, SSP is a good alternative for use in genetic diagnosis.

Comparative study of Gilsanz-Ratib digital atlas and Greulich-Pyle atlas for bone age estimation in a Chinese sample.

BACKGROUND: The applicability of the Gilsanz-Ratib (GR) digital atlas to bone age (BA) determination in China has not been evaluated. AIM: To compare the validity of GR and the Greulich-Pyle (GP) atlas in BA determination for children in Shanghai. SUBJECTS AND METHODS: Left-hand radiographs of 243 girls and 375 boys aged 0-13 years were obtained for suspected trauma. They were divided into eight sub-groups according to gender and age (0-3, 3-7, 7-10 and 10-13 years). Radiographs were read by two radiologists, using both GP and GR atlases. The differences between BA and calendar age (CA) were analysed. The inter- and intra-observer consistency was evaluated. RESULTS: Pearson's correlation coefficients indicated a strong positive correlation between methods and between raters. The differences between BA and CA of two sub-groups (10-13-year-old boys, GR; 0-3-year-old girls, GP) were not only statistically significant, but exceeded 1 SD, suggesting biological significance. CONCLUSION: Both atlases can be used on most age groups. However, the GR atlas is not recommended in boys aged 10-13 years, while the GP atlas is not suitable for girls aged 0-3 years. Therefore, the use of the GP or GR atlas is practical, depending on the age of the child.

Targeted Next-Generation Sequencing of Circulating Tumor DNA Mutations among Metastatic Breast Cancer Patients.

Liquid biopsy through the detection of circulating tumor DNA (ctDNA) has potential advantages in cancer monitoring and prediction. However, most previous studies in this area were performed with a few hotspot genes, single time point detection, or insufficient sequencing depth. In this study, we performed targeted next-generation sequencing (NGS) with a customized panel in metastatic breast cancer (MBC) patients. Fifty-four plasma samples were taken before chemotherapy and after the third course of treatment for detection and analysis. Paired lymphocytes were also included to eliminate clonal hematopoiesis (CH)-related alternatives. A total of 1182 nonsynonymous mutations in 419 genes were identified. More ctDNA mutations were detected in patients with tumors > 3 cm (p = 0.035) and HER2(-) patients (p = 0.029). For a single gene, the distribution of ctDNA mutations was also correlated with clinical characteristics. Multivariate regression analysis revealed that HER2 status was significantly associated with mutation burden (OR 0.02, 95% CI 0-0.62, p = 0.025). The profiles of ctDNA mutations exhibited marked discrepancies between two time points, and baseline ctDNA was more sensitive and specific than that after chemotherapy. Finally, elevated ctDNA mutation level was positively correlated with poor survival (p < 0.001). Mutations in ctDNA could serve as a potential biomarker for the evaluation, prediction, and clinical management guidance of MBC patients with chemotherapy.