[Estimation of molecular clock of Mycobacterium tuberculosis based on whole genome sequencing data].

Objective: To analyze the genomic mutation of Mycobacterium tuberculosis (M. tuberculosis) isolated in endogenous activation period and estimate the molecular clock based on the whole genome sequencing data. Methods: Literatures of the whole genome research of endogenous reactivated tuberculosis were retrieved, and the corresponding whole genome sequencing data were downloaded. We extracted the single nucleotide polymorphisms (SNPs) and strain isolation time of initial treatment and relapse of tuberculosis cases, explored the relationship between the different SNPs and interval between initial treatment and relapse by Poisson regression model, calculated the M. tuberculosis molecular clock, and estimated the mutation rate. Results: When the generation time of M. tuberculosis was 18 hours, the mutation rate in 0-2 years, i.e. short-term endogenous activation, was 6.47×10-10 (95%CI: 5.59×10-10-7.44×10-10), which was significantly higher than that in 2-14 years in long term endogenous activation (3.27×10-10, 95%CI: 2.88×10-10-3.69×10-10). The mutation rates of 0-, 1-, 2-, 3-, 5- and 7-14 years were 7.10×10-10, 6.06×10-10, 4.24×10-10, 5.34×10-10, 2.59×10-10 and 1.26×10-10 respectively. Conclusions: In the period of endogenous reactivation, the mutation rate of M. tuberculosis decreases with the interval time between initial treatment and relapse, which verifies the clinically observed phenomenon that the relapse often occurs within two years after the initial treatment of tuberculosis.

[Risk of bias assessment: (7) Assessing Bias in Studies of Prognostic Factors].

This paper introduces the tools related to Quality In Prognosis Studies (QUIPS) to assess the risk of bias in studies of prognostic factors and the relevant points of assessment and to illustrate the application of QUIPS in published prognostic research. The QUIPS tool identified 6 important areas to consider when evaluating validity and bias in studies of prognostic factors including participation, attrition, measurement on prognostic factors, outcomes, confounding factors, statistical analysis and reporting. It also provided a new method for evaluation on bias in the areas of prognostic research.

Prenatal molecular diagnosis of RET proto-oncogene mutation in multiple endocrine neoplasia type 2A.

We report a case of multiple endocrine neoplasia type 2A (MEN 2A) diagnosed prenatally at 16 weeks gestation. The 35-year-old mother is a MEN 2A patient. She had had three prior pregnancies: one resulted in a stillbirth; one produced a genetically unaffected boy; and the third was terminated in the first trimester owing to a diagnosis of blighted ovum. Autopsy did not reveal the cause of death of the stillborn infant, who was also found to be affected with MEN 2A by molecular study of paraffin-embedded tissue. Because of poor obstetric history and the patient's age, amniocentesis for cytogenetic and molecular studies was performed at 16 weeks' gestation during the pregnancy under discussion. As with other affected members in the mother's family, the missense mutation of TGC to TTC at codon 634 of the RET proto-oncogene was found in amniotic fluid cells. Analysis of DNA extracted from the lymphocytes of the infant's blood at birth confirmed the diagnosis. To our knowledge, this is the first report of prenatal diagnosis of MEN 2A.