Population Genetics Identifies Challenges in Analyzing Rare Variants

Geneticists have, for years, understood the nature of genome‐wide association studies using common genomic variants. Recently, however, focus has shifted to the analysis of rare variants. This presents potential problems for researchers, as rare variants do not always behave in the same way common variants do, sometimes rendering decades of solid intuition moot. In this paper, we present examples of the differences between common and rare variants. We show why one must be significantly more careful about the origin of rare variants, and how failing to do so can lead to highly inflated type I error. We then explain how to best avoid such concerns with careful understanding and study design. Additionally, we demonstrate that a seemingly low error rate in next‐generation sequencing can dramatically impact the false‐positive rate for rare variants. This is due to the fact that rare variants are, by definition, seen infrequently, making it hard to distinguish between errors and real variants. Compounding this problem is the fact that the proportion of errors is likely to get worse, not better, with increasing sample size. One cannot simply scale their way up in order to solve this problem. Understanding these potential pitfalls is a key step in successfully identifying true associations between rare variants and diseases.     

Germline gain-of-function MMP11 variant results in an aggressive form of colorectal cancer

Matrix metalloproteinase-11 (MMP11) is an enzyme with proteolytic activity against matrix and nonmatrix proteins. Although most MMPs are secreted as inactive proenzymes and are later activated extracellularly, MMP11 is activated intracellularly by furin within the constitutive secretory pathway. It is a key factor in physiological tissue remodeling and its alteration may play an important role in the progression of epithelial malignancies and other diseases. TCGA colon and colorectal adenocarcinoma data showed that upregulation of MMP11 expression correlates with tumorigenesis and malignancy. Here, we provide evidence that a germline variant in the MMP11 gene (NM_005940: c.232C>T; p.(Pro78Ser)), identified by whole exome sequencing, can increase the tumorigenic properties of colorectal cancer (CRC) cells. P78S is located in the prodomain region, which is responsible for blocking MMP11's protease activity. This variant was detected in the proband and all the cancer-affected family members analyzed, while it was not detected in healthy relatives. In silico analyses predict that P78S could have an impact on the activation of the enzyme. Furthermore, our in vitro analyses show that the expression of P78S in HCT116 cells increases tumor cell invasion and proliferation. In summary, our results show that this variant could modify the structure of the MMP11 prodomain, producing a premature or uncontrolled activation of the enzyme that may contribute to an early CRC onset in these patients. The study of this gene in other CRC cases will provide further information about its role in CRC development, which might improve patient treatment in the future.     

宝石CT碘-水基图在急性脑梗死介入治疗后的应用

目的探讨宝石CT碘-水基图在急性脑梗死介入治疗后的诊断价值。方法 31例急性脑梗死患者介入治疗后即刻宝石CT平扫QC图发现颅内异常高密度影,采用碘-水基图进行重建分析,同时测定高密度影碘基值、水基值,并与术后24 h普通CT复查诊断结果作比较。结果通过采用碘-水基图,17例诊断为碘对比剂渗出,14例诊断为脑出血转化,与术后24 h普通CT复查诊断结果完全一致(Kappa=1,P0.01);术后即刻碘基图之碘基值:碘对比剂渗出(32.09±5.36) g/L,脑出血转化(6.86±2.26) g/L,二者差异有统计学意义(t=53.291,P0.01);术后即刻水基图之水基值:碘对比剂渗出(1 027.93±8.29) g/L,脑出血转化(1 069.68±7.18) g/L,二者差异有统计学意义(t=-8.897,P0.01)。结论宝石CT碘-水基图可以准确诊断急性脑梗死介入治疗后颅内碘对比剂渗出和脑出血转化,值得向临床介绍推广。     

84例产褥感染的临床特点及常见致病微生物耐药性分析

目的 研究产褥感染的危险因素及常见致病微生物耐药情况，为临床治疗提供参考。方法 回顾性分析我院2017 年1 月～2019 年12 月发生的84 例产褥感染病例的临床资料，与同时期未发生产褥感染的200 例产妇进行对照研究，分析产褥感染的影响因素，并对分离获得的致病微生物进行耐药性分析。结果 感染组妊娠糖尿病、产钳助产、宫口开全后中转剖宫产患者的分布率高于对照组，差异有统计学意义（P＜0.05）；经多因素Logistic 回归分析，妊娠糖尿病是产褥感染的独立影响因素（P＜0.05）。本研究中共检出致病微生物40 株，其中革兰阴性菌13 株（占32.50%），革兰阳性菌10 株（占25.00%），支原体16 株（占40.00%），衣原体1 株（占2.50%），革兰阴性菌中以大肠埃希菌最常见，对二代头孢菌素类抗生素耐药率20%。革兰阳性菌以金黄色葡萄球菌最常见，对青霉素及头孢菌素耐药率高，未发现对亚胺培南及万古霉素耐药。结论 产钳助产、妊娠糖尿病、宫口开全后中转剖宫产是产褥感染可能的危险因素，其中，妊娠糖尿病是产褥感染的独立危险因素。目前临床常见致病微生物谱及耐药率未发生明显变化。     

Continuously moving table 3D MRI with lateral frequency-encoding direction.

A method is presented for 3D MRI in an extended field of view (FOV) based on continuous motion of the patient table and an efficient acquisition scheme. A gradient-echo MR pulse sequence is applied with lateral (left-right (L/R)) frequency-encoding direction and slab selection along the direction of motion. Compensation for the table motion is achieved by a combination of slab tracking and data alignment in hybrid space. The method allows fast k-space coverage to be achieved, especially when a short sampling FOV is chosen along the direction of table motion, as is desirable for good image quality. The method can be incorporated into different acquisitions schemes, including segmented k-space scanning, which allows for contrast variation with the use of magnetization preparation. Head-to-toe images of volunteers were obtained with good quality using 3D spoiled gradient-echo sequences. As an example of magnetization-prepared imaging, fat/water separated images were acquired using chemical shift selective (CHESS) presaturation pulses.     

采用半透明效果实现医学三维整体可视化

目的通过改进直接体绘制技术（DVR）算法中的关键步骤，绘制能表达数据场中不同层次组织的内部结构。方法根据界面对光线的反射和物质本身对光线的衰减，将数据场划分为边界不丰富的简单数据场和边界丰富的复杂数据场，从而采用分段线性函数来构造阻光度传递函数（TF）；将数据场中低灰度体素点看为一种不发光但会导致采样光线衰减的物质；根据采样结束时采样光线的阻光度分布来调整TF，完成三维绘制。结果绘制出了不同层次组织的内部结构。结论本算法有效地解决了体素点相互遮挡的问题，实现了医学三维整体可视化。     

Prognostic index to identify patients who may not benefit from whole brain radiotherapy for multiple brain metastases from lung cancer

Palliative whole brain radiotherapy (WBRT) is often recommended in the management of multiple brain metastases. Allowing for WBRT waiting time, duration of the WBRT course and time to clinical response, it may take 6 weeks from the point of initial assessment for a benefit from WBRT to manifest. Patients who die within 6 weeks (‘early death’) may not benefit from WBRT and may instead experience a decline in quality of life. This study aimed to develop a prognostic index (PI) that identifies the subset of patients with lung cancer with multiple brain metastases who may not benefit from WBRT because of ‘early death’. The medical records of patients with lung cancer who had WBRT recommended for multiple brain metastases over a 10-year period were retrospectively reviewed. Patients were classified as either having died within 6 weeks or having lived beyond 6 weeks. Potential prognostic indicators were evaluated for correlation with ‘early death’. A PI was constructed by modelling the survival classification to determine the contribution of these factors towards shortened survival. Of the 275 patients recommended WBRT, 64 (23.22%) died within 6 weeks. The main prognostic factor predicting early death was Eastern Cooperative Oncology Group (ECOG) status >2. Patients with a high PI score (>13) were at higher risk of ‘early death’. Twenty-three per cent of patients died prior to benefit from WBRT. ECOG status was the most predictive for ‘early death’. Other factors may also contribute towards a poor outcome. With further refinement and validation, the PI could be a valuable clinical decision tool.     

Fat and water separation in balanced steady-state free precession using the Dixon method.

In this work the feasibility of separating fat and water signals using the balanced steady-state free precession (SSFP) technique is demonstrated. The technique is based on the observation (Scheffler and Hennig, Magnetic Resonance in Medicine 2003;49:395-397) that at the nominal values of TE = TR/2 in SSFP imaging, phase coherence can be achieved at essentially only two orientations (0 degrees and 180 degrees ) relative to the RF pulses in the rotating frame, under the assumption of TR < T2, and independently of the SSFP angle. This property allows in-phase and out-of-phase SSFP images to be obtained by proper choices of the center frequency offset, and thus allows the Dixon subtraction method to be utilized for effective fat-water separation. The TR and frequency offset for optimal fat-water separation are derived from theories. Experimental results from healthy subjects, using a 3.0 Tesla system, show that nearly complete fat suppression can be accomplished.