Sequencing‐based microsatellite instability testing using as few as six markers for high‐throughput clinical diagnostics

Microsatellite instability (MSI) testing of colorectal cancers (CRCs) is used to screen for Lynch syndrome (LS), a hereditary cancer‐predisposition, and can be used to predict response to immunotherapy. Here, we present a single‐molecule molecular inversion probe and sequencing‐based MSI assay and demonstrate its clinical validity according to existing guidelines. We amplified 24 microsatellites in multiplex and trained a classifier using 98 CRCs, which accommodates marker specific sensitivities to MSI. Sample classification achieved 100% concordance with the MSI Analysis System v1.2 (Promega) in three independent cohorts, totaling 220 CRCs. Backward–forward stepwise selection was used to identify a 6‐marker subset of equal accuracy to the 24‐marker panel. Assessment of assay detection limits showed that the 24‐marker panel is marginally more robust to sample variables than the 6‐marker subset, detecting as little as 3% high levels of MSI DNA in sample mixtures, and requiring a minimum of 10 template molecules to be sequenced per marker for >95% accuracy. BRAF c.1799 mutation analysis was also included to streamline LS testing, with all c.1799T>A variants being correctly identified. The assay, therefore, provides a cheap, robust, automatable, and scalable MSI test with internal quality controls, suitable for clinical cancer diagnostics.     

Ten novel MSH2 and MLH1 germline mutations in families with HNPCC

Hereditary nonpolyposis colorectal cancer (HNPCC) is one of the most common hereditary cancer-susceptibility syndromes. Germline mutations in mismatch repair genes are associated with the clinical phenotype of HNPCC. We report ten novel germline mutations, three in MSH2 and seven in MLH1. All but one mutation have been found in families fulfilling criteria of the Bethesda guidelines; four of them additionally fulfilled the Amsterdam criteria I or II. Eight mutations were considered pathogenic and predictive diagnostics in healthy family members at risk shall be undertaken; these include five frameshift mutations leading to premature stop codons, in MSH2: c.1672delT (p.S558Xfs) and c.2466_2467delTG (p.C822X) and in MLH1: c.1023delG (p.R341Xfs), c.1127_1128dupAT (p.K377Xfs) and c.1310delC (p.P437Xfs); three mutations leading to splice aberrations, in MSH2: c.1661G>C (r.1511_1661del) and in MLH1: c.677+3A>C (r.589_677del) and c.1990-2A>G predicted to result in a splice site defect. The remaining two mutations are unclassified variants with assumed pathogenicity: one missense mutation in the highly conserved ATPase domain of MLH1 (c.122A>G [p.D41G]) and one in-frame insertion of twelve nucleotides in MLH1 (c.2155_2156insATGTGTTCCACA [p.I719delinsNVFHI]). These two mutations were not found in 102 alleles of healthy control individuals. The corresponding tumors from all patients showed a high level of microsatellite instability (MSI-H). Immunohistochemistry (IHC) revealed complete loss of expression of the affected protein in the tumor cells from all but three patients. The tumors from the patients with the mutations c.1127_1128dupAT and c.1990-2A>G showed a reduction of expression of the MLH1-protein, rather than complete loss. In the tumor from the patient with the missense mutation c.122A>G [p.D41G] a normal expression of the proteins coded by MLH1 and MSH2 was noticed.     

The effects of digital filtering on mismatch negativity in wakefulness and slow-wave sleep

The mismatch negativity (MMN) is a response to a deviant auditory stimulus that occurs infrequently in a sequence of otherwise repetitive, homogeneous standard auditory stimuli. The MMN is presumed automatic and independent of conscious awareness. Recording of the MMN during unconscious states may be problematic. The frequency content of the long-lasting MMN may overlap and summate with other event-related slow potentials and low-frequency background electroencephalogram (EEG) activity. The purpose of this study is to determine the optimal filter settings for recording the MMN during unconscious states. Auditory event-related potentials (ERPs) were recorded from eight subjects in an oddball paradigm during wakefulness and Stages 3 and 4 of sleep [slow-wave sleep (SWS)] using a 0.16-35 Hz analogue bandpass. Deviant probability was 0.033. Stimulus-onset asynchrony was 150 ms. The EEG data were subsequently digitally filtered in the frequency domain. The low-pass filter was set at either 24, 12 or 6 Hz, and the high-pass filter at either 1, 2, 3 or 4 Hz. Applying a low-pass filter down to 12 Hz had a minimal impact on the waking or sleeping MMN amplitude. On the other hand, increasing the high-pass setting from 2 to 3 Hz permitted the visualization of the MMN recorded during sleep. The 4 Hz filter showed a similar trend but also markedly attenuated the amplitude of the waking MMN. A high-pass setting of 3 Hz provides a reasonable compromise. It has only a slight effect on the MMN when the subject is conscious, but still attenuates most of the unwanted slow potential activity when the subject enters SWS.     

Is the failure to detect stimulus deviance during sleep due to a rapid fading of sensory memory or a degradation of stimulus encoding?

The mismatch negativity (MMN) is thought to reflect the outcome of a system responsible for the detection of change in an otherwise repetitive, homogenous acoustic environment. This process depends on the storage and maintenance of a sensory representation of the frequently presented stimulus to which the deviant stimulus is compared. Few studies have been able to record the MMN in non-rapid eye movement (NREM) sleep. This pattern of results might be explained by either a rapid fading of sensory memory or an inhibition of stimulus input prior to entry into the cortical MMN generator site. The present study used a very rapid rate of presentation in an attempt to capture mismatch-related negativity prior to the fading of sensory memory. Auditory event-related potentials were recorded from 12 subjects during a single sleep period. A 1000 Hz standard stimulus was presented every 150 ms. At random, on 6.6% of the trials, the standard was changed to either a large 2000 Hz or a small 1100 Hz deviant. In wakefulness, the large deviant elicited an extended negativity that was reduced in amplitude following the presentation of the small deviant. This negativity was also apparent during REM sleep following the presentation of the large deviant. These deviant-related negativities (DRNs) were probably a composite of N1 and MMN activity. During NREM sleep (stage 2 and slow-wave sleep), only the large deviant continued to elicit a DRN. However this DRN might be overlapped by the initial activity of a component that is unique to sleep, the N350. There was little evidence of the DRN or the MMN during sleep following the presentation of the small deviant. A rapid rate of presentation, therefore, does not preserve the MMN following small deviance within sleep. It is possible that inhibition of sensory input occurs before entry into the MMN generating system in the temporal cortex.     

DNA microarray technique for detection and identification of seven flaviviruses pathogenic for man

A flavivirus microarray was developed for detection and identification of yellow fever (YF), West Nile, Japanese encephalitis (JE), and the dengue 1-4 viruses, which are causing severe human disease all over the world. The microarray was based on 500-nucleotide probe fragments from five different parts of the seven viral genomes. A low-stringent amplification method targeting the corresponding regions of the viral genomic RNA was developed and combined with hybridization to the microarray for detection and identification. For distinction of the generated virus-specific fluorescence-patterns a fitting analysis procedure was adapted. The method was verified as functional for all seven flaviviruses and the strategy for the amplification, combined with the long probes, provided a high tolerance for smaller genetic variability, most suitable for these rapidly changing RNA viruses. A potentially high detection and identification capacity was proven on diverged strains of West Nile and dengue viruses. The lower limit for detection was equivalent, or better, when compared to routinely used RT-PCR methods. The performance of the method was verified on human patient samples containing dengue viruses, or normal human serum spiked with YF or JE viruses. The results demonstrated the ability of the flavivirus microarray to screen simultaneously a sample for several viruses in parallel, in combination with a good lower limit of detection.     

中国人遗传性非息肉病性结直肠癌错配修复基因大片段缺失研究

目的了解中国人遗传性非息肉病性结直肠癌(hereditary nonpolyposis colorectal cancer．HNPCC)家系中MSH和MLH1基因大片段缺失情况及特点，以进一步完善中国人HNPCC家系遗传检测内容。方法取14个符合中国人HNPCC诊断标准的HNPCC家系肿瘤先证者外周血DNA，用荧光标记多重PCR技术结合GeneScan分析系统检测MSH2和MLH1基因大片段缺失。结果14例患者中有1例检测到MSH2基因第1～7外显子缺失，该家系另1例大肠癌患者和3个家系成员有同样的基因片段缺失。结论中国人HNPCC家系错配修复基因大片段缺失可能以MSH2比较常见。建议在中国人HNPCC家系遗传检测中常规包含错配修复基因大片段缺失检测。     

MDC1和MMR蛋白在子宫内膜癌中的表达及临床意义

目的探讨DNA损伤检查点蛋白调节子1(MDC1)与错配修复(MMR)蛋白在子宫内膜癌中的表达及其与相关临床特征的关系。方法回顾性分析126例子宫内膜癌患者的临床及病理资料,收集患者手术或刮宫标本进行HE染色和免疫组化染色,检测MDC1、MMR蛋白(MSH6、MSH2、PMS2、MLH1)的表达,并根据MDC1及MMR蛋白免疫组化结果,分析MDC1、MMR蛋白表达及结合两种蛋白不同表达与患者临床特征的关系。采用Kaplan-Meier法绘制生存曲线图分析MDC1和MMR蛋白联合检测与总生存率的关系。采用Spearman秩相关性分析MDC1与MMR蛋白表达的相关性。结果与MDC1阳性表达患者相比,MDC1阴性表达患者年龄较小,主要为低级别(1~2级)子宫内膜样腺癌(P<0.05);与MMR表达完整(MMR-p)患者相比,MMR表达缺失(MMR-d)患者年龄较小,主要为低级别(1~2级)子宫内膜样腺癌(P<0.05)。MDC1阴性表达/MMR-p、MDC1阳性表达/MMR-p、MDC1阴性表达/MMR-d、MDC1阳性表达/MMR-d各组患者年龄、组织学类型、组织学分级比较,差异具有统计学意义(P<0.05);而临床分期、肌层浸润深度比较,差异无统计学意义(P>0.05)。MDC1、MMR蛋白联合检测与患者的总生存率无关(P>0.05),MDC1阴性表达占所有子宫内膜癌患者的9.5%(12/126),与MMR-d呈正相关(P<0.001)。结论MDC1、MMR蛋白多在低级别子宫内膜癌中失表达,并且MDC1阴性表达与MMR-d具有正相关性,提示MDC1失表达与子宫内膜癌的微卫星不稳定性密切相关。     

靶向PV株核蛋白基因的小分子干扰RNA对不同狂犬病病毒毒株复制的交叉抑制作用

目的研究小分子干扰RNA（siRNA）对狂犬病病毒（RV）不同毒株复制的交叉抑制效果。方法采用体外转录和RNA酶Ⅲ消化长片段双链RNA的方法制备8条以RV的PV株核蛋白（N）基因为靶基因的21nt siRNA，用以转染已经感染了不同滴度PV、CTN或CVS株RV的BSR细胞，采用直接免疫荧光法观察转染的siRNA对已感染BSR细胞的不同毒株RV复制的抑制效果，并分析这种抑制效果与靶基因序列的相关性。结果不同21nt siRNA均对PV株的复制产生了较强的抑制作用：对CTN株和CVS株的交叉抑制作用观察结果表明，21nt siRNA与靶基因在碱基错配高达5个的情况下仍对病毒复制保持抑制效应。然而，siRNA与靶基因碱基错配的位置与抑制作用的丧失高度相关。3’端第2个碱基的错配将使抑制作用表失，随后的碱基错配对抑制作用的影响依次降低；中部碱基错配影响较小；而5’端碱基错配对抑制作用几乎没有影响。结论siRNA对靶基因的抑制作用的丧失与其同靶基因序列碱基错配的位置相关，3’端碱基错配可降低其抑制作用的特异性，产生偏靶效应的范围和概率可能增大，这为设计独特的siRNA序列提供了新的思路。     

Quantitative prediction of ischemic stroke tissue fate

Accurate prediction of ischemic tissue fate could aid clinical decision-making in the treatment of acute stroke. We investigated predictions of tissue fate for three (30-min, 60-min and permanent) stroke models in rats. Quantitative cerebral blood flow (CBF), apparent diffusion coefficient (ADC) and spin-spin relaxation time constant (T(2)) were acquired during the acute phase and at the end point followed by histological examination. Probability-of-infarct profiles based on ADC and CBF data were constructed using a training dataset. Probability-of-infarct maps were predicted using only acute stroke data from a separate experimental dataset, revealing the likelihood of future infarction. Performance measures of sensitivity and specificity showed accurate predictions. Sensitivities (mean +/- SD) for the 30-min, 60-min and permanent stroke were, respectively, 82 +/- 6%, 82 +/- 7%, and 86 +/- 4%, specificities were 83 +/- 5%, 86 +/- 5%, and 89 +/- 6%, and the areas under the receiver operating curve were 87 +/- 3%, 90 +/- 4%, and 93 +/- 3%. Importantly, to improve prediction accuracy, we took into account regional susceptibility to infarction. Spatial frequency-of-infarct maps were constructed and predictions were made by taking the weighted average of the probability-of-infarct map and spatial frequency-of-infarct map. The optimal weighting coefficient of spatial frequency-of-infarct was small (10%) for the permanent occlusion group but surprisingly large (40%) for the reperfusion groups, indicating that regional susceptibility of infarction was important for accurate prediction in reperfusion stroke. We concluded that the likelihood of cerebral infarction in rats can be accurately predicted and that accounting for regional susceptibility of infarct further improves prediction accuracy. Predictive models have the potential to provide a valuable quantitative framework for clinicians to consider different stroke treatment options. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Stress reduction by geometric compliance matching at vascular graft anastomoses

An analysis is presented of stresses developed with different junctional configurations of end-to-end vascular graft anastomoses with severe compliance mismatch. Junctions of circular transverse sections and junctions by bias cuts (beveled ends) are compared with an anastomosis of a graft constructed with an elliptical transverse section and a bevel end cut vessel. This latter substitutes midwall inextensional deformations for extensional deformations that occur with the former, conventional configurations. Applications to end-to-side anastomoses are also discussed. A range of parameters are considered:i.e., vascular wall thickness/radius ratios between 0.1 and 0.5 locations from the anastomotic plane between 1/2 and 3/2 times the vascular wall thickness, host vessel axial stretch by external forces between 0 and 15%, maximal vascular circumferential stretch distal from the anastomosis between 0 and 25%, and perimeter locations at the anastomotic junction 0° and 90°. The graft constructed with an elliptic cross-section developed peak stresses that are orders of magnitude lower than those developed with conventional configurations. The introduction of matching geometric compliance that domimates at the anastomotic junction minimizes consequences of material mismatch between graft and vessel and has the potential to reduce suture line stress greatly. This analysis may suggest designs for experimental studies to confirm relationships between neointimal hyperplasia and suture line stress levels, and provide a relatively simple solution for reduction of such stresses at the anastomotic junction. Choices may be permitted of graft materials with optimal surface properties despite less favorable elastic properties.