Estimating the Efficacy and Efficiency of Cascade Genetic Screening

Screening for genetic variants that predispose individuals or their offspring to disease may be performed at the general population level or may instead be targeted at the relatives of previously identified carriers. The latter strategy has come to be known as "cascade genetic screening." Since the carrier risk of close relatives of known carriers is generally higher than the population risk, cascade screening is more efficient than population screening, in the sense that fewer individuals have to be genotyped per detected carrier. The efficacy of cascade screening, as measured by the overall proportion of carriers detected in a given population, is, however, lower than that of population-wide screening, and the respective inclusion rates vary according to the population frequency and mode of inheritance of the predisposing variants. For dominant mutations, we have developed equations that allow the inclusion rates of cascade screening to be calculated in an iterative fashion, depending upon screening depth and penetrance. For recessive mutations, we derived only equations for the screening of siblings and the children of patients. Owing to their mathematical complexity, it was necessary to study more extended screening strategies by simulation. Cascade screening turned out to result in low inclusion rates (<1%) when aimed at the identification of heterozygous carriers of rare recessive variants. Considerably higher rates are achievable, however, when screening is performed to detect covert homozygotes for frequent recessive mutations with reduced penetrance. This situation is exemplified by hereditary hemochromatosis, for which up to 40% of at-risk individuals may be identifiable through screening of first- to third-degree relatives of overt carriers (i.e., patients); the efficiency of this screening strategy was found to be approximately 50 times higher than that of population-wide screening. For dominant mutations, inclusion rates of cascade screening were estimated to be higher than for recessive variants. Thus, some 80% of all carriers of the factor V Leiden mutation would be detected if screening were to be targeted specifically at first- to third-degree relatives of patients with venous thrombosis. The relative cost efficiency of cascade as compared with population-wide screening (i.e., the overall savings in the extra managerial cost of the condition) is also likely to be higher for dominant than for recessive mutations. This notwithstanding, once screening has become cost-effective at the population level, it can be expected that cascade screening would only transiently represent an economically viable option.     

Screening and self examination for breast cancer.

Breast cancer is the major form of cancer in women, with nearly 30,000 new cases and over 15,000 deaths in the United Kingdom each year. Breast screening by mammography has been shown in randomised trials to reduce mortality from breast cancer in women aged 50 and over. An NHS breast screening programme has been in operation in the United Kingdom since 1988. Its aim is to reduce mortality from breast cancer by 25% in the population of women invited to be screened. The uptake of mammography among the eligible population may be the single most important determinant if the programme is to be effective. Primary care teams have an important part to play in encouraging women to attend for screening and in providing information, advice, and reassurance at all stages of the screening process. To date, routine breast self examination has not been shown to be an effective method of screening for breast cancer and should not therefore be promoted as a primary screening procedure. There is, however, a case to be made for women to become more "breast aware."     

Hemoglobin E disorder: Newborn screening program

Hemoglobin E (Hb E) disorder is an important kind of hemoglobinopathy. It can be seen around the world with the highest prevalence in Southeast Asia. The screening for this disorder becomes the public health policies in many countries. The screening can be performed in several population groups. The newborn screening program for Hb E disorder is an important issue in pediatric genetics. In this brief review, the author discusses on important laboratory tests for screening for Hb E disorder in newborn.     

Comparing disease screening tests when true disease status is ascertained only for screen positives

Disease screening is a fundamental part of health care. To evaluate the accuracy of a new screening modality, ideally the results of the screening test are compared with those of a definitive diagnostic test in a set of study subjects. However, definitive diagnostic tests are often invasive and cannot be applied to subjects whose screening tests are negative for disease. For example, in cancer screening, the assessment of true disease status requires a biopsy sample, which for ethical reasons can only be obtained if a subject's screening test indicates presence of cancer. Although the absolute accuracy of screening tests cannot be evaluated in such circumstances, it is possible to compare the accuracies of screening tests. Specifically, using relative true positive rate (the ratio of the true positive rate of one test to another) and relative false positive rate (the ratio of the false positive rates of two tests) as measures of relative accuracy, we show that inference about relative accuracy can be made from such studies. Analogies with case-control studies can be drawn where inference about absolute risk cannot be made, but inference about relative risk can. In this paper, we develop a marginal regression analysis framework for making inference about relative accuracy when only screen positives are followed for true disease. In this context factors influencing the relative accuracies of tests can be evaluated. It is important to determine such factors in order to understand circumstances in which one test is preferable to another. The methods are applied to two cancer screening studies, one concerning the effect of race on screening for prostate cancer and the other concerning the effect of tumour grade on the detection of cervical cancer with cytology versus cervicography screening.     

不依赖天然外显子的蛋白质内含子定向进化筛选系统

蛋白质剪接技术为在蛋白质水平上直接对蛋白质进行修饰和加工提供了一种全新的解决方案,因而在蛋白质工程及相关领域具有非常广阔的应用前景。现阶段,大部分天然的蛋白质内含子在异源蛋白质中剪接活性非常低,极大限制了蛋白质内含子的开发和应用。为了开发一个可以同时对蛋白质内含子通用性和剪接活性进行筛选的系统,利用Bsa I限制性内切酶识别位点和切割不重合的特性,将Ter ThyX内含子(不含外显子序列)插入到卡那霉素抗性蛋白基因的多个位点。并且摒弃了以往需要结合天然外显子以实现剪接的方法,可以同时对蛋白质内含子的剪接活性和通用性进行筛选。Western blot结果和卡那霉素平板生长结果表明,通过卡那霉素筛选系统可以精确的将蛋白质内含子剪接反应与卡那霉素抗性结合起来,仅从卡那霉素平板上的菌落生长情况即可完成蛋白质内含子剪接活性阳性突变的筛选,是一个快速,稳定的定向进化筛选系统。     

Feasibility of chemical screening of urine for neuroblastoma case finding in infancy in Quebec.

Neuroblastoma is the most common fatal solid tumour of childhood. Studies in Japan suggest that screening urine at 6 months for tumour-derived metabolites greatly improves early case finding and prognosis. The incidence rate of neuroblastoma in Quebec is at least 1 per 10,330 live births, higher than that of all other diseases responding to early treatment except congenital hypothyroidism screened for in the Quebec Network of Genetic Medicine. The feasibility of chemical screening of urine for elevated levels of homovanillic acid and vanillylmandelic acid in Quebec was assessed. The cost-effectiveness of screening 100,000 infants per year would be high (cost-benefit ratio 2.4), with a net saving of about $280,000 and eight lives per year. The estimated cost of adding neuroblastoma screening to the existing urine metabolite screening program is $70,700. The apparent sensitivity of the proposed test is 0.859 and the rate of false-positive results about 0.1%, both acceptable values. The attitude of potential participants toward the present urine screening program and the addition of a "tumour test" was positive. The results indicate that a pilot study of neuroblastoma screening in Quebec could be undertaken.     

On the optimal policies of cancer screening.

Some problems of optimal screening are considered. A screening strategy is allowed to be nonperiodic. Two approaches to screening optimization are used: the minimum delay time approach and the minimum cost approach. Both approaches are applied to the analysis of an optimization problem when the natural history of the disease is known and when it is unknown (a minimax problem). The structure of optimal screening policies is investigated as well as the benefit they can provide compared to the periodic screening policy. The detection probability is assumed to depend only on the stage of the disease, though it may not be constant throughout each stage. It is shown that periodic screening appears to be optimal when one has no information on the natural history of the disease, the minimum delay time criterion being used for optimization. Some applications to lung cancer screening are presented.     

The Health System and Population Health Implications of Large-Scale Diabetes Screening in India: A Microsimulation Model of Alternative Approaches

Background

Like a growing number of rapidly developing countries, India has begun to develop a system for large-scale community-based screening for diabetes. We sought to identify the implications of using alternative screening instruments to detect people with undiagnosed type 2 diabetes among diverse populations across India.

Methods and Findings

We developed and validated a microsimulation model that incorporated data from 58 studies from across the country into a nationally representative sample of Indians aged 25–65 y old. We estimated the diagnostic and health system implications of three major survey-based screening instruments and random glucometer-based screening. Of the 567 million Indians eligible for screening, depending on which of four screening approaches is utilized, between 158 and 306 million would be expected to screen as “high risk” for type 2 diabetes, and be referred for confirmatory testing. Between 26 million and 37 million of these people would be expected to meet international diagnostic criteria for diabetes, but between 126 million and 273 million would be “false positives.” The ratio of false positives to true positives varied from 3.9 (when using random glucose screening) to 8.2 (when using a survey-based screening instrument) in our model. The cost per case found would be expected to be from US$5.28 (when using random glucose screening) to US$17.06 (when using a survey-based screening instrument), presenting a total cost of between US$169 and US$567 million. The major limitation of our analysis is its dependence on published cohort studies that are unlikely fully to capture the poorest and most rural areas of the country. Because these areas are thought to have the lowest diabetes prevalence, this may result in overestimation of the efficacy and health benefits of screening.

Conclusions

Large-scale community-based screening is anticipated to produce a large number of false-positive results, particularly if using currently available survey-based screening instruments. Resource allocators should consider the health system burden of screening and confirmatory testing when instituting large-scale community-based screening for diabetes.     

An economic view of high compliance as a screening objective.

Accepted wisdom holds that high compliance is essential for a screening programme to be successful. Indeed, a reason that the national breast screening programme is not routinely offered to women aged 65 or more is on the grounds of predicted poor compliance by older women. Increasing compliance is often associated with increased costs. These costs represent a lost opportunity for screening alternative target populations. We question the need for screening programmes to achieve high compliance, and we argue that a screening programme can be efficient with very low levels of compliance. Adopting compliance as a screening objective and as a measure of the success of screening may be detrimental to the efficiency of a screening programme.     

American and European recommendations for screening mammography in younger women: a cultural divide?

The American Cancer Society advocates mammography screening for all women from age 40, whereas in Europe it is not recommended for women below the age of 50. Randomised prospective studies have failed to show a significant benefit from screening women aged under 50 and five potentially harmful effects of screening should be considered: lead time, overdiagnosis, radiation exposure, false positive results, and cost. Younger women must be properly informed about the potential for harm as well as for benefit before screening.     

Rapid (partial) prescreening of cervical smears: the quality control method of choice?

Rapid rescreening of all negative and inadequate smears is the quality control method of choice in the UK. The sensitivity of primary screening of laboratory and individual screeners are major indicators of screening quality and are dependent on the number of false negative smears found by rapid screening for their calculation. High sensitivity may indicate good quality primary screening or poor quality rapid review. Quantifiably high quality rapid rescreening is essential if these sensitivity figures are to be meaningful. A 12-month study was undertaken in routine practice using the prescreening mode to ascertain the sensitivity of rapid (partial) screening in our department. The final results of smears were compared with those of rapid prescreening. The calculated sensitivity ranged from 92-54% for high-grade abnormalities and 75-33% for all grades, revealing a wide range of performance between individual prescreeners. Rapid prescreening can identify individuals best suited to rapid screening in routine practice. By using these prescreeners only, the sensitivity of cervical screening could be raised. Rapid (partial) prescreening should be considered as the quality control method of choice.     

Group screening for rare events based on incomplete block designs

Fields such as, diagnostic testing, biotherapeutics, drug development, and toxicology among others, center on the premise of searching through many specimens for a rare event. Scientists in the business of “searching for a needle in a haystack” may greatly benefit from the use of group screening design strategies. Group screening, where specimens are composited into pools with each pool being tested for the presence of the event, can be much more cost-efficient than testing each individual specimen. A number of group screening designs have been proposed in the literature. Incomplete block screening designs are described here and compared with other group screening designs. It is shown under certain conditions, that incomplete block screening designs can provide nearly a 90% cost saving compared to other group screening designs such as when prevalence is 0.001 and screening 3876 specimens with an ICB-sequential design vs. a Dorfman design. In other cases, previous group screening designs are shown to be most efficient. Overall, when prevalence is small (≤0.05) group screening designs are shown to be quite cost effective at screening a large number of specimens and in general there is no one design that is best in all situations. © 2018 American Institute of Chemical Engineers Biotechnol Progress, 35: e2770, 2019.     

不同影响因素对热原实验中兔筛选的影响

目的分析不同影响因素对新西兰兔的初次筛选合格率、二次筛选合格率的影响。方法根据2005版《中国药典》进行测定。结果初次筛选结果中,不同季节、体重值、性别、湿度新西兰兔的筛选率都有显著性差异,筛选时间在7～9月、体重值为1.7～2.0 kg、雄性的新西兰兔、在湿度为61～70%的条件下初次筛选率较高;在二次筛选结果中,不同季节、室温、湿度条件下新西兰兔的筛选率都有显著性差异,筛选时间在1～3月、在室温为22.1～23.0℃、湿度为61～70%的条件下新西兰兔的二次筛选率较高。结论在不同影响因素的条件下,新西兰兔的初次筛选合格率、二次筛选合格率均受到影响。     

Practical approaches to efficient screening: information-rich screening protocol

The past approach of high-throughput screening of everything in the corporate collection has been shown to be very expensive in terms of reagents cost, disposal cost, and compound collection depletion. It is well known that screening campaigns produce several hits, of which only 50% confirm on average. More efficient ways of screening can provide an informative structure-activity relationship (SAR), which in turn can be used to build mathematical models for further probing the activity space and directing chemical synthesis. The authors report new methods and insights to extract the maximum possible information from a screening experiment and find most of the possible hits in the corporate collection while screening as few compounds as possible.     

Cervical screening revisited

Some of the achievements of cervical screening in the reduction of morbidity and mortality in different countries are briefly reviewed, along with a consideration of some of the aspects of cervical cancer screening programs. The latter include the organization of the program (e.g., whether it is organized by the national health authorities), the protection afforded by routine screening, the assurance of quality in cervical sampling and in the screening program, the screening interval, the age groups to be screened, the compliance of women to present themselves for screening and of health care personnel to provide appropriate follow-up and/or treatment for the lesions diagnosed, the problem of false positives and its relation to overdiagnosis and overtreatment and, finally, the cost effectiveness. It is concluded that a centrally organized and well supervised cervical screening program, cautiously executed and with all involved parties closely cooperating, can be a cost-effective means of combatting cervical cancer.     

噬菌体cDNA文库筛选方法的改良

cDNA文库的构建和简便、快速的筛选是获得全长基因的重要途径,基于PCR的筛库方法具有快捷、灵敏的特点。研究改进了基于PCR的噬菌体cDNA文库筛选方法,用液体分装的方法,替代了文库筛选的关键步骤——涂板分区,省去了噬菌体文库铺平板、浸染、培养、划块洗脱的操作过程,使筛库的工作量减少,进一步提高了筛选速度和获得阳性克隆的效率。     

Screening for cancer.

Screening has proved effective for only two cancer sites, the breast and the cervix uteri. Only for these, therefore, should screening be a part of routine clinical practice. The degree to which screening is effective depends on whether appropriate groups are screened. For cancer of the breast, current evidence justifies mammographic screening every two years only from the age of 50, continuing at least to the age of 70. The place of breast self-examination and physical examination of the breasts is under investigation, but these procedures should probably be used in all women after the age of 40. For cancer of the cervix, nearly maximal efficacy is obtained by screening sexually active women every three years from the age of 25 to 60. Older women who have not been screened regularly should be screened. Other screening techniques to detect cancers, such as the rectal examination, sigmoidoscopy, and fecal occult blood tests for colorectal cancer, are still experimental. Organizational and other difficulties will prevent screening programs from making a major contribution to reducing overall cancer mortality by the year 2000. If organizational problems can be overcome, however, screening may control invasive cancer of the cervix and make a major contribution in reducing breast cancer mortality in the future.     

A novel design for estimating relative accuracy of screening tests when complete disease verification is not feasible

The accuracy (sensitivity and specificity) of a new screening test can be compared with that of a standard test by applying both tests to a group of subjects in which disease status can be determined by a gold standard (GS) test. However, it is not always feasible to administer a GS test to all study subjects. For example, a study is planned to determine whether a new screening test for cervical cancer ("ThinPrep") is better than the standard test ("Pap"), and in this setting it is not feasible (or ethical) to determine disease status by biopsy in order to identify women with and without disease for participation in a study. When determination of disease status is not possible for all study subjects, the relative accuracy of two screening tests can still be estimated by using a paired screen-positive (PSP) design in which all subjects receive both screening tests, but only have the GS test if one of the screening tests is positive. Unfortunately in the cervical cancer example, the PSP design is also infeasible because it is not technically possible to administer both the ThinPrep and Pap at the same time. In this article, we describe a randomized paired screen-positive (RPSP) design in which subjects are randomized to receive one of the two screening tests initially, and only receive the other screening test and GS if the first screening test is positive. We derive maximum likelihood estimators and confidence intervals for the relative accuracy of the two screening tests, and assess the small sample behavior of these estimators using simulation studies. Sample size formulae are derived and applied to the cervical cancer screening trial example, and the efficiency of the RPSP design is compared with other designs.     

Predicting the Mortality Benefit of CT Screening for Second Lung Cancer in a High-Risk Population

Patients who survive an index lung cancer (ILC) after surgical resection continue to be at significant risk for a metachronous lung cancer (MLC). Indeed, this risk is much higher than the risk of developing an ILC in heavy smokers. There is currently little evidence upon which to base guidelines for screening at-risk patients for MLC, and the risk-reward tradeoffs for screening this patient population are unknown. The goal of this investigation was to estimate the maximum mortality benefit of CT screening for MLC. We developed a computational model to estimate the maximum rates of CT detection of MLC and surgical resection to be expected in a given population as a function of time after resection of an ILC. Applying the model to a hypothetical high-risk population suggests that screening for MLC within 5 years after resection of an ILC may identify only a very small number of treatable cancers. The risk of death from a potentially resectable MLC increases dramatically past this point, however, suggesting that screening after 5 years is imperative. The model also predicts a substantial detection gap for MLC that demonstrates the benefit to be gained as more sensitive screening methods are developed.     

Critical assessment of the automated AutoDock as a new docking tool for virtual screening

A major problem in virtual screening concerns the accuracy of the binding free energy between a target protein and a putative ligand. Here we report an example supporting the outperformance of the AutoDock scoring function in virtual screening in comparison to the other popular docking programs. The original AutoDock program is in itself inefficient to be used in virtual screening because the grids of interaction energy have to be calculated for each putative ligand in chemical database. However, the automation of the AutoDock program with the potential grids defined in common for all putative ligands leads to more than twofold increase in the speed of virtual database screening. The utility of the automated AutoDock in virtual screening is further demonstrated by identifying the actual inhibitors of various target enzymes in chemical databases with accuracy higher than the other docking tools including DOCK and FlexX. These results exemplify the usefulness of the automated AutoDock as a new promising tool in structure-based virtual screening.