A systematic review of the methodological quality of economic evaluations in genetic screening and testing for monogenic disorders

PurposeUnderstanding the value of genetic screening and testing for monogenic disorders requires high-quality, methodologically robust economic evaluations. This systematic review sought to assess the methodological quality among such studies and examined opportunities for improvement.MethodsWe searched PubMed, Cochrane, Embase, and Web of Science for economic evaluations of genetic screening/testing (2013-2019). Methodological rigor and adherence to best practices were systematically assessed using the British Medical Journal checklist.ResultsAcross the 47 identified studies, there were substantial variations in modeling approaches, reporting detail, and sophistication. Models ranged from simple decision trees to individual-level microsimulations that compared between 2 and >20 alternative interventions. Many studies failed to report sufficient detail to enable replication or did not justify modeling assumptions, especially for costing methods and utility values. Meta-analyses, systematic reviews, or calibration were rarely used to derive parameter estimates. Nearly all studies conducted some sensitivity analysis, and more sophisticated studies implemented probabilistic sensitivity/uncertainty analysis, threshold analysis, and value of information analysis.ConclusionWe describe a heterogeneous body of work and present recommendations and exemplar studies across the methodological domains of (1) perspective, scope, and parameter selection; (2) use of uncertainty/sensitivity analyses; and (3) reporting transparency for improvement in the economic evaluation of genetic screening/testing.     

全身性遗传疾病对角膜移植排斥的影响

角膜移植为治疗角膜盲的主要手段，而角膜移植排斥则是决定角膜植片存活时间和病人术后视力的关键。角膜得益于其特殊的眼前节“免疫赦免”状态，使得角膜移植能够在众多器官移植中享有极低的排斥率，然而排斥反应发生的风险依然存在。当机体处于遗传物质异常的特殊状态时，宿主将通过宏观调控“免疫赦免”状态对植片的保护作用或受体对移植物排异产生的有害作用，延迟或促进角膜移植排斥反应的发生，进而影响移植物的存活时间和透明度。该文综述与角膜移植排斥相关的多种全身性遗传疾病，总结全身性遗传疾病对角膜移植排斥的影响，浅析其发生的病理生理学机制以及诊疗的特殊性。     

Deciphering the molecular landscape of microcephaly in 87 Indian families by exome sequencing

Microcephaly is a frequent feature of neurodevelopmental disorders (NDDs). Our study presents the heterogeneous spectrum of genetic disorders in patients with microcephaly either in isolated form or in association with other neurological and extra-neural abnormalities. We present data of 91 patients from 87 unrelated families referred to our clinic during 2016–2020 and provide a comprehensive clinical and genetic landscape in the studied cohort. Molecular diagnosis using exome sequencing was made in 45 families giving a yield of 51.7%. In 9 additional families probable causative variants were detected. We identified disease causing variations in 49 genes that are involved in different functional pathways Among these, 36 had an autosomal recessive pattern, 8 had an autosomal dominant pattern (all inherited de novo), and 5 had an X-linked pattern. In 41 probands where sequence variations in autosomal recessive genes were identified 31 were homozygotes (including 16 from non-consanguineous families). The study added 28 novel pathogenic/likely pathogenic variations. The study also calls attention to phenotypic variability and expansion in spectrum as well as uncovers genes where microcephaly is not reported previously or is a rare finding. We here report phenotypes associated with the genes for ultra-rare NDDs with microcephaly namely ATRIP, MINPP1, PNPLA8, AIMP2, ANKLE2, NCAPD2 and TRIT1.     

烟雾病临床分型研究进展

烟雾病（moyamoya disease，MMD）是一种颈内动脉末端及其分支起始处进行性狭窄伴颅底异常血管网形成的脑血管疾病，临床上常将其分为缺血型、出血型和无症状型。随着诊疗技术的进步，对MMD临床分型的流行病学特征认识也在不断发展。在成年患者中，缺血型MMD占有重要地位，无症状型亦呈逐渐增多的趋势。不同临床分型MMD的发病年龄、遗传背景、病理生理机制、侧支血管代偿、受累血管分布及其预后存在显著差异。本文总结了对MMD临床分型流行病学特征认识的历史演变，不同临床分型可能的遗传背景、病理生理机制和影像学表现上的差异，为基于不同临床分型的MMD治疗决策提供新的思路。     

CD44基因多态性与宫颈癌及非小细胞肺癌的相关性

背景与目的：CD44分子是众多肿瘤细胞的标志分子，其表达水平与肿瘤细胞的恶性程度有关。该研究探讨CD44基因中的单核苷酸多态性（single nucleotide polymorphism，SNP）位点与云南汉族人群宫颈癌和非小细胞肺癌（nonsmall cell lung cancer，NSCLC）易感性的相关性。方法：选取了CD44基因中的两个SNP位点rs13347和rs8193，采用TagMan基因分型的方法，分析这两个多态性位点在497例宫颈癌患者和500例健康对照个体以及483例NSCLC患者和471例健康对照个体中的分布特征，并分析CD44基因中的多态性位点与云南汉族人群宫颈癌和NSCLC的相关性。结果：rs13347和rs8193位点等位基因和基因型在宫颈癌组和对照组中的分布频率的差异无统计学意义（P>0.05）。而在NSCLC组和对照组的比较中：rs13347和rs8193位点等位基因在NSCLC组和对照组中的分布频率的差异有统计学意义（P=0.020和P=0.004）；这两个位点基因型在NSCLC组和对照组中分布频率的差异有统计学意义（P=0.027和P=0.020）；其中rs13347位点等位基因C在NSCLC组中的分布频率显著高于对照组，可能是NSCLC发生的风险因素（OR=1.250，95% CI：1.035～1.509），rs8193位点等位基因C在对照组中的分布频率显著高于NSCLC组，可能是NSCLC发生的保护性因素（OR=0.768，95%CI：0.641～0.921）。单倍型分析结果显示，rs13347C-rs8193T和rs13347T-rs8193C在NSCLC组和对照组中的分布频率差异有统计学意义（P=0.003和0.022）；该结果说明单倍型rs13347C-rs8193T可能是云南汉族人群NSCLC发生的风险性因素（OR=1.316，95%CI：1.096～1.579）。结论：CD44基因中的两个SNP位点rs13347和rs8193可能与云南汉族人群宫颈癌发病风险无关，而可能与云南汉族人群NSCLC具有相关性。     

输尿管支架管结壳患者尿液菌群的分布特点

目的探讨输尿管支架管结壳患者尿液菌群的分布特点。方法选取2018年10月至2019年3月在山东省立第三医院、山东大学齐鲁医院、济南市中心医院和济南市济钢医院就诊的35例输尿管支架管置入术后患者。纳入标准:年龄18~65岁;输尿管镜碎石术后留置内支架管4周。排除标准:尿液细菌培养阳性;严重肉眼血尿;近期口服抗生素;存在明显残石患者。本研究采用横断面研究方法(临床研究注册号为ChiCTR1800020025),根据有无支架管结壳将患者分为结壳组23例和无结壳组12例。收集拔管当日患者尿液行细菌16s DNA检测。使用UPARSE、UCHIME和RDP calssifier等软件分析两组患者尿液菌群分布特点,明确两组患者尿液中细菌种类总数、细菌丰度,以及丰度占比较大的细菌类别,比较两组患者尿液细菌种类、数量及细菌丰度的差异,明确结壳组患者尿液中丰度占比较大的细菌菌属。结果两组患者的年龄、性别、体质指数、置管侧别、内支架管型号及结石成分差异均无统计学意义(P>0.05)。16s DNA检测结果显示,结壳组丰度占比>1%的菌属数量为11个,丰度占比>0.01%的菌属数量为74个;无结壳组丰度占比>1%的菌属数量为7个,丰度占比>0.01%的菌属数量为11个,两组丰度占比>1%的菌属数量比较差异有统计学意义(t=5.12,P=0.000)。结壳组中菌属丰度占比前3位分别为乳杆菌属(23.1%)、拟杆菌属(18.8%)和未分级拟杆菌属(17.1%),非结壳组中菌属丰度占比前3位分别是为埃希菌-志贺菌属(32.2%)、肠球菌属(24.9%)和假单胞菌属(18.2%)。两组间差异最大的3种细菌是乳杆菌属(P=0.010),拟杆菌属(P=0.004)和未分级拟杆菌属(P=0.004)。结论支架管结壳患者尿液中细菌种类和数量都明显多于非支架管结壳患者。拟杆菌属细菌在支架管结壳患者尿液中的细菌种类丰度较大。     

基于SSR标记与化学成分构建十堰地区天师栗核心种质库＊

目的 利用筛选出十堰的天师栗中高多态性SSR位点评价天师栗种质资源的遗传多样性，结合有效药用成分含量，构建十堰地区天师栗核心种质库。方法 收集十堰地区114份天师栗种质资源，以七叶树基因组为参考，采用荧光毛细管电泳筛选出高多态性SSR位点，对天师栗种质资源进行遗传多样性分析。利用HPLC测定不同种质干燥娑罗子中七叶皂苷的含量。采用最小距离逐步聚类取样策略（LDSS），根据遗传多样性保留程度初步筛选出核心种质，并对该核心种质与原始种质的遗传多样性参数进行T检验，选择与原种质差异不显著的核心种质为最佳核心种质。结果 筛选出13对高多态性SSR分子标记，遗传多样性评价结果表明十堰地区天师栗种质资源遗传多样性较高，遗传分化较小，存在着较大的基因流，114份种质资源未分为不同的亚群，周家坝和辽叶居群间具有较近的遗传亲缘关系，且周家坝居群娑罗子中的七叶皂苷A及七叶皂苷B含量普遍较高。最终筛选出的核心种质共23份，占总种质资源的20.17%，其中周家坝12份样本、辽叶6份样本、普龄5份样本。结论 将SSR分子标记与主要有效药用成分结合，采用LDSS取样策略构建十堰地区天师栗种质资源核心种质库的方法具有可行性，能够有效的保存与管理天师栗种质资源，也为当地天师栗品种改良、新品种选育研究等提供了研究基础。     

NUDT15 is a key genetic factor for prediction of hematotoxicity in pediatric patients who received a standard low dosage regimen of 6-mercaptopurine

6-Mercaptopurine (6-MP) is commonly used for treatment of acute lymphoblastic leukemia (ALL). The incidence of hematotoxicity caused by this drug is quite high in Asians even using a standard low dosage regimen. The present study was aimed to elucidate the impact of thiopurine S-methyltransferase (TPMT), a nucleoside diphosphate-linked moiety X-type motif 15 (NUDT15), inosine triphosphatase (ITPA) and ATP Binding Cassette Subfamily C Member 4 (ABCC4) polymorphisms on hematotoxicity in pediatric patients who received a standard low starting dose of 6-MP. One hundred and sixty-nine pediatric patients were enrolled and their genotypes were determined. Patients who carried NUDT15¹3 and NUDT15¹2 genotypes were at a 10–15 fold higher risk of severe neutropenia than those of the wild-type during the early months of the maintenance phase. Risk of neutropenia was not significantly increased in patients with other NUDT15 variants as well as in patients with TPMT, ITPA or ABCC4 variants. These results suggest that NUDT15 polymorphisms particularly, NUDT15¹3 and NUDT15¹2, play major roles in 6-MP-induced severe hematotoxicity even when using a standard low dosage of 6-MP and genotyping of these variants is necessary in order to obtain precise tolerance doses and avoid severe hematotoxicity in pediatric patients.     

Lung Cancer Risk in Never-Smokers of European Descent is Associated With Genetic Variation in the 5p15.33 TERT-CLPTM1Ll Region

IntroductionInherited susceptibility to lung cancer risk in never-smokers is poorly understood. The major reason for this gap in knowledge is that this disease is relatively uncommon (except in Asians), making it difficult to assemble an adequate study sample. In this study we conducted a genome-wide association study on the largest, to date, set of European-descent never-smokers with lung cancer.MethodsWe conducted a two-phase (discovery and replication) genome-wide association study in never-smokers of European descent. We further augmented the sample by performing a meta-analysis with never-smokers from the recent OncoArray study, which resulted in a total of 3636 cases and 6295 controls. We also compare our findings with those in smokers with lung cancer.ResultsWe detected three genome-wide statistically significant single nucleotide polymorphisms rs31490 (odds ratio [OR]: 0.769, 95% confidence interval [CI]: 0.722–0.820; p value 5.31 × 10^-16), rs380286 (OR: 0.770, 95% CI: 0.723–0.820; p value 4.32 × 10^-16), and rs4975616 (OR: 0.778, 95% CI: 0.730–0.829; p value 1.04 × 10^-14). All three mapped to Chromosome 5 CLPTM1L-TERT region, previously shown to be associated with lung cancer risk in smokers and in never-smoker Asian women, and risk of other cancers including breast, ovarian, colorectal, and prostate.ConclusionsWe found that genetic susceptibility to lung cancer in never-smokers is associated to genetic variants with pan-cancer risk effects. The comparison with smokers shows that top variants previously shown to be associated with lung cancer risk only confer risk in the presence of tobacco exposure, underscoring the importance of gene-environment interactions in the etiology of this disease.     

Molecular characterization of the 17D-204 yellow fever vaccine

IntroductionThe worldwide use of yellow fever (YF) live attenuated vaccines came recently under close scrutiny as rare but serious adverse events have been reported. The population identified at major risk for these safety issues were extreme ages and immunocompromised subjects. Study NCT01426243 conducted by the French National Agency for AIDS research is an ongoing interventional study to evaluate the safety of the vaccine and the specific immune responses in HIV-infected patients following 17D-204 vaccination. As a preliminary study, we characterized the molecular diversity from E gene of the single 17D-204 vaccine batch used in this clinical study.Materials and methodsEight vials of lyophilized 17D-204 vaccine (Stamaril^®, Sanofi-Pasteur, Lyon, France) of the E5499 batch were reconstituted for viral quantification, cloning and sequencing of C/prM/E region.ResultsThe average rate of virions per vial was 8.68 ± 0.07 log₁₀ genome equivalents with a low coefficient of variation (0.81%). 246 sequences of the C/prM/E region (29–33 per vials) were generated and analyzed for the eight vials, 25 (10%) being defective and excluded from analyses. 95% of sequences had at least one nucleotide mutation. The mutations were observed on 662 variant sites distributed through all over the 1995 nucleotides sequence and were mainly non-synonymous (66%). Genome variability between vaccine vials was highly homogeneous with a nucleotide distance ranging from 0.29% to 0.41%. Average p-distances observed for each vial were also homogeneous, ranging from 0.15% to 0.31%.ConclusionThis study showed a homogenous YF virus RNA quantity in vaccine vials within a single lot and a low clonal diversity inter and intra vaccine vials. These results are consistent with a recent study showing that the main mechanism of attenuation resulted in the loss of diversity in the YF virus quasi-species.