Resampling to Address the Winner's Curse in Genetic Association Analysis of Time to Event

The “winner's curse” is a subtle and difficult problem in interpretation of genetic association, in which association estimates from large‐scale gene detection studies are larger in magnitude than those from subsequent replication studies. This is practically important because use of a biased estimate from the original study will yield an underestimate of sample size requirements for replication, leaving the investigators with an underpowered study. Motivated by investigation of the genetics of type 1 diabetes complications in a longitudinal cohort of participants in the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) Genetics Study, we apply a bootstrap resampling method in analysis of time to nephropathy under a Cox proportional hazards model, examining 1,213 single‐nucleotide polymorphisms (SNPs) in 201 candidate genes custom genotyped in 1,361 white probands. Among 15 top‐ranked SNPs, bias reduction in log hazard ratio estimates ranges from 43.1% to 80.5%. In simulation studies based on the observed DCCT/EDIC genotype data, genome‐wide bootstrap estimates for false‐positive SNPs and for true‐positive SNPs with low‐to‐moderate power are closer to the true values than uncorrected naïve estimates, but tend to overcorrect SNPs with high power. This bias‐reduction technique is generally applicable for complex trait studies including quantitative, binary, and time‐to‐event traits.     

1例罕见的B(A)亚型的鉴定

B(A)亚型是一种罕见的ABO亚型,其分子机制为B等位基因在正常B基因序列的基础上发生单碱基突变,使其具有编码双功能活性酶的能力。B(A)亚型在血清学检测中除表现B抗原特异性外,还表现少量A抗原特异性,从而干扰血型鉴定及配血工作。B(A)型如误定为AB型,输入AB型红细胞可引起溶血性输血反应。国内已报道7个等位基因,其中B(A)02型发生率为0.78/10万。现将报道1例工作中遇到的B(A)O2型。     

Gene mutations and three-dimensional structural analysis in 13 families with severe factor X deficiency

Factor X (FX) deficiency is a rare autosomal recessive disorder. The phenotype and genotype of 15 Iranian patients with FX deficiency from 13 unrelated families with a high frequency of consanguinity were analysed. Five different assays identified four patients from three families with a discrepancy between low-FX coagulant activity (FX:C) and higher-FX antigen (FX:Ag) (a type II deficiency). The remaining 11 patients had parallel reductions of FX:C and FX:Ag (a type I deficiency). Nine different homozygous candidate mutations were identified, of which eight were novel. The four type II cases were associated with an Arg(-1)Thr missense mutation in the prepropeptide: Arg(-1) is highly conserved in all vitamin K-dependent proteins. Four type I mutations (Gly78Asp, Cys81Tyr, Gly94Arg and Asp95Glu) were localized to the EGF-1 and EGF-2 domains, for which molecular views showed that the protein folding would be disrupted. The type I mutation Gly222Asp was localized in the catalytic domain of FX, and is sufficiently close to the Asp-His-Ser catalytic triad to disrupt its correct protein folding. The two type I splice site mutations were IVS1+3, A-->T and IVS2-3, T-->G. These novel homozygous FX mutations were consistent with their phenotypes and agree with experimental data from knockout mice, indicating that FX is an essential protein for survival.     

Variability in clinical phenotype of severe haemophilia: the role of the first joint bleed

To quantify variation in clinical phenotype of severe haemophilia we performed a single centre cohort study among 171 severe haemophilia patients. Age at first joint bleed, treatment requirement (i.e. annual clotting factor use), annual bleeding frequency and arthropathy were documented. Because treatment strategies intensified during follow-up, patients were stratified in two age groups: patients born 1968-1985 (n = 91), or 1985-2002 (n = 80). A total of 2166 patient-years of follow-up were available (median 12.0 years per patient). Age at first joint bleed ranged from 0.2 to 5.8 years. Patients who had their first joint bleed later needed less treatment and developed less arthropathy. In patients born 1968-1985 during both on-demand and prophylactic treatment, the 75th percentile of annual joint bleed frequency was consistently four times as high as the 25th percentile. In both age groups variation in annual clotting factor use between 25th and 75th percentiles was 1.4-1.5 times for prophylaxis and 3.8 times for on-demand treatment. To conclude, the onset of joint bleeding is inversely related with treatment requirement and arthropathy and may serve as an indicator of clinical phenotype. Thus, providing a starting point for aetiological research and individualization of treatment.     

儿童混合表型急性白血病15例临床特征分析北大核心CSCD

目的分析儿童混合表型急性白血病(MPAL)的临床特点、治疗及预后, 为临床优化诊疗方案及提高缓解率提供参考。方法基于2016年世界卫生组织(WHO)的诊断标准, 回顾性分析2012年1月至2020年12月苏州大学附属儿童医院收治的15例MPAL患儿的骨髓细胞形态、免疫分型、细胞遗传学、分子生物学特征以及治疗方案、预后等病例资料。计数数据组间比较采用χ^(2)检验, 符合正态分布的计量资料组间比较采用t检验, 非正态分布的计量资料组间比较采用秩和检验。采用Kaplan-Meier(K-M)法估计生存率, 比较应用Log-rank法。结果苏州大学附属儿童医院8年共收治15例MPAL患儿, 男8例, 女7例, 中位年龄为6.8岁;9例患儿表达B淋系+髓系表型, 5例表达T淋系+髓系表型, 1例表达B淋系+T淋系表型;11例患儿进行了染色体核型检查, 2例为正常核型, 2例为复杂核型, 6例为假二倍体, 1例为亚二倍体;5例患儿检测到融合基因, 其中3例AML-ETO阳性, 1例BCR-ABL阳性, 1例MLL阳性;13例患儿在化疗后完全缓解, 总完全缓解率为86.6%, 2年总生存率为(68.2±13.4)%。15例患儿中14例授受了诱导化疗, 1例因个人原因放弃了治疗。首选急性淋巴细胞白血病(ALL)化疗方案10例, 第1个疗程完全缓解1例, 总完全缓解率10%;首选急性髓系白血病(AML)化疗方案4例, 第1个疗程完全缓解3例, 总完全缓解率75%, 未缓解的1例更换ALL方案后缓解;8例行造血干细胞移植(HSCT)和6例未行HSCT组2年总生存率分别为(70.0±18.2)%、(66.7±19.2)%, 差异无统计学意义(χ^(2)=0.318, P=0.573)。结论儿童MPAL是一种罕见的恶性肿瘤, 以淋系和髓系抗原共表达为主, 单纯化疗或HSCT在短期内均可获得较好的预后, 但长期疗效还有待进一步观察。     

早产儿支气管肺发育不良的表型演变

支气管肺发育不良(bronchopulmonary dysplasia,BPD)是早产儿最常见的慢性肺部疾病,与婴儿死亡率、呼吸系统发病率增加有关。随着新生儿重症医学取得进展的同时,BPD的表型已从主要影响晚期早产儿、肺纤维囊性变演变为主要影响胎龄小于28周的超早产儿、肺实质受损和血管生长失调。文章评估了BPD定义演变、病理生理演变、影像演变及临床表型的演变特点,以期寻找新的循证预防和管理策略,改善疾病表型分类,早期识别高危早产儿的临床特点,以改善其预后。     

Genetic variants of alpha-1-antitrypsin (AAT)

Abstract: This paper reviews the genetic variants of alpha-1-antitrypsin (AAT) which have been sequenced with special emphasis on the s.c. deficiency variants. These result in AAT low plasma levels via three main mechanisms: 1) intracellular storage; 2) intracellular degradation; 3) lack of synthesis. Intracellular storage occurs with the classical Z variant and with a few variants called M-like, because of their isoelectric focusing (IF) pattern. The storage phenomen causes liver damage and can be demonstrated at both light and electron microscopic level with the help of immuno-histochemistry. We report a new deficiency variant of AAT (M-Cagliari) characterized by very low plasma levels, massive storage of AAT and liver cirrhosis. By using immunohistochemical techniques and DNA analysis we could demonstrate that M-Cagliari has antigenic and genetic properties other than the Z AAT.     

Genetic analysis of radiation-associated rectal cancer

Genetic aberrations in radiation-associated colorectal cancer have not been studied in detail. We analyzed genetic aberrations in five rectal cancers that developed long after radiotherapy had been performed for cervical cancer. Microsatellite instability (MSI) in tumors was examined at five loci: D2S123, D3S966, TP53, DCC, and BAT26. Mutation of simple repeat sequences within the hMSH3, BAX, and transforming growth factor type II receptor (TGFRII) genes was examined by polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP). Mutation of p53 exons 5–8 was examined by PCR-SSP and direct sequencing. Mutations of the K-ras gene were analyzed by two-step PCR. No MSI was found in tumor specimens at any of the loci examined, and no mutations in the target genes were observed. K-ras mutation was detected in two carcinomas, but not in their irradiated normal mucosa, while p53 mutation was observed in another two carcinomas, but not in their irradiated normal mucosa. Our results suggest that the radiation-associated rectal carcinomas examined in this study did not develop through the mutator phenotype pathway; rather, tumorigenesis was probably mediated through the multistep carcinogenesis pathway.     

Proposed Stages of Myocardial Phenotype Development in Fabry Disease

ObjectivesThis study sought to explore the Fabry myocardium in relation to storage, age, sex, structure, function, electrocardiogram changes, blood biomarkers, and inflammation/fibrosis.BackgroundFabry disease (FD) is a rare, x-linked lysosomal storage disorder. Mortality is mainly cardiovascular with men exhibiting cardiac symptoms earlier than women. By cardiovascular magnetic resonance, native T1 is low in FD because of sphingolipid accumulation.MethodsA prospective, observational study of 182 FD (167 adults, 15 children; mean age 42 ± 17 years, 37% male) who underwent cardiovascular magnetic resonance including native T1, late gadolinium enhancement (LGE), and extracellular volume fraction, 12-lead electrocardiogram, and blood biomarkers (troponin and N-terminal pro-brain natriuretic peptide).ResultsIn children, T1 was never below the normal range, but was lower with age (9 ms/year, r = −0.78 children; r = −0.41 whole cohort; both p < 0.001). Over the whole cohort, the T1 reduction with age was greater and more marked in men (men: −1.9 ms/year, r = −0.51, p < 0.001; women: −1.4 ms/year, r = −0.47 women, p < 0.001). Left ventricular hypertrophy (LVH), LGE, and electrocardiogram abnormalities occur earlier in men. Once LVH occurs, T1 demonstrates major sex dimorphism: with increasing LVH in women, T1 and LVH become uncorrelated (r = −0.239, p = 0.196) but in men, the correlation reverses and T1 increases (toward normal) with LVH (r = 0.631, p < 0.001), a U-shaped relationship of T1 to indexed left ventricular mass in men.ConclusionsThese data suggest that myocyte storage starts in childhood and accumulates faster in men before triggering 2 processes: a sex-independent scar/inflammation regional response (LGE) and, in men, apparent myocyte hypertrophy diluting the T1 lowering of sphingolipid.     

胃癌浸润性淋巴细胞的细胞表型及杀伤活性

目的和方法：本实验用９例胃癌患者ＴＩＬ和ＩＬ２在体外共同孵育后，用流式细胞仪分析胃癌ＴＩＬ的细胞表型特征。结果：ＴＩＬ细胞表型特征是以ＣＤ３为主，ＣＤ４／ＣＤ８为０８３，ＮＫ细胞１６３±３６％。经白细胞介素２（ＩＬ２）激活２０天后，ＣＤ３减少，ＣＤ４／ＣＤ８为１８５，ＮＫ细胞数量增至４１３±１３７％，Ｐ＜００１。ＬＤＨ释放法测定激活后的ＴＩＬ对自体胃癌细胞杀伤率比培养初期高３７４倍，变比对同时培养的７９０１胃癌细胞杀伤率高１７５倍。对自体和异体胃癌细胞杀伤作用均显著高于ＬＡＫ细胞，且具有靶细胞特异性。结论：结果表明胃癌ＴＩＬ对胃癌细胞杀伤作用，可能与ＮＫ细胞数量增多，导致胃癌细胞凋亡有关