全基因组与外显子组测序的应用评估

随着新一代测序技术的不断成熟完善,人类基因组和外显子组测序得到了迅猛发展。测序技术的高通量性致使测序价格越来越低廉,使全基因组和外显子组测序真正用于临床诊断成为现实。作为医学预测和个体化医疗的重要工具之一,全基因组和外显子组测序应用范围广泛,该文针对其在遗传性疾病基因变异中的诊断进行讨论,同时为临床医生如何申请测序,测序报告解释,以及如何与患者沟通检测结果提供了新视角。     

基于全外显子组测序技术的遗传性血液病分子诊断技术体系

目的 探讨通过全外显子组测序技术建立遗传性血液病的分子诊断技术体系.方法 选择2013年6月至2014年3月于上海交通大学医学院附属上海儿童医学中心就诊的临床表现不典型,但高度怀疑为遗传性血液病的3例患者为研究对象.通过全外显子组测序技术筛选3例患者的候选致病基因的突变位点,并采用基于毛细管电泳技术的Sanger法测序和家系分析对其突变位点进行验证.结果 通过全外显子组测序技术发现了3例患者相应的遗传学损伤,并采用Sanger法对患者及其父母的致病基因位点的测序进行验证,验证结果与患者的遗传学损伤相符,每例患儿均获得了明确的分子诊断结果.结论 在遗传性血液病的分子诊断中,全外显子组测序是候选基因靶向测序的重要补充,且在一定程度上可提高疾病的诊断符合率.     

应用下一代测序技术对α地中海贫血进行胚胎植入前遗传学检测

目的 探讨下一代测序(next generation sequencing,NGS)技术在α地中海贫血胚胎植入前遗传学检测中的应用. 方法 选取2对α地中海贫血--SEA缺失型携带者夫妇体外受精胚胎活检后的6个胚胎样本应用全基因组扩增(whole genome amplification,WGA)技术、下一代测序技术进行胚胎植入前遗传学检测,同时采用跨越断裂点荧光PCR(gap-PCR)进行平行对照检测. 结果 2个家系6个胚胎样本的胚胎植入前遗传学诊断(preimplantation genetic diagnosis,PGD)结果分别为--SEA/αα母源携带、--SEA/--SEA、--SEA/αα母源携带、--SEA/--SEA、--SEA/αα母源携带和--SEA/--SEA;胚胎植入前遗传学筛查(preimplantation genetic screening,PGS)结果分别为45,XX,-5、46,XX、46,XY、47,XY,+1、46,XX和46,XY,+1,-2;Family 1 gap-PCR检测结果为父母均为SEA杂合子;E1为正常、E2为SEA纯合子、E3为正常;Family 2检测结果分别为:父母均为SEA杂合子;E4为SEA纯合子、E5为正常、E6为SEA纯合子. 结论 结果显示利用NGS不仅可以检测出23对染色体的核型,同时解决了单细胞扩增等位基因脱扣(allele drop-out,ADO)造成的假阳性和假阴性的风险,更具有市场潜力及应用前景.     

下一代测序技术在遗传病临床检测中的应用

DNA测序技术已广泛应用于生物学研究,很多生物学问题也都可以借助测序技术予以解决.过去10年(2005-2015年),下一代测序技术(next generation sequencing,NGS)逐步从新技术成长为主流的测序技术,并逐渐走进临床诊断领域.NGS以其简单、快速、高分辨率、高通量的特点,在传染性疾病防控、肿瘤的早诊早治、遗传病的早期筛查和诊断、无创产前筛查、胚胎植入前诊断和筛查等领域发挥越来愈大的作用,已成为目前临床领域最具有应用前景的技术之一.同时下一代测序技术领域仍在快速发展,新的测序技术及数据分析技术还在不断涌现,序列数据库和测序数据快速增加.下一代测序技术也有助于以更低廉的价格,更全面、更深入地来分析基因组、转录组及蛋白质相互作用组的各项数据.可以预见,各种测序将成为一项广泛使用的常规实验手段,有望给生物医学研究领域和医学临床诊断带来革命性的变革.本文主要针对下一代测序技术在无创产前诊断、遗传病检测、胚胎植人前诊断和筛查中的临床应用进行介绍和评述.     

新一代高通量测序技术——检验医学发展的挑战与机遇

基因突变以及碱基修饰等可以导致相关疾病的发生发展.个体的基因型也影响个人罹患相关疾病的风险和药物代谢率.随着数据的积累,越来越多与疾病相关的基因突变被发现,DNA测序在疾病预测、诊断、个体化用药等方面显得日益重要.测序技术在短短的数十年间,取得了惊人的进步,从Sanger法为代表的第一代测序技术发展到了第三代高通量测序...     

美国神经病学协会的循证医学指南:横贯性脊髓炎的临床评估和治疗——美国神经病学会治疗与技术评价委员会

横贯性脊髓炎(TM)是脊髓的炎性损害,年发病率为百万分之一(重症)到百万分之八(轻症)。TM常有脊髓磁共振信号的异常和(或)脑脊液细胞的增多。在2002年专家共识已提出典型TM的诊断/排除标准(表1):累及脊髓多个节段,但并不是影像学或病理学的横贯性损害,仍保留"横贯性"是因为脊髓感觉传导通路损害平面对定位诊断的意义。本指南旨在回答下述临     

涉及人的生物医学研究伦理问题——伦理委员会的建设与运作国际研讨会暨上海市医学伦理学会第十三次年会于2009年12月11—12日在上海隆重召开

会议南上海医药临床研究中心、上海市医学伦理学会、上海交通大学医学院附属瑞金医院联合举办．由上海交通大学医学院终身教授、上海医药临床研究中心独立伦理委员会主任委员、上海市医学伦理专家委员会主任、卫生部医学伦理专家委员会委员、联合国教科文组织国际生命伦理委员会委员、前世界卫生组织副总干事、     

Advances in clinical next-generation sequencing: target enrichment and sequencing technologies

The huge parallel sequencing capabilities of next generation sequencing technologies have made them the tools of choice to characterize genomic aberrations for research and diagnostic purposes. For clinical applications, screening the whole genome or exome is challenging owing to the large genomic area to be sequenced, associated costs, complexity of data, and lack of known clinical significance of all genes. Consequently, routine screening involves limited markers with established clinical relevance. This process, referred to as targeted genome sequencing, requires selective enrichment of the genomic areas comprising these markers via one of several primer or probe-based enrichment strategies, followed by sequencing of the enriched genomic areas. Here, the authors review current target enrichment approaches and next generation sequencing platforms, focusing on the underlying principles, capabilities, and limitations of each technology along with validation and implementation for clinical testing.     

Keeping up with the next generation: massively parallel sequencing in clinical diagnostics

The speed, accuracy, efficiency, and cost-effectiveness of DNA sequencing have been improving continuously since the initial derivation of the technique in the mid-1970s. With the advent of massively parallel sequencing technologies, DNA sequencing costs have been dramatically reduced. No longer is it unthinkable to sequence hundreds or even thousands of genes in a single individual with a suspected genetic disease or complex disease predisposition. Along with the benefits offered by these technologies come a number of challenges that must be addressed before wide-scale sequencing becomes accepted medical practice. Molecular diagnosticians will need to become comfortable with, and gain confidence in, these new platforms, which are based on radically different technologies compared to the standard DNA sequencers in routine use today. Experience will determine whether these instruments are best applied to sequencing versus resequencing. Perhaps most importantly, along with increasing read lengths inevitably comes increased ascertainment of novel sequence variants of uncertain clinical significance, the postanalytical aspects of which could bog down the entire field. But despite these obstacles, and as a direct result of the promises these sequencing advances present, it will likely not be long before next-generation sequencing begins to make an impact in molecular medicine. In this review, technical issues are discussed, in addition to the practical considerations that will need to be addressed as advances push toward personal genome sequencing.     

下一代测序技术在分子诊断中的应用

DNA测序是破译人类疾病的一种强大技术,尤其在癌症方面。飞速发展的下一代测序（next—generation sequencing,NGS）极大降低了测序成本,并且实现了高通量,这使我们可以获得整个基因组的序列,以及那些临床上确诊病人的全部基因组信息。然而下一代测序技术带来诸多益处的同时也带来了挑战,那就是怎样使这个技术在临床诊断中成为常规手段。本文就目前NGS的几大技术平台原理,在临床诊断中的应用,以及目前面临的挑战等进行综述。     

A reference method laboratory network for cholesterol: a model for standardization and improvement of clinical laboratory measurements

BACKGROUND: Accurate and precise measurement of blood cholesterol plays a central role in the National Cholesterol Education Program's strategy to reduce the morbidity and mortality attributable to coronary heart disease. Matrix effects hamper the ability of manufacturers to adequately calibrate and validate traceability to the National Reference System for Cholesterol (NRS/CHOL). CDC created the Cholesterol Reference Method Laboratory Network (CRMLN) to improve cholesterol measurement by assisting manufacturers of in vitro diagnostic products with validation of the traceability of their assays to the NRS/CHOL. METHODS: CRMLN laboratories established the CDC cholesterol reference method (modification of the Abell-Levy-Brodie-Kendall chemical method) and are standardized using CDC frozen serum reference materials. CRMLN laboratories use common quality-control materials and participate in monthly external performance evaluations conducted by CDC. The CRMLN performance criteria require member laboratories to agree with CDC within +/-1.0% and maintain a CV < or =2.0%. RESULTS: From 1995 to 200 the CRMLN laboratories met the accuracy criterion 97% of the time and the precision criterion 99% of the time. During this time period, the CRMLN maintained an average bias to CDC of 0.01% and an average collective CV of 0.33%. CONCLUSIONS: CDC established the CRMLN as the first international reference method laboratory network. The CRMLN assists manufacturers in the validation of the calibration of their diagnostic products so that clinical laboratories can measure blood cholesterol more reliably. The CRMLN can serve as a model for other clinical analytes where traceability to a hierarchy of methods is needed and matrix effects of the field methods with processed calibrators or reference materials are present.     

二代测序技术在儿童T淋巴母细胞淋巴瘤全外显子测序中的应用

目的建立从石蜡包埋的儿童T淋巴母细胞淋巴瘤（T-LBL）病理组织中提取基因组DNA,采用二代测序技术行全外显子测序检测的方法并分析其可行性。方法从10例儿童T-LBL石蜡包埋组织中提取基因组DNA,PCR反应扩增后采用二代测序技术行全外显子测序检测并确定致病位点,所获得的致病突变采用Sanger测序法测序确认,比较两种方法的一致性。结果10例石蜡包埋T-LBL组织标本中均成功提取到基因组DNA,采用二代测序技术开展全外显子测序测序均检测到致病突变;二代测序检测结果经Sanger测序法验证,证实致病突变确实存在,且与Sanger测序结果一致。结论基于二代测序技术的全外显子测序测序可用于检测石蜡包埋的儿童T-LBL病理标本的致病突变。     

The clinical implementation of copy number detection in the age of next-generation sequencing

Introduction: The role of copy number variants (CNVs) in disease is now well established. In parallel NGS technologies, such as long-read technologies, there is continual development and data analysis methods continue to be refined. Clinical exome sequencing data is now a reality for many diagnostic laboratories in both congenital genetics and oncology. This provides the ability to detect and report both SNVs and structural variants, including CNVs, using a single assay for a wide range of patient cohorts.

Areas covered: Currently, whole-genome sequencing is mainly restricted to research applications and clinical utility studies. Furthermore, detecting the full-size spectrum of CNVs as well as somatic events remains difficult for both exome and whole-genome sequencing. As a result, the full extent of genomic variants in an individual’s genome is still largely unknown. Recently, new sequencing technologies have been introduced which maintain the long-range genomic context, aiding the detection of CNVs and structural variants.

Expert commentary: The development of long-read sequencing promises to resolve many CNV and SV detection issues but is yet to become established. The current challenge for clinical CNV detection is how to fully exploit all the data which is generated by high throughput sequencing technologies.     

下一代测序技术在胚胎植入前遗传学检测中的应用

以下一代测序技术(next-generation sequencing,NGS)为代表的基因组学技术的迅猛发展给全面深度的染色体筛查和基因诊断提供了机会.NGS也迅速应用于胚胎植入前遗传学诊断(preimplantation genetic diagnosis,PGD)和胚胎植入前遗传学筛查(preimplantation genetic screening,PGS)临床检测中,成为常规检测技术,经济与可靠使其具有更广阔的应用前景.单细胞全基因组扩增(whole genome amplification,WGA)技术的进步使得NGS在PGD和PGS的临床应用中能够更加全面了解植入前胚胎的遗传学信息,可以检测到更加细微的差异;基于NGS技术的PGS和PGD将给移植成功率和试管婴儿(in-vitro fertilization,IVF)出生率带来明显提升.本文主要介绍PGD/PGS的定义、传统的PGD/PGS检测技术,单细胞全基因组扩增技术以及NGS在PGD/PGS中的应用.