云平台解决方案应用于流感监控 - thermofisher.com · chinese center for disease control...
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
云平台解决方案应用于流感监控
赵翔
世界卫生组织全球流感参比和研究合作中心国家流感中心
中国疾病预防控制中心病毒病预防控制所2016
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
Start influenza surveilla
nce
Chinese National Influenza
Center
Became a member of
WHO Global
Influenza Surveillan
ce Network
NISN(8network
laboratories /31 sentinel hospitals)
was established
NISN(63
network laboratories
/197 sentinel
hospitals) was
extended
NISN(411
network laboratories
/556 sentinel
hospitals) was
extended further
WHO CC
History of CNIC
1947 1979 2005
1957 2000 2009
2010
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
发展中国家唯一全球第五个
WHO流感参比和研究合作中心
WHO全球流感监测与应对系统(GISRS)
WHO GISRSWHO GISRS
疫苗监管关键实验室(4家)
疫苗监管关键实验室(4家)
WHO流感参比和研究合作中心(5家)
WHO流感参比和研究合作中心(5家)
141个国家流感中心141个国家流感中心
12个H5参比实验室12个H5参比实验室
WHO动物流感生态学研究中心(1家)
WHO动物流感生态学研究中心(1家)
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
建立了覆盖全国的流感监测网络
411 network labs556 sentinel hospitals
63 network labs197 sentinel hospitals
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
666 total cases/392 fatal
A(H5N1) 人感染病例A(H5N1) 人感染病例
Feb Mar Apr May Jun Jul
Cambodia
FatalChinaEgypt
Indonesia
Aug Sep
H5N1
2005
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
5.10
四川省疾控检测核酸阳性,报疑似病例
5.11
国家流感中心复核阳性
5.17
分离到我国第一株甲流病毒
5.18
获得我国第一株甲流全基因组序列
5.22
序列提交GenBank
GSAID
大陆第一次甲型H1N1流感病例的发现
2009
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
• Excellent performance in the H7N9 control program
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
Timely identification of human infection with novel H7N9 viruses
3.24 Sample from Shanghai
3.25A/H7positive
3.26Sample from Anhui
3.28H7N9 Virus isolated
3.29Full genome Sequence
Gao R et al NEJM J 2013
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
建设深度测序能力
宏基因组学
病原鉴定
进化分析
耐药性分析
指导临床
Next generation Sequencing (NGS)
+
+
四套深度测序平台,两套一代测序平台,两套数据分析系统
为全国流感网络实验室和周边国家提供测序技术指导
24小时完成流感病毒全基因组测序及未知样本宏基因组的病原谱筛查
测序病毒数量提升10倍,测序成本下降10倍
SNP检测灵敏度提升至1%-5%
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
《Clinical and epidemiological characteristics of a fatal case ofavian infl uenza A H10N8 virus infection : a descriptive study》
• Frequency of glutamic acid was 87.6% versus 12.4% for lysine in the sample obtained on day 7, and frequency was 3.3% versus 96.7% on day 9.
Timeline of the clinical course of the patient and identification of causative pathogen
深度测序发现PB2的第627位的杂合突变Glu/Lys,其与病毒感染哺乳动物相关;在治疗过程中,Lys的突变比例增高对应其逐渐增强的毒力
2014
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
Human infection with avian influenza A(H5N6)
H5N1 H6N6
H5N6
Pan M, et al. J Infect, 2015.
Pan et al. J Infect. 2015
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
测序发展
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
测序成本VS测序数据量
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
高通量测序数据分析面临的问题
1. 软件选择
2. 分析效率不高
3. 分析流程中多软件衔接难
4. 各软件资源使用特征差异大
5. 缺少生物信息学的人员
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
思路的转换
• 专业的事交给专业的人
• 分而治之算法
• 减少计算投入成本,加快应用推广
• 化繁为简
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
NGS运用于病原体诊断的意义
致病性病原体的识别对于传染性疾病、病毒学和公共健康具有重要意义。
过去几十年中大规模的疾病爆发几乎都是由病毒引起的,包括SARS和埃博拉病毒。
传染病的精确诊断和及时治疗能够显著地降低持续的传染风险。
降低住院病人死亡率。
二代测序技术通过识别样本基因序列广泛地用于检测临床样本中的病毒、细菌和寄生虫。
识别病原体
精确诊断 公众健康
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
现有分析流程
寄送数据 (2~3工作日)
传统运输数据的方式为快递硬盘
硬盘存储数据的安全性问题
数据分析(8小时)
购买高配服务器
购买大量硬盘存储数据
自行维护计算设备
计算资源无法控制,要么资源不足,
要么资源浪费
10 min
10 min 10 min 10 min 48 hours 10 min
30 min8 hours30 min 8 hours 2 hours
可以改进的空间
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
什么是云计算
• 云计算是通过使计算分布在大量的分布式计算机上,而非本地计算机或远程服务器。
• 好比是从古老的单台发电机模式转向了电厂集中供电的模式。它意味着计算能力也可以作为一种商品进行流通,就像煤气、水电一样,取用方便,费用低廉。
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
利用云计算分析流感病毒
无限存储
强大的可扩展的计算能力
定制化分析算法
随时随地跨区域访问
任何操作都安全可靠
直观的用户体验
自动化上传、分析流程 大数据极速分析
直观的用户界面及数据可视化
易于数据分享及合作
存储及管理海量数据集
云计算的特点
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
云计算解决方案
解决数据运输问题 解决分析速度问题 解决分析算法问题
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
分析workflow
FastQ
Trim
QC报告
DenovoDebujin
OLCblast
Mapping1(vote)
Mapping2(mapping1产生的reference)
Consensus,位点注释等信息
Unmap reads
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
FluCloud系统演示 —主页
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
建立分析流程
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
上传文件至云端
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
查询分析结果
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
下载分析结果
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
资源统计
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
更简单的分析方式
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
自动上传配置
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
• Journal of infection :Aeromonas was identified in blood sample of a fatal case from Western Africa
• Hong Zhang†1, Xiaohui Zou2†, Xiang Zhao2, Liang Cai1, Wenbing Chen2, Lei Yang2, Fuqiang Liu1, Di Qin1, Ge Zeng1, Tian Bai2, Wenfei
Zhu2, Dayan Wang2, Yuelong Shu2*, Lidong Gao1*• To investigate the potential causes of the patient death, we used next generation sequencing
(NGS) with the remaining 8 μl RNA extracted from the blood sample. Approximately 5 μl of RNA was subjected to random reverse-transcription, followed by SPIA amplification using an Ovation RNA-Seq System V2 (NuGEN, San Carlos, CA, USA) and sequenced on an Ion Torrent PGM platform (Life Technologies, New York,USA) with a sequence length of 400bp.
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
不明原因肺炎
不明原因肺炎
病毒/新发病毒
细菌
耐药性
发热。
肺炎影像学特征。
发病早期白细胞数目降低或正常,或淋巴细胞分类计数减少。
使用规范性的抗生素治疗无效。
Real–time PCR
分离培养
药敏试验
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
链球菌, 普氏菌属是主要
的菌群。
部分样本含有比例超高的
不动杆菌。
17份不明原因肺炎咽拭子DNA测序后宏基因组学分析
样本中微生物种类分布
Sample ID
Top
21 M
ost A
bund
ant g
ener
a
Rarefaction analysis
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
Sample ID
样本中微生物种类分布R
elat
ive
frequ
ency
不动杆菌属主要
是鲍曼不动杆菌,
在其中两份样本(
CN04, 21)中的
Reads > 90% 。
链球菌在4份样本
中的Reads比率
>75%。
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
耐药性基因分析
# 所有耐药性基因覆盖区域 ≥70%,匹配的Reads数目 ≥ 1/(100k)Clean reads。
* MLS:Macrolide−lincosamide−streptogramin B
与耐药性数据CARD比对后,发现15/17的样本含有至少两种耐药性基因。
Beta-lactam, Tetracycline, Macrolide 是主要的耐药抗生素。
Antibiotic# CN01 CN04 CN05 CN16 CN19 CN20 CN21 CN22 CN23 CN25 CN26 CN27 CN29 CN30 CN33 TotalBeta-lactam 15.36 14.12 13.52 4.40 23.64 9.35 11.3 23.54 25.27 20.67 35.15 2.97 8.13 24.75 232.17Tetracycline 38.03 35.9 12.96 29.77 15.18 12.2 33.93 30.12 35 40.57 27.69 2.06 5.23 63.81 382.45Macrolide 17.55 14.42 2.29 9.03 13.09 15.58 5.41 4.74 21.81 5.78 109.7MLS* 10.62 3.91 6.17 3.71 15.35 17.09 56.85Lincomycin 2.75 3.08 5.64 1.9 2.81 3.29 3.04 4.94 27.45Acriflavine 71.5 31.55 103.05Ciprofloxacin 3.82 6.02 9.84Multidrug(Efflux) 259.5 163.52 8.74 27.57 6.44 465.77Aminoglycosides 4.12 6.35 4.93 1.38 123.8 140.61Sulfonamide 2.35 1.14 3.49Quinolone 2.72 2.72Streptogramins 3.33 11.95 15.28Chloramphenicol 4.4 1.23 5.63
81.56 405.7 18.56 16.04 52.17 40.72 242.08 52.97 69.24 81.62 75.19 94.68 173.9 31.43 119.1 1555.01
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
Streptoccus 耐药性分析
CN23
CN25
CN27
CN33
对每个样本中匹配的
Reads 归类到各个微生
物属的水平。
Streptococcus 比例很高
的4份样本中(>75%)
,Streptococcus 包含了
>90% 的耐药性Reads。
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
Acinetobacter 耐药性分析
同样的,在 Acinetobacter 比例异常高(>95%)的两份样本CN04 和CN21
中,其耐药性基因相关Reads 几乎全部来自 A. baumannii(>99%)。
CN04
CN21
含有耐药基因比例高的微生物,在样本中的比例也最高。
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
Full-automatic nucleic acid extraction
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
High-throughput qRT-PCR
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
Sequencing machines
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
纳米孔测序仪Mimion
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
全套设备
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
测序原理
• 核心科技为蛋白纳米孔
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
当加入电流后DNA分子单链顺序通过纳米孔,每一种碱基由于分子结构不同产生的电阻信号也不同,以此就可以区分读出碱基的顺序
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
无数个纳米孔被集成在一张石墨烯做成的芯片上,每张芯片上有512个纳米孔,可以同时进行测序
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
每次只需更换内部的流动槽
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
适用于不同的通量
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
Fighting-ebola campaign
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
Danger VS Responsibility
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
The closest contact with Ebola virus
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
Large scale of genome sequencing
More genome data, more accurate prediction!
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CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION
谢 谢