健康管理与深度测序数据解析的挑战
|
摘要
介绍深度测序技术对生物医学研究和社会的影响,讨论深度测序数据解析及其在健康管理应用中所面临的挑战和机遇,包括数据存取、计算技术、数据应用、人才缺失与跨学科人才教育等方面。
The paper introduces impact of deep sequencing technology on biomedical research and the society, discusses challenges confronting and opportunities enjoyed by deep sequencing data parsing and its application in health management, including aspects like data access, computing technology, data application, lack of talent and interdisciplinary talent education, etc.
The paper introduces impact of deep sequencing technology on biomedical research and the society, discusses challenges confronting and opportunities enjoyed by deep sequencing data parsing and its application in health management, including aspects like data access, computing technology, data application, lack of talent and interdisciplinary talent education, etc.
引文
1 Stevens H,Dr Sanger,Meet Mr.Moore:next-generation sequencing is driving new questions and new modes of research[J].Bioessays,2012,34(2):103-105.
2 Erlich Y.A Vision for Ubiquitous Sequencing[J].Genome Res,2015,25(10):1411-1416.
3 Mardis E R.Anticipating the 1 000 Dollar Genome[J].Genome Biol,2006,7(7):112.
4 Abbasi J.23andMe,Big Data,and the Genetics of Depression[J].JAMA,2017,317(1):14-16.
5 Hyde C L,Nagle MW,Tian C,et al.Identification of 15 Genetic Loci Associated with Risk of Major Depression in Individuals of European Descent[J].2016,48(9):1031-1036.
6 Akaev A A,Sadovnichiy V A.A Closed Dynamic Model to Describe and Calculate the Kondratiev Long Wave of Economic Development[J].Herald of the Russian Academy of Sciences,2016,86(5):371-383.
7 Wynn J,Chung W K,23andMe Paves the Way for Directto-Consumer Genetic Health Risk Tests of Limited Clinical Utility[J].Ann Intern Med,2017,167(2):125-126.
8沈百荣主编.深度测序数据的生物信息学分析及实例[M].北京:科学出版社,2017.
9 Vayena E,U Gasser.Between Openness and Privacy in Genomics[J].PLoS Med,2016,13(1):e1001937.
10 Wang S,Jiang X,Singh S,et al.Genome Privacy:challenges,technical approaches to mitigate risk,and ethical considerations in the United States[J].Ann N Y Acad Sci,2017,1387(1):73-83.
11 Huang Z,Anday E,Lin H,et al.A Privacy-preserving Solution for Compressed Storage and Selective Retrieval of Genomic data,2016,26(12):1687-1696.
12 Harris M A,Clark J,Ireland A,et al.The Gene Ontology(GO)Database and Informatics Resource[J].Nucleic Acids Res,2004,32(Database issue):D258-61.
13 Kanehisa M,Goto S.KEGG:kyoto encyclopedia of genes and genomes[J].Nucleic Acids Res,2000,28(1):27-30.
14 Cimino J J,Ayres E J,Remennik L,et al.The National Institutes of Health's Biomedical Translational Research Information System(BTRIS):design,contents,functionality and experience to date[J].J Biomed Inform,2014,(52):11-27.
15 Tryka K A,Hao L,Sturcke A,et al.NCBI's Database of Genotypes and Phenotypes:dbGaP[J].Nucleic Acids Res,2014,42(Database issue):975-979.
16 Chute C G,Beck S A,Fisk T B,et al.The Enterprise Data Trust at Mayo Clinic:a semantically integrated warehouse of biomedical data[J].J Am Med Inform Assoc,2010,17(2):131-135.
17 Murphy S N,Weber G,Mendis M,et al.Serving the Enterprise and Beyond with Informatics for Integrating Biology and the Bedside(i2b2)[J].J Am Med Inform Assoc,2010,17(2):124-130.
18 Bhattacharya S,Andorf S,Gomes L,et al.ImmPort:disseminating data to the public for the future of immunology[J].Immunol Res,2014,58(2-3):234-239.
19 Payakachat N,Tilford J M,Ungar W J.National Database for Autism Research(NDAR):Big Data Opportunities for Health Services Research and Health Technology Assessment[J].Pharmacoeconomics,2016,34(2):127-138.
20 Lowe H J,Ferris T A,Hernandez P M,et al.STRIDE-Anintegrated standards-based translational research informatics platform[J].AMIA Annu Symp Proc,2009,(2009):391-395.
21 Tomczak K,P Czerwinska,M Wiznerowicz.The Cancer Genome Atlas(TCGA):an immeasurable source of knowledge[J].Contemp Oncol(Pozn),2015,19(la):A68-77.
22 Clark K.The Cancer Imaging Archive(TCIA):maintaining and operating a public information repository[J].J Digit Imaging,2013,26(6):1045-1057.
23 Wang X.Translational Integrity and Continuity:personalized biomedical data integration[J].J Biomed Inform,2009,42(1):100-112.
2 Erlich Y.A Vision for Ubiquitous Sequencing[J].Genome Res,2015,25(10):1411-1416.
3 Mardis E R.Anticipating the 1 000 Dollar Genome[J].Genome Biol,2006,7(7):112.
4 Abbasi J.23andMe,Big Data,and the Genetics of Depression[J].JAMA,2017,317(1):14-16.
5 Hyde C L,Nagle MW,Tian C,et al.Identification of 15 Genetic Loci Associated with Risk of Major Depression in Individuals of European Descent[J].2016,48(9):1031-1036.
6 Akaev A A,Sadovnichiy V A.A Closed Dynamic Model to Describe and Calculate the Kondratiev Long Wave of Economic Development[J].Herald of the Russian Academy of Sciences,2016,86(5):371-383.
7 Wynn J,Chung W K,23andMe Paves the Way for Directto-Consumer Genetic Health Risk Tests of Limited Clinical Utility[J].Ann Intern Med,2017,167(2):125-126.
8沈百荣主编.深度测序数据的生物信息学分析及实例[M].北京:科学出版社,2017.
9 Vayena E,U Gasser.Between Openness and Privacy in Genomics[J].PLoS Med,2016,13(1):e1001937.
10 Wang S,Jiang X,Singh S,et al.Genome Privacy:challenges,technical approaches to mitigate risk,and ethical considerations in the United States[J].Ann N Y Acad Sci,2017,1387(1):73-83.
11 Huang Z,Anday E,Lin H,et al.A Privacy-preserving Solution for Compressed Storage and Selective Retrieval of Genomic data,2016,26(12):1687-1696.
12 Harris M A,Clark J,Ireland A,et al.The Gene Ontology(GO)Database and Informatics Resource[J].Nucleic Acids Res,2004,32(Database issue):D258-61.
13 Kanehisa M,Goto S.KEGG:kyoto encyclopedia of genes and genomes[J].Nucleic Acids Res,2000,28(1):27-30.
14 Cimino J J,Ayres E J,Remennik L,et al.The National Institutes of Health's Biomedical Translational Research Information System(BTRIS):design,contents,functionality and experience to date[J].J Biomed Inform,2014,(52):11-27.
15 Tryka K A,Hao L,Sturcke A,et al.NCBI's Database of Genotypes and Phenotypes:dbGaP[J].Nucleic Acids Res,2014,42(Database issue):975-979.
16 Chute C G,Beck S A,Fisk T B,et al.The Enterprise Data Trust at Mayo Clinic:a semantically integrated warehouse of biomedical data[J].J Am Med Inform Assoc,2010,17(2):131-135.
17 Murphy S N,Weber G,Mendis M,et al.Serving the Enterprise and Beyond with Informatics for Integrating Biology and the Bedside(i2b2)[J].J Am Med Inform Assoc,2010,17(2):124-130.
18 Bhattacharya S,Andorf S,Gomes L,et al.ImmPort:disseminating data to the public for the future of immunology[J].Immunol Res,2014,58(2-3):234-239.
19 Payakachat N,Tilford J M,Ungar W J.National Database for Autism Research(NDAR):Big Data Opportunities for Health Services Research and Health Technology Assessment[J].Pharmacoeconomics,2016,34(2):127-138.
20 Lowe H J,Ferris T A,Hernandez P M,et al.STRIDE-Anintegrated standards-based translational research informatics platform[J].AMIA Annu Symp Proc,2009,(2009):391-395.
21 Tomczak K,P Czerwinska,M Wiznerowicz.The Cancer Genome Atlas(TCGA):an immeasurable source of knowledge[J].Contemp Oncol(Pozn),2015,19(la):A68-77.
22 Clark K.The Cancer Imaging Archive(TCIA):maintaining and operating a public information repository[J].J Digit Imaging,2013,26(6):1045-1057.
23 Wang X.Translational Integrity and Continuity:personalized biomedical data integration[J].J Biomed Inform,2009,42(1):100-112.