Next generation sequencing in quality control and analysis of data

doi:10.3969/j.issn.1673-8640.2017.04.003

Abstract

Abstract:

With the development of precision medicine in China,next generation sequencing （NGS） has been improved in clinical practice. Though NGS is a new technology in the field of clinical laboratory medicine,there is a few systematic laws,regulations and guidelines to regulate the development of NGS. Changhai Hospital is one of the first national trial units,which is applying NGS to the diagnosis and therapy of cancer. Now,it has conducted 2 NGS programs,which are genetic testing program and cancer individualized medication program. This review will focus on the problems from practice and provide a useful reference.

Key words: Next generation sequencing, Clinical determination, Quality control, Datum analysis

CLC Number:

R393

YU Dong, GUO Yingjun. Next generation sequencing in quality control and analysis of data[J]. Laboratory Medicine, 2017, 32(4): 255-261.

Figures/Tables 3

References 23

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名称	网址
NCBI	http：//www.ncbi.nlm.nih.gov
Ensembl	http：//www.ncbi.nlm.nih.gov
dbSNP	http：//www.ncbi.nlm.nih.gov/snp
1000 Genomes Project	http：//browser.1000genomes.org
EXAC	http：//exac.broadinstitute.org/
ESP	http：//evs.gs.washington.edu/EVS/
dbVar	http：//www.ncbi.nlm.nih.gov/dbvar
COSMIC（Catalogue of Somatic Mutations in Cancer）	http：//cancer.sanger.ac.uk/cosmic
TCGA	https：//tcga-data.nci.nih.gov/tcga/
ICGC	https：//icgc.org/
ENCODE	http：//genome.ucsc.edu/ENCODE/
ClinVar	http：//www.ncbi.nlm.nih.gov/clinvar/
HGMD	http：//www.biobase-international.com/product/hgmd
DECIPHER	http：//decipher.sanger.ac.uk
HGVS	http：//www.hgvs.org/dblist/dblist.html
DGV	http：//dgv.tcag.ca/dgv/app/home
Leiden Open Variation Database	http：//www.lovd.nl
OMIM	http：//www.ncbi.nlm.nih.gov/omim
HGV	https：//hgv.figshare.com/
HPO（Human Phenotype Ontology）	http：//human-phenotype-ontology.github.io/
PharmGKB	https：//www.pharmgkb.org/
ClinicalTrials	https：//www.clinicaltrials.gov/
DrugBank	http：//www.drugbank.ca/
STITCH	http：//stitch.embl.de/
Therapeutic Target Database	http：//bidd.nus.edu.sg/group/cjttd/
Genomics of Drug Sensitivity in Cancer	http：//www.cancerrxgene.org/
My Cancer Genome	https：//www.mycancergenome.org/
Atlas Genetics Oncology	http：//atlasgeneticsoncology.org/
RefSeqGene	http：//www.ncbi.nlm.nih.gov/refseq/rsg
Biocyc	http：//biocyc.org/
The NCBI BioSystems	http：//www.ncbi.nlm.nih.gov/biosystems/
KEGG	http：//www.kegg.jp/
Locus Reference Genomic	http：//www.lrg-sequence.org
MitoMap	http：//www.mitomap.org/MITOMAP/HumanMitoSeq
Pubmed	https：//www.ncbi.nlm.nih.gov/pubmed
Medline	http：//www.medline.com/home.jsp

名称	网址
NCBI	http：//www.ncbi.nlm.nih.gov
Ensembl	http：//www.ncbi.nlm.nih.gov
dbSNP	http：//www.ncbi.nlm.nih.gov/snp
1000 Genomes Project	http：//browser.1000genomes.org
EXAC	http：//exac.broadinstitute.org/
ESP	http：//evs.gs.washington.edu/EVS/
dbVar	http：//www.ncbi.nlm.nih.gov/dbvar
COSMIC（Catalogue of Somatic Mutations in Cancer）	http：//cancer.sanger.ac.uk/cosmic
TCGA	https：//tcga-data.nci.nih.gov/tcga/
ICGC	https：//icgc.org/
ENCODE	http：//genome.ucsc.edu/ENCODE/
ClinVar	http：//www.ncbi.nlm.nih.gov/clinvar/
HGMD	http：//www.biobase-international.com/product/hgmd
DECIPHER	http：//decipher.sanger.ac.uk
HGVS	http：//www.hgvs.org/dblist/dblist.html
DGV	http：//dgv.tcag.ca/dgv/app/home
Leiden Open Variation Database	http：//www.lovd.nl
OMIM	http：//www.ncbi.nlm.nih.gov/omim
HGV	https：//hgv.figshare.com/
HPO（Human Phenotype Ontology）	http：//human-phenotype-ontology.github.io/
PharmGKB	https：//www.pharmgkb.org/
ClinicalTrials	https：//www.clinicaltrials.gov/
DrugBank	http：//www.drugbank.ca/
STITCH	http：//stitch.embl.de/
Therapeutic Target Database	http：//bidd.nus.edu.sg/group/cjttd/
Genomics of Drug Sensitivity in Cancer	http：//www.cancerrxgene.org/
My Cancer Genome	https：//www.mycancergenome.org/
Atlas Genetics Oncology	http：//atlasgeneticsoncology.org/
RefSeqGene	http：//www.ncbi.nlm.nih.gov/refseq/rsg
Biocyc	http：//biocyc.org/
The NCBI BioSystems	http：//www.ncbi.nlm.nih.gov/biosystems/
KEGG	http：//www.kegg.jp/
Locus Reference Genomic	http：//www.lrg-sequence.org
MitoMap	http：//www.mitomap.org/MITOMAP/HumanMitoSeq
Pubmed	https：//www.ncbi.nlm.nih.gov/pubmed
Medline	http：//www.medline.com/home.jsp