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الأمجد الجيلاني منصور

Professor

أستاذ دكتور

كليات العلوم
قسم علم الحيوان, مبني 5 مكتب رقم 113 الطابق الأرضى

+966-11-46-75789
lmansour@ksu.edu.sa
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Workshop : Genetic Association Studies: From SNP design to analysis and interpretation. Training on open sources software

Workshop:

Genetic Association Studies: From SNP design to analysis and interpretation. Training on open sources software

دراسات الارتباط الجيني: من تصميم SNP إلى التحليل و الإستنتاج مع التدريب على برمجيات المصادر المفتوحة

Pr. Dr. Lamjed Mansour (lmansour@ksu.edu.sa)

 

1- Tools and criteria for selection of informative single nucleotide polymorphisms (SNPs)

2- Methods for SNP genotyping

3- Association analysis and interpretation

4-Functional prediction

Genetic Association Studies: From SNP design to analysis and interpretation. Training on open sources software

In this workshop, we will focus firstly on the website tools and criteria of selection of SNPs polymorphism that will be used on the study. This include the use of HapMap data or dbSNP, determination of all the specifications of the SNPs and the prediction of their function. We will examine the pipeline of “de novo” SNPs after sequencing of a target DNA. We will talk also about the methods for SNP genotyping and the advantage and disadvantage of each one. After that we will examine the methods of data analysis from the row data to final report after logistic regression analysis for reports and publication.

 

 

Gene candidate determination tools:

            - Bibliographic references

            - Genome wide association studies

GWAS Catalog (ebi.ac.uk)

            - Transcriptomic analysis or protein expression

            - ncbi medical genetics portal: https://www.ncbi.nlm.nih.gov/medgen/44264

            DisGeNET database: platform containing collections of genes and variants associated to human diseases https://www.disgenet.org/search

            - Pathway analysis : http://www.snps3d.org/

http://www.snps3d.org/modules.php?name=Search&op=advanced%20search

 

Home - SNP - NCBI (nih.gov)

add your gene name CTLA4

select SNP to be directed to dbSNP

https://www.ncbi.nlm.nih.gov/variation/view/

 

SNP exploration

To explore any SNP we should identify it, get its physical localization (chromosome number, and coordinate, the genome project, major and minor allele frequency (MAF), region (UTR, intron, exon…) protein or gene expression effect…..

add your gene name example PDCD1 or any other gene 

select SNP to be directed to dbSNP

https://www.ncbi.nlm.nih.gov/snp/ (Home - SNP - NCBI (nih.gov)

or ensembl platform:  https://asia.ensembl.org/index.html



you can predict the variant effect through ensemble portal: https://asia.ensembl.org/Homo_sapiens/Tools/VEP

Exemple : CTLA-4 SNPs : Full the table…

SNP ID/assay ID

Common name

Chromosome position :GRCh38

Nucleotide

change

Region

MAF in Human populations (1000genomes Study)

Global

European

rs11571317

 

 

 

 

 

 

rs231775

 

 

 

 

 

 

rs3087243

 

 

 

 

 

 

 

rs11571317,rs231775,rs3087243

Decide which technique you will use for SNPs genotyping:

Methods for SNP genotyping

  • PCR-RFLP: Design primers flanking the region and suitable restriction enzyme (Gene view option, sequence text view); select flanking region, blast and search for primers using primer6, design a restriction enzyme using websites like Sequence Manipulation Suite (SMS), Restriction Digest https://www.bioinformatics.org/sms2/rest_map.html or

    NEBcutter: http://nc2.neb.com/NEBcutter2/

Association analysis and interpretation

Data analysis and processing of genotypes

-Prepare you XLS (VCF) file including all genotyping results

Open this xls file

Open the website snpstat

Reference

Determine de genotype association through the calculation of OR and o values

Determine the haplotype associations and the estimation of D’ and r2

Determine de hardy Weinberg equilibrium and alleles frequency using this website

analyze the overall LD of the selected SNPs through these webapplications 

Functional prediction of SNP

Explore the website

Explore the target 3' UTR region of the gene

For SNP in UTR, explore the website

Variant prediction website (ensemble)

PolyPhen :

Analyse using miRNASNiPer for miRNA interactions

miRNASNP-V3

use the webtool predictSNP platform to predict the deleterious effect of the SNP based on the evaluation of six tools for variant prioritization: CADD, DANN, FATHMM, FitCons, FunSeq2 and GWAVA.

  •  

     Input type for predictSNP

    Chromosome coordinates / accepted format of chromosome names: chr1-chr22, chrX, chrY

    (prefix chr is not required)

    PredictSNP queries must be composed of variants specified by only one input type format

    Simple format

    Definition: CHR,START,[END,]REFERENCE_ALLELE,ALTERNATIVE_ALLELE

    Example (chromosome / GRCh37): chr18,21118528,G,C

Explore SNPs3D; add rs231775, go to KEGG and explore PDB, 3d, sequence-3D view

Linkage disequilibrium and SNPs interactions analysis using SHEsis

Or better use SCHesis Plus web version or download the software

 

Shesis input format

1. Case/control data

sample data for diploidy species

    id1  case G A  C C  1 1  A1 A2
    id2  case A A  T C  1 1  A2 A2
    id3  ctrl A A  T T  2 2  A3 A4
    id4  ctrl 0 0  T T  3 3  A5 A3
    id5  ctrl G G  A A  2 3  A1 A2
    id6  case A A  C A  0 0  A6 A7
  

 

The first column is sample id. The second column is disease status, "case" for cases and "ctrl" for controls. The following columns are genotypes. They should be delimited by space, comma or tab. Adjacent tokens will be compressed and will be treated as a single token. Genotypes can be any string (e.g. 1,2,3,4, or A,T,G,C , or A1,A2,A3,A4, or anything else) except 0, which is the coding for missing genotypes. Use "NA" for missing phenotypes.

 For diploid species, the columns correspond to: sample id, site1-allele1, site1-allele2, site2-allele1, site2-allele2, .

 

Open Webtools for bionformatic analysis

 

 

 

 

Name

Link

Brief description

Category#

1000 Genomes

http://www.1000genomes.org

A deep catalog of human genetic variation

DNA

AFND

http://www.allelefrequencies.net

Allele Frequency Net Database

dbSNP

http://www.ncbi.nlm.nih.gov/snp

Database of single nucleotide polymorphisms

DEG

http://www.essentialgene.org

Database of Essential Genes

EGA

http://www.ebi.ac.uk/ega

European Genome–phenome Archive

Ensembl

http://www.ensembl.org

Ensembl genome browser

euGenes

http://eugenes.org

Genomic information for eukaryotic organisms

GeneCards

http://www.genecards.org

Integrated database of human genes

IMG/HMP

https://img.jgi.doe.gov/imgm_hmp

Human Microbiome MetaGenomes

JASPAR

http://jaspar.genereg.net

Transcription factor binding profile database

JGA

http://trace.ddbj.nig.ac.jp/jga

Japanese Genotype–phenotype Archive

KEGG

http://www.genome.jp/kegg

Kyoto Encyclopedia of Genes and Genomes

MITOMAP

http://www.mitomap.org

Human mitochondrial genome database

NCBI RefSeq

http://www.ncbi.nlm.nih.gov/refseq

NCBI Reference Sequence Database

PolymiRTS

http://compbio.uthsc.edu/miRSNP

Polymorphism in miRNAs and their Target Sites

UCSC Genome Browser

http://genome.ucsc.edu

UCSC Genome Browser database

ChIPBase

http://deepbase.sysu.edu.cn/chipbase

Database of transcriptional regulation of lncRNA and miRNA genes

RNA

DARNED

http://darned.ucc.ie

DAtabase of RNa EDiting in humans

DIANA-LncBase

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=lncBase/index

miRNA targets on lncRNAs

GENCODE

http://www.gencodegenes.org

Encyclopedia of genes and gene variants

H-DBAS

http://www.h-invitational.jp/h-dbas

Human-transcriptome DataBase for Alternative Splicing

HEXEvent

http://hexevent.mmg.uci.edu

Database of Human EXon splicing Events

LNCipedia

http://www.lncipedia.org

Annotated human lncRNA sequences

LncRNA2Target

http://www.lncrna2target.org

Database of differentially-expressed genes after lncRNA knockdown or overexpression

lncRNAdb

http://www.lncrnadb.org

lncRNA Database

lncRNASNP

http://bioinfo.life.hust.edu.cn/lncRNASNP

Database of SNPs in lncRNAs

LncRNAWiki

http://lncrna.big.ac.cn

Human lncRNA Wiki

miRBase

http://www.mirbase.org

miRNA Database

miRTarBase

http://mirtarbase.mbc.nctu.edu.tw

Experimentally-validated miRNA–target interactions

miRWalk

http://mirwalk.uni-hd.de

Database of miRNA–target interactions

NONCODE

http://www.noncode.org

Database of ncRNA genes

NPInter

http://www.bioinfo.org/NPInter

Database of ncRNA interactions

RADAR

http://RNAedit.com

Rigorously Annotated Database of A-to-I RNA editing

piRNABank

http://pirnabank.ibab.ac.in

Database of piwi-interacting RNAs

RBPDB

http://rbpdb.ccbr.utoronto.ca

Database of RNA-binding specificities

RDB

http://ndbserver.rutgers.edu

The nucleic acid database

Rfam

http://rfam.xfam.org

Database of ncRNA families

RNAcentral

http://rnacentral.org

International database of ncRNA sequences

snoRNABase

https://www-snorna.biotoul.fr

Database of human H/ACA and C/D box snoRNAs

starBase

http://starbase.sysu.edu.cn

Database of ncRNA interaction networks

TarBase

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index

Experimentally-validated miRNA:gene interactions

TargetScan

http://www.targetscan.org

Predicted miRNA targets in mammals

CATH

http://cath.biochem.ucl.ac.uk

Protein structure classification

Protein

CPLM

http://cplm.biocuckoo.org

Compendium of Protein Lysine Modifications

DIP

http://dip.doe-mbi.ucla.edu

Database of Interacting Proteins

EKPD

http://ekpd.biocuckoo.org

Eukaryotic Kinase and Phosphatase Database

HPRD

http://www.hprd.org

Human Protein Reference Database

hUbiquitome

http://bioinfo.bjmu.edu.cn/hubi/

Ubiquitination sites and cascades

InterPro

http://www.ebi.ac.uk/interpro

Protein sequence analysis and classification

MEROPS

http://merops.sanger.ac.uk

Database of proteolytic enzymes, their substrates, and inhibitors

MINT

http://mint.bio.uniroma2.it/mint

Molecular INTeraction Database

ModBase

http://salilab.org/modbase

Database of comparative protein structure models

mUbiSiDa

http://reprod.njmu.edu.cn/mUbiSiDa

Mammalian Ubiquitination Site Database

PANTHER

http://www.pantherdb.org

Protein ANalysis THrough Evolutionary Relationships

PDB

http://www.rcsb.org/pdb

Protein Data Bank for 3D structures of biological macromolecules

PDBe

http://www.ebi.ac.uk/pdbe

Protein Data Bank in Europe

Pfam

http://pfam.xfam.org

Database of conserved protein families and domains

PhosSNP

http://phossnp.biocuckoo.org

Genetic polymorphisms that influence protein phosphorylation

PIR

http://pir.georgetown.edu

Protein Information Resource

PROSITE

http://www.expasy.org/prosite

Database of protein domains, families and functional sites

SysPTM

http://lifecenter.sgst.cn/SysPTM

Post-translational modifications

TreeFam

http://www.treefam.org

Database of phylogenetic trees of animal species

UniPROBE

http://thebrain.bwh.harvard.edu/uniprobe

Universal PBM Resource for Oligonucleotide Binding Evaluation

UniProt

http://www.uniprot.org

Universal protein resource

UUCD

http://uucd.biocuckoo.org

Ubiquitin and Ubiquitin-like Conjugation Database

ArrayExpress

http://www.ebi.ac.uk/arrayexpress

Database of functional genomics experiments

Expression

BioGPS

http://biogps.org

Portal for querying and organizing gene annotation resources

Expression Atlas

http://www.ebi.ac.uk/gxa

Differential and baseline expression

Human Protein Atlas

http://www.proteinatlas.org

Tissue-based map of the human proteome

MOPED

https://www.proteinspire.org

Multi-Omics Profiling Expression Database

NCBI GEO

http://www.ncbi.nlm.nih.gov/geo

Gene Expression Omnibus

NRED

http://nred.matticklab.com

Database of lncRNA expression

ONCOMINE

https://www.oncomine.org

Cancer microarray database

PrimerBank

http://pga.mgh.harvard.edu/primerbank

Public resource for PCR primers

PRIDE

http://www.ebi.ac.uk/pride

PRoteomics IDEntifications

TiGER

http://bioinfo.wilmer.jhu.edu/tiger

Tissue-specific Gene Expression and Regulation

WikiCell

http://www.wikicell.org

Unified resource for Human transcriptomics research

CPDB

http://consensuspathdb.org

Database of human interaction networks

Pathway

HMDB

http://www.hmdb.ca

Human Metabolome Database

KEGG PATHWAY

http://www.genome.jp/kegg/pathway.html

KEGG pathway maps

MetaCyc

http://metacyc.org

Metabolic pathway database

Pathway Commons

http://www.pathwaycommons.org

Pathway commons

PID

http://pid.nci.nih.gov

Pathway Interaction Database

Reactome

http://www.reactome.org

Curated and peer-reviewed pathway database

UniPathway

http://www.grenoble.prabi.fr/obiwarehouse/unipathway

Universal Pathway

AlzBase

http://alz.big.ac.cn/alzBase

Database for gene dysregulation in Alzheimer’s disease

Disease

CADgene

http://www.bioguo.org/CADgene

Coronary Artery Disease gene database

COSMIC

http://cancer.sanger.ac.uk

Catalog Of Somatic Mutations In Cancer

DiseaseMeth

http://bioinfo.hrbmu.edu.cn/diseasemeth

Human disease methylation database

DisGeNET

http://www.disgenet.org/web/DisGeNET/v2.1

Gene–disease associations

GOBO

http://co.bmc.lu.se/gobo

Gene expression-based Outcome for Breast cancer Online

GWAS Central

http://www.gwascentral.org

A comprehensive resource for the comparison and interrogation of genome-wide association studies

GWASdb

http://jjwanglab.org/gwasdb

Human genetic variants identified by genome-wide association studies

HbVar

http://globin.cse.psu.edu/hbvar

Hemoglobin variants and thalassemias

HGMD

http://www.hgmd.org

Human Gene Mutation Database

ICGC

http://icgc.org

International Cancer Genome Consortium

IDbases

http://structure.bmc.lu.se/idbase

Immunodeficiency-causing variations

LncRNADisease

http://cmbi.bjmu.edu.cn/lncrnadisease

lncRNA and disease database

LOVD

http://www.lovd.nl

Leiden open (source) Variation Database

MalaCards

http://www.malacards.org

Human maladies and their annotations

MethHC

http://methhc.mbc.nctu.edu.tw

Database of DNA methylation and gene expression in human cancer

MethyCancer

http://methycancer.psych.ac.cn

Database of human DNA Methylation and cancer

miR2Disease

http://www.miR2Disease.org

Database for miRNA deregulation in human disease

MITOMAP

http://www.mitomap.org/MITOMAP

Polymorphisms and mutations in human mitochondrial DNA

NHGRI GWAS Catalog

http://www.genome.gov/gwastudies

Curated resource of SNP-trait associations

OMIM

http://omim.org

Online Mendelian Inheritance in Man

T2D@ZJU

http://tcm.zju.edu.cn/t2d

Connections associated with type 2 diabetes

TCGA

http://cancergenome.nih.gov

The Cancer Genome Atlas

Universal Mutation Database

http://www.umd.be/

Locus-specific database

ViRBase

http://www.rna-society.org/virbase

Virus–host ncRNA associated interactions

GO

http://geneontology.org

Gene ontology

Standard and ontology

HGNC

http://www.genenames.org

Database of human gene names

Europe PMC

http://europepmc.org

Literature database in Europe

Literature

PubMed

http://www.ncbi.nlm.nih.gov/pubmed

Database of biomedical literature from MEDLINE

PubMed Central

http://www.ncbi.nlm.nih.gov/pmc

Free full-text literature archive