genome-wide association s tudy
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Genome-wide Association S tudy. Focus on association between SNPs and traits Tendency Larger and larger sample size Use of more narrowly defined phenotypes(blood lipids, proinsulin or similar biomarkers Limitations Sufficient sample size - PowerPoint PPT PresentationTRANSCRIPT
Genome-wide Association Study• Focus on association between SNPs and traits
• Tendency– Larger and larger sample size– Use of more narrowly defined phenotypes(blood lipids, proinsulin or similar
biomarkers• Limitations
– Sufficient sample size– The massive number of statistical tests performed presents an
unprecedented potential for the positive results– Search the entire genome-->not worth the expenditure
For each of SNPs, allele frequency alters?Odds ratio
Proportion of the same allele Proportion of a specific allele
genotyped for the majority of common known SNPs
Healthy control group Case group
Advantage of Exome Sequecing
• Whole genome sequencing– Redundant raw data(6 Gb in each human diploid
genome )• Exome sequecing(targeted exome capture)– Exons are short and 180,000 exons constitute 1%
of the human genome– The goal is to identify the functional variation that
is responsible for both mendelian and common diseases
Significance• Exome sequencing can be used to identify causal
variants of rare disorders• The first reported study that used exome sequencing as
an approach to identify an unknown causal gene for a rare mendelian disorder
The Shendure Lab• Next-generation human genetics– A multiplex approach to genome sequencing– Targeted sequence enrichment• Protocols relying on molecular inversion probe• Hybrid capture
– Novel analytical strategies to identify the genetic basis of Mendelian disorders by exome sequecing• Autosomal recessive disorders such as Miller syndrome• Autosomal dominant disorders such as Kabuki syndrome
Hapmap project
• Focuse on common SNPs(at least 1% of the population)
• Samples: 4 populations– (30*3 YRI, 30*3 CEU, 45 JPT, 45 CHB)
• Data:– SNP frequencies, genotypes
Work flow
Direct identification of the causal gene for FSS
Read mapping and variant analysis
DNA samples, targeted capture and massively parallel sequencing
a. PCR-based approachb. Molecular inversion probe(MIP)-
based approachc. Hybrid capture-based approach
Mamanova et al. Nat Method 7(2):112-118
Target enrichment Methods
Mamanova et al. Nat Method 7(2):112-118
Figure. ①Probe list of array2
② Probe list of array1③Exome on 1-22, X and Y chromosomes
Work flow
Direct identification of the causal gene for FSS
Read mapping and variant analysis
DNA samples, targeted capture and massively parallel sequencing
Coming…
Direct identification of the causal gene for FSS
Comparison of sequence calls to array genotypes, dbSNP and whole
genome sequencing
Method
Calculation of genome-wide estimates
Variant annotation
Comparison of sequence calls to array genotypes, dbSNP and whole genome sequencing
Variant calling
Target Masking
Read mapping
Sequencing
Targeted capture by hybridization of DNA microarrays
Design of exon capture array
Shotgun library construction
Oligonucleotides and adaptors
Genomic DNA samples
Method
Method 2:MIP and resequencing
Method 3: Whole genome sequencing
Method 4:
Figure. Table of cSNPs of 8 HapMap individuals
Figure. Table of Splice Site Variants of 8 HapMap individuals
Figure. Table of Coding Indels of 8 HapMap individuals
Figure. Table of coverage of 8 HapMap individuals and 4 FSS individual
Figure. Intervals that were exclued….
Figure. ①Probe list of array2
② Probe list of array1③Exome on 1-22, X and Y chromosomes
YRI: Nigeria - Yoruba people of IbadanCHB: China - BeijingJPT: Japan - TokyoCEU: Centre d'Etude du Polymorphisme Humain (CEPH)Eur: European–American ancestry
About mendelian disease
Traditional situation
Current situation
Considerations
• Causal genes may be shared by case group.• Control group may not contain that mutation.• Common mutation may not be causal.• Causal mutation should cause animo acid
change.
Result
Further application
• Typical single gene disorder.• Disorder caused by single but not uniform
gene.• Multiple gene disorder.• Complex disease.• Cancer.