Comments on Rare Variants Analyses Ryo Yamada Kyoto University 2012/08/27 IBC2012@Kobe, Japan.

Comments on Rare Variants Analyses

Ryo YamadaKyoto University

2012/08/27IBC2012@Kobe, Japan

Many difficulties to detect true signals in rare variant analyses

Type 1 error, Power-control, Various Statistics with/without Weights,Data quality, Data load, Platform variations, Missing data, Permutations, Allele freq., Rares with Commons, Replication, Neutral or not,


Type 1 error, Power-control, Various Statistics with/without Weights,Data quality, Data load, Platform variations, Missing data, Permutations, Allele freq., Replication, Rares with Commons integrating all variations,

So many....


• My discussing points– Some problems in rare variant analyses are the

unsolved problems in common variant analyses.


• My discussing points– Some problems in rare variant analyses are the

unsolved problems in common variant analyses.

– Changes in genetic studies along with rare variant analyses• Next-generation sequencing technologies-driven

changes

Common Variant Analyses

• Pre kit-GWAS ~2005– Exonic region-dominant

• kit-GWAS 2005 ~– Genome-wide




• Exome• Whole-genome sequencing

Rare Variant Analyses




• Exome• Whole-genome sequencing

Rare Variant Analyses

déjà vu

What we can learn from SNP LD mapping

• Hypothesis-free approach• All markers vs. 1 trait

Set of Hypotheses

• Hypothesis-free approach• All markers vs. 1 trait• Almost all hypotheses are null.– They work as negative controls.– We obtain distribution under null hypothesis.

• A few hypotheses are “positive”.

• Pick up “outliers” from “null distribution” as positive signals

Many Positive Hypotheses

• Many hypotheses are “truly positive”.– Transctiptome, microarray-chips– False discovery rate



• Different approach to multiple testings from GWAS



• Similar approach to multiple testings in GWAS?



• Similar approach in GWAS?– e-QTL and cis-effect of neighboring SNPs on gene

expression

Nature Genetics 43, 561–564 (2011)

Both are GWAS but different

• Almost all hypotheses are null

• Many positive hypotheses


• Almost all hypotheses are null– All markers vs. 1 trait

• Many positive hypotheses– All markers vs. genes (traits)




Many traits




Many traits

Positives : Neighboring and cis effectsNegatives : Remote or trans effects

Many Positive Hypotheseswith Rare Variant Analyses


• Distribution of statistics is like what?


• Distribution of statistics is like what?• Strategy to detect signals should be cared.



• Many Positive Hypotheses– All markers vs. genes (traits)

Many traits

Positives : Neighboring and cis effectsNegatives : Remote or trans effects

Same GWAS but difference

• Almost all hypotheses are null– All markers vs. 1 phenotype

• Many Positive Hypotheses– All markers vs. genes (traits)

Many traits

Positives : NeighboringNegatives : Trans / Remote genes



• Many Positive Hypotheses– All markers vs. cis-neighboring genes

Many traits


Where are many traits?




Many traits


Where are many traits?• Biobank projects with multiple traits• EHR (Electrical Health Record)-driven genetic

studies– Very many phenotypesNature Reviews Genetics 12, 417-428 (June 2011)




Many traits


Where are many traits?• Physical / pathological conditions vary.• Developmental stages vary.• Cell types/ tissue types/ organs vary.


Many traits


Where are many traits?• Physical / pathological conditions vary.• Developmental stages vary.• Cell types/ tissue types/ organs vary.

Intra-individual diversity


Many traits


Many traitsChange view points


Many genotypes


Many genotypes

Where are many genotypes?


Many genotypes

Where are many genotypes?• Physical / pathological conditions vary.• Developmental stages vary.• Cell types/ tissue types/ organs vary.


Many genotypes


Intra-individual diversityAgain


Many genotypes


Intra-individual diversity

Next generation sequencing technology makes these possible.

Changes by Next Generation Sequencing Technologies

• Individual cell-sequencing detects– Hereditary• Variants from parents to offsprings

– Non-hereditary but genetic• de novo mutations in gamates• Somatic mutations in fetus• Somatic mutations after birth




Before birth

After birth




Before birth

After birth

Hereditary ~ Genetic ~ SomaticDiscriminations are becoming vague.

“Collapsing methods”


• Patterns of possession of rare variants vary with phenotypes.

• “Collapsing methods” make the patterns into a style that can be tested easily; one-dimensional measure




• Information on functionality of variants might be used when collapse to modify the “measure”.




• Is this problem NEW to rare variant analyses?




• Is this problem NEW to rare variant analyses?– NO



• “Collapsing methods” make the patterns into a style that can be tested easily; one-dimensional value

• Is this problem NEW to rare variant analyses?– We do NOT have adequate solutions for patterns

of common variants.

Genetics September 2007 vol. 177 no. 1 535-547



• “Collapsing methods” make the patterns into a style that can be test easily; one-dimensional value

• Is this problem NEW to rare variant analyses?– We do NOT have adequate solutions for patterns

of common variants .

How to handle patterns of variants, BOTH common and rare, should be solved.

Patterns of variants

Patterns of variants

• Rephrase as “Genetic heterogeneity PER GENES”

Notes onGenetic Heterogeneity PER GENES

• Genes vary in their size.


• Genes vary in their size.• Number of variants vary among genes.


• Genes vary in their size.• Number of variants vary among genes.• Allele frequencies vary among genes.


• Genes vary in their size.• Number of variants vary among genes.• Allele frequencies vary among genes.• Haplotype frequencies vary among genes.


• Genes vary in their size.• Number of variants vary among genes.• Allele frequencies vary among genes.• Haplotype frequencies vary among genes.• Functional variations due to genetic variants

vary among genes.

Unsolved Issuesin Common Variant-GWAS

on Genetic Heterogeneity PER GENES

• GWAS



• GWAS– Hypothesis-free approach, targetting genes evenly



• GWAS– Hypothesis-free approach, targetting genes evenly– But...



• GWAS– Hypothesis-free approach, targetting genes evenly– But...– All genes are studied UNEVENLY.



• GWAS– Hypothesis-free approach, targetting genes evenly– But...– All genes are studied UNEVENLY.• Genetic heterogeneity PER GENES affects on sensitivity

and specificity• HLA region and its extreme heterogeneity...



• GWAS– Hypothesis-free approach, targetting genes evenly– But...– All genes are studied UNEVENLY.• Genetic heterogeneity PER GENES affects on sensitivity

and specificity• HLA region and its extreme heterogeneity...

Am J Hum Genet. 2005 April; 76(4): 634–646.

UNEVENNESS Genetic Importance

• GWAS identifies genes of “Genetic Importance” that – are Important for a phenotype,– have functional variants.

UNEVENNESSGenetic Importance

• GWAS identifies genes of “Genetic Importance” that – are Important for a phenotype,– have functional variants.


• Consider a pathway that is important for a phenotype.– Gene X in the pathway is functionally critical

without genetic variants.– Gene Y in the pathway has some functional roles

with genetic variants that make phenotype variations.

• Gene X is “Functionally” important.• Gene Y is “Genetically” important.

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

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


• Consider a pathway that is important for a phenotype.– Gene X in the pathway is functionally critical

without genetic variants.– Gene Y in the pathway has some functional roles


• Gene X is “Functionally” important.• Gene Y is “Genetically” important.


• Consider a pathway is important for a phenotype.– Gene X in the pathway is functionally critical

without genetic variants.– Gene Y in the pathway has some functional role


• Gene X is “Functionally” important.• Gene Y is “Genetically” important.Genetic studies work only on

“genetic” importance.

• Genetic Heterogeneity PER GENES determines “Genetic Importance”

• We do NOT have adequate methods to measure genetic heterogeneity per genes.


• But,...



One-dimensional measuresMeanVariance





How to measure?

Genetic Heterogeneity PER GENESFor Species

OrFor Individuals

Genetic Heterogeneity PER GENESFor Populations

OrFor Individuals


OrFor Individuals

• Heterogeneity in an absolute scale


OrFor Individuals

• Heterogeneity in an absolute scale• Heterogeneity in a relative scale inside of

individuals


OrFor Individuals

• Heterogeneity in an absolute scale• Heterogeneity in a relative scale inside of

individuals

Intra-individul genetic heterogeneity

Intra-individul Genetic Heterogeneity

• They are the source of phenotypic heterogeneity.



• Individuals have to show phenotypic variations that are the basics of living creatures.



• Individuals have to show phenotypic variations that are the basics of living creatures.

• Individual genetic heterogeneity is the resource for the individual to realize phenotypic variations.


• Individual genetic heterogeneity is the resource for the individual to realize phenotypic variations.

• Genetic heterogeneity in a gene for an individual may be relatively more important than others, depending on other genes’ heterogeneity context.


• Individual genetic heterogeneity is the resource to realize phenotypic variations by the individual.

• Genetic heterogeneity in a gene for an individual may be relatively more important than others, depending on other genes’ heterogeneity context.

G x G interaction

G x G with rare variants

• G x G approach in general– Gene set in a functional pathway– Problems with too many combinations

• Same both for common variants and rare variants– Many and scarce variants might G x G approach

less realistic.– Scarce but Many variants could open new ways to

G x G approach ??



• Same both for common variants and rare variants– Many and scarce variants might make G x G

approach less realistic.– Scarce but Many variants could open new ways to

G x G approach ??



• Same both for common variants and rare variants– Many and scarce variants might make G x G

approach less realistic.– Scarce but Many variants could open new ways to

G x G approach with new measures?????

Summary

• Next generation sequencing enabled rare variant analyses.

• Use what next generation sequencing brought us.– Expansion of phenotypes and genotypes– Set of hypotheses and multiple testing– Measures of genetic heterogeneity– Intra-individual heterogeneities

Thank you

Thank you

AnnouncementSymposium and Data Analysis Hands-on Seminar

Jan. 16 – Jan. 19, 2013@ Kyoto University, Kyoto, Japan

Organized by

Marc Lathrop @ CEPHJurg Ott @ Rockefeller Univ.

Fumihiko Matsuda @ Kyoto Univ.

Details will be announced shortly.If you are interested in this seminar

or need updated timely for the details or registration, e-mail to: [email protected] (Ryo Yamada, Kyoto Univ.)

mailto:[email protected]

Comments on Rare Variants Analyses Ryo Yamada Kyoto University 2012/08/27 IBC2012@Kobe, Japan.

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