Common Deletion Polymorphisms in the Human Genome

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Common Deletion Polymorphisms in the Human Genome
Instructor Yao-Ting Huang
Bioinformatics Laboratory, Department of Computer
Science Information Engineering, National Chung
Cheng University.
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Polymorphisms in the Human Population

• So far we have extensively focused on Single
  Nucleotide Polymorphisms (SNPs).

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Polymorphisms in the Human Population

• However, we are distinguished from one another by
  all sorts of mutations in the human genome.
• e.g., deletion, insertion, and inversion.

-A C T T T G C T C-
-A C T T T G C T C-
Deletion polymorphisms
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Types of Deletions

• Recall our human genome is a diploid.
• Each DNA segment should be observed with two
  copies if no deletion.

C CT TT TC CC CA AC C
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Types of Deletions

• Recall our human genome is a diploid.
• Deletion may occur in one or both chromosomes.
• Homozygous deletion
• Hemizygous deletion

C CT TT CC CC CA AC C
C CT TT CC CC CA AC C
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Disease Association with Deletion

• It has been known that deletions can also lead to
  a variety of serious disorders.
• Tumor suppressor gene are often found to be
  deleted in cancer cells.
• With one copy he or she may stay healthy.
• However, the remaining copy of the tumor
  suppressor gene can be inactivated by a point
  mutation, leaving no tumor suppressor gene to
  protect the body.

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References

• McCarroll et al. Common deletion polymorphisms in
  the human genome. Nature Genetics, 2006.
• Conrad et al. A high-resolution survey of
  deletion polymorphism in the human genome. Nature
  Genetics, 2006.
• Hinds et al. Common deletions and SNPs are in
  linkage disequilibrium in the human genome.
  Nature Genetics, 2006.
• Evan E.E. Widening the spectrum of human genetic
  variation, Nature Genetics, 2006.

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The International HapMap Project

• 269 samples from four populations are genotyped
  to provide a dense map of SNPs.
• SNP genotypes are generated at ten genotyping
  centers using seven different genotyping
  technologies.
• SNPs are discarded if they fail to pass the
  quality control (genotyping errors or failure).
• These authors utilize several signatures of
  deletions left in SNP genotyping.
• That is, SNPs of genotyping errors or failure are
  re-scanned for detecting the presence of deletion
  polymorphisms.

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The International HapMap Project

• The deletions usually left two common signatures
  in SNP genotyping.
• (1) Homozygous deletions resulted in null
  genotypes.
• We fail to obtain the SNP alleles of these
  genotypes (i.e. missing data in the microarray
  chip).
• Null genotypes could be due to either the failure
  of genotyping or deletion.
• (2) Hemizygous deletions resulted in SNP
  genotypes miscalled as homozygous.
• We will still obtain SNP alleles for this type of
  deletions.

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Footprints of Deletions in SNPs (1/3)

• (1) Homozygous deletions tend to result in
  cluster of null genotypes.
• Genotyping failure are less likely to be
  clustered and specific to an individual.

deletions
A CT TA AA CT CA CC T
C CT CA CA CT CA CC C
A CT TA CA CT C A AC T
C CT CA CC CC CA AC T
SNP1
SNP2
Genotyping failuare
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Footprints of Deletions in SNPs (2/3)

• (2) Hemizygous deletions resulted in SNPs
  genotypes miscalled as homozygous.
• These hemizygous deletions often violate the law
  of Mendelian inheritance.
• An allele in a child could not have been received
  from any of their parents.

A CT CA CG CA CA CC T
A CT TT TC CC C A AC T
C CT CT CC CC CA CC C
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Gregor Mendel

• Gregor Mendel is called Father of modern
  genetics.
• His study of the inheritance of traits in pea
  plants is the fundamental basis of genetics
  (1866).

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Footprints of Deletions in SNPs (2/3)

• (2) Hemizygous deletions resulted in SNPs
  genotypes miscalled as homozygous.
• These hemizygous deletions often lead to Mendel
  inconsistency.
• e.g., TT of the child violates the Mendelian law.

A CT CA CG CA CA CC T
A CT TT TC CC C A AC T
C CT CT CC CC CA CC C
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Hardy-Weinberg Equilibrium

• Hardy-Weinberg Equilibrium describes a
  relationship between the frequencies of alleles
  and the genotypes observed in a population.
• Frequencies of alleles Pr(A) and Pr(a)
• Frequencies of genotypes Pr(AA), Pr(Aa), and
  Pr(aa).

Father
Mother
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Hardy-Weinberg Equilibrium

• Hardy-Weinberg Equilibrium describes a
  relationship between the frequencies of alleles
  and the genotypes observed in a population.
• Let Pr(A)p and Pr(a)q.
• Ideally, Pr(AA) p2, Pr(Aa) 2pq, and Pr(aa)
  q2.

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Deviation of HWE

• Inbreeding
• Breeding between close relatives, which causes an
  increase in homozygosity for all genes.
• Assortative mating
• When individuals tend to mate with individuals
  like themselves or dissimilar, which increase or
  reduce genetic diversity.
• Small population size (sampling)
• It is easy to observe a random change in
  genotypic frequencies, particularly when the
  population is very small.

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Footprints of Deletions in SNPs (3/3)

• Cluster of deviation from Hardy-Weinberg
  equilibrium.
• We have Pr(A) p gt 0 and Pr(a) q gt 0.
• But no heterozygous SNPs (e.g., AC) are found.

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Methods for Finding Clusters of Null Genotypes
(1/3)

• Formulate each SNP as a binary vector.
• 0 normal genotypes 1 null genotypes.

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Methods for Finding Clusters of Null Genotypes
(1/3)

• Formulate each SNP as a binary vector.
• Genotyping failure tend to scatter in the matrix.

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Genotyping Errors

• Formulate each SNP as a binary vector.
• Homozygous deletions tend to be clustered.

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Methods for Finding Clusters of Null Genotypes
(2/3)

• They cluster is determined based on the
  correlation coefficient r2.

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Methods for Finding Clusters of Null Genotypes
(2/3)

• They cluster is determined based on the
  correlation coefficient r2.
• If SNP3, SNP4, and SNP5 have r2 gt 0.8, they are
  considered to be similar patterns and put in a
  cluster.

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Methods for Finding Clusters of Null Genotypes
(3/3)

• Highly similar patterns (r2gt0.8) of null
  genotypes or Mendel failures tend to be
  physically clustered in the genome.

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Step 1 Identify a list of clusters

• A list of candidate clusters was determined by
  considering every consecutive pair and
  consecutive trio of observations of that pattern,
  together with any other intervening SNP assays.

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Step 2 Compute P value for each cluster
Chromosome
CandidateClusters

• For each candidate cluster, a cluster P value is
  computed to access the binomial probability of
  observing a cluster at least as tight as that
  cluster, given
• the background frequency of the pattern,
• the number of SNPs spanned by the cluster, and
• the total number of SNPs genotyped.

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Clustering P Value

• Suppose the pattern frequency is 0.001.

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Clustering P Value

• A significance threshold is chosen somewhat to
  the left of a knee in the distribution.

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Flow of the Process
Identify clusters of null genotypes or Mendel
inconsistency
CandidateClusters
CandidateClusters
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Results

• They identify 541 deletions ranging from 1 kb to
  745 kb in size.
• 94 are novel and 120 are homozygous deletions.

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Experimental Validation
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How Many Copy Number Polymorphisms (CNPs) are
Deletions?

• CNPs imply a deletion or a duplication.
• Copy number polymorphisms in the human genome,
  Science, 2004. (76 CNPs)
• Detection of large-scale variation in the human
  genome. Nature Genetics, 2004. (255 CNPs)
• Segmental duplications and copy number variation
  in the human genome, AJHG, 2005. (119 CNPs)
• Only 11 deletions are overlapped with previously
  identified CNPs.
• They speculate that most of these CNPs are
  resulted from duplications rather than deletions.

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Exons of Genes Removed by Deletions

• 266 genes are affected by deletions in at least
  one individual.
• Ten genes are found to be deleted with sufficient
  frequency.

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Linkage Disequilibrium (LD) between SNPs and
Deletions (1/2)

• If deletions result from ancestral events, they
  will be often in LD with nearby SNPs.
• Ten deletions (/, /-, -/-) obtained by
  quantitative PCR over 269 HapMap samples are
  tested.
• The phase of deletions and all SNPs flanking
  200kb to one deletion are obtained by Haploview.

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Linkage Disequilibrium (LD) between SNPs and
Deletions (2/2)
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Capture Deletions by Tag SNPs

• SNP3 can be the tag SNP for this deletion.
• i.e., the allele C at this locus indicates a
  deletion.
• This implies that the upcoming genome-wide
  association studies using tag SNPs is also
  sufficient to detect deletions.

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Linkage Disequilibrium (LD) between SNPs and
Deletions

• Six of the ten deletions have a perfect proxy.
• These deletion are connected with the same allele
  across populations.
• This implies they are ancestral deletion before
  migration from Africa to Europe or to Asia.

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More Evidence from Larger Collection

• Based on 51 deletions validated by PCR,
• The haplotype homozygosity of SNPs flanking
  homozygous deletions are significantly elevated.
• This indicates the deletion travel only on
  specific haplotypes.

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Concluding Remarks

• These papers provide a similar method for
  identifying deletion polymorphisms using SNPs.
• Mainly based on cluster of SNPs containg Mendel
  failures or null genotypes.
• The CNPs are mostly resulted from duplications
  instead of from deletions.
• This speculation is not convincible since
  recently discovered deletions are shown to be
  poorly overlapped.
• The deletion polymorphisms and SNPs are in high
  LD.
• A single genotyping platform is sufficient to
  detect both SNPs and deletions.

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Notes of Methods

• The process of patterns of Mendel inconsistency
  are similar to that of null genotypes.
• The vector is changed to length of 60 containing
  two elements per trio in CEU and YRI.
• The Hardy-Weinberg disequilibrium is only used
  for extending the clusters identified by using
  null genotypes or Mendel inconsistency.
• It is estimated by (hetobs/hetexp) and by setting
  a cutoffs of 0.4 or 0.7.