The Correlation of the Human Gene Brain Derived Neurotrophic Factor with Speech Sound Disorder, Usin

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The Correlation of the Human Gene Brain Derived
Neurotrophic Factor with Speech Sound Disorder,
Using Single Nucleotide Polymorphisms from the
HAPMAP Project
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Human Genome Project

• Completed in 2001 by two separate Independent
  organizations.
• A public partnership between the U.S. Department
  of Energy and the National Institutes of Health.
• A private company Celera Genomics

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From Celera Genomics
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Progress made by the genome project

• identify all the approximately 20,000-25,000
  genes in human DNA,
• determine the sequences of the 3 billion chemical
  base pairs that make up human DNA,
• store this information in databases,
• improve tools for data analysis,
• transfer related technologies to the private
  sector, and
• address the ethical, legal, and social issues
  (ELSI) that may arise from the project.

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What Next ??

• 20,000-25,000 genes have been identified but what
  is their purpose?
• How is our DNA different from other species?
• How is our DNA different within our species?

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HAPMAP project

• Starts where the human genome project left off.
• The International HAPMAP Project officially
  started with a meeting on October 27 to 29, 2002.
• The goal of the International HAPMAP Project is
  to compare the genetic sequences of different
  individuals to identify chromosomal regions where
  genetic variants are shared.

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HAPMAP project cont.

• The HAPMAP Project produced a catalog of common
  genetic variants that occur in human beings.
• It describes what these variants are, where they
  occur in our DNA, and how they are distributed
  among people within populations in different
  parts of the world.

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270 samples of people make up the HAPMAP data

• The Yoruba people of Ibadan, Nigeria, provided 30
  samples.
• In Japan, 45 unrelated individuals from the
  Tokyo area provided samples.
• In China, 45 unrelated individuals from Beijing
  provided samples.
• Thirty U.S. trios provided samples, which were
  collected in 1980 from U.S. residents with
  northern and western European ancestry by the
  Centre d'Etude du Polymorphisme Humain (CEPH).

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SNPs

• The HAPMAP Project has identified 40 million SNPs
  among the human population
• SNP is a kind of genetic variation.
• Stands for single nucleotide polymorphism.
• Most SNPs are in non-coding regions of DNA.

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From www.genomenewsnetwork.org
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How is this information useful to current genetic
studies?

• Sequencing DNA is still very expensive.
• SNPs can be used as a surrogate for unknown
  mutant alleles.
• Two techniques for genetic analysis linkage
  analysis and association analysis.

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How does one Interrogate SNPs

• Two types of assays
• One at a time (example Taqman)
• Massively Parallel (example Illumina)

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Illumina

• Studies 96 to 1536 SNPs at a time.
• Uses an array chip of probes that are labeled to
  genotype a persons SNPs.
• A big advantage of Illumina over Taqman is that
  hundreds of SNPs can be studied at once.
• Biggest disadvantage is that it is more expensive.

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Taqman

• Uses florescence labeled probes .

From www.ABS.com
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How do I pick my SNPs

• Go to HAPMAP data
• Look at the information on the CEU population
• Determine which SNPs best represent that
  population
• Design assay

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Selecting SNPs

• LD or Linkage Disequilibrium
• No need to detect SNPS right next to each other
  because they are inherited together.

From http//hmgc.mcw.edu/images/Olivier/Proj-Berke
leyPGA2.jpg
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Linkage studies

• Genetic linkage is the phenomenon whereby alleles
  at loci close together on the same chromosome
  will tend to be inherited together, because it
  will be rare for a crossover to occur between the
  loci at meiosis.
• The closer together the loci are, the less likely
  crossovers will be and the fewer recombinants
  will be observed. If loci are far apart or on
  different chromosomes then recombination will
  occur by chance in 50 of meioses.
• The recombination fraction ranges from 0 (tight
  linkage) to 0.5 (no linkage) and is a measure of
  genetic distance.

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Picture of linkage map
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More Linkage

• Linkage can be used to map disease genes by
  typing polymorphic DNA markers and seeing if
  their alleles cosegregate with disease among
  related subjects. Linkage can be studied in
  multiply-affected families, in which case the
  strength of evidence in favor of linkage can be
  measured as the lod score.
• This is the logarithm (base 10) of the ratio of
  the likelihood of the observed genotypes given a
  recombination fraction less than 0.5 compared
  with the likelihood under non-linkage, i.e. with
  the recombination fraction equal to 0.5.
  Traditionally a lod of 3 or more is taken as
  "significant" evidence for linkage

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Association studies

• Also know as population based association as
  opposed to family based association
• Linkage and association are totally different
  phenomena.
• Association is simply a statistical statement
  about the co-occurrence of alleles or phenotypes.
• Allele A is associated with disease D if people
  who have D also have A more (or maybe less) often
  than would be predicted from the individual
  frequencies of D and A in the population.

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Association studies
From www.charite.de/ch/medgen/eumedis/statistics05
/familyb-association-std.html
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Family based association

• Similar to population based association studies
  except it uses some information from the family
  itself as the control.
• Is intended by design to avoid possible bias
  through inadequate controls and population
  stratification.

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Speech Sound Disorder or SSD

• Example of a complex disease.
• Has a number of different loci that can
  contribute environment can also play a role.
• It is a complex behavioral disorder centered on
  speech production.

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What is SSD?

• Speech-sound disorder can either be problems in
  some of the cognitive tasks of language
  production or problems with the motor skills
  necessary to generate sound.
• SSD is probably not one single disease with one
  single cause.
• It is an umbrella of related diseases and
  linguistically cognitive problems.
• Each of these 'problems' probably has a number of
  different causes that are all interrelated.

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More on SSD

• This makes SSD a very difficult problem to solve.
  SSD can not be considered a binary trait or even
  one continuous trait.
• A broad array of metrics or phenotypes is needed
  to ascertain the very nature of SSD.
• Very powerful statistical methods are needed to
  ascertain a plethora of genetic sources.

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Even more on SDD

• These reasons make this disease somewhat
  subjective. Two different speech therapists may
  disagree if a subject even has speech sound
  disorder or the severity of the problem.
• Strict phenotypic metrics are used to secure
  accurate data

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Phenotype Measures

• Measures of Articulation
• The Percentage of Consonants Correct
• Nonverbal IQ
• Reading Decoding
• The Reading Comprehension Subtest
• Measure of Rapid Naming
• Measure of Verbal Short-Term Memory
• Measures of Vocabulary and Language Comprehension
  

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An example of an Articulation Measure (GFTA)

• Measures of articulation were used to assess
  production of various consonant sounds in
  singleton and cluster contexts in the beginning,
  middle, and final positions of words and blends.
• Subjects were asked to name pictures, and their
  responses were audiotape recorded and
  phonetically transcribed by trained
  speech-language pathologists.
• A percentile score was assigned as the
  quantitative trait for data analysis.

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What is BDNF ?

• The protein encoded by this gene is a member of
  the nerve growth factor family. BDNF was the
  second neurotrophic factor to be characterized,
  after nerve growth factor and neurotrophin 3.
• More specifically, it is a protein that is active
  in certain neurons of the central nervous system
  and the peripheral nervous system.
• It helps to support the survival of existing
  neurons, and encourages the growth and
  differentiation of new neurons and synapses.

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BDNF contd

• It is induced by cortical neurons, and is
  necessary for survival of striatal neurons in the
  brain.
• It is active in the hippocampus, cortex, and
  basal forebrainareas vital to learning, memory,
  and higher thinking.

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Speculation on why BDNF might have a correlation
with SSD

• BDNF helps to support the survival of existing
  neurons, and encourages the growth and
  differentiation of new neurons and synapses.
• In our dataset, we have a phenotype measure of
  verbal short-term memory.

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Speculation on why BDNF might have a correlation
with SSD contd

• BDNF is active in the hippocampus, cortex, and
  basal forebrainareas vital to learning, memory,
  and higher thinking.
• Language and speech are also functions of higher
  thinking. BDNF plays an important role in brain
  development.
• We also have measures of 'other traits' and the
  role of BDNF in these neuro-cognitive traits has
  never been tested.

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Ascertainment

• The data set consists of 161 families
• Probands were enrolled in speech-language therapy
  for moderate to severe errors of SSD with unknown
  origin.
• They were referred from the case loads of
  speech-language pathologists in the greater
  Cleveland metro area.
• Siblings of the probands were also recruited and
  assessed at the same time as the probands.

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My SNPs
frequencies derived from HAPMAP data
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S.A.G.E

• The association analysis was done by a software
  suite known as S.A.G.E. (http//darwin.cwru.edu/)
  
• Ran a test of association
• P-values, based on the likelihood ratio or a Wald
  test, can both be calculated for the
  transformation parameters.

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3 different models were run

• Dominance, Recessive, Additive
• Correspond to the Mendelian terms but applies to
  statistical models.
• So Dominance Treats both homozygote and
  Heterozygote as the same.

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Data results from S.A.G.E

• Results of S.A.G.E are in next 2 slides.
• Looked at all 3 models, but only showed the most
  significant
• Examined 10 different psychometric tests
• Results are in the form P values in the Wald
  statistical test. Below a .01 is significant

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Results

• I have found no supporting evidence to conclude
  that BDNF is in any way related to SSD.
• The data set consists of 161 families pedigrees
  ascertained through a proband with SSD.
• The majority of the sample was white, and most of
  the sample was from the middle- to upper-class
  SES strata.

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Results contd

• Language disorder was present in 23.4 of the
  children.
• Reading disorder was present in 21.6 of the
  children.
• Other co-morbidities were reported by the
  parents, and each represented 15 of the sample.

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Conclusion

• This is the first study that examines the
  association of SSD metrics and variations in the
  BDNF gene.
• I have run statistical family based association
  analysis on four SNPs in BDNF.
• I have found no supporting evidence to conclude
  that BDNF is in any way related to SSD.

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Thank you

• I would like to thank my research advisor Dr.
  Iyengar
• I would like to thank my academic advisor Dr.
  Chiel
• I would like to thank Lara Sucheston for helping
  with the data analysis
• I would like to thank Dmitry Leontiev for helping
  me with all of my lab work