Variome meets the Genome: Challenges and Opportunities

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Variome meets the Genome Challenges and
Opportunities
Human Variome Project (HVP) Forum HGM2008
Satellite meeting 27th September 2008
Mitali Mukerji Institute of Genomics and
Integrative Biology CSIR, Delhi, India
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• SCA as a case study
• Clinically and genetically heterogeneous group of
  neurodegenerative disorders.
• Characterised by progressive cerebellar and
  spinal cord dysfunction.
• Clinical Features Gait ataxia, Dementia,
  Dysphagia, Opthalmoplegia, Retinal degeneration.

Mapped loci (disease gene unknown)
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Why LSDB for ataxia ??
SCAs Shows the phenomenon of Anticipation
Only genotype-phenotype correlation consistently
observed in all populations is anticipation
Confounders in clinical classification

• Due to considerable overlap between the
  symptomatology clinical classification is
  difficult in SCAs
• Clinical features varies among population of
  different ethnic origin
• At early stage disease show characteristic
  distinguishable features but with increasing
• duration symptoms converges to overlapping
  phenotypes
• Not all subtypes reported in populations e.g
  only six SCAs in India
• Some SCAs unique to populations - e.g SCA6 and
  DRPLA in Japan, SCA12 in India

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Total SCA families- 450 Characterized SCAs-
201 Uncharacterized 249
Prevalence and frequencies of ataxia in India
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• Advantage of an LSDB for ataxia
• provide valuable insight into phenotypic
  variability, locus heterogeneity of SCAs
  geographical and ethnicity specific variable
  expression
• Genotype phenotype correlation between repeat
  lengths and more detailed clinical assessment in
  SCAs among different populations would help
  establish accurate clinical classification and
  planning optimal treatment/disease management
  strategies
• It would help compare the variation in
  neurological features among different populations
  and thus enable identification of modifying
  factors responsible for phenotypic variability
• starting point for understanding the molecular
  correlates of phenotypes in ataxia which is a
  multi locus disease where related molecular
  mechanisms converge to overlapping phenotypes.
• Novel candidate regions can be identified

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Phenotype data
Public Submissions
XML Interface
Other Global Databases
PML Central
Blood/Buccal cells DNA isolation
PCR Multiplex PCR for rapid
screening at 5 loci SBE (SNaPshot)
Fragment analysis Direct Sequencing (ABI
sequencer 3130xl)
SCA1 SCA2 SCA3 SCA6 SCA7 SCA8 SCA12 DRPLA SCA17
Indian Genome Variation Database

• Repeat No. at respective loci
• Other sequence variants
• Haplotypes
• HGV accredited nomenclature

Mohd Faruq, Vinod Scaria Mitali Mukerji
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Spino-Cerebellar Ataxia Locus Specific Variation
Database
Built on the Leiden Open Variation Database
architecture Feature for Open Submission and
Curation of Variants and Phenotypes XML
interoperability for exchange of
genotype-phenotype details
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LSDB for SCAs
Patient Data
Variant Data
Standardised Variation annotation as per HGVS
Nomenclature Committee
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Advanced Search Interfaces
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Weakness of LSDB

• LSDB holds locus specific information for a
  particular gene/disease and mutations are mapped
  and curated as static information on a reference
  sequence
• The current configuration of LOVD does not allow
  for dynamic exchange of data from LSDB to genome
  level
• The contextual effect of the locus in the genome
  perspective is lost
• The locus specific information is limited by the
  knowledge of the curator
• Locus/Disease with multiple interacting
  partners/genes cannot be visualised
  comprehensively

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PP2A Assembly
Bß
PPP2R2B encodes subunit of the holoenzyme
assembly of PP2A
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Association of PP2A in Various Diseases
LTD
Sequester in SCA 1 Inclusion
Cellular Growth, Differentiation, Development

• Substrate
• Cellular Protein
• (Tau/Vimentin)
• Viral Proteins

• Signaling Cascade
• MAPK
• JAK/SAPK

Anp32a/Lanp Regulates PP2A
PKCs
PKB/Akt
Alteration In Activity Of PP2A
Alteration of Cellular Growth, Differentiation,
Development

• Hyper-phosphorylation of Tau
• Microtubule Destabilization
• Modification of Synapse Structure

Dysregulated signaling cascade
Implications In SCA 1 Transgenic Mice.
SCA 14
SCA 1
Cancerous Growth (Breast Cancer, Lung Carcinoma,
etc.)
Neurodegeneration (eg. Alzheimer disease)
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Genomic structure of PPP2R2B and alternately
spliced transcripts
Protein varient / divergent N termini
Transcripts alternate 5 splice varients
Bbeta1
Bbeta2
Bbeta3
Bbeta1
Bbeta4
Bbeta5 (predicted)
Bbeta7 (pridicted)
Bbeta6 (predicted)
Holmes et. al.
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c.279CAG1055
g.202694CAG1055
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Adapting a Wiki based approach to LSDB
Vinod Scaria Sridhar Sivasubbu _at_ IGIB
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Approach
LSDB Genome centric
LSDB Locus centric
Variations Mapped as static information
Dynamically integrated into genome
Community participation
Wiki
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