Transcript Gene Hunting

Gene Hunting
Natália F. Martins
Resumo
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Motivação
Estratégia
Automatização (?)
Exemplos
Referências
Motivação
• A Busca de genes pode ser motivada pela
necessidade de desenvolvimento de drogas
inibidoras,
• Por aplicações biotecnológicas, biofábricas
• Ciência básica.
Traditional Organization of Gene Hunting
Physicians - working
with families, gather
medical information Families - cooperating
thru an interest in their
own families
Biomedical scientists
-- analyzing DNA,
Coordination -- informal, based on the
disease biochemistry
Generating public knowledge on
the disease -- publication key
medical & scientific norms of the
professions, with complex patterns of
cooperation.
Methodology
1.
A qualitative phase
Selection of words, therms and related literature
2.
A quantitative phase
Expression levels, microarray data, experimental data.
Combinatorial chemistry, drug design
Whole genomes
References
Key words
interactions
Arrays data
Top10 list
Experimental
phase
Automatização é Possível
Exemplos
• Cell signaling
• Zebra fish
• Virulence
Cell signaling pathways in Paracoccidioides brasiliensis inferred from comparisons with other fungi
• The identification of putative genes involved in the cellular signaling
pathways was performed by the “search by key word” service provided
by the bioinformatics group of the PbGenome project (Felipe et al.,
2003). The classification of candidates according to the signaling
category families was performed by a BLASTx (Zhang, 2003)
comparison of sequences against a database with all the signaling
protein sequences from Genbank (Benson et al., 2004). The analyzed
clusters were assembled by CAP3 software in the sequence-processing
pipeline from the PbGenome project. The multiple sequence alignment
of the candidates was performed using CLUSTAL W software (Aiyar,
2000).
Transcriptome Analysis of Zebrafish Embryogenesis
Using Microarrays
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PLoS Genet. 2005 August; 1(2): e29. Published online 2005 August 26. doi:
10.1371/journal.pgen.0010029.
• Methods
– Embryo collection
– RNA isolation and reference RNA
– Zebrafish oligonucleotide probe design and
microarray construction
– Data acquisition and statistical analysis
Vibrio cholerae recovered
directly from patient specimens
• Methodology
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Collection of clinical samples
RNA and genomic DNA extraction.
Microarrays and hybridization
Statistical analysis
Differential expression of genes in the TCP island
during early compared with late human infection,
represented as log10 fold change. Expression of the
transposase sequence (tnp) of the TCP island is
shown at the left, and that of the integrase gene
Gene Hunting and Drug Design
Genetic basis of disease
Phenotype
Disease state
– Complex, often
contested definitions &
diagnoses, arising at
different ages etc.
Genotype
Genetic mutations
(polymorphisms)
– Located over 50,00080,000 genes, subject
to high levels of
natural variation or
noise
Added Statistical complexity
• Two types of disease
• Monogenic -- mutation in one gene leads to disease follows
Mendelian inheritance
• Polygenic -- mutations in several genes lead to disease follows
complex inheritance patterns
• Susceptibility -- genes may confer susceptibility
rather than necessarily the disease itself
(penetrance)
• Very high levels of background noise making the
search for mutations difficult
Population genetics projects very complex and
difficult – access to desirable population a key
Key Types of Knowledge
for Population Genetics
Medical Records: Provides information on phenotypes, but
this can be complex, difficult to define, not available to the
patient in full detail.
Genetic Records: Also known as genetic maps. Developed
from tissue samples, blood etc. using a range of different
techniques including search for genetic markers.
Genealogical Records: Given the complexity of finding
statistical correlation, family records provide improved
“roadmaps” by reducing the background noise, using
inheritance information & common markers.
Summary and Implications
• A market exists for genetics exists, but is
constrained
– Very little buying and selling of property rights to
populations
– The “borrowing” strategy has, along with fears of group
revolts, necessitated the imposition of medical research
norms that limit the degree to which information can be
exploited
• A “moral economy” surrounds this market
• Competition between public and commercial
projects may be increasing
Fonte : www.genomeprairie.ca/gels/news/crsgovrdocs/Casper.ppt
2005
Future
What the bleep do we know?