Gene Hunting

Natália F. Martins

Resumo

• 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

Biomedical scientists -- analyzing DNA, disease biochemistry

Families - cooperating thru an interest in their own families

Coordination -- informal, based on the medical & scientific norms of the professions, with complex patterns of cooperation.

Generating public knowledge on the disease -- publication key

Methodology

1. A qualitative phase

Selection of words, therms and related literature

2. A quantitative phaseExpression levels, microarray data, experimental data.Combinatorial chemistry, drug design

Whole genomes

Key words

interactions

References

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 • 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

– 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

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Developing the Market: Monogenetic Disorders

basic gene or protein encodingsequence

diagnostic method/assay

therapeutic molecule/treatment forspecific disease

other

Genetic basis of disease

Phenotype

Disease state

– Complex, often contested definitions & diagnoses, arising at different ages etc.

Genotype

Genetic mutations (polymorphisms)

– Located over 50,000-80,000 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?