Common disease - Rare variant (CD-RV) hypothesis is an alternative to Common disease - Common Variant (CD-CV). It says that the disease is caused by multiple strong-effect variants, each of which is found in only a few people. Instead of the common signpost pointing to a common weak-effect variant, it might be pointing to many strong-effect variants. According to CD-RV, a few people have one strong-effect variant (which causes the disease), a few have another, and so on.
This hypothesis does not necessarily claim that common disease cannot have common variant. It rather suggests that rare variants possibly requires careful consideration. Here, whole genome sequencing, instead of SNP polymorphism, can help a lot.
Two important links:
Showing posts with label Population genetics. Show all posts
Showing posts with label Population genetics. Show all posts
March 15, 2012
Common Disease - Common Variant
Common disease - common variant (CD-CV) hypothesis says that the common disease-causing allele (or variant) will be found in all human populations commonly having that disease.
Common variants (not necessarily disease-causing) are known to exist in coding and regulatory sequence of genes. CD-CV says, some of these variants lead to cause that disease.
Common example is SNP (Single Nucleotide Polymorphism) - single nucleotide base change in DNA. SNP variants tend to be common in different human population. This polymorphism have been valuable as "markers," in search for common variants causing a common disease.
In complex disease, the effect (additive or multiplicative) of a variant at a gene to cause the disease will be very small and it will be evolutionarily neutral, as so many genes influence a complex disease.
Common variants (not necessarily disease-causing) are known to exist in coding and regulatory sequence of genes. CD-CV says, some of these variants lead to cause that disease.
Common example is SNP (Single Nucleotide Polymorphism) - single nucleotide base change in DNA. SNP variants tend to be common in different human population. This polymorphism have been valuable as "markers," in search for common variants causing a common disease.
In complex disease, the effect (additive or multiplicative) of a variant at a gene to cause the disease will be very small and it will be evolutionarily neutral, as so many genes influence a complex disease.
March 14, 2012
Talk - Introduction to Population Genetics (2010)
Topics:
- Human genetic variation / diversity (including continental variation)
- Ancestry & race
- Linkage disequilibrium (with mutation and recombination)
Recombination Hotspot
Recombination hotspots are regions in a genome that exhibit elevated rates of recombination, relative to a neutral expectation. The peak recombination rate within hotspots can be hundreds or thousands of times that of the surrounding region.
60% of crossovers occur only in 10% of the genome. [http://www.youtube.com/watch?v=ZPnLTmJfUu0&feature=g-hist&context=G2ac1660AHT179vAAAAA Time:1:17:40]
60% of crossovers occur only in 10% of the genome. [http://www.youtube.com/watch?v=ZPnLTmJfUu0&feature=g-hist&context=G2ac1660AHT179vAAAAA Time:1:17:40]
March 13, 2012
March 6, 2012
Basic Terms in population genetics
Population Genetics: Study of naturally occurring genetic differences among organisms.
Genetic Polymorphism: Genetic differences that are common among organisms of the same species.
Genetic Divergence: Genetic differences that accumulate between species.
So, Population Genetics is the study of genetic polymorphism and divergence.
Gene: Roughly, gene is a genetic term meaning physical entity transmitted from parent to offspring during the reproduction process that influences heredity.
Genotype: Set of genes present in an individual.
Phenotype: Physical or biochemical expression of genotype.
Same genotype can result in different phenotype depending on environmental factors and same phenotype can result for 2 or more genotypes. Although genes do not determine complex phenotype owing to interacting genes and environmental factors, genes do determine molecular phenotypes.
Allele: Genes can exist in different forms or state. The alternative forms of gene are call alleles.
A gene corresponds to a specific sequence of constituents (called nucleotides) along DNA. Different sequences of nucleotides that may occur in a gene represent allele.
Transcription is the process in which sequence of nucleotides present in one DNA strand of a gene is faithfully copied into the nucleotides of RNA molecule. RNA has nucleotides A, U (instead of T in DNA), G & C.
After transcription, certain segments of the RNA transcript are removed by splicing. The eliminated segments are known as introns. The regions between the introns that remained in fully processed RNA are called exons.
In addition to splicing of exons, RNA processing also includes modifications to both ends of the RNA transcript. The fully processed RNA consitutes the messenger RNA (mRNA).
mRNA undergoes translation on ribosomes in the cytoplasm to produce polypeptide. In mRNA, each adjacent group of 3 nucleotides constitutes codon. Codon specifies the corresponding amino acids and subunits in the polypeptide chain.
Genome: The totality of DNA in a cell is the genome.
Within a cell, genes are arranged in linear order along the chromosomes. The position of a gene along the chromosome is called locus. In eukaryote, at any locus, every individual contains 2 alleles - one from mother, other from father. If both alleles are same, then the individual is called homozygous. On the other hand, if they are different, then that is called heterozygous.
Each human reproductive cell contains a complete set of 23 chromosomes. A human chromosome contains averagely 3500 genes. A cell has a genome size of approximately 3x10^9 base pairs.
Genetic Polymorphism: Genetic differences that are common among organisms of the same species.
Genetic Divergence: Genetic differences that accumulate between species.
So, Population Genetics is the study of genetic polymorphism and divergence.
Gene: Roughly, gene is a genetic term meaning physical entity transmitted from parent to offspring during the reproduction process that influences heredity.
Genotype: Set of genes present in an individual.
Phenotype: Physical or biochemical expression of genotype.
Same genotype can result in different phenotype depending on environmental factors and same phenotype can result for 2 or more genotypes. Although genes do not determine complex phenotype owing to interacting genes and environmental factors, genes do determine molecular phenotypes.
Allele: Genes can exist in different forms or state. The alternative forms of gene are call alleles.
A gene corresponds to a specific sequence of constituents (called nucleotides) along DNA. Different sequences of nucleotides that may occur in a gene represent allele.
Transcription is the process in which sequence of nucleotides present in one DNA strand of a gene is faithfully copied into the nucleotides of RNA molecule. RNA has nucleotides A, U (instead of T in DNA), G & C.
After transcription, certain segments of the RNA transcript are removed by splicing. The eliminated segments are known as introns. The regions between the introns that remained in fully processed RNA are called exons.
In addition to splicing of exons, RNA processing also includes modifications to both ends of the RNA transcript. The fully processed RNA consitutes the messenger RNA (mRNA).
mRNA undergoes translation on ribosomes in the cytoplasm to produce polypeptide. In mRNA, each adjacent group of 3 nucleotides constitutes codon. Codon specifies the corresponding amino acids and subunits in the polypeptide chain.
Genome: The totality of DNA in a cell is the genome.
Within a cell, genes are arranged in linear order along the chromosomes. The position of a gene along the chromosome is called locus. In eukaryote, at any locus, every individual contains 2 alleles - one from mother, other from father. If both alleles are same, then the individual is called homozygous. On the other hand, if they are different, then that is called heterozygous.
Each human reproductive cell contains a complete set of 23 chromosomes. A human chromosome contains averagely 3500 genes. A cell has a genome size of approximately 3x10^9 base pairs.
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