Genetics - Genome Variation and Trait Analysis Part 2 - Exam 4/Final - Dr. Shi

A particular SNP can predict the existence of a nearby gene in the....

same haplotype

What do genome-wide association studies do?

seek correlations between SNP patterns and phenotypes in large groups of individuals, seek SNPs that are shared with much greater frequency among individuals with the same trait than among others

Describe the Manhattan plot.

the -log10 p value from chi squared test is plotted, rare peaks indicate a significant association

What is linkage disequilibrium?

the presence of two or more loci on a chromosome with limited recombination between them, presence of LD at particular loci in a population can be evidence of common ancestry

What is positional cloning?

the process that enables researchers to obtain and locate a gene of interest without any prior knowledge of its protein product or function

What is the genetic marker of Fragile X syndrome?

the tip of X chromosome end dangled, separated by a thin thread, in affected individuals chromosome region has 200-2000 CGG repeats

What does chi square test determine/show in genetics?

used to show a significant difference between control and diseased groups

What is a haplotype?

a particular combination of alleles along a chromosome

Give an example of how a large family pedigree and positional cloning were used to map Huntington's Disease in 1984.

detection of linkage between the DNA marker G8 and the HD locus was found, linkage was between G8-C and HD

What are genetic markers?

identifiable DNA sequences with known physical locations on chromosomes, DNA sequence variations that can be used as a point of reference

How are frequencies of variants determined?

in large samples of control and disease groups

Individuals who carry a particular SNP allele at one site often carry specific alleles at other nearby variant sites. What is this correlation known as?

linkage disequilibrium (LD)

Genome wide association (GWAs) studies allow for the ______________ of complex-trait genes and do not use _________ _____________.

mapping, family pedigrees

What is Fragile X syndrome? What does it cause?

mental retardation, long and narrow face by adulthood, unusual X chromosome

What is the locus of the huntingtin gene?

4p16.3

What is the CFTR gene locus?

7q31

There are many different diseases and conditions associated with the localization of common SNPs. Give some examples.

Heart Disease, Type 1 and 2 diabetes, obesity, HIV disease progression, and prostate, breast, and colorectal cancers

What linkage analysis or association between the phenotype and the genetic marker?

all affected males have the fragile site at the x chromosome

How is positional cloning performed/analyzed?

all members of disease carrying family are genotyped with a series of DNA markers, candidate genes in the smallest genetically defined area that must contain gene locus are identified by a series of linkage analysis between trait and markers, compare sequence and expression of candidate genes in many diseased versus non diseased individuals

What does positional cloning require?

family pedigree, genetic markers, linkage analysis combining many DNA markers with the disease locus of interest

Scientists can map the location of genes to specific human chromosomes by...

positional cloning