2 Identifying Disease Genes/genetic Susceptibility Flashcards
Indications for cytogenetic analysis
Gross physical or mental retardation - especially associated with abnormalities
Ambiguous internal or external genitalia
Girls with 10 amenorrhea and boys with delayed pubertal development
Males w learned behavior disorder or who are taller then expected
Specific malignant and premalignant diseases
Family history of similar affected children
Couples with multiple spontaneous abortions of unknown cause
Tracing ancestors/ biological relationships
Prenatal diagnosis
Indications for cytogenetic analysis - prenatal diagnosis
Advanced maternal age, carrier status, h/o affected child, IUGR
Biochemical disorder
Congenital abnormality
Screening for neural tube defects and trisomy
Challenges to diagnosis
Big challenge - to identify genes underlying complex (multifactorial) diseases, in which there is no obvious predominant disease locus
Monogenic - influenced predominantly by single gene locus
Ogliogenic - disease phenotype may be dependent on a few genes
Polygenic - multiple gene factors determine phenotype eachmaking a small contribution EX: type 1 and 2 DM, coronary artery disease, stroke, RA, AD
Genes have been identified as genetic risk factors and protective factors
Next generation sequencing
Whole genome sequencing
Sequencing by synthesis
Most common and 99.9% accurate
Cut DNA -> add linkers -> flow cell -> in Situ PCR -> sequencing -< image of hundreds of extended molecules
Advantages : accurate and quick
Disadvantage: expensive ($1000) not worth it when looking at less then 20 genes
Karyotype
Test for chromosome abnormalities in a sample of cells usually in metaphase or prometaphase when chromosomes are mostly condensed
use GMIC staining that binds to AT regions
Preimplantation in genetic testing -> IVF
Advantages: cheap, easy, show major deletions and insertions, preimplantation genetic testing
disadvantages: Slow and labor intensive - 1 to 2 weeks, bas resolution, many mutations cannot be identified
Chromosome FISH
Chromosomal abnormalities
FISH - fluorescence in situ hybridization
Fix chromosome preparations on microscopic slides, treat the slides to denature DNA and hybridized flourescently labeled probes of interest to the denatured DNA
Locations of the four escape signals are recorded against a background stain that binds to all DNA sequences
Fix Cr -> denature DNA -> Flu. Probe hybridization -> record Flu. Signals
Advantages: increased resolution, show single mutations, fast
Disadvantages: must have premodern primer - no exploring
Ex: MYCN oncogene and Williams syndrom (deletion of long arm on chromo 7)
Identifying monogenetic disorders
Exome sequencing
Linkage analysis
Exome sequencing
Testing for monogenetic disorders
Some genetic disorders have not been well studied because they are very rare - useful in looking at rare or unknown disease
Majority of disease causing mutations - occur in the exons of protein-coding genes
Cost effective, less laborious - sequencing this fraction,just over 1% of the genome is an easier and cheaper option then genome sequencing
Linkage analysis
Testing for monogenetic disorders
Fundamental principle of genetic linkage: alleles at very closely neighboring loci (<50 map units) on a DNA molecule are co-inherited because the chance they are separated by recombination is very low
Statistical estimate of whether two loci are likely to lie near each other on a chromosome and are therefor likely yo be inherited together is called a LOD (logarithm of odds) score
LOD of 3 or more is generally taken to indicate that 2 loci are linked and close to one another
Thrifty phenotype
An adaptation that maximizes the chance of surviving in an adverse environment with limited calorie intake
Fetal nutrient starvation -> thrift phenotype -> low metabolic rate and reduced pancreatic beta cell mass and islet function
Altered metabolism is not well adapted to a later life where food is plentiful, increasing risk type 2 DM, obesity and HT
Phenocopies
Phenocopies- same phenotype with different genotype
Some affected people who do not have genotype commonly associated with the disease are phenocopies that have been wrongly classified as having the disease under the study
EX Alzheimer’s disease:
Rely on post-mortem brain pathology so we give provisional AD diagnosis - post mortem exam might reveal different type of dementia such as Levy dementia, frontotemporal dementia etc
For other phenocopies the phenotype might have an environmental origin
Genome-wide association studies (GWAS)
Complex diseases -> difficulty identifying susceptible locus -> GWAS
Rapidly scanning markers (SNPs) across the complete sets of DNA, or genomes of many people to find genetic variations associated with a particular disease
New genetic associations -> better strategies to detect, treat and prevent disease
Useful in finding genetic variations to common, complex diseases - asthma, cancer, diabetes heart disease and mental illness
GWAS in IBS
Very suvessful in Chron’s diseasesand ulcerative colitis
GWAS identified total of 163 risk loci for IBS
30 - specific for chron’s
23 specific for ulcerative colitis
110 risk factors for both
Autophagy machinery is now known to interact with many stress pathways - immune response and inflammation
Case-control studies
Most widely used method of investigating genetic and environmental basis of complex disease
Cases and controls investigated retrospectively - studies are open to bias
Prospective cohort studies
Boing advantage of removing bias
Study individuals over a long period of time before onset of disease
Periodic assessments of subjects - recording detailed info on the subjects and collecting samples for future lab tests
