Home / Summaries / FM2004 / mapping-genome-genetic

Tutorial title - Gene mapping and disease gene identification

59 important questions on Tutorial title - Gene mapping and disease gene identification

How many genes does the human genome contain?

20,000 to 25,000 genes

What does the human genome project identify?

Physical location of every element in the human genome

What are the diagnostic application of gene mapping/identification?

1. Genotype-phenotype correlations (how a patient may progress or present depending on their mutation)
2. Prenatal, presymptomatic, carrier testing, spectrum of mutation
3. Genetic counselling, disease frequency

What is the purpose of gene mapping?

- to understand diseases or traits
- understand the pathogenesis (how is it doing that?)
- develop therapies accordingly

What is the limitation of the human genome project (HGP)?

Doesn't identify a gene or implicate it in a trait/disease, requiring gene mapping

What is the difference between physical mapping and gene mapping?

Physical mapping
- assign genes to a chromosal location using measurements of physical distance
Genetic mapping
- estimation of how close 2 loci are based on how frequently recombination is detected

What are the tools of measurement used for physical mapping?

1. Chromosomal abnormalities
2. FISH (fluorescent in situ hybridisation)
3. DNA sequencing

What is FISH (fluorescent in situ hybridisation)?

A fluorescent probe complimentary to gene of interest hybridises/binds to a specific chromosomal location

What are the two methods of DNA sequencing?

Whole genome sequencing (WGS)
Whole exome sequencing (WES)

What are the two methods used for genetic mapping?

Linkage analysis and association analysis

Linkage analysis is best suited for what type of disorders?

Family based, single gene disorders

What pattern suggests linkage in a family?

Consistent, repeated inheritance of a particular genomic region with the trait

Association analysis is best suited for what type of disorders?

Population based, complex/single gene disorders

What does recombination/crossover do?

Breaking and reforming of chromosomes during meiosis

Is crossover more likely to happen in 2 loci that are far apart or close together on a chromosome?

Far apart

What does lots of reshuffling between 2 loci on a chromosome imply?

2 loci are far apart

What does reduced/absence of reshuffling between 2 loci imply?

2 loci are close together

What are the essential components for genetic mapping?

1. A marker of known location that can be tracked
2. A phenotype (observable trait) that can be tracked

What is determined from the essential components of genetic mapping?

If the marker and trait are inherited independently or together.

What are the possible reasons behind a marker and phenotypic trait being inherited independently?

2 loci on different chromosomes or far apart on same chromosome

What is the possible reason behind a marker and a phenotypic trait being inherited together?

2 loci are physically close to one another on the same chromosome

What makes a good genetic marker?

Follows Mendelian inheritance

Easily accessible material (blood, buccal swab)

Easy and cheap to genotype

Highly polymorphic (high chance of heterozygotes)

What are the features of DNA VNTRs (microsatellites) make them an ideal genetic marker?

- 10⁵ loci in the genome (abundant)

- many alleles = highly polymorphic

- highly informative

- can be assayed by automated multiplex PCR = easy and relatively cheap to genotype

- easy physical localisation

- distributed throughout genome

What are the features of DNA SNPs that make them an ideal genetic marker?

- 10⁷ loci across the genome (abundant), densely distributed across genome
- More stable over evolutionary time than microsatellites
- has massively parallel technologies that allow a sample to be assayed for thousands of SNPs in a single operation

What is the variation detected in polymorphic microsatelite markers?

The variation in the number of repeats of a microsatelite (short DNA sequence)

What are the steps for polymorphic microsatelite marker detection?

1. Amplification via PCR
2. Separation depending on size by electrophoresis

Why do microsatellite alleles differ in size?

Because individuals have different numbers of repeat units

How is a polymorphic marker applied to pedigree analysis?

1. Assign marker alleles to family members (numbers, letters, bp sizes, etc..)
2. Track the inheritance of the specific piece of DNA through a pedigree

What does linkage analysis examine the inheritance of in a pedigree?

1. Disease locus with unknown location
2. Polymorphic marker locus with known location

What are the characteristics of inheritance of two unlinked loci?

- transmitted independently of each other
- not physically close

What are the characteristics of inheritance of two linked loci?

- transmitted toegether
- physically close on the same chromosome

After detecting linkage of two loci, what is the next step?

- check if nearby markers also display the same non-random pattern of inheritance
- try to identify smallest region shared by affected individuals

How are candidate genes selected within the region?

Use knowledge of disease biology --> candidate genes
Screen all genes in the region regardless of function (location-based)

Why is gene screening necessary after mapping?

Linkage analysis only gives you a rough range of genes that might be causing the disorder. Gene screening allows you to actually identify the causative gene from a big number of candidate genes.

Which regions of a gene are typically screened?

Coding regions of a gene: exons, splice sites

What common mutation types are screened for?

Missense
Nonsense
Splice-site mutations

How do you determine if a DNA variation is disease-causing (a mutation)?

Compare the DNA samples with other individuals in the family and the control samples (population)

What are the characteristics that confirm a variation is a mutation?

- alteration in protein (amino acid, splicing, conserved residue)
- functional change (demonstrated through cell and animal models)

What are candidate genes?

Genes that are likely to be involved with the disease based on disease mechanism or location

How can positional cloning help identify candidate genes?

1. Identify chromosomal region that contains disease gene
2. Narrow down by considering what genes in that region may cause disease

Example of a candidate gene approach in Retinitis Pigmentosa (RP)?

1. Disease locus mapped to chromosome 3
2. Rhodopsin gene also located on chromosome 3
3. Therefore, rhodopsin is a strong candidate gene
Retinitis Pigmentosa = progressive retinal degeneration, loss of night vision
Rhodopsin = essential for night vision

What are the main steps in disease gene identification?

1. Linkage analysis: map disease region
2. Genetic databases: identify genes in region
3. Find candidate genes by either animal homology or identification of map breakpoints by analysis of chromosomal translocation or deletion in patient
4. Use of whole-genome or exome sequencing to identify the pathogenic mutation from the candidate genes

What is whole exome sequencing (WES)?

Analysis of coding regions of all known genes in an individual

What is whole genome sequencing (WGS)?

Analysis of entire genome of an individual

What are the common steps that follow whole exome and genome sequencing?

1. Identify variants by filtering against known databases
2. Identify novel variants and the genes from those novel variants
3. Confirm the variant gene in other affected individuals by performing functional analysis

What is a novel variant?

newly discovered, distinct genetic alteration that has never been previously reported in population databases

What is dbSNP (single nucleotide polymorphism database)?

A catalogue of all known SNPs (single nucleotide polymorphism) that includes population frequency data.

What is the HapMap project?

A resource cataloguing ~5 million SNPs (single nucleotide polymorphisms) across different populations and identifying representative SNPs due to clustering

What is the 1000 Genomes Project?

Whole-genome sequencing of diverse individuals to document human genetic variation across multiple populations.

Which variants are filtered out from millions of variants from WES/WGS?

- not located within or near an exon
- appears too frequently in variant databases to cause disease
- variant has no predicted functional consequence
- inconsistent with inheritance model

How much of the 3 billion base pair long human genome encodes proteins?

Less than 1.5% of the human genome encodes proteins

What is comparative genomics?

Comparison of genomes from different populations/species to see what genes/sequences are conserved

What is functional genomics?

The study of gene expression and function + protein function and protein-protein interactions after genome sequencing by using tools like microarrays (gene expression), proteomics, and interactome analysis.

What is the purpose of The Cancer Genome Atlas (TCGA)?

Understand the molecular basis of cancer through the application of genome analysis technologies

What are the results of improved features of sequencing technologies?

1. Highly automated
2. Reduced cost (from $1 million in 2007 to $600 now)
3. Very high throughput
4. Improved efficiency

What are bioinformatics tools used for?

To efficiently use large biological datasets with the use of sequencing or microarrays to identify patterns, predict, and compare with other species

What is the aim of 1000 genomes project?

Provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations

What is the precision medicine initiative?

Aim to understand how genomic variations and other health factors (genome, lifestyle, clinical data) affect the development of diseases.

Why is gene analysis a bottleneck?

Because gene analysis is a much slower and expensive process than gene sequencing

The question on the page originate from the summary of the following study material:

FM2004

View summary

A unique study and practice tool
Never study anything twice again
Get the grades you hope for
100% sure, 100% understanding

Remember faster, study better. Scientifically proven.