Genes L14 Notes

Question 1

Describe the characteristics of Mendelian Diseases in Humans

Answer 1

•	Mendelian Diseases in Humans:
-	3 x 109 base pairs -> haploid genome
-	20,000 protein-coding genes
-	Mendelian / monogenic disease
	1% affected -> birth
	5% affected
	40% paediatric hospital referral -> Mendelian diseases

Question 2

What are the benefits of identification of disease genes?

Answer 2

•	Benefits of identifying disease gene?
-	Genetic testing:
Whole pop / high risk pop
Eg. Newborn blood spot test -> sickle-cell, hypothyroidism, inherited metabolic diseases. 
-	Development of new therapies:
Eg. Drugs, gene therapy
-	Provide insights into causes of other types of the disease
Eg. Alzheimers

Question 3

Describe the 3 steps in location of disease

Answer 3

Location of disease:
• Pedigree Analysis:
- Investigate disease occurrence -> families
 Determine mutation type
• Linkage Analysis:
- Search -> evidence -> genetic linkage between disease gene & markers
 Map disease gene
• Positional cloning:
- Select designated genes in region of chromosome
 Search -> disease-associated mutations -> each gene selected.

Question 4

Name the three stages in location of disease?

Answer 4

• Pedigree Analysis:
• Linkage Analysis:
• Positional cloning:

Question 5

Describe the function of pedigree analysis

Answer 5

• Pedigree Analysis:
- Investigate disease occurrence -> families
 Determine mutation type

Question 6

Describe the function of linkage analysis

Answer 6

• Linkage Analysis:
- Search -> evidence -> genetic linkage between disease gene & markers
 Map disease gene

Question 7

Describe the function of Positional cloning

Answer 7

• Positional cloning:
- Select designated genes in region of chromosome
 Search -> disease-associated mutations -> each gene selected.

Question 8

Describe the characteristics of autosomal recessiveness in Mendelian inheritance

Answer 8

• Autosomal recessive:
   Phenotype can skip generations
   Both parents -> carriers -> pass trait to offspring.
   Equally affects both genders.

Question 9

Describe the characteristics of autosomal dominance in Mendelian inheritance

Answer 9

• Autosomal dominant:
   Phenotype -> every generation
   Equally affects both genders
   Homozygous mutant -> sometimes lethal.

Question 10

Describe the characteristics of x-linked recessiveness in Mendelian inheritance, including examples of types of transmission using crosses

Answer 10

• X-linked recessive:
   More males affected
  -> males with one mutant allele -> hemizygous.
   Types of transmission:
  1. Transmission -> Female heterozygous carrier
   Half -> sons affected
   Half -> daughters carriers.

> > XAXa x XAY
> XAXA ; XAY ; XAXa ; XaY

2. Transmission -> Hemizygous affected male
    No sons affected / carriers
    All daughters -> carriers

 XAXA x XaY
XAXa ; XAXY ; XAXa ; XAY

3. Transmission -> Affected female:
    All sons -> affected
    All daughters -> carriers.

 XaXa x XAY
XAXa ; XaY ; XAXa ; XaY

Question 11

Describe the characteristics of x-linked recessiveness in Mendelian inheritance & the consequences of different types of transmission

Answer 11

	More males affected 
-> males with one mutant allele -> hemizygous. 
	Types of transmission:
1.	Transmission -> Female heterozygous carrier 
	Half -> sons affected
	Half -> daughters carriers. 
2.	Transmission -> Hemizygous affected male
	No sons affected / carriers
	All daughters -> carriers
3.	Transmission -> Affected female:
	All sons -> affected
	All daughters -> carriers.

Question 12

Describe the characteristics of x-linked dominance in Mendelian inheritance, including the consequences of different types

Answer 12

• X-linked domiant:
   Affected male parents
  » All daughters affected
  » No sons affected / carriers

           >> XdXd       x        XDY
               XDXd ; XdY ; XDXd ; XdY

 Affected heterozygote females
» Half -> sons affected
» Half -> daughters affected.

> > XDXd x XdY
XDXd ; XDY ; XdXd ; XdY

Question 13

What is the result of an x-linked recessive mendelian inheritance in which transmission occurs from female heterozygous carrier?

Answer 13

Transmission -> Female heterozygous carrier
 Half -> sons affected
 Half -> daughters carriers

Question 14

Describe the problems affecting pedigree analysis

Answer 14

Problems affecting pedigree analysis:
• Incomplete penetrance / Variable expressivity
 Not all carrying disease allele express phenotype.
• Delayed onset
Eg. Huntington’s, familial breast cancer.
 Even though dominant genetic disease, phenotype only expressed later in life ->
after reproduction -> already potentially passed to offspring.
• Genetic Heterogenity
- Mutations -> different genes -> produce same disease
Eg. 3 genes -> familial early-onset Alzheimers
- Can solve this by observing genetically homogenous populations
Eg. Icelanders & Mormons
• Non-paternity / misattributed paternity

Question 15

Explain why there are difficulties using linkage analysis to study disease genes. State what method is used as an alternative solution.

Answer 15

• Difficulties using linkage analysis to study disease genes as requires at least 2 genetic disease genes present in a family at any one time.
 Solved by DNA markers.

Question 16

Describe the requirements of DNA Markers

Answer 16

•	DNA Markers:
-	Requirements:
	Polymorphic:
>> 2 or more alleles -> significant proportion of population
>> Easy to assay 
   -> Easy to distinguish alleles.

Question 17

Name the types of DNA markers commonly used

Answer 17

Short Tandem Repeats (STRs)

Single Nucleotide Polymorphisms (SNPs)

Question 18

What are STRs/ Short tandem repeats?

Answer 18

 Short Tandem Repeats (STRs)
Microsatellite repeats
Tandem repeats -> Short, non coding sequences (2-4 nucleotides)
Eg. GAGAGA / TTATTATTATTA
Longer repeats (>10 nucleotides) -> minisatellite repeats.

Question 19

Describe how STRs can be used in forensic analysis

Answer 19

 Forensic Analysis -> STRs
Polymerase Chain Reaction (PCR)
»_space; Amplifies 10 STRs & Gender DNA marker
>Separated -> electrophoresis -> DNA profile.
Forensic uses -> DNA profiles:
»_space; Each individual excl. identical twins -> unique DNA profile
»_space; Individuals placed at scene -> analysis -> hair, blood, saliva / semen
samples.
»_space; DNA profiles of crime -> compared -> suspect / database profiles
»_space; Close matches -> indicate close relatives.

Question 20

What is a Single Nucleotide Polymorphism?

Answer 20

 Single Nucleotide Polymorphisms (SNPs)
Non-coding DNA
Most common type found -> Human genome
Abundant & easy to identify -> gene chip technology

1 Nucleotide difference per 1000 nucleotides -> Any 2 individuals.

Question 21

Describe the HapMap project

Answer 21

HapMap Project:
»_space; Gene chip technology -> identification -> common SNPs -> across
ethnic groups.
SNP genotyping -> GeneChip
»_space; Each individual -> pedigree
-> 0.5-1 mill SNPs genotyped
-> Each SNP tested -> linakge w/ disease phenotype -> using genetic
model.
-> Identifies several SNPs in region -> genome where disease must be
located.

Question 22

Describe what is occurring in this family inheritance of the homozygous female offspring in terms of x-linked inheritance

{} -> Family/siblings [] - Reproduction
- Generation 1:
[ XAY x { XAXB ] + XAY }
Generation 2:
{ XAY + XBY + [ XAXA } x XBY ]
Generation 3:
{ XAXB x XAXB XAY }

Answer 22

• Pedigree Analysis -> X-linked SNP -> 2 alleles -> family w/ Haemophillia A
   Allele A -> Always associated -> haemophilia -> hemizygous males
  »Evidence -> linkage to disease in family.
  »Allele A not causing disease -> a disease allele linked to this haemophilia
  allele on chromosome is.
   Female (Generation 2) -> Homozygous AA -> not affected
  » 2nd allele -> father (Generation 1)
  ->Family didn’t suffer with Haemophillia A
  »Haemophillia allele not actually causing disease
   Disease allele linked to haemophilia allele on mother’s side of family is.
  -»Therefore homozygous female -> not affected -> only one of the
  haemophillia alleles inhertited -> linkage with disease allele ->
  haemophilia allele from father’s family not linked to disease allele.
  -> So heterozygous for disease allele.

Question 23

What is a haplotype?

Answer 23

• Haplotype:

 Particular combination of SNPs -> small chromosomal region.

Question 24

Describe how the haplotype of individuals are determined.

Answer 24

• 6,000 bp -> 20 of which are SNPs.
  Each individual -> one of 4 possible haplotypes
  -> 1 haplotype -> same differences in nucleotide seq. to other haplotypes.
  Therefore identification of Haplotype can be done using tag SNPs rather than assessing all differences in SNP bases.
  »_space;For example -> at particular nucleotide base -> A/G tag
  -> if A nucleotide -> Haplotype 1/2/4/
  At 2nd tag -> T/C ->
  -> if C nucleotide -> Haplotype 2/4
  At 3rd tag -> C/G ->
  -> if C nucleotide -> Haplotype 4
  Therefore identifying haplotype.
  »Genotyping 3 tags of 20 sufficient to identify haplotype.

Question 25

Describe a factor affecting linkage of a disease allele & SNPs regarding location on the chromosome. Explain the consequences of these possible factors that may occur.

Answer 25

- The closer a mutation occurs to a particular SNP on the chromosome, the higher the linkage illustrated by that SNP to the disease in future generations / the higher the no. of future generations with SNPs associated to the disease. - The further away an SNP is located from the original mutation on the chromosome, less likely association will still be present as the no. of future generations/pedigrees incr. Eg. Muatation closest -> SNP1 & furthest -> SNP3. ->> SNP3 -> least linkage with disease ->> SNP2 -> linkage in some pedigrees. ->> SNP1 -> linkage -> all pedigrees.

Question 26

What is positional cloning

Answer 26

• Positional Cloning:  Identifies candidate genes -> inspection -> specific region -> human genome sequence .  Sequences -> Candidate genes -> affected & unaffected observed.  Location within genome of SNPs -> disease linkage known.

Question 27

Describe Disease Gene Discovery using Next Generation Sequencing (NGS)

Answer 27

• Disease Gene Discovery -> Next Generation Sequencing (NGS): - Sequencing -> Whole genomes (WGS) & whole exomes (WES) -> unaffected & affected pedigree individuals. - Identification -> rare variants ->> shared only by affected individuals. - Identification -> potential causative variants in candidate genes - Investigation -> functional consequences -> potentially causative variants.  Highly effective -> identification -> de novo mutations -> parent-child trios.

Question 28

Symbols in pedigree analysis? Male ; Female ; Affected & Non-affected ; Deceased ; Heterozygous ; Twins ; Monozygotic twins ; Consanguineous relationships / mating between individuals.

Answer 28

• Symbols in pedigree analysis: - Circle -> Female - Square -> Male - Coloured -> Affected - Half-coloured -> Heterozygous carrier - Diagonal line through shape -> Deceased - 2 individuals -> same generation -> joined by = -> Mating between relatives (Consanguineous) - 2 individuals -> same generation -> joined by ^ - 2 individuals -> same generation -> joined by triangle -> monozygotic twins