Human Genetics 1

Question 1

Who do human genetic disorders effect?

Answer 1

… affect at least 2% of all new born babies
… account for 50% of all childhood deafness, mental retardation and death
… affect 5% of the total population by the age of 25
… genetic variation also impacts on diseases in old age e.g. Alzheimer’s, osteoporosis and cancer

Question 2

Classification of Human Genetic Disorders

Answer 2

1) single gene disorders
2) chromosome disorders
3) multifactorial disorders (the most common)

Question 3

Locating the Genes / Variations Responsible for Human Phenotypes

Answer 3

• segregation of hereditary traits studied in families
• family trees drawn to determine mode of inheritance
• statistical associations sought between genetic variation and hereditary traits to locate ‘disease alleles’ and genes responsible for other phenotypes

Question 4

Autosomal Dominant Conditions

Examples

Answer 4

-Huntingdons
-myotonic dystrophy
-early onset Alzheimer’s
and >3160 others

Question 5

Autosomal Dominant Conditions

Characteristics

Answer 5

• affected person usually has one affected parent
• can affect either sex
• transmitted by either sex
• a child of an affected x unaffected mating has a 50% chance of being affected

Question 6

Penetrance

Definition

Answer 6

-the percentage of individuals with a particular genotype that express the phenotype expected of that genotype

Question 7

Expressivity

Definition

Answer 7

• the degree to which a trait is expressed

- variations in the expressed phenotype

Question 8

What is an example of incomplete penetrance?

Answer 8

osteogenesis imperfect - brittle bone disease

Question 9

Osteogenesis Imperfecta

Answer 9

• caused by a mutation in collagen encoding genes
• the mutations alter glycone by adding a bulkier side chain to the molecule which disrupts the tertiary structure
• affects the ability of collagen to bind to mineral components of bone causing them to become brittle

Question 10

What is an example of variable expressivity?

Answer 10

polydactyly

Question 11

Polydactyly

Answer 11

• a common condition seen in 1 in 500 births
• variable expressivity can affect the number / size / appearance of digits
• caused by mutations in a number of different genes

Question 12

Autosomal Recessive Conditions

Examples

Answer 12

-cystic fibrosis
-beta-thalassaemia
-tay-sachs disease
and >3000 others

Question 13

Autosomal Recessive Conditions

Characteristics

Answer 13

• affected individuals usually born to unaffected parents (carriers)
• carriers are asymptomatic
• parental consanguinity increases incidence
• affect either sex
• 2 carriers have a 25% chance of having affected offspring

Question 14

Cystic Fibrosis

Frequency

Answer 14

• most common inherited disorder in the UK and in Caucasian European populations
• 1/25 Europeans of Caucasian descent carry a defective CF allele

Question 15

Cystic Fibrosis

Cause

Answer 15

• loss of phenylalamine at position 508 in the cystic fibrosis transmembrane conductance regulator
• a membrane located ATPase responsible for secretion of Cl- ions from cells

Question 16

Cystic Fibrosis

Symptoms, Treatment and Prognosis

Answer 16

• build up of viscous mucus affects breathing and provides a fertile site for bacterial infection
• management by physiotherapy
• gene therapy has been developed but the success rate is currently quite low
• survival beyond age 35 is rare but improving

Question 17

Beta - Thalassaemia

Cause

Answer 17

• nonsense mutation in haemoglobin B (HBB) gene encoding beta-globin
• results in reduced synthesis of haemoglobin
• reduced oxygen carrying capacity of the blood

Question 18

Beta - Thalassaemia

Malaria

Answer 18

• beta-thalassaemia affects blood cells
• upon interaction with malaria, blood cells in affected individuals disintegrate as they are relatively fragile
• this means that sufferers have an enhanced resistance to malaria

Question 19

Beta - Thalassaemia

Frequency

Answer 19

• the recessive allele is most prevalent in Mediterranean and Middle Eastern populations
• this is in areas where malaria is more prevalent as this gives a selective advantage to carriers of the disease allele

Question 20

Sickle Cell Anaemia

Cause

Answer 20

• mutation in the haemoglobin B (HBB) gene encoding beta-globin
• point mutation resulting in the change of an amino acid from glutamic acid to valine
• effects folding preventing correct binding with oxygen
• also gives red blood cells a characteristic sickle shape

Question 21

Sickle Cell Anaemia

Malaria

Answer 21

• heterozygous individuals (carriers) are resistant to malaria
• sickle trait is incompletely recessive so heterozygotes will have a small number of sickled red blood cells which malaria cannot infect

Question 22

X-Linked Recessive Conditions

Examples

Answer 22

-haemophilia
-ducheme muscular dystrophy
-fragile X syndrome
-red green colour blindness
and >1100 others

Question 23

X-Linked Recessive Conditions

Characteristics

Answer 23

• mainly affect males as they only have one copy of the X chromosome
• affected males are usually born to unaffected parents
• females always affected if father is affected and mother is at least a carrier
• females can also be affected by non random X inactivation
• no male to male transmission as males pass on their X chromosome to their daughter and their Y chromosome to their sons

Question 24

X-Linked Dominant Conditions

Examples

Answer 24

-X linked vitamin D resistant rickets
-CMTX
and ~500 others

Question 25

X-Linked Dominant Conditions | Characteristics

Answer 25

- can affect either sex but females more than males - females are more often mildly and more variably affected than males - the child of an affected female has a 50% chance pf being affected regardless of sex - for an unaffected male, all of his daughters will definitely be affected

Question 26

Mitochondrially Inherited Conditions | Examples

Answer 26

- Leigh's disease - leber optic distrophy - kearns-sayre syndrome - MELAS - MERF

Question 27

Mitochondrially Inherited Conditions | Characteristics

Answer 27

- affected individuals born only to affected females - all offspring of affected females are affected to some degree - affected males cannot pass on the condition - this is because the zygote gets its mitochondria from the egg

Question 28

Leigh's Disease

Answer 28

- neurological syndrome - usually results in early infant mortality - symptoms: ataxia, neurodegeneration, lactic acidosis - progressive death of brain cells eventually leads to death - several causes which might be autosomal recessive, X-linked recessive ot mitochondrial inheritance

Question 29

Triparental IVF

Answer 29

- two possible procedures i) obtain zygote from father and affected mother, transplant zygote nucleus into enucleated donor egg from healthy donor female ii) transplant nucleus of affected mother's egg cell into enucleated egg of healthy donor female, then fertilise the 'recombinant' egg

Question 30

First Question Asked When Trying to Determine the Sequence of a Phenotype

Answer 30

-is the biochemical basis of the phenotype known?

Question 31

Finding the Sequence of a Phenotype | Biochemical Basis of Phenotype Known

Answer 31

- protein sequence can be used in a genome database search - identify the gene sequence in the human genome - PCR amplify the gene from the affected and unaffected individuals - identify any mutations in the affected individual and their family

Question 32

Finding the Sequence of a Phenotype | Biochemical Basis of Phenotype Unknown

Answer 32

- have to locate gene in genome, identify the correct coding sequence, determine the nature of the mutation - there are two statistical approaches which can be used to achieve this: i) analysis based on genetic linkage ii) analysis based on allelic association - both methods rely on genetic variation (polymorphism) between individuals

Question 33

Autozygosity Mapping

Answer 33

- pedigree analysis in families with a high incidence of consanguineous marriage - offspring homozygous for the causal mutation are also likely to be homozygous for a large region of DNA either side of the mutation as well - by comparing the genomes off individuals with the disorder you can identify the disease interval, the smallest section of chromosome required for the disorder - this means that the causal mutation is somewhere in that genetic interval - the genetic interval in which the causal mutation lies will be homozygous in affected individuals and heterozygous in unaffected family members

Question 34

Genetic Polymorphism | Definition

Answer 34

- existence of two or more variants at significant frequency in the population - any DNA sequence variant present at a frequency of >1% in the population - any non-pathogenic variation

Question 35

Uses of Genetic Polymorphisms in Human Genetics

Answer 35

-polymorphic regions of DNA that segregate with the target allele can be used to track the inheritance of certain alleles through a family tree

Question 36

Genetic Markers | RFLPs

Answer 36

- restriction fragment length polymorphisms - can be used to identify genotypes if it associated with a disease allele - not convenient to use - detection of RFLPs requires southern blot using a cloned probe, a relatively slow and laborious process

Question 37

Genetic Markers | SSRs

Answer 37

- simple sequence repeats - sequence length variants at defined positions in the genome resulting from DNA replication errors - easily detected by PCR - used for genetic fingerprinting - but only about 10^5 exist in a genome

Question 38

Genetic Markers | SNPs

Answer 38

- single nucleotide polymorphisms (snips) - very common, 1 every 100-300 bp in the human genome - easily detected by PCR - identified in whole genome sequencing so we know what the sequences of DNA to either side of them are making it easy to design primers - use a gene specific primer which binds to the sequence before the SNP - use allele specific primer which include the SNP so can be used to distinguish between different alleles - competitive PCR between gene specific and allele specific primers is the basis of a number of medium-through put genotyping assays that can score the allelic status of thousands of different SNP loci simultaneously in large numbers of individuals

Question 39

Analysis Based on Genetic Linkage

Answer 39

- ideally requires large multi-generational families (OR many small families considered collectively) - known mode of inheritance - useful for single gene disorders

Question 40

What do linkage and association studies rely on?

Answer 40

-co-segregation of alleles and phenotype

Question 41

Co-segregation - Parental Genotype AaBb | 2 genes on different chromosomes

Answer 41

- independent assortment in meiosis - 25% of getting each combination - cannot detect any genetic linkage

Question 42

Co-segregation - Parental Genotype AaBb | 2 genes far apart on the same chromosome

Answer 42

- recombination is frequent enough for loci to assort independently - 25% chance of getting each combination - cannot detect any genetic linkage

Question 43

Co-segregation - Parental Genotype AaBb | 2 genes close together on the same chromosome

Answer 43

- close linkage between loci - cosegregation of linked alleles - most of the time you get parental combinations - but very rarely you get recombinants

Question 44

Close Linkage Between Polymorphic and Disease Locus

Answer 44

- if the polymorphic locus is sufficiently closely linked to an autosomal dominant disease gene, we can score the presence of a particular allele at the polymorphic locus as a predictor of affected status - variation at the polymorphic locus is NOT responsible for the disease phenotype, but is LINKED to the genotype that is responsible for the phenotype

Question 45

Haplotype Analysis

Answer 45

- by increasing the number of markers tested you have a better chance of defining the chromosomal region carrying the affected gene - alleles at linked loci distinguish maternal and paternal chromosomal regions - haplotypes consisting of co-segregating alleles are common because recombination is infrequent and not entirely random

Question 46

Is recombination random?

Answer 46

- no - there are locations on a chromosome where recombination is supressed e.g. at the centromere - and regions where recombination is frequent, recombination hot spots

Question 47

Linkage Disequilibirum

Answer 47

- loci between which there is very little recombination, causing allelic co-segregation, are said to be in linkage disequilibrium - linkage disequilibrium describes a measure of the 'correlation of co-segregation' - it can be calculated as a correlation coefficient which decreases as distance between loci increases

Question 48

Co-segregation and Recombination

Answer 48

-cosegregation and recombination can be used to locate chromosomal regions where genes of interest must lie