single gene pathology

Question 1

what will a genome browser show?

Answer 1

the reference to identify what is normal - it will show a chunk of a chromosome and the genes within in and their relative locations along chromosome

Question 2

why might a gene be represented multiple times?

Answer 2

variations in splicing and mRNA

Question 3

what is OMIM?

Answer 3

It is a catalogue of human disease - shows which genes in the chromosome are associated with which conditions

Question 4

what are two sources of pathology?

Answer 4

repeat sequences or point mutations - these cause the bulk of single gene inherited disease

Question 5

what are interspersed repeats?

Answer 5

they are the important parts of repeat sequences that move themselves around the genome by retrotransposition - DNA - RNA - DNA
LINE and SINE both have a role in generating single gene pathology

Question 6

what are the characteristics of interspersed repeats?

Answer 6

they are scattered around the genome, with individual copies at many locations, they are generally at the same point in everyone and may be within or inbetween genes

Question 7

how big is a LINE1?

Answer 7

a long interspersed nuclear element has around 100,000 copies, 6000bps and makes up around 20% of the genome

Question 8

how does LINE regulate itself?

Answer 8

it promotes it’s own motility - it encodes two gene products that are involved in catalysing the reverse transposition of itself - ORF1 and 2

Question 9

what is an ALU repeat?

Answer 9

short interspersed nuclear element - 500,000 copies with 300bps and makes up 5% of genome.

Question 10

where are SINE found?

Answer 10

they are primate specific and are dispersed around genome by retorotransposition and therefore dependent on LINE 1

Question 11

what is one of the first processes in meiosis?

Answer 11

it is in prophase
chromosomal homologues will pair up - recognise each other precisely as it is sequence dependent
they will then exchange genetic material through recombination at the chiasm

Question 12

what are derivative chromosomes?

Answer 12

they are the chromosomes that give rise to gametes that are from maternal and paternal material

Question 13

how can interspersed repetitive elements affect recombination?

Answer 13

similar copies of repeats close to each other can result in misalignment which means there is staggered alignment - this results in illegitimate recombination and unbalanced gametes resulting in DNA being repeated or deleted in tandem

Question 14

what can unequal crossing over result in?

Answer 14

intragenic pathology, recurrent large scale duplications or deletions or reciprocal duplication or deletions that can be pathological

Question 15

what is Mbp?

Answer 15

a mega base pair that is equal to one million base pairs

Question 16

what are examples of recurrent duplications/deletions that are large scale from unequal crossing over?

Answer 16

DiGeorge - 3Mbp deletion in 22q11.2 and this is a repeated mediated combination - always the same deletion
William’s syndrome - 1.5Mbp - 7q11.23

Question 17

what is a microdeletion in 17p11.2?

Answer 17

potoki-lupski syndrome - 1.5Mbp deletion - reciprocal

Question 18

give an example of a reciprocal deletion and duplication that is pathogenic?

Answer 18

peripheral myelin protein 22 - PMP22 gene - myelin in the central nerves
duplication - HMSN1 - hereditary sensory and motor neuropathies
deletion - HNPP - hereditary neuropathy with pressure palsies
mechanism is dependent on the gene dosage

Question 19

where would you find intragenic pathologies?

Answer 19

they sit within genes

Question 20

what are intragenic pathologies?

Answer 20

they are single gene disorders where duplication and deletion are both pathogenic - duchenne muscular dystrophy is an example. The presentation will depend on reading frame effects and how much it changes the frame.

Question 21

what happens if the change is not a multiple of three?

Answer 21

the reading frame cannot be read therefore deletion or truncation - out of frame disposition is much more likely to have a serious effect on sequences - there is a genotype phenotype correlation

Question 22

what types of mutations are there?

Answer 22

gross rearrangements, large deletions or insertions, point mutations or trinucleotide repeat expansions

Question 23

what are the characteristics and examples of large scale deletions and insertions?

Answer 23

the effects are variable
they may not be detected to PCR methods if heterozygous as the normal gene will amplify as it should
Duchenne Muscular Dystrophy from deletion
Charcot Marie Tooth Disease in duplication

Question 24

what is an example of a gross rearrangement?

Answer 24

haemophilia A

Question 25

what is the basis of haemophilia A?

Answer 25

haemophilia A is a X linked recessive disorder that involves the F8 clotting factor gene on the tip of the X chromosome. It involves repeat sequences that are present in the F8 gene, near the X chromosome and in the opposite direction. It is a recurrent inversion event whereby the tip of the chromosome is bent back on itself meaning that the segment inbetween the two gets flipped upside down - this means the exons are intact but the gene is chopped in half so cannot transcribe. Further to this there is also most of the time another process of illegitimate recombination

Question 26

what is a point mutation?

Answer 26

most single gene pathology results from point mutations. They occur in a single point in the genome and generally involve a single nucleotide or base pair. It can be:
a single nucleotide substitution
frameshifting
single nucleotide indels
indel insertion or deletion where you lose or gain a single nucleotide

Question 27

what is a silent mutation?

Answer 27

when there is no effect even in the protein coding region and no effect on function as generally if you do not change the sequence the function remains the same. This is because there are four codons for an amino acid - polymorphisms frequency is over 1%

Question 28

what is a missense mutation?

Answer 28

when the amino acid is changed - underlie many genetic diseases but not all are pathogenic - can be part of normal genetic variation. It can be described with how conservative it is - i.e. is the new AA chemically similar to original and therefore more likely to be tolerated

Question 29

what is a nonsense mutation?

Answer 29

a mutation that incorporates a stop codon - truncation. Diagnostic tests exploit this - protein truncation test. They are not all random - there is some patterning especially with CG dinucleotides

Question 30

what are CG dinucleotides?

Answer 30

they are the symmetrical, principal site of DNA modification after replication - methylation which eventually occurs on both strands. This deamination can convert AAs mostly cytosine to thymine, and therefore mean that they do not match the Watson Crick Base Pairing Rues. There are mismatch repair mechanisms in place but these occasionally fail or repair the wrong strand

Question 31

what is a frameshift mutation?

Answer 31

it is when you change the reading frame due to maybe loosing a single nucleotide. Therefore you change the structure and function of the protein which will almost certainly be pathogenic

Question 32

how can splicing go wrong?

Answer 32

not all single nucleotides are involved in AA sequence. Splicing depends on the AG/GT regions after and before the spliced region. Therefore changing the exon position from G to A for example means it will not function and swill splice elsewhere instead

Question 33

how would you report a new mutation?

Answer 33

genomic DNA (g.)
cDNA (c.)
protein (p.)
start with ATG nucleotide and number as go
additional terminology with splice junction mutations

Question 34

what would C.658delG mean?

Answer 34

on cDNA at position 658 there has been a deletion of a G

Question 35

what is TER and how would you write this another way?

Answer 35

terminator/stop - *

Question 36

what are considerations for inferring pathogenicity?

Answer 36

is it present in healthy controls?
is it consistent inheritance?
is it a mutated residue that is catalytically important or highly conserved?
has it previously been proven to affect gene function?

Question 37

how do you report pathogenicity?

Answer 37

pathogenic 
likely pathogenic 
uncertain significance 
likely benign 
benign

Question 38

what is often a loss of function mutation?

Answer 38

recessive - 50% of the gene function is adequate

Question 39

what is mutational heterogeneity?

Answer 39

it is frequent - affected individuals are compound heterozygous therefore mutation testing is challenging
examples are CF and beta thalassaemia

Question 40

when are new mutations rare?

Answer 40

when both parents are carriers

1/4 offspring will be affected by carrier condition

Question 41

what can dominant inheritance sometimes result in?

Answer 41

it can sometimes result in an alteration in function or a gain not a loss

Question 42

what is the difference in mutational spectrum between dominant and recessive inheritance?

Answer 42

in dominant new mutations are comparatively common and there is a narrower spectrum

Question 43

what is achondroplasia?

Answer 43

it is a dominant condition where a glycine residue turns into an arginine

Question 44

what are trinucleotide repeat expansions?

Answer 44

stretched of DNA where the same triplet is repeated multiple times. They can be in the protein coding sequence - usualyl code for polyglutamine as CAG is glutamine and is repeated or can be outside of the protein coding sequence and elsewhere in the genome.

Question 45

what are polyglutamine expansions usually?

Answer 45

they usually give rise to late onset neurodegenerative diseases

Question 46

how are expansions outside of the protein coding region different?

Answer 46

mutations in these are more unstable and can change from one generation to another

Question 47

what are some polyQ repeat conditions?

Answer 47

huntington’s (occassional mutations)

spinocerebellar ataxis

Question 48

what are large non-coding repeat expansions conditions?

Answer 48

Fragile X syndrome (frequently mutates - instability) - transcriptional silencing
Myotonic Dystrophy

Question 49

what does HD affect?

Answer 49

it is a neurodegenerative disorder: involuntary movements, psychiatric changes, cognitive loss leading to dementia and neuronal loss in the corpus striatum and cortex

Question 50

what is the mode of inheritance for HD?

Answer 50

autosomal dominant - heterozygous CAG expansions showing mutational instability and anticipation

Question 51

what is the difference between the normal CAG repeat and that of HD?

Answer 51

normally the polyglutamine repeat is of variable length but in HD it is expanded. This means that the spectrum is shifted to the right and is centred around larger repeat averages.

Question 52

what is anticipation?

Answer 52

each succeeding generation seems to have HD worse as the CAG expands on transmission and therefore the symptoms are more severe and earlier onset

Question 53

how are Fragile X and HD sex dependent?

Answer 53

The expansion only seems to show when it is transmitted by a) fathers for HD and b) mothers for Fragile X

Question 54

what is Fragile X syndrome?

Answer 54

it is one of the commoner single gene causes of mental handicap where females seem to be less severely affected

Question 55

why is Fragile X described as semi dominant?

Answer 55

it is an X linked recessive condition where it seems as if the end of the X chromosome seems to be snapped off. The symptoms are more severe in males - large ears and testes

Question 56

what is the basis of Fragile X syndrome?

Answer 56

progressive expansion from normal to very large size of the CGG repeat - adjacent to the FMR1 gene

Question 57

why is the inheritance of fragile X peculiar?

Answer 57

it is from normal males - the condition does not seem to be inherited from anywhere - the mother can be a carrier of a pre-mutation state which will expand in the offspring