Week 1 Flashcards
What is the structure of DNA?
double helix strand
WHat are the 4 DNA nucleotide?
AGCT
What are the 4 RNA nucleotides?
AGCU
Which nucleotide does A bind to?
T
Which nucleotide does C bind to?
G
What nucleotide does T bind to?
A
What nucleotide does G bind to?
C
Between which nucleotides do stronger bonds form and why?
C-G because there are 3 hydrogen bonds instead of 2
Describe the process of gene expression
RNA polymerase forms primary mRNA mRNA undergoes splicing to remove introns and mature mRNA is formed Translation then occurs in the ribosome. Transfer RNA is involved in translation 1st amino acid is methionine. Codon (mRNA) anti-codon(tRNA) Then post translational modifications occur
What relation is the child of your cousin?
First cousin once removed
What is meant by penetrance?
Chance that inherited mutation will lead to disease
How do you calculate the chance of someone developing a genetic form of cancer?
chance of inheriting mutation multiplied by the chance that the mutation will lead to disease
What capabilities must be acquired for a cell develop into cancer?
proliferative signalling
avoidance of apoptosis
bypassing replicative senescence
insensitivity to anti-growth signalling
WHat part of chromosomes are involved in replicative senescence?
telomeres
Describe tumour suppressor genes
normally inhibit progression through the cell cycle
Promote apoptosis or act as stability genes
Give examples of tumour suppressor genes
Rb
TP53
DNA repair (BRCA)
Describe proto-oncogenes
normally stimulate cell cycle
Describe how oncogenes are formed
1 copy of mutated proto-oncogene leads to gain of function effects
What is meant by wt?
wild type - normal (non-mutated copy of allele)
Describe stability genes
a type of TSGs
act to minimise genetic alterations
account for commonest hereditary cancer predisposition syndromes
Describe sporadic cancer
common
late onset
single primary tumour
Describe familial cancer
uncommon
early onset
often multiple primaries
How are most common familial cancers inherited?
autosomal dominant
How do you identify the risk of a cancer being hereditary?
more than one individual in the same family
affected by similar cancers or cancers at related sites with early onset
multiple primary tumours
early age of onset
WHat would a cancer family history clinic offer?
draw family tree and verify diagnoses
estimate likelihood of predisposing gene mutation
discuss screening, risk factors, preventative measures
What are the main mutations involved in hereditary breast cancers?
BRCA 1
BRCA 2
TP53
PALB2
Which BRCA mutation is more likely when there is a family history of ovarian cancer?
1
Which BRCA mutation is most likely when there is a history of male breast cancer?
2
WHat is meant by modifier genes?
loci that confer to increased susceptibility to cancer
these are common and each confers a small effect on increased risk
These are mutations outwith genes - enhancer and silencer parts that control the expression of neighbouring genes
WHat is the function of the BRCA1 and BRCA 2 proteins?
DNA repair by homologous recombination of double-strand breaks
what treatment may BRCA 1 and BRCA 2 carriers offered?
examinations
screening
prophylactic bilateral mastectomies
prophylactic oophorectomies
Which mutated genes can lead to ovarian cancer?
BRCA 1
BRCA 2
HNPCC - MLH1 or MSH2
Describe how olaparib works
selective lethality
BRCA cell uses different type of DNA repair mechanism involving PARP - this is inhibited by drug and causes cell death
WHat is PARP?
poly ADP polymerase
what is the main form of familial colonic cancer?
hereditary non-polyposis colon cancer
What is a rare form of familial colonic cancer?
familial adenomatous polyposis
Describe HNPCC
usually only a few polyps
uterus, stomach, ovary
Due to inheritance in mutation in MMR systemic genes (repairs point mutations)
Which genes are associated with HNPCC?
MLH1 MSH2 MSH6 PMS2 these genes encode proteins that act together in a complex to carry out miss-match repair
Which eye condition is associated with familial adenomatous polyposis?
congenital hypertrophy of the retinal pigment epithelium
What is unusual about MYH polyposis?
autosomal recessive inheritance
attenuated form of FAP
base excision repair (BER) gene DNA glycosylase
WHat cancers can be caused by Li fraumeni syndrome?
breast brain sarcoma leukaemia adrenocortical carcinoma
What mutation is involved in Li fraumeni syndrome?
TP53
What is TP53 involved in?
control of cell cycle, apoptosis and replicative senescence
what is typically meant by a mendelian disorder?
single gene
How many genes are there?
20-25 thousand
What type of inheritance is achondroplasia?
autosomal dominant
Describe autosomal dominant inheritance
effects every generation
vertical pattern of inheritace
only need 1 faulty gene
males and females effected
What is meant by variable expression?
2 people in the same family with the same mutation can have different severities of it
What is meant by incomplete penetrance?
inheriting the mutation does not necessarily meant you are affected by the condition
What is gonadal mosaicism?
When some of the germ cells have undergone mutation and therefore there is a small chance of it being passed on to a child
What gene can effect the severity or penetrance in people who carry the BRCA2 gene?
FGFR2
Give examples of AD conditions
inherited breast or colon cancer
ADPKD
NF1
What are the clues that a condition is autosomal recessive?
usually horizontal pattern of inheritance
both males and females effected
there may be consanguinity in the family
What is meant by consanguinity?
parents may be related to each other. This increases the risk that both will carry the same mutation
Give examples of AR conditions
cystic fibrosis
phenylketonuria
spinal muscular atrophy
congenital adrenal hyperplasia
What are the features of recessive X-linked conditions?
Knight’s move pattern
No male to male transmission
only males afffected
Why can there be some “manifesting carriers” in recessive X-linked conditions?
Skewed X inactivation
Normally 50% of each X chromosome turned off, but if this balance is skewed then it can lead to a faulty gene being more highly expressed
Describe X-linked dominant inheritance
Pattern is like AD but with no male to male transmission
Females more likely to be affected than males
Give examples of X-linked dominant conditions
Vitamin D resistant rickets
incontinentia pigmenti
Rett syndrome
What is meant by genetic anticipation?
mutation gets bigger as more repeats are added
increasing severity of onset in successive generations
Give examples of conditions that involve genetic anticipation
Huntington disease
Fragile X syndrome
myotonic dystrophy
What is meant by pseudo-dominant inheritance?
If an AR condition but has a very high carrier frequency or consanguinity - it appears like AD
Give an examples of a condition that can show pseudo dominant inheritance patterns
Gilbert syndrome
What is unusual about mitochondrial DNA?
much smaller genome circular much smaller than nuclear DNA 37 genes no introns
Describe mitochondrial inheritance
inherited only from the mother
all children inherit it from the mother but to a variable extent
there is a threshold of the number of mutations that are required for disease to occur
heteroplasty
syndromes often affect muscle, brain and eyes
What is the presentation of Huntingtons disease?
onset between 30 and 50
progressive chorea (involuntary movement)
dementia and psychiatric symptoms
What repeat is found in HD?
CAG
mainly prone to expansion during meiosis in the father
Describe the pathophysiology of HD
CAG repeat within the coding sequence
encodes polyglutamine tract
expansion of tract causes insoluble protein aggregates and neurotoxicity
Describe the clinical aspects of myotonic dystrophy
AD with genetic anticipation
progressive muscle weakness in early adulthood
also myotonia and cataracts
more risk of increased repeat sequence in mother
Describe the genetic basis of myotonic dystrophy
unstable length mutation of a CTG repeat
in the 3’ transcribed but untranslated region of DMPK gene
affected if 50 or more repeats
Describe the pathogenic mechanism in myotonic dystrophy
abnormal DMPK mRNA
indirect toxic effect upon splicing of other genes
e.g. the chloride ion channel gene (causing myotonia)
Describe the clinical aspects of cystic fibrosis
AR
carrier frequency of 1 in 20-25
recurrent lung infections
exocrine pancreas insufficiency
How is CF diagnosed?
screening of newborns by immunoreactive trypsin (IRT) level
confirmation by DNA testing and or sweat testing
Describe the pathogenic mechanism of CF
CFTR mutations
defective chloride ion channel
increased thickness of secretions
Describe the most common mutation in cystic fibrosis
F508del
in frame deletion of 3bp (one codon)
loss of phenylalanine (F) at position 508
prevents normal folding of protein and insertion into the plasma membrane
What is meant by cascade screening?
identification of mutations permits prenatal diagnosis if desired and subsequent identification of carrier relatives
Describe NF1
neurofibromatosis 1 commonly cafe au lait macule and neurofibromas short stature macrocephaly learning difficulties very variable expressivity lisch nodules in eyes
What are the possible complications of NF1?
increased risk; hypertension scoliosis pathological tibial fractures significant tumours
Describe the DMD gene
Largest human gene but doesn’t encode the largest protein
What does dystrophin normally do?
forms link between F-actin intracellular and the dystroglycan complex in the cell membrane
What test can be carried out at birth in DMD?
serum creatine kinase
leaks out of damaged muscle cells
massively increased level of DMD from birth before any symptoms occur
What sort of mutation is DMD?
out of frame mutation
What sort of mutation is BMD?
in frame mutation
What does BMD stand for?
Becker muscular dystrophy
Describe fragile X syndrome
X linked recessive
genetic anticipation
most common inherited cause of learning disability
phenotype in males can be severe
some carrier females are affected but more mildly
Describe Edward’s syndrome
trisomy 18 small chin clenched hands with overlapping fingers malformations of heart, kidneys etc if survive first year generally have profound LD
Describe patau syndrome
trisomy 13
congenital heart disease is usual
about 50% die in first month
Describe the clinical features of patau syndrome
cleft lip and palate micropthalmia abnormal ears clenched fists post axial polydactyly
How do trisomies mutations occur?
normally from maternal non-disjunction in meiosis
What does PGD stand for?
Pre-implantation genetic diagnosis
What are the pros of PGD?
permits implantation of unaffected embryos
TOP then unnecessary
What are the cons of PGD?
possible long wait
not available to all woman
difficulty with multiples visits and procedures
<50% success
Describe genetic counselling
providing genetics-related advice and information
information re investigation and interpretation
thinking about implications for relatives
What are the main principles of a screening programme?
clearly defined disorder appreciable frequency advantage to early diagnosis few false positives few false negatives benefits outweigh the costs
How is sensitivity calculated?
true positives/(all affected)
How is specificity calculated?
True negatives out of all unaffected
What is CUB screening?
ultrasound and biochemical testing for Downs syndrome
Describe chorionic villous sampling
10-12 weeks
1/50 miscarriage
quick results
Describe amniocentesis
16-18 weeks
1/100 miscarriage
result 1-2 weeks
how is DNA sequencing carried out?
automated fluorescent dideoxycytidine (Sanger) sequencing Massively parallel (next gen) sequencing
What is allele-specific (ARMS) PCR used for?
for specific known point mutations
What is MPLA used for?
to look for specific duplications and deletions
What is Array CGH used for?
to detect abnormalities when the location is not known
What is quantitive flouresenct PCR used for?
Raoid detection of aneuploidies
What are the chromosome based analysis methods?
karyotyping
FISH
Which tests are used to detect sub-microscopic deletions/duplications?
FISH
MLPA (position known)
aCGH
What techniques are used to detect point mutations?
DNA sequencing or ARMS
What can be analysed with NGS?
single gene
several genes at once
come
genome
What are the steps in data analysis in NGS?
DNA massively parallel sequencing FASTQ file Sequence alignment BAM file Variant calling VCF file Data filtering steps (removing common variants)
WHat is meant by pharmacogenetics?
the study of the genetically controlled variation in response to medication
Describe ivacaftor
G551D - the 3rd most common CF mutation
Blocks opening of CFTR chloride channel
Ivacaftor re-opens the channel
Describe examples of future therapies in DMD
exon skipping: convert DMD to BMD phenotype by altering splicing patterns to correct the reading frame
or using drugs that allow read-through of premature stop codons
What are meant by splicing factors and relate it to DMD
proteins necessary for normal splicing of other genes - include “muscle blind” proteins
These are mopped up (sequestered) by the abnormal DMPK mRNA to which they bind.
