Week 1 Genetics Flashcards
Describe transcription and translation
Transcription (takes places in nucleus) DNA copied into pre- mRNA by RNA polymerase pre-mRNA gets spliced. Exons remain, introns get taken out. Forms mature RNA Translation (takes place in cytoplasm) tRNA has an anticodon which binds specifically to mRNA codon in ribosomes. The other end of tRNA has amino acid, so eventually forms polypeptide methionine – first amino acid
What capabilities must cell have to become cancerous?
- Avoid apoptosis - Proliferative signalling - Avoid replicative senescence (normal cells have limit of amount of times they can divide) - insensitivity to anti-growth signalling
Chance of daughter getting breast cancer of mum has br Ca
50% risk of inheriting it 80% risk of having breast cancer if you inherited gene Overall chance: 50%x80% = 40%
What is a tumour suppressor gene?
Inhibit progression through cell cycle (e.g. RB) Promote apoptosis (e.g. BAX) Act as stability genes (minimised genetic alterations e.g. BRACA1/2) Mutations cause loss of function Need to lose 2 copies for tumourigenic effect (2 hit hypothesis - require 2nd hit after the inheritance of one inactivated gene) Usually AD with incomplete penetrance
What is a proto-oncogene?
Stimulates cell cycle Mutations cause gain of function - forms oncogene One mutated copy forms tumourogenic effect Mutations in them not usually inherited, except e.g. RET causes condition MEN2
Complete penetrance vs Incomplete penetrance
Complete - inherited mutated gene and develop disorder Incomplete - inherited mutated gene but don’t develop disorder
Why does the same gene cause variable phenotype in people?
Environment Modifier genes (affects severity and penetrance e.g. FGFR2 in BRACA2) Gonadal mosaicism
What is gonadal mosaicism?
Mosaicism: Genetic abnormality that occurs after fertilisation, during mitosis. Causes individual to have a normal cell line and a genetically abnormal cell line. So some of the individual’s cells may show phenotype e.g. segmental neurofibromatosis type 1 Gonadal mocaisim: genetic abnormality only in some germ cells. So can be healthy individual but pass on to their children e.g. DMD
Autosomal dominant conditions
Achondroplasia NF1 neurofibromatosis) Myotonic dystrophy
Autosomal dominant inheritance pattern
Vertical inheritance Male to male transmission (as mutation not just in X chromosome so not X-linked) Affects female and males
If both parents have a AR condition, what are the chances of their children inheriting it?
75% carriers 25% healthy 25% affected
Examples of autosomal recessive conditions
Sickle cell CF SMA Congenital adrenal hyperplasia Phenylketonuria
Autosomal recessive inheritance pattern
Horizontal inheritance Both females and males affected May be consanguinity in family
Differences in AD vs AR
AD Vertical pedigree Disease expressed in heterozygotes Offspring usually 50% chance affected Variable expressitivity May have incomplete penetrance AR Horizontal pedigree Disease expressed in homozygotes (2 mutant alleles) Offspring usually low risk of being affected Expressitivity more constant in family Consanguinity important Both females and males affected in both
X-linked recessive conditions
Duchenne muscular dystrophy Fragile X syndrome
X-linked recessive pattern
Knight’s move No male to male transmission Mostly/only males affected Manifesting carriers - due to skewed X-linked inactivation (when one of X chromosomes in female are switched off. So if good copy switched off, bad copy is active)
Proportion of children with the condition, if mother/father has X linked recessive condition
Carrier mother - 50% sons affected - 50% daughters carriers Carrier father - No sons affected (as Y chromosome passed on) - All daughters carriers
X linked dominant conditions
Vit D resistance rickets Rett syndrome
X linked dominant pattern
Vertical inheritance No male to male transmission If father affected - all daughters affected If mother affected - 50% daughters affected
X linked rec vs. X linked dom
Both no male to male transmission X linked recessive Knights move If father affected: all daughters carrier, no males affected If mother affected: 50% daughters carrier, 50% males affected Affects more males than females X linked dom Vertical transmission If father affected: all daughter affected, no males affected If mother affected: 50% daughters affected, 50% males affected Affects females:males 2:1
How lovely is John?
Really lovely
How good looking is John?
Unbelievably
Is John probably the best looking guy?
Yes
Should I buy John lots of presents?
Yes
Should I buy John Coffee daily?
Yes
Should I be nasty to John?
No.
Out of 10 how great is John?
11/10
What are stability genes?
Type of tumour supressor gene Minimises genetic alterations Account of commonest hereditary cancer predispositions e.g. BRACA1, BRACA2
Difference between sporadic and familial cancer
Sporadic: Common Late onset Single primary tumour Familial: Uncommon Early onset Multiple primaries
How are most common cancer predisposition syndromes inherited?
Autosomal dominant Most due to inheriting tumour supressor gene - Involves Knudson’s 2 hit hypothesis: first mutation inherited, then 2nd mutation would lead to cancer
Breast cancer genes
BRCA1 (ch. 17) (breast and ovarian cancer) BRCA 2 (ch. 13) (male breast ca) On autosomes, not sex chromosomes TP53 PALB2 PTEN
Function of BRCA1 and BRCA2 genes
DNA repair by homologous recombination of double stranded breaks
Ovarian cancer genes
BRCA1/2 HNPCC e.g. MLH2, MSH2 Possible treatment: PARP inbhition - olaparib
Types of colon cancer
- Hereditary nonpolyposis colorectal cancer (HNPCC) - most common - Familial adenomatous polyposis - MYH-associated polyposis Aspirin reduces CRC (colorectal cancer)
Hereditary nonpolyposis colorectal cancer (HNPCC)
- From the inheriting mutations in MMR (mismatch repair) system - MMR mutation present (80% risk in males, 40% risk in females) - usually only few polyps - screening by colonoscopy - MLH1, MSH2
Familial adenomatous polyposis
APC gene Causes congenital hypertrophy of retinal pigment epithelium
MYH polypopsis
Auto recessive Normal function of MYH: base excision repair High risk of carcinoma
Li Fraumeni syndrome
Auto dominant cancer pre disposition syndrome Breast ca, brain tumour, sarcoma TP53 mutation (master control gene)
What is heteroplasmy
More than one type of genome in organelle e.g. MT
HD
30 - 50 Progressive chorea, psychiatric symptoms, dementia Autosomal dom Genetic anticipation HTT gene - CAG (glutamine) repeats (36-39 normal)
What is genetic anticipation?
Genetic disorder passes on to each generation, the symptoms become apparent (usually more severe) at an earlier age with each generation HD, MD. Fragile X
Myotonic dystrophy
Autosomal dom, genetic anticipation Progressive muscle weakness, myotonia (muscle can’t relax), cataracts - abnormal DMPK mRNA - causes indirect toxic effect (deregulates splicing) on other genes - CLCN1 (chloride ion channel) - causes increased risk of diabetes (splicing insulin receptor gene affected)
Cystic Fibrosis
Autosomal recessive Carrier frequency: 1 in 20/25 Childhood onset (always look at age in pedigree) - Recurrent lung infections - Pancreatic exocrine insufficiency (thick mucous secretions block pancreatic ducts) - CFTR gene mutations - Defective chloride ion channel, leading to increased thickness of secretions - F508del (loss of phenylalanine) Diagnosis: Screening of newborns by immunoreactive trypsin (IRT) levels Confirmed by DNA testing (CF mutations) or sweat (increased Cl conc)
What is cascade screening?
When one person is diagnosed, the other carrier relatives are identified
NF1
- AD - Cafe au lait macules, short stature, macrocephaly - Learning difficulties, Lisch nodules - Increased risk of hypertension, scoliosis, phaeochromocystomas
DMD
- X linked rec - Can be inherited by gonadal mosaicism - DMD gene in Xp21 - Dystrophin forms link between F actin and dystroglycan complex - Creatnine kinase leaks out of damaged muscle fibres into blood, so DMD pts will have increase serum creatnine kinase (SCK) from birth
DMD vs BMD (becker muscular dystrophy)
DMD Onset 3yrs Wheelchair by 12 Out-of-frame deletions BMD Onset 11 yrs Wheelchair later or not at all In-frame deletions
Fragile X syndrome
- X linked rec - Genetic anticipation (due to repeats in FMR1 gene) - If more 200 repeats: phenotype in males severe, carrier females can be affected - Significant learning disability
Trisomy 21
Downs syndrome - Risk for young parents 1/1000 - Due to maternal non-disjunction (chromosome fails to separate in meiosis), or 14:21 (Robertsonian) translocation - Learning difficulties, heart conditions, hypothyroidism
Trisomy 18
Edward’s syndrome - Small chin, clenched hands with overlapping fingers, heart conditions, if survive in 1st year learning difficulties
Trisomy 13
Patau syndrome Congenital heart disease 50% die within 1 month Cleft palate, abnormal ears, post axial polydactyly (extra little finger)
Preimplantation genetic diagnosis (PDG)
1 or 2 cells removed, when embryo 3 days old QF-PCR or PCR or FISH to check for mutations Unaffected embryos transferred in uterus Pros: Allows implantation of unaffected emvryos Cons: Long wait Difficulty with multiple visits/procdures 50% success rate of having a baby
When is genetic screening test offered
Offered: - Pregnancy - Neonatal - Adulthood
Main principles of genetic testing
- Whole population offered test, but risk to each individual is low - Cheap, non-invasive - Clearly defined disorder - Advantage to early diagnosis - Few false positives (specific) - Few negatives (sensitive) - Benefits outweigh costs
Neonatal screening tests
Mass spectrometry: - Phenylketonuria Immuno-assay - CF HPLC: - sickle cell
Prenatal diagnostic tests
- Family history of serious disorder - High risk from prenatal screening Chorionic villous sampling 10-12 wks 1/50 miscarriage rate Amniocentesis 16-18 wks 1/100 miscarriage rate
Genomics
Involves all DNA nuclear: 3 billion bp MT: 17 kbp 1.5% coding: exome
Detection of point mutations
DNA sequencing - don’t need to know mutation as uses whole gene - 1 gene at a time (Sanger) - many or all genes (massively parallel/Next generation sequencing) Allele specific (ARMS) PCR - only for known point mutations
Detection of submicroscopic duplications and deletions (few thousand bp)
MLPA (PCR-based) Array comparative genomic hybridisation (aCGH)
Rapid detection aneuploidies (abnormal no. of chromosomes not multiple of 23)
QF-PCR (2 signals = 2 chromosomes, 3 signals = 3 chromosomes) - rapid Chromosome based analysis: Karotyping - stain chromosomes, look using microscope FISH (fluorescent in situ hybridisation) - look for certain parts of chromosome
Whole chromosome analysis
Karyotyping QF-PCR
Sub-microscopic deletions/duplications
FISH or MPLA -to detect deletions/duplications of certain genes aCGH - if position of duplication/deletion unknown
Point mutation
DNA sequencing or ARMS
Non-invasive prenatal testing
- Tests free fetal DNA in maternal plasma - Detect if male e.g. for X linked conditions - Father’s mutations - Aneuploidy
Ivacaftor
For CF patients with mutation G551D. Causes Cl- ion channel to be blocked. As Cl- can’t pass, secretions become too thick Ivacaftor re-opens Cl- channel
Gefitinib
EGFR in lung cancer
Trastuzumab (Herceptin)
HER2 in breast cancer
Possible future therapies
- Exon skipping: converting DMD to BMD phenotype by changing splicing patterns to correct reading frame - using antisense oligonucleotides - Drugs that allow read through of premature stop codons (Ataluren) - CRISPR-Cas9: Allows mutation correction
Are 2 different mutations located on same copy of gene be enough to cause an AR disorder?
No, as there is still a healthy copy of gene remaining
What is MLPA most commonly used to detect?
Deletion of a gene
What is QF-PCR used most often for?
Rapid method in detecting trisomys
What is ARMs most often used for?
Nucleotide substitution for known gene
Does NF1 have genetic anticipation?
No
Clinical Assessment of a patient
Patient’s Clinical History - age of symptoms, progression Family history Consanguinity? Miscarriages? Examination Dysmorphic features Growth Investigations DNA, chromosomes, biochem
What is pseudodominant inheritance?
Inheritance pattern looks auto dominant when actually auto recessive. - Due to high carrier frequency or consanguinity in family - If affected person has a partner who is a carrier, their offspring can be affected with apparent vertical transmission - Gilbert syndrome (intermittent jaundice - due to insufficient amount of enzyme encoded by UDG-1A1 leading to increased insoluble bilirubin which can’t be excreted.
