Genetics Flashcards
Give 4 examples of autosomal dominant conditions
- Inherited breast or colon cancer
- Adult polycystic kidney disease (APKD)
- Neurofibromatosis type 1 (NF1)
- Huntington disease (HD)
Explain autosomal dominant pattern of inheritance, including its characteristics
- Only one copy of the faulty gene is needed to be affected by the condition (homozygotes + heterozygotes)
- Multiple generations affected (vertical pattern of inheritance)
Characterised by
- Variable expression: range of symptoms in people with same condition
- Incomplete penetrance: some individuals who carry the pathogenic variant express the associated trait while others do not
- Modifier gene variants
- Offspring of affected individuals usually have a 50:50 risk
List features of neurofibromatosis type 1
- Cafe au lait macules
- Neurofibromas
- Short stature
- Macrocephaly
- Learning difficulties in 30%
- Variable expressivity
- Lisch nodules in the eyes
Describe autosomal recessive pattern of inheritance including its characteristics
- 2 copies of the faulty gene needed to express phenotype
- Single generation affected - horizontal pattern of inheritance
Characteristics include
- Likely consanguinity in the family
- Disease expressed in homozygotes or compound heterozygotes
- Offspring of affected individuals have a low risk
- Expressivity more constant within family
List examples of autosomal recessive conditions
Cystic fibrosis (CF)
Phenylketonuria (PKU)
Spinal muscular atrophy (SMA)
Congenital adrenal hyperplasia
Wilson disease
Tay-Sachs disease
Describe the pathophysiology of cystic fibrosis
Mutation in CFTR gene in chromosome 7
> Leads to a defective chloride ion channel and increased thickness of secretions
> Mutation is usually p.F508del, in-frame deletion of 3bp (one codon)
> Deletion of phenylalanine prevents normal folding of protein & insertion into plasma membrane
Presents with
> Salty sweat
> Thick mucus blocking airway (High rates of sinus infection)
> Blockage of pancreatic duct
> Male infertility (congenital bilateral absence of vas deferens)
> Liver disease
> Meconium ileus
How is cystic fibrosis diagnosed?
Screening of newborns by immunoreactive trypsin (IRT) level
Confirmation by DNA testing for CF mutation (ARMS kit) or sweat testing for increased chloride concentration
Described X-linked recessive inheritance and its characteristics
X chromosome carries the faulty gene so
- No male to male transmission
- Mostly or only males affected
- Occasional manifesting carriers due to skewed X inactivation
- Knight’s move: two males who are related through an unaffected female are affected
> Likely to be X-linked recessive as female has an additional unaffected X chromosome which protects her
Describe the pathophysiology of Duchenne Muscular Dystrophy (DMD)
Frameshift mutation (mostly out of frame deletions) results in shorter dystrophin protein, which damages the myocyte cell membrane
> allows creatine kinase exit and calcium entry, destroying myocytes
Muscle damage leads to progressive degenerative weakness
> onset 3y, wheelchair by 12y
> Mean life span of <30 years as heart and diaphragm are affected by muscle weakness
Describe the tests used to diagnose Duchenne Muscular Dystrophy
- MLPA (multiplex ligation-dependent probe amplification) test to detect deletions
- SCK test : measures serum creatine kinase released by damaged muscle
> confirmed by muscle biopsy then tested for absence of presence of dystrophin gene and expression in muscle fibres via immunohistochemistry (IHC)
Describe the pathophysiology of Becker Muscular Dystrophy (BMD)
- Mutations in dystrophin gene, but in-frame deletions, so there is reduced quantity of fully functional dystrophin OR full quantity of partially functional dsytrophin
- Mild phenotype of DMD
- onset age 11
- may never need a wheelchair
Explain X-linked dominant inheritance and its characteristics
- Pattern is like AD but no male-to-male transmission
- Vertical pattern of inheritance
- Male-female transmission: all daughters affected
- Female-female transmission: 50% daughters affected
- appears to be more females affected - due to male lethality
Give examples of X-linked dominant conditions
Vitamin D resistant rickets
- caused by pathogenic variants of PHEX gene
Incontinentia pigmenti
- Skin condition that causes rashes and patches of pigmentation
- Caused by partial deletions of IKBKG gene
Rett syndrome
- Causes child development to stop at 6-18 months with subsequent regression
- Due to pathogenic variants of MECP2
- Male lethality
Explains pseudo-autosomal and pseudo-dominant inheritance
- Pseudo-autosomal: seems autosomal but is actually on the sex chromosomes
- Pseudo-dominant (actually AR): if there’s a high carrier frequency or cosanguinity
> e.g. Gilbert syndrome (TA insertion within promoter region of UGT1A1 gene) - causes intermittent jaundice due to episodes of mild unconjugated hyperbilirubinaemia
Describe mitochondrial inheritance giving an example
- Smaller genome (37 genes, 17 kbp, no introns, circular)
- Inherited only from mother
> all children affected to variable extents - Syndromes often affect muscle, brain and eyes
E.g. Leigh’s disease
> In mitochondrial DNA, MT-ATP6 gene coding for ATP synthase
Heteroplasmy is when there is more than one type of mtDNA in an individual
Describe the causes of Down’s syndrome and its phenotypic features
Causes: trisomy 21 due to maternal nondisjunction or Robertsonian translocation (inheritance risk)
- Phenotypic features
> Upward slanting palpebral fissures and epicanthic folds
> Sandal gap
> Single transverse palmar crease
> Small nose
> Low set ears
>macroglossia
> High incidence of heart malformations, hypothyroidism, childhood leukaemias, early onset Alzheimer’s
Describe the cause of Edwards’ syndrome and list its clinical features
Caused by trisomy 18
Features
> Often stillborn or miscarried, survival usually <4 months due to infections/heart failure; profound intellectual disability if they survive
> Rockerbottom feet
Syndactyly
Malformations of ears, heart, kidneys…
Micrognathia: small lower jaw
Exomphalos: umbilical hernia at birth
Describe the cause of Patau syndrome and its clinical features
- Caused by trisomy 13
Features
> Not compatible with life past a few week safter birth; many miscarriages
> Hypotelorism: eyes close together; cyclopia; microphthalmia
> Abnormal ears
> Clenched fists
> Cleft lip & palate
> Scalp defects, microcephaly
> Post-axial polydactyly
> Organ problems e.g. heart difficulties
Describe the cause and inheritance of myotonic dystrophy type 1 (DM1)
DM1 is caused by a CTG repeat expansion in the 3’ UTR of the DMPK gene (serine-threonine kinase)
> Inheritance is autosomal dominant with genetic anticipation
Repeat number of alleles increases with each generation; severity of disease is directly related to the number of repeats present
Describe the pathogenesis and clinical presentation of DM1
DM1 is characterised by abnormal DMPK mRNA which has an indirect toxic effect upon the splicing of other genes, e.g. chloride ion channel CLCN1 gene, causing myotonia
> Insulin receptor also affected, causing diaberes in some
Presents as adult-onset muscular dystrophy; myotonia (muscle relaxation is impaired) and cataracts
Describe the cause and inheritance of Huntington’s Disease (HD)
Caused by a CAG repeat sequence near the 5’ coding end of the huntingtin gene (HTT) on chromosome 4, which encodes a polyglutamine tract
> Expansion of the tract causes insoluble protein aggregates & neurotoxicity
Inheritance is autosomal dominant with genetic anticipation
Describe the pathogenesis and clinical features of HD, including diagnosis
Protein is cytoplasmic and ubiquitously expressed; may be involved in transport and trafficking within the brain as well as transcription and anti-apoptotic processes
> Selective neurodegeneration: neostriatum and cerebral cortex
Features include Huntington’s chorea (progressive) and dementia
Diagnosis via triplet primed PCR (TP-PCR)
Describe the cause and clinical features of Fragile X
Caused by an expansion of the CGG repeat in the 5’ UTR of the FMR1 gene
Inheritance is X-linked recessive; most common inherited cause of learning difficulties
Can cause premature ovarian failure in female carriers and Fragile X-associated tremor ataxia in males
Define 1) genetic heterogeneity 2) pleiotropy
- Genetic heterogeneity is a term used to describe a disorder having several different genetic causes
- Pleiotropy describes when one gene causes more than one condition e.g. RET gene causes MEN2 (AD) and Hirschprung’s disease
List different types of gross lesions in genes
- Large deletions
- Inversion
- Insertion
- Duplication
Explain the different types of microlesions in genes
Substitution
- Replacing one base for another
Can be missense if it changes a codon from coding from one amino acid to coding for another OR nonsense if the coding codon is exchanged for a stop codon
Splicing
- If splice site is abolished, some exons may be spliced to different locations so the resulting mRNA has a missing exon
Regulatory
- Altering transcription start site can change the affinity for transcription factors
Small insertions/deletions
- Can result in a frameshift mutation if not a mutliple a 3; changes codons downstream (out of frame)
- In-frame mutations result in a loss or altered amino acid at a specific point but does not change others
Give an example of 1) gain of function mutation 2) loss of function mutation
- Mutant FGFR1 can dimerize without a growth factor leading to osteoglophonic dysplasia, which presents with craniosynostosis and dwarfism
- Kallman syndrome (haploinsufficiency) presents with anosmia and hypogonadotrophic hypogonadism
List the 9 characteristics of cancer cells
- Self-sufficiency (proliferation in absence of growth factors)
- Insensitivity to growth-inhibitory signals (inactivation of TSGs)
- Evasion of apoptosis (overexpression of BCL2)
- Limitless replication potential (upregulation of telomerase)
- Sustained angiogenesis
- Tissue invasion & metastasis
- Avoiding immune destruction
- Genome instability and mutation
- Deregulating cellular energetics
Define oncogenes and give examples
Oncogenes are mutated forms of normal genes (proto-oncogenes) involved in signalling pathways that regulate cell proliferation, inducing tumour formation
E.g. in the nucleus; Myc & cyclin D
Define proto-oncogenes and give examples
Proto-oncogenes are normal cellular genes that encode proteins involved in regulating cell growth/division
- Only need one mutated gene copy (dominant effect) for tumorigenic effect (oncogene)
E.g.
> Growth factors such as PDGF & growth factor receptors e.g. EGFR, HER2
> Cytoplasmic signalling intermediates e.g. Ras, MEK, BRAF
> Nuclear proteins e.g. Myc, Fos, Jun
> Cell cycle regulators e.g. BCL1, cyclin D
> Proteins influencing cell survival e.g. BCL2
Define tumour suppressor genes and give examples
TSGs are genes whose encoded proteins inhibit cell cycle progression
Loss of function mutation is oncogenic; usually recessive (both copies must be mutated) but the EXCEPTION is p53 (acts as a tetramer, dominant negative)
Examples: RB, BRCA1, MEN1
Mutation in p53 (TP53) results in Li Fraumeni syndrome - inherited predisposition for cancer (AD inheritance)
Describe the causes and management of familial adenomatous polyposis (FAP)
Caused by APC gene mutations, AD inheritance
Results in a carpet of small adenomatous polyps: high risk of adenocarcinoma so total colectomy done at young age
Describe the causes and management of familial breast cancer
BRCA1/2 mutations as these proteins are involved in DNA repair by homologous recombination of double-stranded breaks
> Increased risk of ovarian and breast cancer
Other mutations include TP53, PALB2, PTEN
Prevention; testing via next generation sequencing, examinations, screening by mammography or MRI, prophylactic bilateral mastectomy/oopherectomy
List mutations that increase the risk of ovarian cancer and the treatment for this cancer
Mutations in BRCA1/2, MLH1, MSH2
Treatment is surgical or via a PARP (poly ADP ribose polymerase) inhibitor - olaparib
Why would you suspect an inherited cancer syndrome in an individual?
- Young age of onset for cancer
- Multiple primary tumours in one individual
- Several genetically related individuals with same/related cancer
List the tests used to detect point mutations
- DNA sequencing
> Sanger sequencing
> Next generation sequencing (NGS)
> Allele specific (ARMS) PCR
Explain the mechanism behind Sanger sequencing
Sequences 1 gene at a time using fluorescent dideoxynucleotide sequencing to detect point mutations
Explain the mechanism behind next generation sequencing (NGS)
- Aka massively parallel or high throughput sequencing
- Illumina method
> Hundreds of millions of DNA fragments sequenced at once on a flow cell
> Use computer to identify variants compared to the reference sequence
> Produces a variant call format (VCF) file - a list of all the variants
> User filters variants to just those that are not common (Not polymorphisms) and are predicted to be damaging to the protein
Can sequence a single gene, several genes (gene panel); exome (all protein coding regions of all genes) or the genome
Explain the mechanism behind an ARMS PCR
Special PCR that analyses only specific known mutations
List the tests used to detect sub-microscopic duplications and deletions
- MLPA
- Chromosomal microarray (CMA)
- FISH
Explain the mechanism behind MLPA
Multiplex ligation dependent probe amplification is a PCR-based method that targets a group of specific known positions - chromosomal loci - where there might be a deletion
Explain the mechanism behind FISH
Fluorescence in-situ hybridisation (FISH) uses a specific DNA probe that binds to a location on a chromosome
E.g. FISH using a Williams syndrome probe can find a deletion of the elastin gene at 7q
List methods for the detection of aneuploidies
- Karyotyping; examining chromosomes using light microscopy
- Quantitative fluorescence PCR (QF-PCR): whole chromosome analysis
Explain the mechanism behind non-invasive prenatal testing (NIPT)
Aka cell free foetal DNA (cffDNA) screening
> Uses complex new DNA analysis techniques to identify tiny amounts of foetal DNA in maternal blood
> cffDNA migrates into the maternal bloodstream via apoptotic trophoblast cells shed from placental tissue
Testing involves taking a blood sample from the mother and performing massively parallel sequencing - no risk to foetus
List the appliactions of NIPT
- Sex determination; detecting Y chromosome sequences to test for X-linked conditions
- Single gene disorders: detects paternally inherited alleles e.g. FGFR3 causing achondroplasia; also where parents are carriers of different mutations in the same gene for AR conditions such as CF
- Non-invasively determined foetal Rh type
> detection of RHD gene in an RhD negative pregnant woman indicates RHD positive foetus - Aneupolidy: screening for trisomies, may need confirmation via CVS or amniocentesis
- Microdeletion syndromes/other chromosomes
Explain the function of the CF drug ivacaftor (and tezacaftor, elexacaftor…)
Targets G551D - 3rd most common CF mutation - which blocks the opening of the CFTR chloride ion channel; ivacaftor reopens the channel, improving CFTR function
Explain the system used for gene editing
CRISPR/CAS9 system can be used to correct mutations in the DNA sequence
> CRISPR is a guide RNA that finds a target sequence
> in trials for beta-thalassaemia and sickle cell disease
> important to avoid off-target effects (other genes)
> gene replacement: Zolgensma for spinal muscular atrophy (SMA); introduces normal SMN1 gene copy to motor neurons via an adenovirus vector
Describe new therapies used for DMD
Oral drug (ataluren or translarna)
> small molecule that may cause read-through of premature stop codons, allowing the ribosome to finish synthesising dystrophin
Describe the cause hereditary non-polyposis colon cancer (Lynch syndrome)
AD inherited cancer predisposition (colorectal + uterus + stomach + ovary)
- usually only a few polyps
Mutations inherited in one of they key DNA mismatch repair genes: MLH1, MSH2, MSH6, PMS2
> Screening if at high risk, 2 yearly colonoscopies from 25 & 2 yearly upper GI endoscopy from 50
> aspirin reduces risk of colorectal cancer
Describe the cause of MYH/MUTYH polyposis
AR inheritance
15-200 polyps, like mild FAP
> Normal function: base excision repair gene (BER gene) - encoding DNA glycosylase
Mutation leads to high risk of carcinoma; 2 yearly colonoscopy for screening
Explain the DNA mismatch repair complex
Heterotetramer of proteins that track along DNA following DNA polymerase
> MSH2/MSH6 (MSH2/MSH3) heterodimer recognises and binds mismatch
then recruits MLH1/PMS2 (MLH1/PMS1, MLH1/MLH3) heterodimer
DNA exonuclease digests nucleic acids and DNA polymerase adds on new bases
Explain nucleotide excision repair
Used for single base repair; NER multi enzyme complex tracks along DNA molecule and identifies lesion
Endonuclease cuts within the molecule; DNA polymerase fills gap and DNA ligase seals it
Describe the repair of double strand breaks
2 types
- Homology-dependent repair: germline cells
> single stranded overhang is used to search entire genome to find homologous chromosome as a template - Non-homologous end-joining: somatic cells
> 2 broken ends of DNA are tested against each other and through coincidence some bases match and are attached together
Describe the cause of MutYH-associated polyposis
AR inherited loss of function mutation of MYH gene - encodes a component of the base excision repair pathway
- MutYH recognises oxoguanine paired with A, another chance is given for OGG1 to pick up damage and repair it, returning to G-C base pair
- If this is not repaired, O (Oxo-G) pairs with A, resulting in T-A base pair during replication (oncogenes, TSGs)
