Genetics Flashcards
autosomal dominant inheritance
· More than one generation involved
· Male to male transmission
· Males and females affected with equal severity
· Penetrance: affected person showing clinical symptoms
· Expressivity: variation in clinical presentation
autosomal recessive inheritance
One or more affected children with unaffected parents
Usually only one generation involved
Males and females affected with equal frequency and severity
A higher incidence of consanguinity
X-linked inheritance
Usually only males affected
More than one generation involved with the disease appearing to be passed on through normal females
No male to male transmission
X inactivation
Carrier females affected by X-linked disorders as a consequence of X-inactivation/lyonization -> random, normal X chromosome switched off in excess of cells leaving diseased X= manifestation of disease
Fragile X Syndrome
commonest non chromosome cause of mental retardation
- 1:4000
Symptoms:
- Mild-severe mental retardation
- Macroorchidism (post pubertal)- abnormally large testes
- Long face, prominent jaw, thick nasal bridge, large ears
- Joint hypermobility
- Autistic features
Consanguity of first, second and third degree relatives
first= 50% (100% if identical) second= 25% third= 12.5%
Fetal Sex on Maternal Blood- cell free fetal DNA (cffDNA)
- Originates from placental trophoblast & shed into maternal blood stream, detectable from 4-5w gestation (increases with progression)- Can be analysed to detect Y specific sequence of male
- 3-6% of total DNA in maternal plasma, cleared rapidly post delivery
- Used for early non-invasive prenatal determination of sex for foetuses at risk of X linked disorders (avoid invasive CVS for female foetus)
Chorionic Villus Sampling- invasive
- Piece of placenta -> DNA extraction and chromosome analysis
- performed 11w gestation, miscarriage risk= 1.5-2%
- PCR based test (DNA extracted without culture), result in three days
Amniocentesis
- Removal of 10-20ml amniotic fluid under ultrasound control, contain cells from baby and placental membranes: chromosome analysis and DNA molecular analysis
- Performed 15w gestation onwards, miscarriage risk= 0.5-1%
Amnio-PCR
- Amplification of polymorphic markers on chromosomes 21, 18 and 13 based on limited PCR cycles= quantification of results
Preimplantation Genetic Diagnosis
IVF creation of embryo from egg and sperm of couple, each embryo tested for particular genetic disorder and one unaffected embryo is transferred into womb -> pregnancy
- for couples at risk of having a child with a single deep gene disorder or chromosomal disorder
Criteria for PGD (NHS funded)
known genetic condition, female age >39, no unaffected living child, female BMI< 30, non-smoker, AMH>/= 6, antral follicle count >8
Haemoglobinopathies Antenatal Screening Programme
- Screening for sickle cell anaemia and other haemoglobin variants based on Family Origin Questionnaire to assess risk, women and/or partners in high risk groups
- Screening for thalassemia based on inspection of routine blood indices
Screening for Trisomy 21, Trisomy 18 & Neural Tube Defects
- First trimester screening (nuchal transparency, HCG, PAPP-A) offered 11-14w
- Second trimester screening (missed first) offered 15-20w, measure AFP, HCG, unconjugated oestridiol & inhibin A
High HCG: AFP ratio increases
chances for Down Syndrome
AFP<2 multiples of median adjusted for maternal wight indicates
increased risk of neural tube defect, 90% identified in second trimester detailed screening
When is ultrasound screening for fetal anomaly carried out in low risk women?
Ultrasound screening for fetal anomaly in low risk women performed 18-20w gestation
endophenotypes
if 1 person in family has disease, other people in family may have it with low expressivity eg. on the spectrum
How do you know if a disease is genetically determined?
- Segregation analysis– this looks for patterns in the family history of affected individuals
- Using twin studies which compare the concordance of disease between monozygous (identical) twins to the concordance of the same disease in dizygous (fraternal) twins
Both of these techniques provide a quantitative measure of how “genetic” a disease is. Diagnostic genetic testing is currently only available in mendelian disease.
Newborn Screening in Scotland
- phenylketonuria (PKU)
- congenital hypothyroidism (CHT)
- cystic fibrosis (CF)
- medium chain acyl-CoA dehydrogenase deficiency (MCADD)
- sickle cell disorder (SCD)
- hearing loss
Phenylketonuria (PKU)
- 1/6000 in Scotland
- clinically silent in first months
- eczema, hypopigmentation, severe developmental delay by toddler age, ‘mousy’ smell to urine (from build-up of intermediate phenyl-acetate)
- all babies have testing at 7 days
what mutation leads to PKU?
mutation in both copies of PAH gene- no phenylalanine hydroxylase activity > build-up of phenylalanine (neurotoxin) leading to intellectual disability
Treatment for PKU
phenylalanine-restricted diet started <21 days, continue diet for life and leads to normal outcome in most children
Criteria for population based screening:
- Well defined disorder
- Known incidence
- Significant morbidity or mortality
- Effective treatment available
- Period before onset during which intervention improves outcome
- Ethical, safe, simple and robust screening test
- Cost effective
Criteria for Presymptomatic Genetic Testing- medical reasons
- If done for medical reasons:
o Should result in a preventative intervention
o Family implications need to be considered - Testing of children is appropriate if intervention starts in childhood
when is Pre-symptomatic Genetic Testing carried out for non-medical Reasons?
Carried out in adult onset neurodegenerative disorders eg. HD:
- autosomal dominant
- DNA diagnosis available
- No effective treatment
- No accurate prediction of age of onset
- Restricted to adults
what kind of mutation is the majority of developmental disorders caused by?
de novo mutation (78%)
Cornelia de Lange- causes, symptoms
- caused by mutation of NIPBL (loading protein during metaphase for cohesion)
- causes severe limb malformation, characteristic facial features, short stature
- mutations in SMC1A, RAD21, SMC3 give similar phenotypes
Modularity
mutations in different components in the same complex causing similar disorder
There are specific genes commonly seen associated with severe mental retardation > chromatin associated protein has a general effect on genes expressed
- effects can be so severe because transcription of many different genes if affected by a single protein
channel proteins are common targets for
genetic epilepsy & epileptic encephalopathies
What is the difference between somatic and germline mutations?
Somatic mutations- non germline tissues, non-heritable
Germline mutations- present in egg/sperm, heritable, cause cancer family syndrome
Difference between familial and sporadic retinoblastoma?
- Familial= presents in childhood & bilateral, multifocal
- Sporadic= presents later on & unilateral, unifocal
Knudson’s 2 Hit Hypothesis
If first hit is a germline mutation, second somatic mutation more likely to enable cancer
Mutations and Inheritance of Tumour Suppressor Genes
Tumour suppressor genes control cell growth and differentiation and function as ‘cellular recessives”- both alleles must be affected but a first hit germline mutation is inherited in a dominant fashion.
-% of RB is familial
risk of - is increased in germline mutation
10%
non-ocular tumours
Neurofibromas Type 1 (NF1)
· Autosomal dominant · Affects 1 in 2,500 · Multisystem disorder · Dominant · Fully penetrant · Highly variable expressivity- Great variability between affected individuals in the same family
NF1 gene function
The NF1 gene (v large) on chromosome 17 encodes the protein neurofibromin. Neurofibromin suppresses Ras, a potent activator of cell growth and proliferation.
Clinical Features of NF1
· Neurofibromas (anywhere in body)- cutaneous, subcutaneous, nodular, plexiform
· Other skin manifestations- axillary freckling
· Lisch Nodules- in the eye
· Optic Glioma- growth around optic nerve, usually asymptomatic and can present with deteriorating vision, 15%
- Scoliosis- 10%, usually v mild, small number with severe presentation
- Learning disability- usually mild, 30-50%
- Large head
NF1 Cancer Predisposition
- Malignant tumor of the peripheral nerve sheath
o Life time risk of 13%
o Usually from pre-existing plexiform neurofibroma - Astrocytoma 2%
- Phaeochromocytoma 0.7%
- Rhabdomyosarcoma 1.4%
Von Hippel Lindau Disease
- Autosomal dominant
- Affects 1 in 35,000 individuals
- High penetrance
- Associated with a wide variety of tumours
vHL protein function
The vHL protein suppresses tumour growth and downregulates angiogenic factors.
vHL mutation identification
~90% of individuals with a clear diagnosis of vHL will have mutation identified- myoclonic testing is 1st line investigation
Screening Regimen for vHL (yearly)
MRI of brain and spine (2-3 yearly)
Ages 5-18
- Eye/retinal examination
- 24 hour urine collection for catecholamines
Ages 18-65
- Eye/retinal examination
- Physical examination
- 24 hour urine collection for catecholamines
- MRI of abdomen
If tumour found early- easier to treat with less severe complications
Familial Adenomatous Polyposis
- Autosomal dominant
- 1 in 10,000
- polyps develop during second decade
- colonic malignancies third decade
- Associated features
o CHRPE
o Desmoid tumours
o Osteomas
APC mutation types
APC (large) mutations are mostly truncating mutations. You can also have attenuated FAP- milder, later onset and better prognosis.
what is genomic imprinting?
Genomic imprinting is the difference in gene expression depending on whether a gen is maternally or paternally inherited.
what does genomic imprinting lead to?
Leads to functional hemizygosity i.e loss of biparental contribution
Examples of genetic imprinting
Example: deletion of 15q11.13 region on maternal chromosome= Angelman’s but on paternal= Prader Willi
Angelman’s Syndrome
- Severe global developmental delay
- No speech
- Inappropriate laughter
- Drooling
- Seizures
- Cannot walk without help
- No family history
Prader Willi Syndrome
- Floppy at birth, poor feeding
- Short stature, small hands and feet
- Hyperphagia and obesity
- Hyponadism
- Mental retardation (mild to moderate)
Mechanisms of Loss in Imprinting
- Chromosome deletion of maternal/ paternal chromosome
- Methylation abnormality- takes of paternal/ maternal pattern, loss of biparental expression
- Uniparental disomy- maternal regions on the chromosome have gone and been replaced by paternal genome
- Mutation in UBE3A gene/ General Gene Mutations
Imprinting and Cancer Associations
o Wilm’s tumour – maternal chrom 11p15
§ Neuroblastoma – maternal chrom 1p36 & paternal chrom 2
Mitochondrial DNA and Mutations
• Contains important genes for mitochondrial metabolic pathways and ribosomal RNAs
• High rate of mutations- no repair mechanism
– Point mutations and deletions occur
Mitochondrial Inheritance
only passed on by affected mothers, affected fathers do not pass it on (paternal wiped out after fertilisation)
Phenotypes of Mitochondrial Mutations
- Multiple phenotypes (clinical heterogeneity)- gene mutations can cuase multiple presentations, one family can have multiple presentations
- Mitochondrial diseases are respiratory chain disorders (disorders of high energy tissue)
Heteroplasmy
different daughter cells contain different proportions of mutant mitochondria compared to normal
when do genetic disorders follow mendelian inheritance and not mitochondrial?
- Mitochondrial DNA does not code for all mitochondrial protein
- If abnormal mitochondrial protein is coded from genomic DNA then genetic disorders follow mendelian patterns of inheritance
packing ratio
The degree to which DNA is condensed is expressed as its packing ratio (length of native DNA / length after condensation).
what is condensin I responsible for in mitosis?
lateral compaction of chromosomes (metaphase)
what is condensin II responsible for in mitosis?
axial shortening of chromosomes (prophase)
what can mutations in parts of the condensins lead to?
microcephaly (not enough brain growth)
Cohesin cycle
- cohesin is loaded onto DNA by NIPBL
2. cohesin can release DNA through action of separase (ESPL 1)
Cohesin actions at metaphase and anaphase
cohesin molecules lock chromosomes together at kinetochore and assemble the centromere at metaphase
separase activation in anaphase pulls chromosome and once pulling forces gets to a point DNA is released from cohesin and they are neatly pulled into daughter cells
Roberts Syndrome cause
- Caused by biallelic mutations in ESCO2- viral loss of function mutation, signals on & off chromosomes can lead to cohesion getting stuck on chromosomes
- Premature centromere separation
- Lagging chromosomes- can’t release cohesin so daughter chromosomes can’t be released
telomere function and sequence
- End structure that stops chromosomes getting stuck together (long strand of single stranded DNA using internal RNA template & TERT enzyme), added to chromosomes by telomerase
repeat sequence: TTAGGG
Dyskeratosis Congenita cause
Caused by short telomeres by a mutation of both TERT enzymes, present in young adults/children.
Dyskeratosis Congenita symptoms
- Dysplastic nails
- Reticular pigmentation
- Oral leukoplakia
- Bone marrow failure
- Myelodysplastic syndrome
- Acute myelogenous leukaemia
polyploidy, trisomy and monosomy definitions
- Polyploidy- extra copy of whole genome
- Trisomy- extra copy of 1 of the chromosomes
o Autosomal- more severe
o X chromosome - Monosomy- loss of 1 of pair of chromosomes
o Turner syndrome- affects girls
Triploidy
extra copy of maternal genome in female embryo
- Extra paternal copy of the genome leads to
hydatidiform mole- rare, cancer-like
Live born infants are usually
diploid/triploid mosaic- 2 types of cells in the body rather than just 1
trisomy 21
Down’s syndrome
trisomy 18
Edward syndrome- small, multiple malformations, usually die in 1 month
trisomy 13
Patau syndrome- cleft lip, postaxial polydactyly
what chromosomes can’t have trisomy?
Chromosome 1 and 19 cannot have trisomy as 1 is the largest chromosome and 19 is gene rich. They can only have a triploidy mutation
47XXY is?
Klinefelter syndrome
(common), hypogonadism- testes cannot produce sufficient testosterone, small testes, usually infertile
45X is?
Turner syndrome (monosomy) endocrine function fine at first but regress over time, ovarian regression supplements oestrogen postnatally- healthy but infertile
recombination before 1st meiotic division
extensive recombination of DNA occurs between homologous chromosomes
euploidy and aneuploidy
Euploidy- normal balanced state of ploidy in an organism
Aneuploidy- unbalanced state- significant deviation from the standard diploid (2n) genome of a cell is almost always deleterious
MI non disjunction
failure of homologous chromosome pair separation in anaphase 1 leading to two daughter cells with n+1 and two with n-1 (non-viable)
M2 non-disjunction
failure of sister chromatid separation in anaphase 2 leading to sister gametes being pulled into 1 gamete
2 normal daughter cells and
- n+1 gamete
- n-1 gamete
most common type of aneuploidy
numerical chromosomal abnormalities
constitutional and mosaic
If the abnormality is seen in every cell it is called constitutional. If it is seem in only a proportion of cells it is known as mosaic.
Chromosomal trisomy increases with
mothers age as there is increased time spent in cell meiosis.
types of structural chromosomal abnormalities
deletions and duplications
genetic mechanisms that lead to structural chromosomal abnormalities
non-homologous end joining (NHEJ) and non-allelic homologous recombination (NAHR)
NHEJ and NAHR targets
The boundaries of NHEJ structural chromosome anomalies are essentially random whereas NAHR targets specific regions of the genome.
interstitial NHEJ
deletion occurs in one arm of chromosome and these ends are joined maintaining the proximal and end parts
terminal NHEJ
deletion at the end of the chromosome & telomerase repairs it leading to shortened end, more common
WAGR syndrome
Wilms tumour, aniridia (absence of iris), genitourinary anomalies, mental retardation
Caused by deletion in non-homologous end joining.
how are NHEJ Continuous Gene Syndromes recognised?
NHEJ Continuous Gene Syndromes are recognised via phenotype as a result of haploinsufficiency for one or more high-penetrant genes (individual genes that have strong effect on genotype so going from 2 to 1 makes a big difference.
non specific signs of NHEJ Continuous Gene Syndromes
- Short
- Learning difficulties
- Heart malformation
- Seizures
reciprocal translocation
NHEJ between chromosomes– no genetic materal lost and doesn’t alter genomic copy number so no medical abnormality but there will be problem with reproductive health
why do reciprocal translocation cause problems with reproductive health?
During pairing of homologous chromosomes in meiosis, quadrivalents need to be formed which is complex- less efficient, lower sperm count.
classes of daughter cells that can be made in segregation during meiosis in reciprocal translocation
- balanced- normal embryo
- balanced- all genetic materal present
- imbalance- major chromosomal abnormality
inheritance in reciprocal translocation
Reciprocal translocations can be inherited by offspring. Even if the original translocation is balanced, future inherited translocations can be unbalanced.
De novo reciprocal translocation (passed on from neither parent)
mechanism of NAHR
within each homologue there are low copy tandem repeats which are identical to each other
recombination at the wrong repeats can lead to deletions and duplications of different loops in chromosomes
acrocentric chromosomes
13, 14, 15, 21, 22
- Have centromeres at the end of chromosomes
- Short arms are factories for creating components of ribosomes- mediate translation
- Ribosomes are the most abundant proteins in cells
Williams Syndrome
7q11.23
supravalvular aortic stenosis (elastin), learning difficulties, good expressive language but poor comprehension
Di George syndrome
22q11.2
TBX1 gene- cardiac outflow tract defects, cleft palate
Structural chromosome anomalies that change the order of sequence in the genome without altering the copy number are known a
balanced structural chromosome anomalies
If the change in order occurs within a chromosome it is known as an inversion. If they occur between non-homologous chromosomes they are known as balanced reciprocal translocations
Robertsonian translocations
arise from NAHR fusing of chromosomes 13, 14, 15, 21 or 22 (similar, highly repetitive sequences on their short arms)
when are Balanced inversions and translocations associated with disease?
mostly not associated with disease unless one of the breakpoints has interrupted a haploinsufficient disease gene
gametes of a carrier of a balanced translocation
when the carrier of a balanced translocation makes gametes there is a high risk on an unbalanced results due to the requirement to pair structurally unusual and normal chromosomes.
problems with Robertsonian translocations carriers
Individuals can have some infertility but most problems arise in reproduction as can cause problems in meiosis like trisomy and monosomy.
Triple Repeat Expansion Dynamic Mutations
- Mutations are evolving
- Not stably inherited
- Mutations are (usually) increasing in size with successive generations but can also contract
- More severe in succeeding generations
- Has a threshold effect
- Exhibit a relationship between severity and repeat copy number
- Most common are triplet repeats
examples of gender bias in Triple Repeat Expansion Dynamic Mutations
• Expansion of repeats usually has gender bias
– e.g. HD – expansion when transmitted from paternal line
– Fragile X – expansion when transmitted from maternal line
anticipation
The signs and symptoms of some genetic conditions tend to become more severe and appear at an earlier age as the disorder is passed from one generation to the next.
explained by triple repeat dynamic mutations
Myotonic Dystrophy Symptoms
- Frontal balding
- Cataracts
- Muscle weakness
- Myopathic facies
- Myotonia
- Dysphagia
- Intellectual deterioration
Myotonic Dystrophy Repeat Expansions and Disease Alleles
- CTG trinucleotide repeat in 3’ UTR of Myotonic dystrophy gene.
- Normally 5-27 copies of repeat
- Disease alleles 50-2000 repeats- there are intermediate alleles that are high risk of expansion
- Repeat expands on male or female transmission- sudden increase usually comes from maternal side
- Disease shows anticipation
Digenic Inheritance
• >100 genes involved
• Usually conform to mendelian patterns of inheritance
Double heterozygotes- no deficit found in patients who were only carriers of a mutation in a single locus but deficit occurred where patients were carriers of mutations in 2 gene loci
Contiguous Gene Deletion Syndromes caused by
a microdeletion that spans two or more genes tandemly positioned along a chromosome
Microdeletion in Williams-Beuren Syndrome
7q11.23 • Dysmorphic facial features • Cocktail party demeanour • Excessive non-social anxiety • Preserved vocabulary • Cardiovascular problems • Supravalvular aortic & renal stenosis (elastin) • Transient hypercalcaemia (paediatric)
Subtelomeric Deletions
• Majority of translocations involve chromosome ends (shared telomere-associated repeats)
• Gene rich adjacent regions (rearrangements likely to have phenotypic consequences)
Moderate-severe mental retardation:
• for sporadic cases (7%)
• for familial cases (25%)
Mosaicism may become clinically important if:
- mutant cells has tendency to grow and replace normal cells (cancer cells)
- mutation arose early in embryonic development, so becomes a large proportion of the whole body
- mutation occurred in the germ line
When an individual is made up of populations of cells with different genetic constitutions, can be mosaic for:
- chromosomal aneuploidy
- molecular mutations
Somatic Mosaicism
All cells suffer mutations as they divide
• At meiosis and at mitosis
• Repair Mechanisms Exist
• Can give rise to reversion
• Given the numbers of cells in the body everybody will have some cells which have a mutation of some sort
Gonadal Mosaicism
• Commoner in some diseases
– Duchenne Muscular Dystrophy
– Osteogenesis Imperfecta (6% recurrence rate)
• Can offer prenatal diagnosis for a second child, even when parents are unaffected (if a mutation is identified)
• Causes recurrence risk for fatal dominant conditions
Duchenne muscular dystrophy
X-linked neuromuscular disorder caused by mutations in the dystrophin gene
- late walkers
- Muscle weakness develops through childhood as muscle fibres are replaced with fat and boys become usually wheelchair bound in their teens.
Early treatment with steroids may slow progression of the disease but death often occurs in young adulthood.
Haploinsufficiency
one copy of normally diploid gene is insufficient to allow development to proceed normally or health or homoeostasis to be maintained
allelic and locus heterogeneity
Allelic heterogeneity occurs when two or more alleles of a single locus are independently associated with the same trait, while locus heterogeneity occurs when two or more DNA sequence variations at distinct loci are independently associated with the same trait.
linkage
When two loci are close together on the same chromosome, so that the chance of crossing over between the two loci at meiosis is less than 50%, they are said to be linked.
Linkage analysis
allows location of unknown disease genes. It also allows tracking of a disease of known location through a family.
not necessary to know the mutation in the gene for this, just the location of the gene involved. Locus heterogeneity, however, limits the application of this technique.
Charcot Marie Tooth mutation
duplication on short arm of chromosome 17
dicentric chromosomes are a common feature of
Robertsonian translocations
HD number of CAG repeats to cause disease
Healthy: 8-35
27-35: unstable, have potential to expand and cause disease in the next generation.
Over 36 to cause Huntington’s disease
