Case 16: genetics

Question 1

Lynch management: MLH1 or MLH2

Answer 1

• Bowel cancer risk: 2 yearly colonoscopy screening, generally 25-75
• Gynaecological cancer risk: no screening. Hysterectomy with bilateral saplingo-oophorectomy after age 35 and once childbearing is complete
• Gastric cancer risk: H.pylori testing/eradication. Regular endoscopy screening not offered
• Symptom awareness: GI tract, gynae, urological
• Chemoprophylaxis: regular aspirin for at least 2 years

Question 2

Lynch management: MSH6 or MPS2

Answer 2

• Bowel: 2 yearly colonoscopies aged 35-75 (review at 75). H.pylori screening
• Gynae: Hysterectomy alone >45 and once childbearing is complete

Question 3

FAP

Answer 3

• Inherited mutations in the APC tumour suppressor gene: Autosomal dominant
• Hundreds of polyps form by 30-40
• Highly penetrant: majority of patient will develop colorectal cancer in middle age
• Causes large amount of polyps to grow in the bowel ‘adenomas’
• Classical FAP:1000s of colonic adenomas (100% risk of colorectal cancer)
• Attenuated FAP: 10-100 adenomas, not as penetrating. Can just offer long term colonic surveillance: colonoscopy 1-2 years

Question 4

FAP: management and extracolonic features

Answer 4

• Extracolonic features: Gastric fundus polyps, Duodenal polyposis, CHRPE (retinal findings), desmoid tumours, jaw osteomas
• Prophylactic total proctocolectomy with ileal pouch anal anastomosis (IPAA) formation in their twenties.
• Annual sigmoidoscopy/colonoscopy from 10-12

Question 5

Other rare single gene bowel cancer conditions

Answer 5

• MUTYH (Recessive mutations cause attenuated FAP like condition): lifelong colonoscopy follow up
• Peutz-Jeghers syndrome (STK11 gene) – perioral and digital hyperpigmentation; GI polyposis, other malignancy risk (breast and pancreatic). Dominant inheritance
• Juvenile Polyposis (e.g. SMAD4 gene) – GI polyposis, features of HHT (Hereditary Haemorrhagic Telengiectasia), internal organ bleeding and Telngiectasia’s with SMAD4. Dominant inheritance

Question 6

Bowel cancer: risk FH

Answer 6

• If no single gene identified base recommendations on strength of family history
• Population: no strong fhx
• Moderate: one FDR <50, 2 FDR’s at any age. One off colonoscopy at 55
• High: 3 FDR’s, Lynch excluded. 5 yearly colonoscopy from 40
• Very high: single gene cause like Lynch or FAP. Disorder specific screening i.e. 2 yearly for Lynch syndrome or 1 year for attenuated FAP

Question 7

Other colorectal genetics

Answer 7

• Retinoblastoma: germ line mutation in the retinoblastoma gene (Rb) predisposes to Retinoblastoma which occurs in childhood
• LI Fraumeni syndrome: a rare autosomal dominant condition. Due to a germline mutation in the p53 suppressor gene. Increases risk of sarcoma and cancer of the breast, brain and adrenal gland

Question 8

Noonan syndrome

Answer 8

• An autosomal dominant condition due to a defect in a gene on chromosome 12
• Features similar to Turner’s: Webbed neck, widely spaced nipples, short stature, pectus carinatum and excavatum
• Due to a mutation in the PTPN11 gene
• Cardiac: pulmonary valve stenosis
• ptosis, wide set eyes
• triangular-shaped face
• low-set posteriorly rotated ears, broad forehead, down-slanting palpebral fissures, a high arched palate
• coagulation problems: factor XI deficiency

Question 9

Noonan syndrome: associated conditions

Answer 9

• Congenital heart disease, particularly pulmonary valve stenosis,hypertrophic cardiomyopathy and ASD
• Cryptorchidism(undescended testes) can lead toinfertility. Fertility is normal in women.
• Learning disability
• Bleeding disorders (Thrombocytopaenia)
• Chest deformity (pectus excavatum), scoliosis, kidney deformity
• Lymphoedema
• Increased risk ofleukaemia and neuroblastoma

Question 10

Definitions: Dysmorphology and Syndrome

Answer 10

Dysmorphology: the recognition and study of birth defects and syndrome

Syndrome: condition characterised by a set of associated symptoms with a known or assumed single aetiology.

Question 11

Malformation definition

Answer 11

Morphological abnormality present at birth and of prenatal origin, it can involve a single organ or a body part and arises because of an abnormal developmental programme. A malformation is a structured birth defect. Fault in the genetic blueprint preventing the body from developing properly

Question 12

Aims of dysmorphology

Answer 12

• diagnosis (to end uncertainty and unnecessary investigations, to allow better management and prevention of complications)
• prognosis
• recurrence risk
• family planning

Question 13

Classifying structural defects

Answer 13

• Clinical impact: normal variant, minor, major
• Pathogenesis: Malformation, Deformation, Dysplasia, Disruption
• Recognizable patterns: syndrome, sequence, association

Question 14

Classifying structural defects clinical impact- normal

Answer 14

Relatively frequent morphological characteristics with no medical/pathological impact. Normal variant i.e. 2-3 toe syndactyly (webbing of toes)

Question 15

Classifying structural defects clinical impact- minor

Answer 15

• structural anomalies that don’t cause significant clinical disease, functional abnormality or cosmetic problem. No impact on life expectancy or QoL. Even if >1 doesn’t necessarily mean they have a syndrome
• head → scalp defect.
• ears → small, posteriorly rotated.
• face and neck → hyper-hypotelorism, cleft uvula, mild micrognathia,
• skin → sacral dimples, preauricular tags, single palmar crease.
• thorax/abdomen → supernumerary nipples, small hernias
• limbs → cubitus valgus, clinodactyly, large thumb

Question 16

Classifying structural defects clinical major

Answer 16

• Structural anomaly causing significant clinical, functional or cosmetic problems
• Impact on life expectancy and/or quality of life
• For example: ectrodactyly (missing central finger and fusion of other fingers), spina bifida

Question 17

Classifying structural defects pathogenesis- Malformation

Answer 17

• Morphologic abnormality that arises because of an abnormal developmental process- its a primary defect
• Bilateral cleft lip: non fusion of the maxillary prominence with the intermaxillary process
• Ectrodactyly: abnormal formation of hands and fingers with central fingers and fusion of other fingers

Question 18

Classifying structural defects pathogenesis- deformation

Answer 18

• Distortion of normal structure by an external factor- secondary defect
• Amniotic bands
• Intrauterine constraint: lack of intrauterine space can consequent congenital deformation as club feet or facial asymmetry. For example, Bicornate uterus or lack of amniotic fluid (oligohydramnios)
• Amniotic bands: Limb or part of the foetus becomes tangled in a strand of amnion, can impair blood supply to the distal limb

Question 19

Classifying structural defects pathogenesis- disruption

Answer 19

• Disruption: destruction of a tissue that was previously normal, normally due to impairment in blood supply- it is a secondary defect
• Interruption of a blood supply to a limb or muscle
• Poland sequence- absence of pec major and other muscles on one side due to interrupted blood supply

Question 20

Classifying structural defects pathogenesis- Dysplasia

Answer 20

• Abnormal cellular organisation within a tissue resulting in structural changes/abnormal growth of a tissue: its a primary defect.
• Abnormal organisation within a cell line or group of cells causing it to function differently. Wont affect all tissue. For example, skeletal dysplasia
• Cartilage hair hypoplasia
• Achondroplasia (drawfism)

Question 21

Classifying structural defects: Recognisable patterns

Answer 21

• Syndrome: a pattern of anomalies known or thought to have the same cause/gene mutation (i.e. Noonan syndrome- PTPN11)
• Sequence: a single primary malformation which leads to a set of morphological abnormalities (Potter sequence- occurs when a foetus grows within a restricted uterine cavity causing rocker bottom feet and a squashed face. Pierre Robin)
• Association: A pattern of at least 2 anomalies that occur together more often than expected by chance. No common cause identified. Gene in common might be found in the future. i.e. VACTERL

Question 22

What is the aim of Dysmorphology

Answer 22

• Diagnosis: better management and prevention of complications
• Prognosis and follow-up (are any other potential problems?)
• Recurrence risk (appropriate counselling for parents and relatives)
• Family planning and pregnancy management (PND- prenatal diagnosis/PGD?)

Question 23

Conditions that may present with a cleft palate

Answer 23

• Isolated Pierre Robin sequence
• DiGeorge syndrome: inherited, autosomal dominant. Due to microdeletion of gene. Presents with small chin, cleft palate and heart defect
• Stickler syndrome: inherited

Question 24

Trisomy 21: Downs syndrome

Answer 24

• face:upslanting palpebral fissures,epicanthic folds,Brushfield spots in iris, protruding tongue,small low-set ears, round/flat face
• flat occiput
• single palmar crease,pronounced ‘sandal gap’ between big and first toe
• hypotonia
• congenital heart defects (40-50%, see below)
• duodenal atresia
• Hirschsprung’s disease

Question 25

Down’s syndrome: Cardiac complications

Answer 25

• multiple cardiac problems may be present
• endocardial cushion defect(most common, 40%, also known as atrioventricular septal canal defects)
• ventricular septal defect
• secundum atrial septal defect
• tetralogy of Fallot
• isolated patent ductus arteriosus

Question 26

Down’s syndrome: later complications

Answer 26

• subfertility: males are almost always infertile due to impaired spermatogenesis. Females are usually subfertile, and have an increased incidence of problems with pregnancy and labour
• learning difficulties
• short stature
• repeated respiratory infections(+hearing impairment from glue ear)
• acute lymphoblastic leukaemia
• hypothyroidism
• Alzheimer’s disease
• atlantoaxial instability

Question 27

Down’s syndrome screening and prevention

Answer 27

• the combined test is now standard: nuchal translucency measurement + serum B-HCG + pregnancy associated plasma protein A
• these tests should be done between 11 - 13+6 weeks
• if women book later in pregnancy either the triple* or quadruple test should be offered between 15 - 20 weeks

Question 28

Trisomy 18 (Edwards syndrome)

Answer 28

• Life expectancy is usually less <1 year
• Small head, small jaw, clenched fist with overlapping fingers, profound intellectual disability
• Heart defects: VSD, ASD, PDA

Question 29

Trisomy 13 (Patau syndrome)

Answer 29

• Life expectancy is <1 year
• Heart, brain, kidney abnormality
• Incomplete fusion of the of the lip/palate (clefting)
• Microcephaly, Podacytyl (extra digits), Omphalocele
• Severe developmental and intellectual disability

Question 30

Autosomal recessive inheritance chance of children affected

Answer 30

• Affected individuals are normally born to unaffected carrier parents
• Carrier couples have a 1 in 4 chance of having an affected child
• Unaffected children have a 2 in 3 (2 in 4 of all children) chance of being a carrier

Question 31

Autosomal recessive: inheritance of carrier status

Answer 31

• If one parent is a carrier each child has a 1 in 2 chance of being a carrier
• Siblings of a carrier have a 1 in 2 chance of being a carrier (presuming no one in the family is affected)

Question 32

Autosomal recessive: one parent has the condition

Answer 32

• All offspring are obligate carriers if one parent is affected and the other parent isn’t a carrier
• If the other parent is a carrier offspring have a 1 in 2 chance of being affected

Question 33

‘3 things’ autosomal recessive rule

Answer 33

• 1= Father must be a carrier
• 2= Mother must be a carrier
• 3=They must both pass on their mutation (if both carriers this chance is 1 in 4)
• To calculate the chance of a pregnancy being affected you must multiple the possibilities (1) x (2) x (3)

Question 34

What to consider for carrier testing

Answer 34

• Prevalence and carrier frequency of the condition?
• Does the gene have a mutation which accounts for the majority of cases?- don’t want to read the whole gene
• Is their a biochemical test which can identify carrier status? (i.e. in metabolic conditions carriers might be the middle ground between being normal and pathogenic)

Question 35

The most common autosomal recessive conditions per ethnicity

Answer 35

• North western Europe: Alpha-1-antitrypsin deficiency, Cyststic fibrosis, Spinal muscular atrophy, Smith Lemli Opitz syndrome
• African American: Sickle cell disease/ B thalaessemia, Alpha 1 antitrypsin deficiency, Cystic fibrosis, Pompe disease
• Ashkenazi Jewish: Factor XI deficiency, familial mediterranean fever, Gaucher disease, Cystic fibrosis
• Eastern Asia: sickle cell disease/ B thalaessemia, Spinal muscular atrophy, Gaucher disease, Achromatopsia
• Middle East: Familial Mediterranean fever, sickle cell disease/B thalassaemia, Hereditary thymine uraciluria, Achromatopsia

Question 36

How do you do carrier testing

Answer 36

• Genetic testing: Mutation analysis for known common mutation. May test for specific mutations in an ethnic population
• Biochemical analysis i.e. looking or levels of alpha-1-antrypsin
• May do different tests for those at population risk then relatives at increased risk

Question 37

Common genetic mutations

Answer 37

• Alpha 1 antitrypsinogen deficiency: SERPINA1
• Haemochromatosis: HFE
• Tay-sachs disease: HEXA
• Spinal muscular atrophy: SMN1

Question 38

Why carrier testing can be wrong

Answer 38

• De novo mutations
• Chromosome abnormalities
• Rare or unidentified mutation not picked up on carrier testing
• Counsel that carrier testing can reduce the risk of a child being affected but cannot exclude the possibility

Question 39

When is carrier testing useful

Answer 39

• First degree relatives of those affected by the condition: main purpose is to determine likelihood of having an effected child
• Useful in conditions where the gene has a common mutation which accounts for a large proportion of cases

Question 40

Reproductive options for reproductive disease

Answer 40

• Pre-conception: accept risk of recurrence, choose not to have further children, adoption, donor gamete. Pre-implantation genetic diagnosis
• 1st trimester: Non invasive prenatal testing
• 11-14 weeks: Chorionic villous sampling
• 15+ weeks: Amniocentesis
• Throughout pregnancy: detailed foetal anomaly scanning. Repeat US so they can pick up changes early and management plan can be present from birth i.e. cleft palate
• Neonatal period: testing of cord blood, test or monitor for features of the condition following birth

Question 41

What determines if someone is eligible for pre-implantation genetic diagnosis

Answer 41

• There is a list of approved conditions set out by the Human Fertilisation and Embryology Authority
• the patient has to meet NHS IVF eligibility criteria which takes into account their age, health, chance of success, smoking, BMI, whether they already have a child etc

Question 42

Pre-implantation Genetic Diagnosis (PGD)

Answer 42

• Assisted reproduction with embryo biopsy to screen embryos for a specific genetic condition prior to implantation (only done in IVF)
• Done after egg is fertilised. At day 5-7 a biopsy is taken
• Testing on embryo biopsy= FISH analysis, SNP array or testing for a known mutation in a single gene disorder
• Stimulation of the ovaries → Collection of eggs from the ovaries → Insemination/Injection of sperm → Fertilisation → Embryo biopsy → Embryo testing → Embryo transfer (for embryos not containing the genetic change)

Question 43

Pre-implantation Genetic diagnosis (PGD): advantages and conditions

Answer 43

• Done for HFEA approved conditions. For example: Huntington’s, Muscular dystrophy, CF, Spinal muscular atrophy, Duchenne muscular dystrophy, Haemophilia
• Advantages: Avoid difficult decisions following testing during a pregnancy, can be part of already planned Fertility treatment

Question 44

Pre-implantation conditions considerations

Answer 44

• Success rate: 1 in 3- not great if you can have a child naturally
• Length of treatment: long 8-18 month before pregnancy, emotional
• Travel: have to travel to London and Leeds for appointments
• Side effects: Ovarian Hyperstimulation syndrome. Multiple pregnancy

Question 45

Chorionic Villous sampling

Answer 45

• Invasive pre-natal testing
• Needle is inserted in lower abdomen with US guidance
• Sampling of cells taken from the chorion (developing placenta) between 11 and 14 weeks gestation to test for specific genetic condition
• Chorion derived from the fertilised egg and shares genetic make-up with embryo
• Chance of uncertain results due to placental mosaicism (de novo mutation)- more significant in chromosomal abnormalities
• Risk of complications: Miscarriage (1%), Vascular disruption defects

Question 46

What is placental mosaicism

Answer 46

the placenta and foetus may have different chromosomal makeup as de novo mutation may have occurred in the cells that have become the chorion rather than the cells of the foetus.

Question 47

Amniocentesis

Answer 47

• Invasive pre-natal testing
• Us guidance and needle insertion in the lower abdomen
• Testing of fetal cells present in the amniotic fluid
• Performed from >15 weeks gestation, done later than CVS meaning termination is more difficult
• Chance of failing to achieve a result increases with gestational age
• Risk of complications: Miscarriage (0.5%)- less than CVS, Amniotic fluid leak causing oligohydramnios

Question 48

Non invasive prenatal diagnosis/testing

Answer 48

• Compared to invasive testing no risk of miscarriage or complications
• Analysis of cell-free fetal DNA (cffDNA) fragments in the mums bloodstream. This DNA is from the foetus and the placenta. Use a blood sample from Mum
• Fetal DNA accounts for approximately 10% of cell free DNA in the maternal bloodstream
• cffDNA detectable from 4 weeks but reaches sufficient levels for analysis from 10 weeks
• NIPT: Non-invasive Prenatal Testing for aneuploidies
• NIPD: Non-invasive prenatal Diagnosis

Question 49

Application of NIPD: determining fetal sex

Answer 49

• Don’t offer routinely to find the sex of the child but used in:
• X-linked disorders (Duchene Muscular Dystrophy).
• Disorders with gender specific phenotypes (e.g. Congenital Adrenal Hyperplasia).
• Test for Y chromosome DNA sequence

Question 50

Applications of NIPD: testing for a specific mutation in a single gene disorder

Answer 50

• De novo mutation identified in a previous pregnancy or affected child.
• Dominant disorders affecting the father. Cant do maternal as mutation will be present in blood from mum even if foetus doesn’t have it)
• Known paternal mutation in a recessive condition where both parents carry a different mutation
• If mutation detected offer CVS/amniocentesis. If mutation absent foetus is unlikely to be affected