Chromosome Abnormalities Flashcards
What is cytogenetics?
Study the genetic constitution of cells through the visualisation and analysis of chromosomes
Why do cytogenetic analysis?
Accurate diagnosis/prognosis of clinical problems
- identify the syndrome associated with abnormality
- account for phenotype
- account for pregnancy loss
Better clinical management
- e.g. hormone treatment for Klinefelter syndrome
Assess future reproductive risks
- risk of live born abnormal child
- previous downs pregnancy, approx 1% increase above pop risk of another
Prenatal diagnosis
- TOP of affected pregnancy/planning for management at birth
What are referral reasons for cytogenetic analysis?
Constitutional abnormalities
- prenatal diagnosis
- birth defects
- abnormal sexual development
- infertility
- recurrent fetal loss
Acquired abnormalities
- leukiaemias e.g. AML ALL CML
- solid tumours
- specific translocations/abnormalities van give prognostic information
Name 2 prenatal diagnosis methods
Chorionic villus sampling - 11-12 weeks gestation, 1.2% miscarriage risk
Amniocentesis - 15 weeks onwards, 0.8% miscarriage risk
Describe prenatal diagnosis
Maternal serum screening for Down’s syndrome
- biochemical markers 1:150 offererd PND
First trimester screening - biochemical and ultrasound scan
- nuchal translucency and biochemical markers
FH chromosome abnormality
Abnormal ultrasound scan
- cystic hygroma, cleft lip/palate, heart abnormality, limb abnormalities
DNA studies e.g. CF, SMA
What are some birth defects
- dysmorphism
- congenital malformations
- mental retardation
- developmental delay e.g. abnormal behaviour, learning difficulties
- specific syndromes
- Down’s syndrome (trisomy 21)
- Williams syndrome (deletion 7q11.23)
- DiGeorge syndrome (deletion 22q11.2)
Name methods of cytogenetic testing
Karyotyping, chromosome analysis
FISH
Microarray comparative genomic hybridisation (aCGH)
Describe chromosome analysis
- systematic sorting of chromosomes = karyotyping
- whole genome screen 5-10Mb resolution
- metaphase chromosome Staines, paired up and grouped together
- abnormalities described using standard nomenclature ISCN 2013
How is chromosome analysis carried out?
Count the number of chromosomes
Identify each chromosome pair
Assess if there is any missing or extra material - are bands in the right place
All pars must be seen at the correct resolution twice
All chromosomes independently rechecked once
How is a karyotype written
Standard format to describe the karyotype: ISCN 2016
Chromosome number, sex complement and structural changes separated by commas
46,XX - normal female
46,XY - normal male
47,XX+21 - female with trisomy 21
46,XY,inv(7)(p11.2q11.23) - male with chromosome 7 inversion
No spaces
What are numerical cytogenic abnormalities?
Aneuploidy - loss and gain of whole chromosomes
Arise due to errors at cell division in meiosis
Trisomies e.g9m. Down’s +21, Patau +13, Edwards +18
Monosomies (missing whole chromosome) e.g. Turner syndrome 45,X which is the only full monosomy to be viable - X inactivation
Polyploidy
What is polyploidy?
Gain a whole haploid set of chromosomes
Triploidy 3NA
The most common cause is polyspermy
Triploidy occurs in 2-3% in all pregnancies and ~15% of all miscarriages: term deliveries die shortly after birth
Name causes of aneuploidy
Originates from non-disjunction at one of the meiosis cell divisions
Forms gametes with a missing chromosome and extra chromosome - which chromosomes involved will influence viability
Can occur during mitotic cell division - causes mosaicism i.e. 2 cell populations in an individual
Describe Down’s syndrome
Frequency 1:650-1000 Hypotonia Characteristic facial features Intellectual disability Heart defects Increased prevalence of leukaemia Increased incidence of early Alzheimer’s 21q22 DSCR
Describe Edwards syndrome
Incidence 1:6000; female predominance
Maternal meiosis II error
Modal lifespan 5-15 days
Nearly all diagnoses made prenatally
Small lower jaw Prominent occipital Low set ears Rocker bottom feet Overlapping fingers
Describe patau syndrome
Multiple congenital abnormalities Polydactyly Holoprosencephaly Incidence 1:12000 Majority die in neonatal period
What is X chromosome inactivation?
Only 1 X chromosome is ever active in a human cell
Males have 1
Females have 2
X inactivation ensures individuals have same X chromosome complement that is active
Decsribe Turner syndrome
45,X
Incidence 1:2500
Majority of cases absent paternal X; phenotypic differences depending on parental origin of C
Short stature, heart defects, mild learning difficulties, neck webbing, puffy feet, infertility
What is mosaicism?
Presence of 2 or more cell lines in an individual
- usually caused by mitotic non-disjunction
- throughout the body or tissue limited
Degree of mosaicism depends on when the mitotic error occurred
Trisomic conceptus rescued to give mosaicism - anaphase lag
Name some cytogenic structural abnormalities
Translocations - reciprocal and robertsonian Inversions - paracentric and pericentric Deletions Duplications Insertions Rings Marker chromosomes Isochromosomes
What are reciprocal translocations?
Two break rearrangements
Usually unique to a family t(11;22) is an exception
Carriers produce balanced and unbalanced gametes
If unbalanced offspring will have an abnormal phenotype dependant on regions of trisomy and monosomy
Segregation analysis using patchy teen diagram to assess this imbalance
What are types of segregation in meiosis I?
Alternate - balanced
Adjacent 1 - non homologous centromeres - most common form to give imbalance
Adjacent 2 - homologous centromeres
3:1 non disjunction
What is a balanced/unbalanced rearrangement?
Translocations can be balanced (in an even exchange of material with no genetic information extra or missing, and ideally full functionality) or unbalanced (where the exchange of chromosome material is unequal resulting in extra or missing genes).
What is meiosis disjunction
Matching segments pair
Translocation forms quadrivalent
Produces balances and unbalanced products depending on type of segregation
Describe alternate segregation
Alternate centromeres segregate together
Always produce normal or balanced gametes
What are adjacent-1 and adjacent-2 segregation?
Adjacent-1 - different centromeres - most likely mechanism for imbalance
Adjacent-2 - like centromeres - large degree of imbalance but very rare
Both produce unbalanced gametes - monosomy and trisomy
How are unbalanced segregate outcomes assessed?
Establish likely segregation Have the imbalances been reported before? - DECIPHER - ECARUCA - literature search e.g. PubMed Quote risks if established
What are robertsonian translocations?
Two acrocentric chromosomes fused together: 13,14,15,21,22
Mono or dicentric: 13;14 most common
Chromosome count of 45 in balanced carriers
Trivalent formed at meiosis - not very stable
Aneuploidy risk - females have higher risk than males, homologous carriers cant have normal pregnancy
Name some FISH probe types
Locus/gene specific probes - used for microdeletion syndromes - too small to see on G-added chromosomes
Centromere probes - used to identify chromosome of origin
Telomere probes
Whole chromosome paints - used to identify a chromosome in aa rearrangement
What is interphase analysis?
Give an example
PND - up to 14 days in culture - causes anxiety
Uncultured cells
FISH probes for 13,18,21,X&Y - common aneuploidies
Results in 24-48 hours
Full karyotype 14 days
99+% concordance with full karyotype
Many patients TOP after FISH
Example: leukaemia FISH
Look for different types of chromosome abnormalities
Translocation - fusion problems for the genes involved
Gene rearrangements - break apart probes
Amplifications - locus specific problems e.g. her2, c-myc oncogenes
What is microarray comparative genomic hybridisation (aCGH)
Examines the whole genome at high resolution
Copy number changes
- cant detect balanced rearrangements
- not used for mutation detection
Uses patient DNA not chromosomes
- compare normal control DNA to patient DNA
15-20% abnormality rate in developmental delay cohort
What are aCGH referral groups?
Learning difficulties/developmental delay/multiple congenital abnormalities
Normal karyotype - balanced de novo karyotype - is it really balanced?
Unbalanced karyotype to assess gene content
What are advantages of array CGH
Examines entire genome at high res
Targeted against known genetic conditions and sub telomere regions
1 array is the equivalent of many FISH (1000s) and can be automated
Detailed info on genes in del/duo region
Better phenotype/genotype correlation
What are disadvantages of array CGH?
Arrays are more expensive than karyotyping
Will not detect balanced rearrangements
Copy number variation (CNV)
Mosaicism may be missed
How is array analysis performed?
Scan array slides Input scans into software Run appropriate algorithm for array type Results lie produces Quality criteria must be reached Interpret any copy number calls Follow up using FISH/MLPA/array
Results
Normal result
Pathogenic change
- clear pathogenic finding
- specific genes or syndromic region
Uncertain change
- possibly pathogenic
- novel copy number change wit no genes or those unlikely to be relevant to phenotype
Benign finding
- polymorphic finding
- generally not reported
