Lecture 11: Introduction to Cytogenomics Flashcards
What does Medical Cytogenomics STUDY? INVESTIGATES? EMPLOYS?
- Studies GROSS HUMAN GENOME VARIATION IN HEALTH AND DISEASE
- Investigates HEREDITY AT THE CELLULAR LEVEL
- Employs VARIETY OF METHODS REQUIRING HIGHLY SPECIALISED SKILLS
highly specialised skills
What are Human Chromosomes? =4
- Cellular structures
- Compacted DNA (1 DNA molecule = 1 chromosome)
- DNA-protein interactions
– ‘compaction’
– ‘regulation of gene expression’
- DNA-protein interactions
4.* Ensure CORRECT CELLULAR INHERITANCE’ VIA CELL DIVISION
CELL DIVISION
MITOSIS AND MEIOSIS
UNDERTSAND PROCESSES
Human diploid chromosome set?
KARYOGRAM =?
1 - #22 – autosomes;
Karyogram - ordered image of the chromosomes from a single cell..
on metaphase spread
X , Y – sex chromosomes
22 + sex chr = 23
Metaphase chromosome morphology
‘p’ arm (short) =2
‘q’ arm (long) = 2
telomere at each end
- hence 4 on each arm
- CENTROMERE in middle
—-
…LOCATION OF CENROMERES…
Metacentric - in middle
Submetacentric - above middle
Acrocentric - near top of both chr
= will have ‘satellite’ and ‘stalk’ …above the acrocentric line
Selected methods for cytogenomic analysis: 5
- Conventional cytogenetics
- chromosomal microarray
- quantitative fluroescence -PCR (QF-PCR)
- Genomic sequencing
- FISH - Fluorescence IN SITU HYBRIDIASTION
Selected methods for cytogenomic analysis: Conventional cytogenetics = 2
- requires dividing cells
- resolution 5-10Mb
Selected methods for cytogenomic analysis:
chromsomal array- 2
- DNA - based
- Resolution approx 50Kb
Selected methods for cytogenomic analysis:
Quantitative Fluorescence – PCR (QF-PCR)
- DNA - based
- Resolution single locus
Selected methods for cytogenomic analysis:
‘Fluorescence in situ hybridisation (FISH)’
- Dividing/non-dividing cells
- Resolution ~200Kb
Selected methods for cytogenomic analysis:
‘Genomic sequencing’
- DNA - based
- Resolution single locus
what are chromosomal abnormalities?
types?
Deviations from the standard pattern
of 23 pairs of chromosomes with known morphology
types:
–Numerical abnormalities
–Structural abnormalities
What is ‘Numerical chromosome abnormalities’
= 2
- Deviations in chromosome number
- Usually occur de novo – low recurrence risk
example of ‘Numerical chromosome abnormalities’
- Down syndrome
- Prevalence ~ 1:1000 births
(Roizen N & Patterson D, 2003 Lancet 361:1281-1289) - Additional copy of chromosome 21 (trisomy 21)
Mechanisms of numerical chromosome abnormalities = 2
- cell division errors
- fertilisation errors
Mechanisms of numerical chromosome abnormalities: ‘CELL DIVISION ERRORS’
= 4
- Checkpoint defects
- cohesion defects
- centrosome amplification
- microtubule defects
‘diagram on slide 11’
Mechanisms of numerical chromosome abnormalities:
‘FERTILISATION ERRORS’
Example
- ovum = 23, X
- 2 SPERM ON IT
- 23, Y AND 23 X
HENCE = DISPERMY
Euploid numerical abnormalities means =
examples -2
Euploid numerical abnormalities means =
‘(multiples of the haploid set)’
- TRIPLOID = 3 Sets of chromosomes for each order
- TETRAPLOID = 4 sets of chromosomes for each order
Aneuploid numerical abnormalities means?
examples? - 2
Aneuploid numerical abnormalities means
‘(gain or loss of one or a few chromosomes)’
- TRSIOMY 21 (3 chromosomes for order 21)
- Monosomy X (X or Y missing only one sex chro = (X, …)
Structural chromosome abnormalities?
MECHANISIM?
TYPES?
INHERITANCE?
- ‘Mechanism: chromosomal breakage and reunion
in a different configuration’
TYPES
* Balanced – no net gain or loss
* Unbalanced –gain/loss of chromosomal material
- May be inherited –’ high recurrence risk’
Balanced structural abnormalities:
Balanced structural abnormalities:
‘Robertsonian translocations’
Translocation (14;21)
NOTE: 45 chromosomes
Risk for chromosomally abnormal offspring…
(14, 14 and 21, 21) + ‘balanced translocation’ (14, t14;21, 21)
= 14, 14;21 and 21,21
UNBALANCED TRANSLOCATION (TRANSLOCATION TRISOMY 21)
DIAGRAM ON SLIDE 16
Other balanced rearrangements:
‘reciprocal translocations’
Other ‘balanced’ rearrangements:
‘reciprocal translocations’
=
Translocation of (11;22)
der(11) and der(22)
Meiosis I pairing
diagram on slide 17
Balanced structural rearrangements challenging
for detection = 2
- INSERTION
(“cut and paste”) - INVERSION
(‘FLIP’)
- Paracentric (near above)
- Pericentric (near below)
Unbalanced structural abnormalities 1
- chr 13 pair
NO ABNORMALITY - CAN LEAD TO
– DELETION
of chr 13 …OF TERMINAL SEGMENT
—DUPLICATION
of genes on chr 13 ..becomes longer
- INTERSTITIAL DELETION on chr 16
LOOK AT DIAGRAM ON SLIDE 19
Unbalanced structural abnormalities 2 =
- Sister chromatid recombination
- loss of both termini
- ring chromosome (x)
- Isochromosome (x)
- Marker chromosomes (unknown origin)
define :
Mosaicism
Presence of ‘cell lines’ with ‘different chromosomal
constitution’ in the ‘same individual’ – ‘numerical or
structural changes’
Clinical impact of cytogenomic variants = 3
1 * No apparent effect
2 * Reproductive issues
3 * Apparent clinical concerns
– Ambiguous genitalia
– Multiple congenital anomalies
– Neuro-developmental issues
– Cancer
Clinical impact of cytogenomic variants:
‘Apparent clinical concerns’ =4
1 – Ambiguous genitalia
2 – Multiple congenital anomalies
3 – Neuro-developmental issues
4 – Cancer
A major proportion of chromosomal abnormalities are ‘detected prenatally’
TABLE ON SLIDE 23
‘Maternal age’ and risk of chromosomal
abnormality
Maternal age and risk of chromosomal
abnormality = PROPORTIONAL
HIGHER AGE = HIGHER RISK OF CHROMOSOMAL ABNORMALITY IN INFANTS
EXAMPLE ON GRAPH WAS ON TRISOMY 21
…Risk increased from age 35/36 ish (frequency = 0.1 ish or less)
- great at 45 approx frequency of 0.10
Subject of human cytogenomics?
mechanisms?
recurrence risk?
clinical impact?
- Chromosome variation in health and disease is a subject of human cytogenomics
- Different mechanisms underlying
chromosomal aberrations
- Different mechanisms underlying
3 * Different recurrence risk associated with
numerical and structural chromosomal
anomalies
4 * Different clinical impact of chromosomal
abnormalities
