Chromosome Pathology

Question 1

what is cytogenetics?

Answer 1

study of chromosomes - anything more than a single gene

Question 2

what is the improved name for cytogenetics and why?

Answer 2

molecular cytogenetics and genome disorders as there is a blurred boundary between cytogenetics and molecular genetics

Question 3

why are we diploid and what are the exceptions?

Answer 3

all cells have 23 pairs of chromosomes per cell, but gametes are haploid - they only gave 23 chromosomes

Question 4

what are the autosomes?

Answer 4

chromosomes 1-22, X/Y are sex chromosomes

Question 5

what percentage of births is cytogenetics implicated in?

Answer 5

0.7% live births, 5% of stillbirths and 50% of miscarriages - major contributor to congenital malformation and learning difficulties

Question 6

what do most cytogenetic changes result in?

Answer 6

copy number variations - this is a DNA sequence with a variable copy number compared to the reference genome - can be 1Kb to several Mb

Question 7

what is a continguous gene?

Answer 7

it is a disorder that results from a chromosomal abnormality resulting in the duplication/deletion etc of numerous genes next to each other

Question 8

what was the earliest cytogenetic technique still used now occasionally to detect copy number variation?

Answer 8

G banding

Question 9

what are some whole genome techniques for CNV detection?

Answer 9

G banding, next generation sequencing or microarrays

Question 10

what are some techniques for targeted testing and what do they look at?

Answer 10

they look for CNVs in particular parts on the genome and examples are FISH, QF-PCR and microarrays

Question 11

what types of CNV are there?

Answer 11

numerical (polyploidy, aneuploidy or mosaicism)

structural - the gain or loss of one or more genes - duplication or deletion

Question 12

what is more severe loss or gain?

Answer 12

loss is more deleterious than gain - dosage effect describes the loss or gain of part of or a whole chromosomes

Question 13

what is the position effect?

Answer 13

this is a cytogenetic abnormality that will cause an abnormal phenotype - a gene in a new chromosomal environment will function inappropriately

Question 14

what is aneuploidy?

Answer 14

it is trisomy (the gain of just one chromosome) or monosomy (the loss) of a chromosome

Question 15

what is polyploidy?

Answer 15

when you gain whole sets (triploidy - 3 of every chromosome or tetraploidy)

Question 16

what can increase the change of aneuploidy occurring during meiosis/gametogenesis?

Answer 16

the increase in maternal age - paternal age increase has no significant effect

Question 17

what occurs when there are errors in meiosis?

Answer 17

non-disjunction - failure of chromosome or chromatid separation - majority happen in meiosis I

Question 18

what is the result of non disjunction in meiosis I?

Answer 18

it is nullisomic (no chromosomes in a gamete therefore resulting in monosomy when fertilised) or disomic (2 copies of a chromosome in each gamete) gametes

Question 19

why do we only see trisomy 1, 18 and 13?

Answer 19

most aneuploidys do not make it past full term - trisomy 21 only has a 75% chance of making it past full term

Question 20

when do the errors resulting in polypoidy occur?

Answer 20

most are triploidy and occur at fertilisation

Question 21

what is the difference between diplospermy and dispermy?

Answer 21

in diplospermy the sperm does not reduce it’s chromosome number, in dispermy two sperm will fertilise the same egg. Digymy is when the egg doe not reduce it’s chromosome number

Question 22

what is the difference in presentation between a maternal and paternal triploidy?

Answer 22

double maternal - underdeveloped placenta and a disproportionately large head
double paternal - large cystic placenta

Question 23

what is a hydatidiform mole?

Answer 23

when a sperm fertilises and egg that is empty and therefore there is no foetus but a placenta develops

Question 24

when do the errors resulting gin mosaicism occur?

Answer 24

these occur at early cleavage and result in normal and abnormal cells - mitotic nondisjunction

Question 25

what is trisomic rescue?

Answer 25

when cells kick out the extra copy of the chromosome during early stages of division

Question 26

why is there variable clinical expression in structural rearrangements?

Answer 26

theses can be deletions or duplications, and there can be a variable size of imbalance, and other genetic and environmental effects

Question 27

what is inverted duplication?

Answer 27

a duplication that is followed downstream by it's inverted component

Question 28

what techniques are used in conventional cytogenetics?

Answer 28

metaphase chromosome analysis and G banding

Question 29

what techniques are used in molecular cytogenetics?

Answer 29

FISH, QF-PCR and microarray

Question 30

what is the karyotype for G banding?

Answer 30

there are 3000 genes and 550 bands

Question 31

what is the difference in duplication and deletion results in array CGH?

Answer 31

deletion will appear to left and duplication to the right

Question 32

what is a decipher track?

Answer 32

it is used to detect deletion - may show haploinsufficiency - low score indicates higher levels of pathogenicity

Question 33

what techniques do you use in parental studies?

Answer 33

targeted arrays or FISH

Question 34

what are the advantages of aCGH?

Answer 34

early diagnosis - reduced need for other tests, can show the location and size of imbalances, high resolution and therefore high diagnostic hit rate, and information only on relevant genes

Question 35

what are the disadvantages of aCGH?

Answer 35

low level mosaics are not detected, less than 10% are not detected, only dosage is detected not structural rearrangement and mutations, needs good quality and fresh DNA, non pathogenic and uncertain pathogenic changes are also detected

Question 36

what is QF-PCR?

Answer 36

quantitative fluorescence polymerase chain reaction - amplification of short tandems repeat (chromosome specific repeated DNA sequences) using fluorescent primers

Question 37

what are STRs?

Answer 37

they are short tandem repeats - they are highly repetitive regions of genome with four particular bases that are duplicated many times in a sequence

Question 38

in aneuploidy detection what shows positive result?

Answer 38

2 or more markers with abnormal dosage (up to 4/5)

Question 39

what is the size of the product related to?

Answer 39

it is directly related to the number of ATTT repeats

Question 40

what is the process for non-invasive prenatal testing?

Answer 40

take mothers blood sample and extract foetal DNA (<10%) - assess aneuploidy (if there is a risk then invasive test needed)

Question 41

what is the process for spontaneous abortion testing?

Answer 41

extract tissue (skin, lung, cord, cartilage, placenta), macerate and extract then do QF-PCR or aCGH

Question 42

what is neuroblastoma and how can we identify it?

Answer 42

FISH to identify it - it is a rare fast growing cancer in the abdomen of children

Question 43

what will FISH show in neuroblastoma?

Answer 43

multiple double minutes and paired episomal structures - MYCN gene is massively overproduces and amplified within gene - poor prognosis and needs high dose chemo

Question 44

what is a balanced chromosomal translocation?

Answer 44

can be reciprocal or robertsonian - there is no net loss or gain of chromosomal material

Question 45

what is a reciprocal translocation and what is the risk of this?

Answer 45

it is when two or more chromosomes break and exchange material, there is no loss or gain of genetic material and is usually of no issue to the individual however there is a 5% risk of hitting an important gene every time a chromosome breaks

Question 46

what is the result of pairing after reciprocal translocation?

Answer 46

quadrivalent structure - pachytene cross - 50% of gametes abnormal

Question 47

what chromosomes are acrocentric and what does this mean?

Answer 47

13,14,15,21 and 22 are acrocentric - where the centromere is quite near one end of the chromosome - usually long q and short p

Question 48

what is a robertsonian translocation?

Answer 48

when the chromosomes break close to the centromere, the p parts are lost and q pair up - not deleterious because the p part does not contain any coding DNA - not phenotypic risk but there is a fertility risk

Question 49

what is the prevalence of robertsonian and reciprocal?

Answer 49

1 in 500 = reciprocal and 1 in 1000 for robertsonian

Question 50

what is next generation sequencing?

Answer 50

sequence based analysis of chromosome changes