Chromosome Pathology Flashcards
what is cytogenetics?
study of chromosomes - anything more than a single gene
what is the improved name for cytogenetics and why?
molecular cytogenetics and genome disorders as there is a blurred boundary between cytogenetics and molecular genetics
why are we diploid and what are the exceptions?
all cells have 23 pairs of chromosomes per cell, but gametes are haploid - they only gave 23 chromosomes
what are the autosomes?
chromosomes 1-22, X/Y are sex chromosomes
what percentage of births is cytogenetics implicated in?
0.7% live births, 5% of stillbirths and 50% of miscarriages - major contributor to congenital malformation and learning difficulties
what do most cytogenetic changes result in?
copy number variations - this is a DNA sequence with a variable copy number compared to the reference genome - can be 1Kb to several Mb
what is a continguous gene?
it is a disorder that results from a chromosomal abnormality resulting in the duplication/deletion etc of numerous genes next to each other
what was the earliest cytogenetic technique still used now occasionally to detect copy number variation?
G banding
what are some whole genome techniques for CNV detection?
G banding, next generation sequencing or microarrays
what are some techniques for targeted testing and what do they look at?
they look for CNVs in particular parts on the genome and examples are FISH, QF-PCR and microarrays
what types of CNV are there?
numerical (polyploidy, aneuploidy or mosaicism)
structural - the gain or loss of one or more genes - duplication or deletion
what is more severe loss or gain?
loss is more deleterious than gain - dosage effect describes the loss or gain of part of or a whole chromosomes
what is the position effect?
this is a cytogenetic abnormality that will cause an abnormal phenotype - a gene in a new chromosomal environment will function inappropriately
what is aneuploidy?
it is trisomy (the gain of just one chromosome) or monosomy (the loss) of a chromosome
what is polyploidy?
when you gain whole sets (triploidy - 3 of every chromosome or tetraploidy)
what can increase the change of aneuploidy occurring during meiosis/gametogenesis?
the increase in maternal age - paternal age increase has no significant effect
what occurs when there are errors in meiosis?
non-disjunction - failure of chromosome or chromatid separation - majority happen in meiosis I
what is the result of non disjunction in meiosis I?
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
why do we only see trisomy 1, 18 and 13?
most aneuploidys do not make it past full term - trisomy 21 only has a 75% chance of making it past full term
when do the errors resulting in polypoidy occur?
most are triploidy and occur at fertilisation
what is the difference between diplospermy and dispermy?
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
what is the difference in presentation between a maternal and paternal triploidy?
double maternal - underdeveloped placenta and a disproportionately large head
double paternal - large cystic placenta
what is a hydatidiform mole?
when a sperm fertilises and egg that is empty and therefore there is no foetus but a placenta develops
when do the errors resulting gin mosaicism occur?
these occur at early cleavage and result in normal and abnormal cells - mitotic nondisjunction
what is trisomic rescue?
when cells kick out the extra copy of the chromosome during early stages of division
why is there variable clinical expression in structural rearrangements?
theses can be deletions or duplications, and there can be a variable size of imbalance, and other genetic and environmental effects
what is inverted duplication?
a duplication that is followed downstream by it’s inverted component
what techniques are used in conventional cytogenetics?
metaphase chromosome analysis and G banding
what techniques are used in molecular cytogenetics?
FISH, QF-PCR and microarray
what is the karyotype for G banding?
there are 3000 genes and 550 bands
what is the difference in duplication and deletion results in array CGH?
deletion will appear to left and duplication to the right
what is a decipher track?
it is used to detect deletion - may show haploinsufficiency - low score indicates higher levels of pathogenicity
what techniques do you use in parental studies?
targeted arrays or FISH
what are the advantages of aCGH?
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
what are the disadvantages of aCGH?
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
what is QF-PCR?
quantitative fluorescence polymerase chain reaction - amplification of short tandems repeat (chromosome specific repeated DNA sequences) using fluorescent primers
what are STRs?
they are short tandem repeats - they are highly repetitive regions of genome with four particular bases that are duplicated many times in a sequence
in aneuploidy detection what shows positive result?
2 or more markers with abnormal dosage (up to 4/5)
what is the size of the product related to?
it is directly related to the number of ATTT repeats
what is the process for non-invasive prenatal testing?
take mothers blood sample and extract foetal DNA (<10%) - assess aneuploidy (if there is a risk then invasive test needed)
what is the process for spontaneous abortion testing?
extract tissue (skin, lung, cord, cartilage, placenta), macerate and extract then do QF-PCR or aCGH
what is neuroblastoma and how can we identify it?
FISH to identify it - it is a rare fast growing cancer in the abdomen of children
what will FISH show in neuroblastoma?
multiple double minutes and paired episomal structures - MYCN gene is massively overproduces and amplified within gene - poor prognosis and needs high dose chemo
what is a balanced chromosomal translocation?
can be reciprocal or robertsonian - there is no net loss or gain of chromosomal material
what is a reciprocal translocation and what is the risk of this?
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
what is the result of pairing after reciprocal translocation?
quadrivalent structure - pachytene cross - 50% of gametes abnormal
what chromosomes are acrocentric and what does this mean?
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
what is a robertsonian translocation?
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
what is the prevalence of robertsonian and reciprocal?
1 in 500 = reciprocal and 1 in 1000 for robertsonian
what is next generation sequencing?
sequence based analysis of chromosome changes
