GEN: Chromosome Abnormalities and Genomic Rearrangements Flashcards
what is the study of chromosomes called?
cytogenetics
number, strucutre, deletions, duplications, instability
why has it been difficult to establish chromsome numbers in the past?
karyotyping techniques produced low quality images
what is aneuploidy?
any number of chromosomes in humans that is not 46
what 3 kind of chromosome abnormalities can you have?
- chromosome rearrangements
- whole chromosome aneuploidy
- copy number imbalance (missing/extra)
what 2 techniques are used to investigate chromosomes?
traditional cytogenetics
molecular cytogenetics
whats involved in traditional cytogenetics
G-banding
fluorescence in situ hybridisation (FISH)
breakage
whats involved in molecular cytogenetics
Quantitative Fluorescence-PCR
MLPA
Array CGH
what is required for traditional cytogenetics?
cell culture to collect metaphase cells
what are molecular cytogenic tests carried out on?
DNA
what does this image show?
G-banded chromosomes
what are consequences of chromosome rearrangements?
recurrent miscarriages and infertility (meiosis issues)
what are consequences of copy number imbalances?
dysmorphism, developmental delays, learning difficulties, specific phenotypes (epilepsy, diabetes, cardiac malformations)
what are consequences of chromosome breakage syndromes?
fanconi anaemia, ataxia telangiectasia
how does whole chromosome aneuploidy arise?
non-disjunction at meiosis/mitosis
why are chromosomes 13, 18 and 21 the live birth autosomal trisomies?
as they are gene-poor chromosomes as large genomic imblanaces lead to conception loss
what happens in meiosis I and II?
how do trisomic conceptus come about?
how do monosomic conceptus come about?
how do uniparental disomy’s come about?
when does uniparental disomy become important?
if chromosome carries imprinted gene
what can you get mosaicism from?
whole chromosome aneuploidy
what is mosaicism?
anaphase lags in cell division from an aneuploid cell so one cell line/daughter cell losing its extra chromosome ⇒ normal chormosome complement
what else can mosaicism arise from other than whole chromosome aneuploidy
can arise in an initially normal conceptus. This can be due to either non-disjunction or
anaphase lag.
what happens if it is a somatic conception in mosaicism
abnormal phenotype improved by normal cell line
what happens if it is a gonadal conception in mosaicism?
arises in germ cells identified by 2 pregnancies with same de novo abnormality
what happens if it is a CPM in mosaicism?
confined to extraembryonic tissue, can have normal outcome or compromise placental function, may also result in UPD following trisomy rescue
what 4 chromosome rearrangements can you have?
- Robertsonian translocations
- reciprocal translocations
- inversions
- intrachromosomal insertions
what are Robertsonian translocations?
fusions of two acrocentric chromosomes (13, 14, 15, 21, 22) where balanced carriers are phenotypically normal but have reproductive risks - recurrent miscarriages, Patau syndrome, Down syndrome and male infertility
what are reciprocal translocations?
any segment of non-homologous chromosomes, almost always unique to the family where balanced carriers are phenotypically normal but have reproductive risks
what are the reproductive risks of reciprocal translocations dependent on?
size of translocated segment
what are the two inversion types?
pericentric - including centromere
paracentric - excluding centromere
what happens in ‘Fluorescence In Situ Hybridization’
(FISH)
denaturation and re-annealing
what can FISH be used for?
investigation of structurally abnormal chromosomes using FISH
looking for specific deletions
what is segmental copy number imbalance?
imbalance of bits within chromosome
what was the traditional prenatal cytogenetics test?
G banded chromosomes, which requires 2 weeks for results
what can be used instead the traditional prenatal cytogenetics test?
FISH, QF-PCR: more accurate
what is the resolution for G-banded chromosome analysis?
~5-10Mb
what causes syndromic disease?
many small imbalances (microdeletions) - cannot pick up via G-banding
what are microdeletion syndromes?
- submicroscopic chromosomal deletions (100-3000kb)
- called syndrome because they occur at low freq. in all populations
why does microdeletion happen?
genomic structure at disease locus predisposing gene to deletion-duplication by unequal recombination
what are microdeletions mediated by
low copy repeats
what are 5 micro deletion syndromes?
what test detects microdeletions?
Array CGH
how does array CGH work
- chop up and label patients DNA with fluorescent marker red
- chop up reference DNA and label with green
- apply both to microarray slide
- denature and re-anneal to complementary oligonucleotide sequences
- red= more patient ⇒ duplication, green=more control ⇒ deletion
- plotting
what 4 things can array CGH detect
- whole chromosome aneuploidy
- micro deletion/duplication syndromes
- subtelomere imbalance
- other imbalance regions (CNVs -maybe benign or pathogenic)
what does array CGH not give?
position effect - G-banding is used for infertile males
how can we determine the clinical consequence of a previously unreported imbalance?
- inheritance
- de novo or inherited from affected parent ⇒ pathogenic
- inherited from unaffected parent ⇒ benign
- number of genes (burden)
- specific gene content (phenotype correlation?)
what will array CGH soon be replaced by
Whole exome/genome sequencing (NGS)
