Chromosomal Abnormalities Flashcards
How many base pairs per octamer of histone?
166
How are histones stabilised?
h1 stabilises DNA wrapped around on tamer
What is epibenthic modification?
Demethylation, histone acetylation changes inactive chromatin to active chromatin
Methylation, histone deacetylation changes active chromatin to inactive chromatin
At what stage of mitosis are chromosomes analysed?
Metaphase
How are chromosomes isolated for analysis?
Spindle inhibitor - colcemid
Fix with 3:1 methanol : acetic acid
Stain with geimsa- banding
Light microscopy
What specimens can be used for chromosome analysis, and how long do they take to culture?
Bone marrow 0–1 days T lymphocytes 2-3 days (Grow in suspension) Amniotic fluid 7-21 days (Grow on substrate) Chorionic villus sampling Solid tissue
What are the relative sizes of chromosomes harvested from blood, bone marrow and amniotic fluid?
What is the implication?
Blood>amniotic fluid >bone marrow
Can detect smaller abnormalities in bigger chromosomes
Which chromosomes are acrocentric?
D and G groups - 13, 14, 15, 21, 22
Which of chromosomes 21 and 22 is larger?
22
What groups are chromosomes X and Y in?
X is C, Y is G
How are chromosomes stained?
Trypsin digests proteins of metaphase chromosomes
Stain with geimsa or leishman (romanowksi type dye)
AT rich = gene poor. Stain darkly
GC rich = gene rich. Stain lightly
What is c banding?
Stains heterochromatin at centromeres, 1, 9, 16 and Yq
Who do cytogenetic analysis?
Better management eg hormonal treatment of Klinefelter syndrome
Accurate diagnosis - account for phenotype/pregnancy loss
Assess future reproductive risks
Prenatal diagnosis
Why are people referred for cytogenetic testing?
Birth defects Abnormal sexual development Prenatal diagnosis Infertility Recurrent fetal loss Leukaemia ALL/AML/CML/myelodysplasia/myeloproliferative disorders Solid tumours
What might prompt the offer of prenatal diagnosis?
Maternal serum screening - downs
First trimester biochemical markers and ultrasound
Familial hypercholesterolaemia
Abnormal ultrasound - cleft lip and palate, abnormal limbs/heart
Whats Williams syndrome?
Deletion 7q11.23
What’s DiGeorge syndrome?
Deletion 22q11.2
WHat are the viable aneuplodies?
Trisomy 21 - downs
Patau trisomy 13, Edwards +18
Turners monosomy X
What is polyploidy?
Gain of a whole haploid set of chromosomes
What causes polyploidy?
Polyspermy
What is the consequence of triploidy?
15% of miscarriages, 2-3% of pregnancies - die shortly after birth
WHat causes aneuplodies?
Meiosis non disjunction
Mitotic non disjunction- mosaicism
WHat is anaphase lag?
Chromosomes left behind due to defects in spindle formation or attachment to chromosomes. Mitosis or meiosis
What is the incidence of Down syndrome?
1 in 650-1000
What are the symptoms of downs?
Hypotonia Intellectual disability Characteristic facial features Heart defects Increased incidence of leukaemia Increased incidence of early Alzheimer's
What is the cause of Edwards syndrome?
Trisomy 18 due to maternal meiosis two error
What is the prevalence of Edwards syndrome?
1 in 6000
What are the symptoms of Edwards syndrome?
Prominent occiput Rocker bottom feet Lifespan 5-15 days Small lower jaw Low set ears Overlapping fingers
What is patau syndrome?
Trisomy 13 Death in neonatal period Holoprosencephaly Polydactylyl Congenital abnormalities
What is the incidence of pataus syndrome?
1:12000
What is the incidence of turners syndrome?
1:25000
What are the symptoms of turners?
Short stature, neck webbing, infertility, heart defects, mild learning difficulties
What is x inactivation?
Ensures only one x chromosome is active in any cell so males and females have same chromosome complement
Why is monosomy of X a problem?
Pseudo autosomal regions at the ends of the chromosomes X and Y are essential for meiosis
SHOX gene in PAR, explains short stature
What causes mosaicism?
Mitotic non disjunction
What cell line is usually lost in mosaicism?
Monosomic cell lines
What are the four UPDs?
Isodisomy - 2 identical chromosomes from 1 parent
Heterodisomy - 2 different chromosomes from one parent
Segmental UPD - only part of chromosome involved
Acquired UPD - solid tumours and leukaemias
Why does UPD matter?
Some chromosomes are imprinted - chromosomes are expressed depending on their parental origin
What is UPD15?
Prader willi/angel an
What is Russell silver?
UPD 7
What is beckwith weidemann?
UPD 11
Ow does UPD arise?
Monosomy rescue
Trisomy rescue
Gamete complementation
Mitotic error
How does trisomy rescue occur?
Disomic gamete -> trisomic conceptus
Lies a chromosome in post zygotic mitosis
How do you test for UPD?
Use repetitive markers - micro satellites - to identify parental origin of chromosomes
Which reciprocal translocation is not unique to a family?
Immanuel syndrome t(11;22)
What gametes may someone affected with a reciprocal translocation produce and how is this determined!
Balanced or unbalanced
Pachytene diagram
How can chromosomes be separated in a pachytene diagram, implications?
Alternate - balanced
Adjacent 1 homologous centromeres
Adjacent 2 non homologous centromeres
Both unbalanced
How do you assess the impact of unbalanced segregation in reciprocal translocation?
Assess likely segregation
Literature search
What’s a robertsonian translocation?
Two acrocentric chromosomes fused (13,14,15,21,22)
How would you write in standard notation a female with robertsonian translocation of 14 and 21?
45,XY,der(14;21)(q10;q10)
What probes are used in FISH?
Centromere probes
Telomere probes
Whole chromosome paints
Gene specific probes
WhY use centromere probes?
Large, easy to see, use for copy number analysis
Why use chromosome paints?
Identify rearrangements
Why use prenatal aneuploidy analysis?
PND takes two weeks causes anxiety
FISH is quick 99% accuracy,common aneuplodies
What FISH is used in leukaemias?
Interphase analysis- look for translocations, rearrangements, amplifications of genes
HOw long are oligonucleotides in a microarray?
60bp
How long should you hybridise in a microarray?
48hrs
What is Cot-1 used for?
In microarrays to suppress repetitive sequences
What is aCGH?
Array comparative genome hybridisation
Microarray
Why use aCGH?
Check if an apparently balanced karyotype really is balanced
Investigate learning difficulties and congenital abnormalities
Investigate unbalanced karyotypes
Hat different arrays are available?
Cancer gene arrays (copy number and loss of heterozygosity LOH)
Chromosome/gene specific (X/DMD)
Oligo arrays and SNPs (copy number and LOH)
Exon arrays - small intergenic copy number changes
WHole genome screen - copy number changes
How are microarrays assessed?
3um laser
WHat are the benefits of aCGH?
Can target many thousands of genes, can automate
Examine whole genome
Detailed information on genes in deleted/duplicated region
Target against known conditions
WHat are the disadvantages of aCGH?
Expensive
Doesn’t detect balanced rearrangements
Might not detect mosaicism
What can the outcomes of variation be?
Pathogenic, normal or uncertain - dilemma - no genes, assume not pathogenic
What is NIPT?
Non invasive prenatal testing
Cell free fetal DNA in maternal plasma (5%) at nine weeks gestation
Technically challenging -research.
Early in pregnancy. Non invasive
WhAt can you use NIPT for?
Sexing RhD status Soon +21 X linked conditions excluding haemophilia Congenital adrenal hyperplasia Achondroplasia Thanatophoric dysplasia
What is NGS?
Next generation sequencing - fragment genomic DNA, sequence in parallel
Realign to reference genome - full sequence
How is NGS used in diagnosis?
Generate lots of data - hard to analyse
Useful for NIPT, copy number analysis, mutation scanning, epigenetic analysis, expression analysis, tumour profiling, RNA sequencing
Reduces cost compared to Sanger sequencing
What is whole genome sequencing?
Look at all exons
Compare with parents - de novo mutations
Easier to interpret
