Cytogenetics Review Questions

Unit 1

List the three broad categories of clinical indications for chromosomal analysis.
Prenatal, Constitutional, Cancer/Acquired

List 5 prenatal indications for cytogenetics analysis.
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Which family members should have chromosomal analysis?
Both parents of a child with structural chromosome rearrangement, deletion, duplication 2) all family members at risk of having a chromosome rearrangement

What are the indications for chromosomal analysis of products of conception?
1)Abortuses (missed abortions) of unknown reason, 2)Malformed stillbirths, 3)Stillbirth of undetermined etiology

Compare amniocentesis and chorionic villus sampling with regards to gestational age, complication rate, turn around time, and false results

What are the clinical indications for tissue sampling instead of blood for cytogenetic analysis?
1)Suspicion of chromosomal mosaicism, 2) blood is not available (e.g. POC), 3) surgical or post-mortem tissue.

List 8 standard techniques for cytogenetics analysis.
1) Geimsa / G-Banding, 2) Quinacrin / Q-banding 3) Reverse / R-banding, 4)Centromere / C-banding, 5)NOR staining (nucleolus organizer regions), 6)DAPI staining, 7) Chromosomal breakage, 8) Sister chromatid Exchange (SCE)

List 5 Molecular cytogenetics techniques.
1)FISH (flourescence in situ hybridization), 2) Multi-colour FISH, 3) SKY (spectral karyotyping), 4) CGH (comparative genomic hybridization), 5) CGH array

What is g-banding?
Chromosomes are treated with trypsine and then stained with Geimsa (or wrights) which darkly stains the AT rich regions (heterochromatin), and lightly stains the GC rich regions of the chromosome.

Outline the general procedure for cytogenetics study.

1) cell culture at 37C 5%CO2 in medium (dividing and stimulation), 2) Chromosome elongation Thymidine BrdU, 3) Metaphase arrest with Colcemide, 4) Cell swelling with hypotonic KCl,* Hardening with acetic acid* 5) Fixation with Cournay's (Methanol: Acetic acid, 3:1), 6) Slide making (chromosome spread with ideal temperature and humidity), 7) Slide aging (air dry slide warmer), 8)Staining (G, Q, C, R-banding), 8) Molecular cytogenetic technique (FISH, multi-FISH, CGH, SKY, array CGH).

Broadly what at the three main morphological groups of chromosomes?
Metacentric, acrocentric, submetacentric.

What are the 4 minimum items included in a standard banding nomenclature?
1. Chromosome number, 2) short or long arm, 3) region on that arm, 4) band number within that region

What are the clinical indications for an individual to have chromosomal analysis?
1)suspected classic chromosome syndrome, 2) Mental retardation of undetermined etiology, 3) dysmophic features, 4) multiple congenital abnormalities, 5) abnormalities of sexual development, 6) ambiguous genitalia, 7)pubertal failure, 8)abnormalities of growth, 9) certain types of malignancies.

What is q-banding?
Chromosomes are prepared with quinacrine which produces flourescent bands in the AT rich regions, particularly useful in identifying polymorphisms on the acrocentric chromosomes ( ) and the Y chromosome.

What is R-banding?
Darkly stains the GC rich regions of the chromosome (Euchromatin), aka Reverse-banding, and is used to detect subtle deletions or rearrangements that may not be detected by Q or G banding.

What is C-banding?
C-Banding stains the constituitive heterochromatin that is localized to the pericentromeric regions of all chromosomes and on the distal long arm of Y. Used to identify pericentric inversions and polymorphisms in centromeric regions of 1,9,16, and Yq, as well as confirming translocations of Y

What is NOR?
NOR is a silver staining procedure which stains the nucleolus organizer regions of satellited chromosomes (used to study the size of stalks and satellites in the acrocentric chromosomes)

List the metacentric chromosomes.

List the submetacentric chromosomes.

List the acrocentric chromosomes.

What is Bloom syndrome?
Bloom syndrome is a rare AR genetic disorder with a defect in the BLM gene with a phenotype of short stature, tendency to sunburn, increased risk of malignancy, reduced or absent fertility, and prone to sister chromatid exchange [[1]]

What is SCE (Sister chromatid exchange?
SCE (sister chromatid exchange) is the interchange of homologous segments between two chromatids of one chromosome, grow the cells under special conditions to produce a differential staining of sister chromatids.

What is DAPI staining?
DAPI staining produces bright flourescence of the heterochromatin regions of 1,9,16, and Y, as well as the centromere of 15, and is used to id marker chromosomes or translocations of Y.

Explain how chromosomal breakage studies are used to diagnose Fanconi's anemia.
Cultured cells are treated with DEB (Diepoxybutane) or mitomycin C to induce breakage, those cells with chromosomes prone to breakage are especially susceptible and this can be seen as gaps, breaks, deletions, triradial, quadriradial, dicentric, and complex figure in the metaphase.

Unit 2

Describe the 4 steps of mitosis.
Prophase, metaphase, anaphase, telophase

List the 8 steps of meiosis.
Meiosis 1(Prophase 1, Metaphase 1, Anaphase 1, Telophase 1), Meiosis 2( Prophase 2, Metaphase 2, Anaphase 2, Telophase 2).

What is the main difference between constitutional and acquired chromosome anomalies.
1) Constitutional affects the whole patient, acquired usually limited to 1 organ.

What at the three main categories of patient features associated with unbalanced constitutional chromosomal anomalies?]1) dysmophy, 2) Visceral malformations, 3) developmental/psychomotor delay.
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What is meant by a homogeneous chromosomal anomaly?
Homogeneous chromosomal anomalies mean that all the cells STUDIED carry the anomaly, may be constitutional or acquired.

What is meant by a mosaic chromosomal anomaly?
Mosaic chromosomal anomalies mean that only some of the cells STUDIED carry the anomaly, may be constitutional or acquired.

What are chromosomal polymorphisms?
Chromosomal polymorphisms are variants of chromosomes that are widespread in a particular population which to date are not known to have any effect on the phenotype, they vary in size, position, and staining properties but must occur in heterochromatin regions usually near the centromere.

List 3 known chromosomal polymorphisms, according to ISCN 2013.
Chromosomal polymorphisms

Classify numerical abnormalities of chromosomes.
1) polyploidy (multiple complete sets of chromosomes, e.g. 3N), 2) Aneuploidy (monosomy (e.g. Turner's syndrome), trisomy (e.g. trisomy 18, 13, or 21), tetrasomy))

What are the four main types of abnormalities in chromosome structure?
1) Deletion, 2) duplication, 3) rearrangement (inversion or insertion), 4) translocation

What is the key difference between a balanced and an unbalanced chromosomal rearrangement?
Balanced translocations imply that there is no missing or excess genetic material, while unbalanced translocations have either missing or excess genetic material from that of a normal genotype.

List three types of balanced chromosomal rearrangements.
Translocation, inversion, insertion.

List three unbalanced numerical chromosomal rearrangements.
trisomy, monosomy, multiploidy

List 5 structural unbalanced chromosomal rearrangements.
deletion, duplication, derivative chromsome, recombination chromosome, marker chromosome, ring chromosome, Dm & HSR

What is the karyotype for a female infant with cri-du-chat?
46,XX,del(5)(p15.1)

Unit 3

What is FISH?
FISH is a molecular cytogenetic technique in which flourescently labelled DNA probes are hybridized to metaphase spreads or interphase nuclei.

When is interphase FISH more helpful than metaphase?
Interphase FISH is particularly useful in samples where there is poor culture growth such as bone marrow or cancer tissue.

What is the approximate resolution of cytogenetic FISH?
3-5Mb

What are the three types of FISH probes?
1)Probes for repetative sequences (Centromeres, telomeric sequences), 2) Unique sequence probes hybridized to a single copy of DNA sequences in a specific gene or chromosome, 3) Whole chromosome paints (or arms) which are cocktails of probes that are chromosome specific and cover the entire length.

List 7 applications of FISH technology?
1) Microdeletion syndromes, 2) Characterization of chromosomal structural abnormalities, 3) identification of marker chromosomes, 4) Aneuploidy detection, 5) Cancer cytogenetics, 6) Gene mapping, 7)Rapid detection of sex chromosomes and the SRY gene

List 5 microdeletion syndromes.
List of Microdeletion Syndromes