Cytogenetics

Question 1

What is the best stage for karyotyping and why?

Answer 1

Metaphase, because DNA is the most tightly packed.

Question 2

G-banding patterns

Answer 2

Light bands = higher GC and lower AT content, early replicating, housekeeping genes
Dark bands = lower GC and higher AT content, late replicating, tissue specific genes

Question 3

Metacentric chromosomes

Answer 3

Two arms of equal length

Question 4

Submetacentric chromosomes

Answer 4

Two arms not of equal length (long arm q longer than short arm p)

Question 5

Acrocentric chromosomes

Answer 5

Only has coding DNA on long arm

Question 6

Band designation nomenclature

Answer 6

Chromsome # / p or q / Region / Band /Sub-band (e.g. 14q32.3)

Question 7

Why do telomeres cap chromosomes?

Answer 7

To maintain structural integrity, ensure complete replication, and help establish chromosome pairing

Question 8

Why are subtelomeric domains subject to translocations?

Answer 8

Because they have low copy repeats that are homologous across chromosomes

Question 9

Numerical chromosome abnormality:
Euploid
- Haploid
- Diploid
- Polyploidy

Answer 9

Exact multiple of haploid set

• Haploid: normal number in gametes (N)
• Diploid: normal number in zygote and somatic cells (2N)
• Polyploidy: complete extra set(s) of chromosomes (#N)

Question 10

Numerical chromosome abnormality
Aneuploid
- Monosomy
- Trisomy

Answer 10

Loss or gain of single chromosome

• Monosomy = 45
• Trisomy = 47

Question 11

Recombination occurs during ____.
Why is recombination important? What does lack of recombination lead to? Which gender has more recombination? Where does it occur more closely to?

Answer 11

Meiosis I.
Recombination is important for proper alignment and segregation of chromosomes and for increasing genetic diversity. Lack of recombination leads to nondisjunction. Females have more recombination and it occurs more closely to telomeres.

Question 12

Male v. female meiosis timing

Answer 12

Male meiosis begins at puberty and is ongoing through life. Female meiosis being prior to birth and arrests in M1 prophase until puberty. During ovulation, M1 completed and M2 is completed after fertilization

Question 13

What is nondisjunction? What does it lead to? What is it correlated with and why?

Answer 13

Nondisjunction is a failure of paired chromosomes in meiosis I or sister chromatids in meiosis II to separate. It results in aneuploidy (monosomy or trisomy) It is correlated with advanced maternal age (particulalry trisomy) (but not paternal age) and likely because likelihood of recombination error goes up over time.

Question 14

Trisomy 21

Trisomy 18

Trisomy 13

Other trisomies?

Answer 14

21 = Down's syndrome 
18 = Edward's syndrome; early lethality
13 = Patau syndrome; early lethality

Other trisomies results in spontaneous abortion. Most common Trisomy 16 (results in miscarriage)

Question 15

Where do most translocations occur and what do they involve?

Answer 15

Most translocations occur at the distal end of chromosomes and involve homologous parts of subtelomeric regions. They can be balanced or unbalanced.

Question 16

What is a balanced rearrangement? Does it result in altered gene expression? Will karyotyping show it? What can it result in?

Answer 16

A balanced rearrangement is a type of reciprocal translocation that has no loss or gain in genetic material. It can still result in altered gene expression even though no material is lost due to small changes at insertion or breakage point. A balanced translocation can become unbalanced when passed on. Karyotyping will not show small deletions since we can’t see chromosomes at a resolution

Question 17

What is a Robertsonian translocation? What does it result in?

Answer 17

A translocation occurring between 2 acrocentric chromosomes. It results in loss of short arms (which do not have coding DNA) but does not affect DNA content of long arms. It can result in improper alignment during meiosis leading to improper segregation and aneuploidy. Note: 14/21 Robertsonian translocation is the source of familial Down syndrome.

Question 18

Intrachromosomal abnormalities (4)

Answer 18

(1) Deletions (terminal or interstitial: at end or within chrom.)
(2) Duplications: duplication of region of DNA in chrom.
(3) Isochromosome: chrom. with two identical arms
(4) Ring formation: ends of chromosomes fuse to form ring.

Question 19

FISH technique (fluorescence in situ hybridization)

Answer 19

Can probe ~200kb segments using specific DNA probe (but have to know what sequence you’re looking, not exactly but closely). Useful for ID’s microdeletions

Question 20

CGH arrays

Answer 20

Used to detect unbalanced chromosome abnormalities (copy number variations in particular). Resolution of about 100kb. Not great for doing entire genome because lots of noise. Can’t detect polyploidy.

Question 21

Sequencing (two types)

Answer 21

• Has 1bp resolution; good for learning the DNA sequence, but can’t detect copy number variations
  (1) Sanger (dideoxy) sequencing: high fidelity, low error rate, best for ID’ing small sequence changes in limited region
  (2) Next-generation sequencing: can do whole genomes or specific subset; have to run multiple times bc of sporadic errors; expensive

Question 22

The ____ of X and Y chromosomes allow them to pair during ___.

Answer 22

The pseudoautosomal regions of X and Y chromosomes allow them to pair during meiosis.

Question 23

What happens to make a 46, XX individual phenotypically male?

Answer 23

SRY gene, which initiates development of male characteristics is translocated onto an X chromosome

Question 24

X-inactivation

Answer 24

Prevents overexpression of X-linked genes in poly-X individuals. Relies on XIST protein.

Question 25

Sex chromosome anomalies

(1) Turner syndrome
(2) Polysomy X
(3) Klinefelter syndrome
(4) 47, XYY

Answer 25

(1) 45, X: short, infertile, heart defects. Mosaicism.
(2) 47+, Xn: developmental disability (worse with more Xs)
(3) 47+, XnY (usually 47, XXY): infertile, small testes, breast development
(4) slightly lower IQ, often taller

Question 26

Nonsense mutation

Answer 26

Mutation results in stop codon in aa sequence

Question 27

Missense mutation

Answer 27

Mutation results in different aa being incorporated in aa sequence

Question 28

Frameshift mutation

Answer 28

deletion or insertion of 1 or 2 bases, thus latering the reading frame of the aa sequence

Question 29

Splicing mutation

Answer 29

Mutation in splicing regions, resulting in improper splicing

Question 30

Regulatory mutations

Answer 30

Mutations in promoter resulting in gene not being expressed or being expressed at lower levels

Question 31

Single common mutation is? Detected by?

Answer 31

Every individual with disease phenotype has same mutation. Can be detected via restriction length polymorphisms.

Question 32

Multiple common mutations? Detected by?

Answer 32

Multiple types of mutations in same gene. Use allel specific oligonucleotide hybridization to detect.

Question 33

No common mutations. Detect?

Answer 33

Vast majority of diseases, no single gene linked to disease. DNA sequencing is most direct way to detect.

Question 34

What is a polymorphism? Can be used for?Types?

Answer 34

DNA sequence changes that don’t cause disease. Occurrence of multiple alleles at a locus where 2 or more alleles have frequencies greater than 1% in the population. Most are in noncoding regions. They can be used for gene apping and linkage analysis, to detect uniparental disomy (both copies of chromosome from one parent), and play a role in drug metabolism.

(1) SNPs: single nucleotide variant at particular site. Highly abundant. Can create/destroy a restriction enzyme site.
(2) VNTRs (minisatellites): tandem repeats of 15-65 bps that go up to 20kb. Used in forensics and paternity.
(3) Short tandem repeats (microsatellites): tandem repeats of 2-4bps. Detected by PCR. Can use to determine parental origin of chromosome.