Cytogenetics, Chromosome Abnormalities, Imprinting

Question 1

How can leukemia and lymphoma be diagnosed?

Answer 1

Chromosome analyses of bone marrow is performed in order to detect the common cytogenetic abnormalities associated with a diagnosis of leukemia or lymphoma. Specific chromosome abnormalities can also alert clinicians to the use of specific therapies

Question 2

What are the two common translocations common to leukemias and what treatments are used to treat them?

Answer 2

t(9;22) is diagnostic for chronic lymphocytic leukemias, which can be treated with a specific tyrosine kinase inhibitor, Imatinib mesylate, also known as Gleevec.t(15;17) is diagnostic for a specific acute myeloid leukemia, which can be treated with retinoic acid and arsenic trioxide.

Question 3

What are the common FISH probes?What are they used for?

Answer 3

FISH probe panels are used for differential diagnosis, and as a means to monitor treatments or disease progression. The following is a short list of the fluorescence-labeled probes used for specific diseases, primarily hematologic malignancies, but also solid tumors (breast cancer, brain cancer, lung cancer, and selected sarcomas).

Question 4

What can chromosomal microarrays help diagnose?

Answer 4

Genomic deletions and duplications, but not translocations

Question 5

Characterize the laboratory test algorithm for children or adults who present with learning disorders, developmental delays, autism dysmorphic features, and/or failure to thrive

Answer 5

1. CMA to detect duplication or deletion, consult DGV2. If >3 are abnormal, and not common, study with FISH (patient and parental chromosomes)3. If abnormality found in parents, test other family members4. If not found in parents or DGV, consult literature5. If step 4 fails, and family has history of spontaneous abortions, perform standard cytogenetics to rule out balanced translocations.

Question 6

What is the mechanism of the two most common chromosome rearrangements?

Answer 6

Double strand breakage is often fixed by non homologous end joining,and crossing over between DNA fragments can result in many new combinations.

Question 7

What are the three types of balanced chromosomal rearrangements? What is their phenotypic effect?

Answer 7

InversionsReciprocal translocationsRobertsonian translocationsNo effect

Question 8

Please describe inversions.

Answer 8

Inversion: occurs when one chromosome undergoes two double strand breaks of the DNA backbone and the intervening sequence is inverted prior to the rejoining of the broken ends.a. Paracentric inversions exclude the centromere.b. Pericentric inversions include the centromere. Normally, there is no phenotypic effect, but this can lead to errors in meiosis and the production of irregular gametes.

Question 9

Please describe reciprocal translocations.Do they have reproductive consequences?

Answer 9

Reciprocal translocation: results from the breakage and rejoining of nonhomologous chromosomes, with a reciprocal exchange of the broken segments. As with inversions, carriers of reciprocal translocations have an increased risk of producing unbalanced gametes; balanced translocations are often found in couples that have had two or more spontaneous abortions, and also in infertile males.

Question 10

Please describe Robertsonian translocations.What are the reproductive consequences?

Answer 10

Robertsonian translocation: the fusion of two acrocentric chromosomes within their centromeric regions, resulting in the loss of both short arms (containing rDNA repeats). Robertsonian translocations result in the reduction of chromosome number, but are considered balanced rearrangements because the loss of some rDNA repeats is not deleterious.Carriers of Robertsonian translocations are phenotypically normal, but these rearrangements lead to unbalanced karyotypes for their offspring, resulting in monosomies and trisomies. The most common example is a translocation involving chromosomes 14 and 21, karyotype 45, XX or XY der(14q;21q).Note that Thompson and Thompson text abbreviates a Robertsonian translocation as “rob”, but this is now simplified to “der” to indicate a chromosome derivative.

Question 11

What is an unbalanced chromosomal rearrangements, and what is the general result?What are the four general types?

Answer 11

The chromosome set has additional or missing material. Phenotypes of these individuals are likely to be abnormal. Duplication of genetic material can lead to partial trisomy, while deletions lead to partial monosomy.Deletion, duplication, ring chromosome, isochromosome.

Question 12

Please describe the two types of deletions.

Answer 12

Terminal deletion: the deleted segment on one chromosome arm: produces a deleted fragment (not stably transmissible) and the transmissible rest of the chromosome.Interstitial deletion: the deleted segment contains the centromere (ie goes from one arm to the other). Notice that the deleted segment can form into a ring chromosome

Question 13

Please describe duplications.

Answer 13

Duplication: gain of genetic information, which is generally less harmful than deletion, but can lead to abnormalities (i.e. partial trisomy 21).Duplications can also result from unequal crossing-over or by abnormal segregation during meiosis in a carrier of a translocation or inversion.

Question 14

What is a ring chromosome?

Answer 14

A chromosome fragment that circularizes and acquires kinetochore activity for stable transmission to daughter cells (also called a marker chromosome). Sample karyotype: 46, XY r(13)(p11q34), which is a male with a supernumary ring chromosome derived from the p11 to q34 region of chromosome 13.

Question 15

What is an isochromosome?

Answer 15

A chromosome in which one arm is missing and the other duplicated in a mirror-image fashion, possibly occurring through an exchange involving one arm of a chromosome and its homolog at the proximal edge of the arm, adjacent to the centromere.

Question 16

What are the recurrence risks for the progeny of carriers of these rearrangements?

Answer 16

Most chromosome structural abnormalities found in fetuses and newborns that are associated with serious clinical effects are attributable to a random event. They are therefore unlikely to occur again. Moreover, a recurrence can be diagnosed in utero.Occasionally a serious chromosomal abnormality can be inherited from a seemingly normal parent who carries a balanced chromosomal abnormality such as a translocation. In these comparatively rare cases, the recurrence risk could be much increased.

Question 17

What are contiguous gene syndromes? What are some examples?

Answer 17

Abnormal phenotypes caused by over-expression or loss (haploinsufficiency) of neighboring genes. Velocardiofacial syndrome (del 22q11). Leads to cleft palate and septal defects, and DiGeorge syndrome (del 22q11), absent or hypoplastic thymus and parathyroids, congenital heart disease

Question 18

Please define epigenetics.

Answer 18

Mitotically and meiotically heritable variations in gene expression that are not caused by changes in DNA sequence

Question 19

How can modifications in DNA and chromatin affect gene expression?

Answer 19

Reversible, post-translational modifications of histones and DNA methylation are examples of epigenetic mechanisms that alter chromatin structure, thereby affecting gene expression.

Question 20

What is genetic imprinting?What is its molecular basis?

Answer 20

It is now known that a small number of autosomal genes in the mammalian genome are inherited in a silenced state from one of the two parents, and in a transcriptionally active form from the other, thereby rendering the individual functionally hemizygous for these genes.Allele-specific methylation of CpG dinucleotides in the promoters of imprinted genes, established in one of the two germ lines and maintained throughout embryogenesis, has been implicated in the maintenance of imprinting in somatic cells.

Question 21

How can DNA methylation act as a gene silencer? Activator?

Answer 21

DNA methylation as a gene silencing mechanism: Hypermethylation may directly inhibit transcription either by repelling transcription factors (some DNA binding factors are known to be methylation-sensitive), or methylation may actively recruit factors that repress transcription.DNA methylation as a gene activation mechanism: The molecular basis of this activation is poorly understood, but a current model postulates that DNA methylation may prevent the binding of a transcriptional repressor.

Question 22

What is the process of imprinting in germ line cells?

Answer 22

Whole scale erasure of all of the methylation marks in an embryo leads to demethylation of chromosomes. X chromasome reactivation and biallelic expression also occur. Then, remethylation occurs through denovo methyltransferases happens in a sex specific manner. Occurs prior to initation of meiosis in primordial germ cells.

Question 23

What is the DNA methylation pattern in somatic cells?

Answer 23

When fully methylated, double stranded DNA divides to be replicated, we end up with two hemi-methylated DNA strands. Maintenance methyltransferase methylates the newly synthesized strand.

Question 24

Describe the relevance of genetic imprinting in Prader-Willi and Angelman syndromes.

Answer 24

Chromosomal mutations involving imprinted loci lead to parent of origin effects, meaning that the phenotype observed will depend upon which homologue (i.e. paternally derived or maternally derived) in the affected person’s genome has been deleted or duplicated. This phenomenon is illustrated in two contiguous gene syndromes called Prader-Willi and Angelman syndromes.

Question 25

What happens with imprinting in Prader Willi Syndrome?

Answer 25

In 70% of patients, the syndrome is the result of a cytogenetically observable deletion involving the long arm of chromosome 15 (15q11-q13), occurring on the chromosome 15 homolog inherited from the patient’s father.These patients have a normal, maternally derived homolog of chromosome 15.However, this region on the maternally derived chromosome is methylated, and transcriptionally silenced.Prader-Willi syndrome is characterized by obesity, excessive and indiscriminate eating, short stature, small hands and feet, hypogonadism, and mental retardation.

Question 26

What happens with imprinting in Angelman syndrome?

Answer 26

These patients have a deletion of approximately the same region of chromosome 15 described in PWS, but on the maternally derived homolog.Angelman syndrome is characterized by an unusual facial appearance, short stature, severe mental retardation, spasticity and seizures. In this case, the information contained on the normal paternally derived chromosome 15 is inactivated due to DNA methylation.

Question 27

Describe the origin and clinical effects of uniparental disomies with regard to Prader-Willi and Angelman syndromes.

Answer 27

Uniparental disomy most commonly occurs when a trisomic conceptus (e.g. trisomy 15, maternal nondisjunction leading to two maternal, one paternal 15s) loses one of its extra chromosomes due to mitotic nondisjunction in early gestation.This chromosomal sorting error in effect “rescues” the developing pregnancy from spontaneous abortion but may result in an abnormal phenotype if both remaining homologs are derived from the same parent (e.g. reduction of the trisomy 15 genome above to the normal 46 chromosomal complement by loss of the paternally derived homolog. Since both remaining 15 homologs are maternal in origin, both carry maternally repressed loci. Normal development is dependent on expression of genes at the missing paternal 15q11-13 locus. Prader Willi- means have 2 maternal loci, Angelman is 2 paternal loci