Bocian Chromosome Structure and Variation Flashcards
(174 cards)
1
Q
Describe chromosome morphology
A
Two arms connected at the centromere
2
Q
Arms of a chromosome
A
Short arm = p
Long arm = q
3
Q
Three general shapes of a chromosome
A
a) Metacentric (centromere is in the middle)
b) Submetacentric (centromere is off-center)
c) Acrocentric (centromere is near the end)
4
Q
Acrocentric chromsomes have?
A
Satellites at the top end of the short arm
Code for rRNA and are called Nucleolar organizing regions
5
Q
Ends of chromsomes are claled?
A
The ends of the chromosomes are called telomeres; the small portions just next to the
telomeres are called the sub-telomeric regions.
6
Q
Chromosome during the cell cycle (early and after replication)
A
Each chromosome consists of 1 chromatid in early cell cycle and two sister chromatids after
replication (but before cell division)
7
Q
Number of chromosomes in normal human somatic cell
A
46 chromosomes (23 pairs)
8
Q
What are homologus chromosomes?
A
Each pair consists of one maternally-derived and one paternally-derived chromosome
(homologs or homologous chromosomes)
9
Q
What are autosomes?
A
22 pairs of chromosomes, non-sex chromsomes
10
Q
Sex chromosomes number?
A
1 pair of sex chromosomes (XX or XY)
11
Q
What is a Karyotype?
A
conventional arrangement of metaphase chromosomes for analysis
12
Q
Cells must be what to do a Karyotype?
A
Cells must be living and dividing in order to get metaphase chromosomes to construct and analyze a karyotype
a) Samples are grown in tissue culture to obtain dividing cells (therefore, you cannot freeze samples, or place them in preservatives such as formalin, or get them contaminated with bacteria, or let them dry out, etc.)
13
Q
Common type of sample for individual chromosome Karyotype
A
To study an individual’s chromosomes: blood lymphocytes (a type of white cell) are by
far the most commonly used
14
Q
Common type of sample for karyotype of fetus
A
To study the chromosome of a fetus: amniotic fluid (contains fetal epidermal cells) is by
far the most commonly used; also, chorionic villi (placental cells)
15
Q
Common type of sample for the karyotype of tumors
A
Bone marrow, tumor tissue
16
Q
What must be added to do a karyotype? What is used for lymphocytes?
A
Must add a mitogen (i.e., an agent that causes mitosis) for blood lymphocyte cultures (phytohemagglutinin—stimulates lymphocytes to divide)
17
Q
What is added to accumulate cells in metaphase for a karyotype?
A
Colcemide – a compound related to colchicine - destroys the mitotic spindle
18
Q
What is Banding?
A
Each chromosome has a unique sequence of bar code-like stripes, allowing
identification of individual homologs and the analysis of abnormalities of their structure by
disruption of the normal banding pattern
19
Q
Describe the staining of G-(Giemsa) Banding. What is dark? Light?
A
AT-rich regions stain (G-dark bands); GC-rich regions do not stain (G-light bands)
20
Q
Describe high resolution analysis of chromosomes (high res karyotype)
A
Chromosomes are prepared in prometaphase (or even late prophase) instead of metaphase to make them longer and increase the number of sub-bands that can be seen
21
Q
Compare routine and high res karyotype
A
Routine can see 450-500 bands
High res caan see 550-800 bands
22
Q
Each chromosome is divided into what notationally?
A
Divided into standard regions
23
Q
Describe the numbering of chromosome regions
A
The regions are numbered, in order, from the centromere toward the ends
a) e.g., the long arm (q) of chromosome 1 consists of four regions numbered consecutively
from the centromere outward: 1q1, 1q2, 1q3, 1q4
The regions are further subdivided, e.g. 1q11, 1q12, 1q13, etc.
a) Then further subdivision: 1q11.1, 1q11.2, etc.
24
Q
Give examples of chromosome cytogenetic shorthand notation
A
a) 46,XY
(1) 46 chromosomes total, with one X and one Y (a normal male karyotype)
b) 46,XX
(1) 46 chromosomes total, with two Xs (a normal female karyotype)
c) 47,XY,+21
(1) 47 chromosomes total, with an X and a Y and an extra (+) chromosome #21
d) 45,XX,-22
(1) 45 chromosomes total, with two X’s and a missing (-) chromosome #22
25
Describe how to write out chromsomes with duplication, deletion, and translocation in shorthand notation
e) 46,XY,dup(7)(q11q31)
(1) 46 chromosomes total with an X and a Y; there is a duplication of the material on the
long arm of chromosome 7 from region q11 to region q31
f) 46,XY,del (22)(q11.2)
(1) 46 chromosomes total with an X and a Y; one of the chromosomes #22 is missing a
portion of the long arm located at region q11.2 (del = deletion)
g) 46, XX, t (7;9) (p21.2;q34.1)
(1) A female with a balanced translocation, i.e., an even exchange [more about this
below] of portions of chromosome 7 starting at 7p21.2 and chromosome 9 starting at
9q34.1
26
Karyotype results should state the?
Band level (the resolution)
27
Molecular cytogenetics are used to detect?
Deletions of duplications smaller than 4 Mb
A DNA probe is used to detect the presence or absence of a specific chromosomal
segment
28
What can be detected by molecular cytogenetics?
A DNA probe is used to detect the presence or absence of a specific chromosomal
segment
Chromosomal abnormalities can be detected in both dividing and non-dividing cells
29
What is FISH?
FISH (Fluorescence In Situ Hybridization)
Identification of specific chromosomes and parts of chromosomes by in situ hybridization with labeled DNA probes
30
FISH is useful for (5 things)?
(1) Detecting submicroscopic deletions and duplications
(2) Detecting subtle chromosome rearrangements
(3) Identifying marker chromosomes (see definition below)
(4) Identifying the content of multiple rearranged chromosomes
(5) Detecting aneuploidy (extra or missing chromosomes) in interphase cells in
cancers
31
3 types of FISH used in clinical studies
Centromeric probes
Whole Chromosome Paint probes
Unique sequence probes
32
Describe centromeric FISH probes
Centromeric probes (Satellite repeat-sequence probes)
(a) Target only the centromeres of specific chromosomes
```
(b) Useful in determining the number of chromosomes in cases of possible
aneuploidy syndromes (disorders due to extra or missing chromosomes) or in cancer cells
```
(c) Can use with interphase cells if metaphase cells are not available
33
Describe whole chromosome paint FISH probes
Cover an entire chromosome
Used as a screening tool in the characterization of an abnormal chromosome.
34
Describe unique sequence FISH probes
Target a specific locus (or gene) on a chromosome
(b) Use for diagnosis of chromosome microdeletion or microduplication
syndromes
(c) Certain acquired translocations that are unique to specific cancers can be
detected in interphase cancer cells with dual-color unique sequence probes.
35
Describe FISH nomenclature
Capital letters and numbers are used for the locus, and “+” or “−” given immediately afterward indicates whether the locus has been identified as being present or absent,respectively.
36
Describe subtelomere analysis
FISH analysis of individuals with idiopathic (i.e., unexplained) intellectual disabilities, with
or without congenital malformations, shows that a significant proportion (5-10%) of these
patients have unbalanced abnormalities involving the subtelomeres. Many or most (~50%)
of these abnormal subtelomere cases are familial (i.e., inherited from a carrier parent),
which has important implications for genetic counseling and recurrence risk estimates.
37
Describe Chromosomal microarray analysis
A very high-resolution molecular cytogenetic technique that is used to detect
submicroscopic chromosomal duplications and deletions (copy number variants, CNVs).
A series of DNA or RNA probes is placed on a glass slide or silicon wafer (chip) and
hybridized with DNA or RNA from the patient
38
Three types of Chromosomal microarray analysis
Genomic Array
Expression Array
Molecular probe inversion array
39
Describe genomic array chromosomal microarray analysis
(i) DNA-based
| (ii) Looks for changes (loss or gain) in a patient’s DNA
40
Describe expression array chromosomal microarray analysis
RNA-based
(i) Looks for expression of a series of genes
(ii) Often used in cancer profiling
41
What is array-based comparative genomic hybridization (array CGH)
Compares a sample of patient’s DNA to normal control DNA…..by observing their ability to compete with each other for hybridization to an array of thousands of reference DNA probes immobilized on a slide or chip
42
Array CGH tells us?
Copy number variations (CNV) are determined by the differences in hybridization pattern intensities between patient DNA and control DNA. The copy number of each clone (i.e., how many copies of that clone determined based on the ratio of the hybridization signal between the patient’s DNA and normal control DNA for each chromosome
43
What is a copy number variation?
In Array CGH
A copy number variation (CNV) is a segment of extra or missing DNA
detected by microarray analysis
44
Normal CNV in a CGH tells us?
Normal: The amount of patient DNA equals the amount of control DNA (1:1 ratio of patient to control DNA)
45
CNV in a CGH with duplication?
Duplications of chromosomes in patient DNA result in favorable hybridization of the patient sample to the spots on the array (ratio 1.5 patient DNA : 1 control DNA)
46
CNV in a CGH with deletion?
Deletions of chromosomes in patient DNA result in favorable hybridization of the normal DNA to the spots on the array (ratio 0.5 patient DNA : 1 control DNA)
47
Array resolution of a CGH depends on?
Array resolution depends on probe size and spacing along the genome and by the
specific statistical algorithms used to set the criteria for gains and losses.
48
Describe the three types of CGH
Comparative using Bacterial artificial chromosome arrays or oligonucleotide arrays
Single nucleotide polymorphism arrays
49
Describe targeted probes for CGH
Targeted probes: Uses probes mainly from specifically defined regions of known
microdeletion or duplication syndromes and all centromeric and telomeric regions
50
Describe constitutional probes for CGH
Uses probes from the entire genome
(including the centromeric and telomeric regions), relatively evenly-spaced across
the genome, e.g. fragments spaced at 1 Mb intervals or 300 kb intervals throughout
the genome, or they may use overlapping (contiguous) clones
51
Compare the accuracy of an oligo array and a BAC array for CGH
copy number changes that were missed on a BAC array – therefore, if a patient had a normal BAC array in the past, an oligo array (or a SNP array) may pick up an abnormality that was missed on the BAC array.
52
What is a SNP?
A single nucleotide polymorphism (SNP), a variation at a single site in DNA, is the
most frequent type of variation in the genome.
53
A SNP is what genetically?
A SNP has a single base pair substitution (A, T, C, or G) of one nucleotide for another
But it’s not considered to be a mutation
(“Polymorphism” = normal population variant
54
What is the criteria to be a SNP?
To be considered a SNP, the substitution must be found in at least 1% of the general population
55
Where can SNPs occur?
SNPs can occur within the coding sequence of a gene, the non-coding regions of genes,
or the inter-genic regions (between genes)
56
What do SNP arrays detect?
Copy number changes, and also……….
Certain types of copy-neutral changes (no change in copy-number) that are not
detected by CGH arrays:
(a) Can detect long contiguous stretches of homozygosity (hmz) (LCSH) that are associated with uniparental disomy or with consanguinity or incest, each of which increases the risk for autosomal recessive disorders
57
Describe what SNP arrays are really good at detecting?
This advantage of SNP arrays has a huge potential in cancer diagnostics, since loss of heterozygosity (LOH) is a prominent
characteristic of most human cancers. LOH is a form of allelic imbalance that can result either from the complete loss of an allele (by
deletion) or from UPD (uniparental disomy, in which an individual
has two copies of certain stretches of genes from one parent and no
copies from the other parent)
58
SNP arrays can detect what type of genetic disorder?
Triploidy (extra copy of every chromosome)
59
Difference between SNP and CGH?
SNP arrays differ from CGH arrays in that only the patient’s genome is hybridized to the slide (do not need a control patient’s DNA)
60
Copy number assesssment of SNP and CGH?
SNP arrays allow a more comprehensive assessment of copy number than CGH arrays
61
What is B allele frequency?
Metric provided by SNP array
B allele frequency (BAF) is the proportion of the total allele signal (A+B) explained by a single allele (A)
BAF can detect copy numbers from 0 to 4
62
How is microarray diagnoses written? Normal male? Normal Female?
```
Female arr(1–22)x2,(X)x2
Male arr(1–22)x2,(XY)x1
```
63
Examples of microarray deletions or duplications?
(1) For example, a 698 kb interstitial duplication in chromosome 1q43:
(a) arr 1q43(241,822,181-242,519,964)x3 [hg19]
(2) Another example: an interstitial deletion of the short arm of chromosome 20:
(a) arr 20p12.2(10,454,698–10,818,327)x1 [hg19]. This specifies a 323,630 bp
(324 kb) deletion within chromosome 20p12.2.
The (numbers) are molecular coordinates related to the location of base pair on
the gene map and can be used to look up genes within that segment and to
compare features of other patients with overlapping copy number variations
[hg19] refers to the version gene map that was used to interpret this analysis
64
CNV can be?
Microdelections or microduplications (not SNPs)
65
Describe the types of CNV?
Everyone has CNV
Pathogenic
Benign
Variants of unknown clinical significance
66
Are CNV typically helpful?
Often the CNV are not easy to interpret
67
Microarray advantage over karyotype?
Provides analysis at much higher resolution than karyotyping. Detects an additional 5-20% of patients with unexplained intellectual disabilities and/or congenital anomalies (compared with those who have had normal karytoype
analysis and subtelomere FISH analysis)
68
Microarray advantage for supply material?
Uses DNA - does not need cultured, dividing cells
69
Array CGH data compared to FISH?
Array CGH provides the equivalent of multiple, concurrent FISH analyses over hundreds or thousands of loci
(a) Single-probe FISH requires clinical suspicion of a specific disorder so that the correct probe(s) can be used
70
Microarray correlation with phenotype?
Allows correlation of phenotype with genes (deleted or duplicated) in the affected region
(a) Inclusion of the genomic coordinates for each of these abnormalities allows the laboratory or physician to go to the genomic databases to determine the precise gene content of the deletion or duplication.
(b) Allows more precise characterization of imbalances, providing a better analysis of the phenotype
71
Balances on Microarray versus karyotype?
Microarray can identify imbalances at the breakpoints of translocations that on karyotype analysis appear to be balanced and may even identify gene disruptions at the places where the chromosome(s) have broken
72
SNP arrays can detect what that CGH cannot?
SNP arrays can identify UPD (isodisomy), consanguinity or incest, polyploidy (CGH arrays cannot identify these)
73
Microarray analysis can tell us what about cancer?
the unexpected finding of tumor susceptibility
74
What type of information does microarray not tell us?
do not provide any further positional information
| regarding the imbalance.
75
Array CGH cannot differntiate what?
Array CGH cannot differentiate free trisomies from unbalanced Robertsonian translocations
76
CGH can tell us copy number variation relative to what?
The ploidy level of the reference DNA
77
Microarray does not detect what type of chromosome anomaly?
Does not detect balanced chromosome anomalies (i.e., abnormalities in which
pieces of chromosomes have been moved around but are neither lost nor gained)
78
Regions that are not represented on a microarray are?
Not assayed
79
Describe limitation of microassay interpretation
Some of the changes it identifies are benign DNA variations (polymorphisms);
others are VUS that cannot be interpreted yet
80
Microarrays and small base-pair duplications/deletions?
Array CGH cannot detect very small base-pair duplications or deletions (but
these can be detected by SNP array) or point mutations
81
Triploidy and microarray?
Triploidy will not be detected by some forms of microarray (Yes in SNP and No in CGH)
82
Aneuploidy and microarray?
Some aneuploidies can be missed, such as XYY if the wrong gender control is used.
83
Marker chromsomes and microarray?
Marker chromosomes may also be missed, depending on the size, the composition of the marker, and whether there is good coverage in the array of the specific chromosomal region present on the marker.
84
Microarrays and mosaicism?
The accuracy of detecting low levels of mosaicism (≤5-10%) is still in question
85
Test for whether whole extra or missing chromsome?
Use routine karyotype
86
Test for suspected specific, well-described microdeletion or microduplication
Use single-probe FISH analysis if a specific, well-described microdeletion or microduplication syndrome is suspected (e.g., Williams syndrome or the 22q11.2 deletion)
87
Test for looking for a balanced translocation?
Use karyotype analysis ± FISH in cases where you are looking for a balanced translocations (microarray will not detect them because DNA is neither gained nor lost)
88
When to use CGH or SNP array?
Use array CGH or SNP microarray as the first test in patients with multiple congenital anomalies and/or with unexplained intellectual disabilities if you don’t recognize the diagnosis, or when standard studies (karyotype, FISH) have not provided a diagnosis in patients suspected of being chromosomally abnormal
89
Microarrays have markedly increased ability to do? (5 things)
(1) Find new microdeletion and microduplication syndromes
(2) Further delineate known syndromes
(3) Identify genes responsible for genetic disorders (candidate genes within duplicated or deleted regions)
(4) Detect mosaicism
(a) may miss low-level mosaicism
(5) Detect uniparental disomy (UPD) and consanguinity (SNP arrays)
90
When should parental studies be done?
For pathogenic deletions and duplications, parental studies (by FISH or metaphase
preparations, if possible) should be conducted to rule out the presence of a chromosomal rearrangement such as an insertion or inherited duplication. Although these are rare, for a family in which such a rearrangement is found, recurrence risk can be as high as 50%
91
What is Cell-Free Fetal DNA screening?
Analyzes circulating cffDNA from maternal blood in women at increased risk for fetal aneuploidy
1. Source of cff DNA:
a) Placental cells break down, and fetal DNA enters maternal circulation
b) ~10% of circulating DNA in maternal plasma is fetal
92
What does ploidy mean?
“Ploidy” – Having to do with entire sets of chromosomes
93
What is haploid
Haploid – 23 chromosomes
94
What is euploid?
Euploid – Any number of chromosomes that is an exact multiple of the haploid number
95
What is aneuploid?
Aneuploid – Cells deviating from the multiples of the haploid number are called aneuploid
(i.e., not euploid), indicating a missing or extra chromosome (e.g., 47 or 45 chromosomes)
96
What is diploid?
Diploid - 46 chromosomes (23 pairs present) (“di” = 2 sets)(2n)
97
What is polyploid?
Polyploid – having more than the normal two haploid sets of chromosomes:
98
What is triploid?
Triploid – 69 chromosomes (an extra chromosome in each pair) (“tri” = 3n)
99
What does somy mean?
Having to do with a single chromosome
100
What is nullisomy?
both copies of the chromosome are missing (a non-viable state)
101
What is monosomy?
A missing chromosome (e.g., monosomy-22, which means 45 chromosomes total
with only one chromosome #22)
102
What is trisomy?
an extra chromosome (e.g., trisomy-21, which means 47 chromosomes total with three chromosomes #21)
103
What is meant by constitutional chromosomal abnormality?
A chromosome abnormality that is present from conception or early fetal development and
involves the entire body
104
Describe what is meant by acquired chromosome abnormality
New or added. “New” in the sense that it was not inherited, and “added” in the sense that it was
not congenital (present at birth) but came along later; usually used with respect to tumor or
cancer cells.
Acquired chromosome abnormalities are important in analyzing cancer cells
105
What is a numerical chromosome abnormality?
An abnormality in the number of chromosomes present
1. May be constitutional or acquired
2. This is where you use the “ploidy” or “somy” terms
106
What is a structural chromosome abnormality?
Structural chromosome abnormalities – An abnormality in the structure of one or more of the
chromosomes
“Somy” also may be used here, but it is usually used along with the word, “partial,” e.g., partial
trisomy of chromosome 8, which means that only a part of chromosome is duplicated
107
What is mosaicism?
One or more additional cell lines with different chromosome complements arise in embryonic or pre-embryonic life and become an integral part of the organism; the individual has more than one kind of cell, e.g., some normal cells and some cells with trisomy 8
108
What is a chimera?
Individuals with 2 or more cell lines, due specifically to the fusion of originally separate zygotes
109
What is polyploidy?
Abnormalities involving the entire chromosome complement (sets of
chromosomes)
110
What is triploidy? What does it result from?
Triploidy: 3 sets of chromosomes (3n=69); may be 69,XXX, 69,XXY, or 69,XYY.
Triploidy can result from dispermy (the extra set comes from the father) or digyny
(the extra set comes from the mother).
111
What is tetraploidy?
Tetraploidy: 4 sets of chromosomes (4n); may be 92,XXXX or 92,XXYY
112
Numerical abnormality involving a single chromosome is often from?
Usually result from meiotic non-disjunction (failure of homologous chromosomes to
separate symmetrically at cell division) occurring in egg or sperm. Infrequently due to
mitotic non-disjunction in the zygote. After non-disjunction, one daughter cell has an
extra chromosome and the other daughter cell has a missing chromosome.
113
Example of a monosomy?
45,X (Turner syndrome)
114
Examples of Trisomy?
(i) Trisomy 21 (Down syndrome)
(ii) Trisomy 13 (Patau syndrome)
(iii) Trisomy 18 (Edwards syndrome)
115
Examples of sex chromosome trisomy?
(i) 47,XXY (Klinefelter syndrome)
(ii) 47,XXX (Triple-X syndrome)
(iii) 47,XYY syndrome (has no other name)
116
Age of mother and correlation to type of chromosome abnormality?
The incidences of autosomal trisomy and of sex chromosome trisomy (XXY and XXX but not XYY) in offspring increase with the age of the mother, but the incidences of monosomy, polyploidy, and structural changes do not.
117
Describe chromosomal mosaicism
The coexistence, within one embryo, of two or more distinct cell lines that are genetically identical except for the chromosomal difference between them. The different cell lines are established by the time embryonic development is complete (the point at which the embryo becomes a fetus), are fixed in the individual, and are part of his/her chromosomal constitution. There may be more than one cell line within a single tissue (e.g., two different cell lines found in the blood) or different cell lines among different tissues (e.g., one type of cell in the blood and another type of cell in the skin).
Notation: 47,XY,+21[8]/46,XY[42] denotes an individual in whom a total of 50 cells were
examined; [8] cells had an extra chromosome #21, and [42] cells were normal.
118
What is somatic mosaicism?
the body consists of more than one type of cell
119
What is germ line mosaicism?
the mosaicism exists in the eggs or sperm (sometimes also called
gonadal mosaicism)
120
What is placental mosaicism?
Placental mosaicism, or confined placental mosaicism – About 1-2% of placentas have a
different chromosome constitution from that of the embryo; usually the embryo is normal
and the placenta is trisomic, but one or both can be mixed.
121
What is trisomy rescue?
A trisomic zygote or early embryo loses the extra chromosome and becomes normal with respect to the number of chromosomes in each pair
122
Structural abnormalities due to chromosomal rearrangements occur when?
can occur either during meiosis (more
| common) or mitosis (less common)
123
What are normal chromosomal heteromorphisms?
Normal chromosome heteromorphisms (“polymorphisms”) - Normal variations that are not associated with phenotypic abnormality and that usually are also found in one of the normal parents of the individuals in whom they occur
124
Describe deletion
A portion of a chromosome is missing
Notation: 46,XY,del(22)(q11.2). The q11.2 segment is missing from one of the
chromosomes 22.
125
What is a partial monosomy? Cryptic translocation?
Results in partial monosomy for the deleted segment
| 1) May be a cryptic translocation (“hidden” - too small to be seen without FISH
126
Once a deletion is diagnosed, what must be done?
Once a deletion (or any other type of structural change) is diagnosed, you must rule
out a rearrangement in one of the patient’s parents
127
What is microdeletion?
Microdeletion – The deletion is so small it cannot be seen by
conventional microscopic methods; a cryptic deletion. FISH or other
molecular techniques must be used to diagnose it. A microdeletion often
includes several gene loci.
128
List three examples of autosomal microdeletions
(a) Williams syndrome (del 7q11.2)
(b) Prader-Willi syndrome — due either to del 15q11-q13pat (i.e., deletion ofna small portion of the chromosome #15 that was inherited from the
father) or to maternal UPD 15 (UPD = uniparental disomy and will be explained in your lecture on nontraditional inheritance)
(c) Angelman syndrome — due either to del 15q11-q13mat (i.e., deletion of a small portion of the chromosome #15 that was inherited from the mother) or to paternal UPD 15 (also several other mechanisms)
129
Cri du Chat is what type of deletion?
Can be seen with routine microscopy or can be small enough to be considered a microdeletion
130
What is duplication?
Duplication – Results in partial trisomy for the duplicated segment
a) Notation: 46,XY,dup(1)(q22q25). The segment of one of the chromosomes 1 has been
duplicated (dup) from q22 to q25.
b) Notation: 46,XY,add(8)(p23). There is a piece of additional (add) chromosomal material
on the short arm of chromosome 8, attached at 8p23, but the origin of the additional material
is not identified yet.
131
Once a duplication is diagnosed, what must be done?
If a duplication (or any structural abnormality) is diagnosed, you must rule out a
rearrangement in one of the patient’s parents
132
What is contiguous gene syndrome?
Usually refers to a phenotype caused by a deletion of several genes, but could also be a duplication of several genes (a microduplication). Since about 1/3 of all our genes relate to brain development and many of the other loci relate to the control of morphogenesis of the embryo, most microdeletions involving several genes will result in a phenotype comprising dysmorphism (abnormal physical features), organ malformations, and intellectual deficit. Many
of these were previously thought to be dominant or recessive syndromes caused by single genes.
133
What are translocations?
Translocations – Relocation of a whole chromosome or portion of a chromosome to another chromosome
134
What is a balanced versus unbalanced translocation? Potential complication effect?
What is most important for the individual to be normal is that the correct amount of genetic material is present (the translocation is balanced –there are neither extra nor missing “pages” – one just has to look in one of the other “books”
to finish reading the “recipe”) and that none of the “recipes” (genes) has been disrupted –
i.e., that all the information remains able to be read, or that portions of two genes have not
been placed next to each other so that they make up a new, deleterious product (position
effect) (e.g., a peanut butter and jelly sandwich recipe translocated with a liver and onions
recipe could result in peanut butter and liver sandwiches…..). If the individual has too
much or too little genetic material, or if a gene has been disrupted so that it cannot be used
properly, the translocation is called unbalanced.
135
Compare outcomes of balanced versus unbalanced translocations
(1) Individuals with unbalanced rearrangements are usually physically and/or intellectually abnormal.
(2) Individuals with balanced rearrangements are phenotypically normal. However, during reproduction they may pass on their translocation in either balanced or unbalanced form – therefore, they have increased risk to have
abnormal offspring.
136
What are reciprocal translocations?
Exchange of genetic material between non-homologous chromosomes (i.e.,
chromosomes from different pairs) or between homologous chromosomes at nonhomologous
sites (much less common).
137
Carriers of balanced reciprocal translocations have an increased risk of?
Carriers of balanced reciprocal translocations have an increased risk to have offspring with partial monosomy for one of the involved chromosomes and/or partial trisomy for the other chromosome.
138
What is robertsonian translocation?
A translocation involving two acrocentric (#13, 14, 15, 21, or 22) chromosomes (may involve homologous chromosomes —e.g., two #13s— or nonhomologous chromosomes —e.g., a #14 and a #21) which have joined at or near the centromere (i.e., the front covers of two books are torn off and the two books are stapled together front-to-front.) The short arm material is lost, but there are no phenotypic consequences of losing this material from acrocentric chromosomes. This is because the acrocentric short arms only code for ribosomal RNA (the nucleolar organizing regions, NOR’s, are in the stalks of the satellites).
139
Risk of robersonian translocation?
The normal, balanced carrier
has a risk of having unbalanced offspring with trisomy or monosomy (those
with monosomy are unlikely to survive past early pregnancy).
140
Describe the balanced carrier of robertsonian translocation
Balanced carrier of a Robertsonian translocation: Notation: 45,XX,der(14;21)(q10; q10). The total number of chromosomes is 45 because
two of them have joined together to form a single, larger chromosome, which was derived (der) from the long arms of chromosomes 14 and 21.
141
Describe the unbalanced carrier of robertsonian translocation
Unbalanced carrier of a Robertsonian translocation: Notation: 46,XX,der(14;21)(q10;q10),+21. This individual has a total of 46 chromosomes, but one of her 14’s has a #21 attached to it. Therefore, this individual has an
extra chromosome 21 (a total of 47 chromosomes’ worth of DNA, but you only
see 46 individual pieces…….).
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What are insertions?
Insertions – A segment from one chromosome is inserted into another chromosome
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What are inversions?
Inversions – a piece of chromosome breaks out, turns upside-down, and re-inserts itself in the
same place
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How does inversion occur?
At meiosis, in order for the inverted chromosome to pair with its homologue along its entire
length, it has to flip over at the inverted part and form a reversed loop (inversion loop).
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Inverted DNA will lead to embryos with?
The resulting conceptuses (embryos)
would have either a partial trisomy for one distal segment and a partial monosomy for
the other, or vice versa. In general, the one with the least amount of monosomy is the only
one likely to be viable (i.e., the less that’s missing, the better it is…..)
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What is a pericentric inversion?
Pericentric inversions – the inverted segment includes the centromere. Recombinant
results in partial monosomy and partial trisomy.
Notation: 46,XY,inv(7)(p14.2q36.3).
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What is a paracentric inversion?
Paracentric inversions – the inversion occurs to one side or the other of the centromere and
does not include it.
Notation: 46,XY,inv(3)(q13q24).
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What is an isochromosome?
Isochromosome – a “mirror-image” chromosome comprising either two copies of the long arms and no short arms, or vice versa.
a) Normally, chromosomes divide by longitudinal separation at the centromere into two
chromatids. However, if a chromosome undergoes transverse separation at the centromere, the two daughter chromosomes will not be equal but rather will represent a smaller
chromosome (2q’s, no p) and a larger chromosome (2 p’s, no q).
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What is a ring chromsome?
Results from loss of telomeres from both the short and long arm of a chromosome and fusion of the “sticky ends”. Results in partial monosomy of the end of the short arm and also of the end of the long arm.
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What is a marker chromosome?
An abnormal, usually smaller, chromosomethat cannot be identified by banding. FISH is
often useful in the characterization of the marker chromosome; array CGH also can be used.
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What are autosomal fragile sites?
Autosomal fragile sites - not associated with clinical abnormality
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What is Fragile X?
Fragile X: an abnormality in the distal long arm of the X chromosome (Xq27) due to unstable DNA trinucleotide repeat sequences.
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What is spontaneous abortion? Frequency?
The term, “spontaneous abortion” (SAb) is used for pregnancy loss (miscarriage) up to 20 weeks’
gestation.
1. The frequency of pregnancy loss is estimated to be from 10-50% of all conceptions,
depending on the method used to detect the pregnancy,
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Most common cause of miscarriage?
The most common cause of miscarriage is a chromosome abnormality.
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Chromosome anomalies account for what amount of miscarriages? When? Percentage that are trisomies?
Chromosome abnormalities account for at least 50% of all SAbs and for ~70% of SAbs occurring in the 1st trimester (up to the 12th week of pregnancy).
50% of the chromosome abnormalities are trisomies
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Chromosomal anomaly in couples with many miscarriages?
In ~5% of couples who have had ≥3 SAbs, one partner carries a balanced chromosomal
rearrangement (compared with 0.55% of the general population); their risk of chromosomally abnormal offspring in future pregnancies is increased. Therefore, couples with this history should be karyotyped.
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Describe the Y chromosome. Variation in size?
The Y chromosome is in the same size range as the two smallest pairs of autosomes (#21-22).
It has relatively few genes (59 genes and disorders as of January 2014)
The size of the Y can vary markedly without any clinical effect because there is a variable-length distal segment of the Y long arm that does not contains any genes.
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Sex determination and the Y chromosome
The Y chromosome (or, more specifically, a gene on the Y chromosome short arm (Yp), is a
dominant determinant for testis development and determines gender in humans (the testis determining factor, TDF), known as SRY (sex-determining region on Y). That is, human
embryos develop as females unless SRY is present and causes the indifferent gonad to develop into a testis.
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What is the pseudoautosomal region?
Unlike autosomal pairs of chromosomes, the heteromorphic X and Y are not completely homologous. There are two regions of complete homology between the X and Y chromosomes at the distal ends of their short and long arms. The X and Y chromosomes pair and cross over in these regions during prophase I. This appears to
be essential for correct segregation of the sex chromosomes. As a result of this crossing over, female offspring of males can inherit DNA sequences from the Y chromosome distal to the point of exchange and vice versa. Therefore, genetic markers in this region of pairing and exchange between the X and Y segregate
independently of sexual phenotype, and so this region is called the pseudoautosomal region.
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X genes and sexual differentation?
majority of genes on the X have nothing to do with sexual differentiation.
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What is the Lyon Hypothesis?
Despite the fact that males have one X and females have two X’s, the sexes really do not differ from each other very much, apart from sexual development and secondary sexual characteristics. The relative similarity of male and female mammals is due to a mechanism of dosage compensation that allows all but one X chromosome in each cell to be almost
entirely turned off (inactivated). (The “almost” is very important – there are some genes on the X that escape inactivation.)
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Describe why Turner phenotype is not so irregular
Single X is enough
Patients missing an entire X chromosome (i.e., Turner syndrome) or those with an entire extra X chromosome (e.g., XXY or XXX individuals) are not very different overall from normal individuals.
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Difference between genotypes with variable levels of X
It is those few genes on the X that escape inactivation that cause the differences between an XX individual and an XO or XXX individual, or between an XY and an XXY individual.
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X inactivation is what type of process?
Epigenetic (non-permanent)
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What is XIC? XIST?
XIC (for X inactivation center) in the human refers to a region on the X chromosome that isrequired for the initiation of X-inactivation and is invariably present on all X chromosomes that
undergo inactivation, including those with structural rearrangements.
There is a specific gene in that region called XIST (X-inactivation-specific transcript), a complex specialized control locus located in the proximal q arm of the human X chromosome (at Xq13.2) that is the master regulatory switch locus for X-inactivation. XIST is necessary for X inactivation (but alone is not sufficient).
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How to help the lab?
The more clinical information you give the laboratory, the better analysis and interpretation they can provide.
1. If you tell the lab the specific abnormal clinical features, they can look closely in any regions
known to cause those abnormalities or suggest other techniques to use.
2. If you are looking for a specific microdeletion or other specific anomaly that requires special
techniques, you must tell the lab which anomaly or condition you are looking for so they can
use the proper probe(s).
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Parental analysis with numerical abnormality?
For patients who have numerical abnormalities, e.g. trisomy, monosomy, or triploidy, chromosome analysis of their parents is not needed because these anomalies arise de novo.
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Parental analysis with structural abnormality?
For patients who have structural abnormalities, e.g. duplications, deletions, translocations, etc.,
parental karyotype analysis is essential because:
1. One of the parents may have the rearrangement in balanced form
2. Knowing whether the rearrangement in the patient was inherited from a parent or occurred
de novo will help assess recurrence risk (the chance that they may have another abnormal
baby) for the parents’ future pregnancies.
3. If the patient’s parent carries a balanced rearrangement, one of his or her parents (i.e., the
patient’s grandparent) may also carry the balanced rearrangement and may have passed it to others of his/her children (i.e., the patient’s aunts and uncles), who probably are not aware
that they may be at-risk to have chromosomally abnormal children.
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What to consider if test is normal, but phenotype is off?
If you suspect a specific chromosome abnormality on the basis of the phenotype of the patient but the blood karyotype, FISH, microarray, etc. are normal, and you are still suspicious, consider the possibility of mosaicism and either examine a much larger number of cells or test another tissue, e.g. skin
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Two modes of Prader Willi
Deletion of 15q for father
| Inheritance of only mom 15s
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What is a haplotype?
A haplotype (from the Greek: ἁπλοῦς, haploûs, "onefold, single, simple") in genetics is a combination of alleles (DNA sequences) at adjacent locations (loci) on a chromosome that are inherited together. A haplotype may be one locus, several loci, or an entire chromosome depending on the number of recombination events that have occurred between a given set of loci, if any occurred.
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What is difference between introns and exons?
Exons are expressed
Introns are not expressed
Splicing
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What is a locus?
In genetics, a locus (plural loci) is the specific location of a gene or DNA sequence or position on a chromosome
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Simplex vs sporadic?
“Sporadic” refers to a chance event. “Simplex” refers to a single occurrence of a condition in a family.
