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Integrated Medical Science > Test 1 > Flashcards

Test 1 Flashcards

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1
Q

Del(5q) is commonly seen in…

A

Myelodysplastic syndrome (MDS) (sometimes in AML as well)

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2
Q

Difference between an interstitial deletion and a terminal deletion:

A

Interstitial: two break points in the chromosome
Deletion: one break point in the chromosome

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3
Q

Del(5q) genetic mechanism of oncogenesis:

A

Deletion: Gene dosage effect caused by deletion of multiple genes contained in the 5q region

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4
Q

t(9;22) is commonly seen in…

A

Chronic myeloid leukaemia (CML), and also some cases of acute lymphocytic leukaemia (ALL)

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5
Q

t(9;22) genetic mechanism of oncogenesis:

A

Translocation resulting in formation of the novel hybrid fusion gene BCR-ABL1 on der(22).

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6
Q

t(14;18) is commonly seen in…

A

Follicular lymphoma and some cases of non-Hodgkin’s lymphoma

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7
Q

t(14;18) genetic mechanism of oncogenesis:

A

Translocation resulting in juxtaposition of BCL2 gene with IGH@ causing de-regulated expression of BCL2

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8
Q

Double minutes (dmins) are commonly seen in…

A

AML

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9
Q

Dmins genetic mechanism of oncogenesis:

A
  • Amplification leading to c-myc oncogene over expression
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10
Q

Pericentric inversions:

A

Pericentric inversions include the centromere in the inversion i.e. in both arms of the chromosome

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11
Q

inv(16) is commonly seen in…

A

AML

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12
Q

FISH with inv(16):

A
  • Pericentric inversion visualised using a break-apart probe for 16q22, the region that includes the CBFβ gene.
  • The component of the probe that binds upstream of the CBFβ gene is labelled red, while that which binds downstream is labelled green.
  • Native state: red and green signals combine to produce a yellow colour
  • Inversion state: red and green signals appear distinct from each other
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13
Q

Paracentric inversions:

A

Only occur in one arm of the chromosome

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14
Q

inv(16) genetic mechanism of action:

A
  • Inversion resulting in formation of a novel hybrid fusion gene CBFβ-MYH11
  • MYH11 encodes transcription factor that interacts with RUNX1
  • RUNX1 function is inhibited with binding
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15
Q

t(8;21) is commonly seen in…

A

AML of the M2 subtype

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16
Q

t(8;21) genetic mechanism of action:

A
  • Translocation resulting in formation of a novel hybrid fusion gene RUNX1-RUNX1T1.
  • The chimeric fusion protein has transforming oncogenic activity
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17
Q

t(8;14) is commonly seen in…

A

Burkitt’s lymphoma (sometimes in non-Hodgkins lymphoma)

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18
Q

t(8;14) genetic mechanism of action:

A
  • Translocation resulting in juxtaposition of myc gene with IGH@ causing overexpression and increased proliferation
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19
Q

t(15;17) is commonly seen in…

A

Acute promyelocytic leukaemia, also called AML M3

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20
Q

t(15;17) with FISH

A
  • Visualised using a dual-fusion probe set
  • One probe is green, one is red, each labelled to chromosome 15 or 17
  • Unaffected 15 and 17: labelled red and green respectively
  • Derivative 15 and 17: a combination of red, green and yellow signals
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21
Q

What two genes are involved in the abnormality t(15;17)?

A

PML and RARa

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22
Q

How does the abnormality t(15;17) cause AML?

A

t(15;17) forms a novel hybrid fusion gene PML-RARa

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23
Q

What prognosis does t(15;17) PML-RARa have?

A

Favourable

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24
Q

How does trisomy 8 result in AML?

A

There is amplification of oncogene c-myc

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25
Q

What prognosis does trisomy 8 have?

A

intermediate

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26
Q

What prognosis does t(8;21) RUNX1-RUNX1T1 have?

A

favourable

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27
Q

What prognosis does inv(16) CBFβ-MYH11 have?

A

Favourable

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28
Q

Explain Knudson’s Two-Hit Hypothesis for carcinogenesis:

A
  • Knudson’s two-hit hypothesis is based on the theory that the tumour suppressor genes on both chromosomes in a cell need to be inactivated in order to produce a cancer (i.e. two hits)
  • This can either be sporadic, so two events need to happen to mutate each gene, or one mutated gene can be inherited from parents, and then only one event needs to occur to mutate both genes
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29
Q

Explain the multi-step nature of carcinogenesis:

A
  • The multi-step nature model has three phases: initiation, promotion, tumour progression
  • initiation: a mutation occurs where the metabolism and repair processes of the cell are altered
  • promotion: involves proliferation of the affected cell (this is irreversible but not yet cancer)
  • progression: a series or mutations of epigenetic changes occur in these cells, and with selection they continue proliferating
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30
Q

Explain the somatic mutation theory vs. tissue organised field theory:

A
  • Somatic mutation Theory (SMT): Carcinogenic agents lead to a higher number of new mutations or increase in already mutated genes which can affect cell growth, differentiation or function.

Tissue Organization Field Theory (TOFT): Carcinogenic agents disrupt interactions between cells that maintain the tissue architecture

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31
Q

What is the role of proto-oncogenes?

A
  • regulate cell growth and differentiation
  • potential to become oncogenes
  • involved in signal transduction and execution of mitogenic signals
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32
Q

What is the role of onco-genes?

A
  • have the potential to increase the malignancy of a cell
  • once they become activated they are constitutively expressed
  • e.g. c-myc, k-ras
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33
Q

What are the different classification of oncogenes?

A
  • growth factors
  • growth factor receptors
  • cytoplasmic tyrosine kinases
  • cytoplasmic serine/threonine kinases
  • regulatroy GTPases
  • transcription factors
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34
Q

Mechanism of action of growth factor receptors and an example

A
  • overexpression or amplification
  • they add phosphate groups to tyrosine in target proteins
  • this can cause cancer by switching the receptor permanently on without signals from outside of the cell
    e. g. platelet derived growth factor receptor (PDGFR)
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35
Q

Mechanism of action of regulatory GTPases and an example

A
  • mechanism: point mutations leading to deregulated overactivity
  • e.g. Ras in many common cancers (lung, colon)
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36
Q

Mechanism of transcription factors and an example

A
  • mechanism: point mutation, amplifications ot translocations
  • e.g. c-myc amplicaton in dmins
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37
Q

How oncogenes become activated:

A
  • through mutations, gene amplification and chromosomal rearrangements
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38
Q

How mutations work to activate oncogenes:

A
  • alter structure of proto-oncogene -> produces an oncogene
  • dominant-gain-of-function mutation: affected gene has a new molecular function
  • involve protein regulatory regions –> leads to uncontrolled activity of the mutated protein
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39
Q

How gene amplification works to activate oncogenes:

A
  • repeated copying in DNA replication -> more copy numbers -> higher gene expression -> deregulated cell growth
  • Amplification can result in d-mins (double minutes)
  • Amplified regions can contain hundreds of copies
  • e.g. c-myc is amplified in small-cell lung cancer, breast/ovarian cancer and leukaemias
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40
Q

How chromosomal rearrangements work to activate oncogenes:

A
  • When these rearrangements happen, oncogenes can be activated by:
    1. Regulatory control of IGH@
  • oncogene is moved close to an immunoglobulin gene and falls under its control -> deregulated expression -> neoplastic transformation
    1. Formation of novel hybrid fusion genes
  • Juxtaposition of 2 genes to form a novel fusion gene -> codes for chimeric protein -> transforming activity
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41
Q

What is a tumour suppressor gene and what are its functions?

A
  • They suppress cellular growth/survival when needed to prevent tumours forming.
  • Outcomes triggered by tumour suppressor activation:
  • Arrest cell cycle to inhibit cell division
  • Induce cell cycle to DNA damage repair mechanisms
  • Promote apoptosis if damage cannot be repaired
  • Induce senescence
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42
Q

Six biological capabilities acquired by cancer cells:

A
  • Sustaining growth signalling
  • Evading growth suppressors
  • Resisting cell death
  • Enabling replicative immortality
  • Inducing angiogenesis
  • Activating invasion and metastasis
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43
Q

How cancer cells sustain growth signalling:

A
  • send their own signals to normal cells in extracellular matrix around tumour -> react and supply tumour with growth factor
  • An increase in receptor proteins at the cancer cell surface -> hyper responsive to usually limited supply -> an increase of growth signalling
  • this keeps growth signalling switched on
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44
Q

How cancer cells evade growth suppressors:

A
  • Function of a growth suppressor is to control growth (regulatory pathways/factors)
  • Many of these are dependent on tumour suppressor genes e.g. TP53
  • Defects in pathways/genes -> cancer cells resist inhibitory signals that would usually stop their growth
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45
Q

How cancer cells resist cell death

A
  • Apoptosis = programmed cell death
  • Different pathways regulating/affecting apoptosis (e.g. TP53 mediated/BCL2 regulated)
  • Opportunities for cancer cells to resist apoptosis through defects in these pathways
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46
Q

p53/BCL2 regulatory pathway to Apoptosis:

A
  • BCL2 has anti cell death function-> cell lives
  • TP53 can: promote cell death and DNA repair
  • Apoptosis acts to control cancer cells but it can be overcome if:
  • 1) Over expression of BCL2 (
  • 2) Mutation/loss of TP53
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47
Q

How cancer cells induce angiogenesis:

A
  • angiogenesis: formation of new blood vessels (this process is balanced by inducers and inhibitors)
  • For cancer cells to grow they need a blood supply. During carcinogenesis an “angiogenicswitch” is tripped and remains on. Inducers & inhibitors control this switch
  • e.g. TP53 loss or mutation can dysregulate TSP-1and induce angiogenesis as seen in growth of breast and melanoma cancers
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48
Q

How cancer cells activate invasion and metastasis:

A
  • Metastasis: distant areas attach to ECM and recruit normal cells for support
  • Activated by changes in molecules needed for cell adhesion: cadherins and integrins
  • Genetic alteration in cadherins/integrins or factors that regulate/affect their pathways –> activation of invasion/metastasis
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49
Q

Defintion of AML:

A
  • Accumulation of clonal immature cells from the myeloid lineage in the bone marrow that interferes with normal production
  • More than 20% blasts
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50
Q

Risk factors for AML:

A
  • There are few known proven risk factors for AML and it is relatively unknown what causes AML to develop.
  • Smoking
  • Chemicals
  • Radiation
  • Viruses
  • Congenital syndromes (some - increase risk)
  • Certain blood disorders
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51
Q

AML genetic mechanisms:

A
  • Homeostasis: balance in proliferation/regulation/apoptosis
  • Cancer-associated genes: oncogenes, tumour suppressor genes
  • Activation of oncogenes by: mutation/amplification/translocation
  • Switching off tumour suppressors by: mutation
  • Outcome: alteration of gene expression
  • Leads to: alteration in growth/apoptosis/differentiation/function
  • 2nd event or multi-step process leads to cancer being formed.
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52
Q

Cancer stem cell theory

A
  • involves stem cells, progenitor cells or differentiated cells
  • cell becomes mutated -> loss of regulated cell divison -> cancer stem cell
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53
Q

Two hit model for AML:

A

Involves class I and class II mutations

Class I:

  • these mutations give prolierative or survival advantages but do not affect differentiation
  • e.g. BCR/ABL mutations
  • produce a CML-like mutation

Class II:

  • these mutation impair haematopoietic differentiation which leads to apoptosis
  • e.g. PML/RARa fusions
  • produce an MDS-like mutation

These two class mutations in combination –> produce AML

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54
Q

Lab investiagtions for AML

A
  • Morphology and blood film
  • Coagulation studies
  • Immunophenotyping
  • HLA typing
  • Molecular Haematology
  • Cytogenetics
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55
Q

PB film and bone marrow aspirate/trephine in diagnosing AML

A
  • Peripheral blood film - mostly diagnostic, blasts & accompanying changes provide good clues
  • Bone marrow aspirate - detailed morphology of cells, good for quantitating
  • Bone marrow trephine - marrow cellularity & cellular pattern of involvement , IHC testing & assessing fibrosis esp in a “dry” tap aspirate
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56
Q

Features of an AML blood film:

A
  • nucleated RBCs
  • Pelger Huet anomaly
  • large platelets

Blasts:

  • auer rodes
  • high n:c ratio
  • obvious nucleoli
  • pale blue-grey cytoplasm
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57
Q

AML coagulation studies:

A
  • Disseminated intravascular coagulation (DIC) is common

- Acute promyelocytic leukemia (APML) results in: higher PT, lower fibrinogen -> +ve fibrin split products

58
Q

AML immunophenotyping:

A
  • Myeloid Antigens: CD11b, CD13, CD33, CD34, CD45, CD117, HLA DR
59
Q

AML Human Leukocyte Antigen testing:

A
  • Major Histocompatability Complex
  • Genes encode cell-surface antigens - involved immune function
  • HLA-typing for allogeneic stem cell transplant
  • Donors: Matched related donors, Matched Unrelated Donors, Cord
60
Q

AML molecular haematology and its role:

A
  • Denaturing: 94, Annealing: 50-65, Extension: 72 -> repeat 30-40 cycles
  • Detect fusion transcripts generated by novel fusion genes
  • Monitors engraftment post BMT
  • Sensitivity levels (good for minimal residual disease):
61
Q

AML cytogenetics and its role:

A
  • Includes conventional cytogenetics and molecular analysis (FISH)
  • Confirm diagnosis of disease
  • Classify haematological malignancies and the subsets
  • monitors MRD
  • Predictive factors for prognosis
62
Q

What are the prognostic markers of AML and what do they mean for the patient?

A
  • three prognostic groups: favourable, intermediate and adverse
  • Favourable … overall survival at 5yrs = 60 - 80%
  • Intermediate … overall survival at 5 years = 24 - 42%
  • Adverse … overall survival at 5 years < 20%
63
Q

Cytogenetic abnormalities with a favourable prognosis:

A
  • t(15;17)
  • t(8;21)
  • inv(16)/t(16;16)
64
Q

Cytogenetic abnormalities with an intermediate prognosis:

A
  • Normal karyotype
  • Entities not classified as favourable or adverse
  • Trisomy 8
  • t(9;11)
  • t(11;19)
65
Q

Cytogenetic abnormalities with an adverse prognosis:

A
  • inv(3)
  • del(5q)
  • del(7q)
  • abn(17p)
  • t(9;22)
  • Complex ( ≥3 unrelated abnormalities)
66
Q

Follicular lymphoma definition

A
  • ~30 % of adult NHL’s
  • Originates from follicular germinal centre
  • Centroblasts/centrocytes - somatic hypermutation of Ig HV genes -> ongoing mutations -> Ig heavy and light chain genes rearranged
  • Immunophenotype: CD5-, CD10+, CD19+, CD20+, CD22+, sIg +, BCL2+
67
Q

Diffuse large B cell lymphoma definition

A
  • ~40% adult NHL’s
  • Originates germinal or post-germinal centre – mostly centroblasts
  • Large transformed B-cells with somatic hypermutations of Ig HV genes -> ongoing mutations, ->Ig heavy and light chain genes rearranged
  • Immunophenotype: CD5-, CD10±, CD19+, CD20+, sIg +, BCL2 ±, BCL6±
68
Q

Myeloma defintion

A
  • Originates post-germinal centre
  • Bm based disease >with 10% clonal malignant plasma cells
  • Immunophenotype: CD79a+, CD138+, CD38+, CD19- , CD56+
69
Q

Lymphoid neoplasm definition

A
  • Neoplastic proliferation of cells that are clonal and derived from the lymphoid lineage
  • Can either be T-cell and NK cell or B-cell derived
  • 85% of lymphoid neoplasms are B-cell derived
  • 15% of lymphoid neoplams are T-cell and NK-cell derived
70
Q

Cytogenetics of Follicular lymphoma

A
  • t(14;18) IGH@-BCL2 ~ 90%
  • BCL2 has 2 breakpoint cluster regions:
  • 1) MBR - major breakpoint region
  • 2) MCR – minor cluster region
  • Karyotypes become more complex with histological grade and transformation
71
Q

Cytogenetics of diffuse large B cell lymphoma

A
  • most are complex karyotypes
  • 20%: t(14;18), IGH@-BCL2 p53 mutations
  • 10-30%: t(3;V), IGH@-BCL6
  • about 10%: t(8;14), IGH@-MYC
72
Q

Cytogenetics and FISH of myeloma

A
  • Interphase FISH only on plasma cells
  • CD138+ selection of plasma cells
  • High risk: t(4;14) IGH@-FGFR3 or TP53 deletion
  • Standard risk: The absence of high risk features and presence of hyperdiploidy (5,9 and 15)
73
Q

Somatic hypermutation

A
  • Somatic hypermutation = extremely high rate of mutation ≥10⁵ - 10⁶ times
  • Mistargeted somatic hypermutations is a likely mechanism in the development of B-cell lymphomas
74
Q

Course of disease from MGUS to myeloma:

A

MGUS -> smouldering myeloma -> myeloma -> plasma cell leukaemia

75
Q

FISH probes for myeloma:

A
  • t(4;14)– IGH@-FGFR3 -> Dual fusion probe
  • t(14;16) – IGH@-MAF -> Dual fusion probe
  • TP53 deletions -> Locus specific indicator
  • Hyperdiploidy of 5, 9, 15 (extra copies) -> Locus specific indicators
76
Q

B cell differentiation in follicular lymphoma

A
  • Follicular lymphoma matures from germinal centre (follicular area) of the b cell
  • antigen driven side of maturation
77
Q

B cell differentiation in DLBCL

A
  • mostly displays germinal centre differentiaton
78
Q

B cell differentiation in myeloma

A
  • post germinal centre b cell differentiation

- caused by exogenous carcinogens

79
Q

Principle of FISH:

A
  • DNA probes bind to target sequences
  • Probes are labelled with fluorescent dyes
  • Hybridisation -> single stranded DNA anneals to complementary DNA
  • this hybridisation is seen as a brightly coloured signal by fluoresence microscopy
80
Q

Direct and indirect probe labelling in FISH:

A
  • Indirect: labelled with reporter molecules (strepavidin)

- Direct: by incorportating fluorescein dUTP

81
Q

Types of FISH probes:

A
  • Multiple chromosome sequences
  • specific chromosome structure
  • unique DNA sequences
82
Q

Multiple chromosome sequence probes:

A
  • Whole chromosome paints (WCP) for the entire chromosome
  • Available for each of the human chromosomes
  • Useful for detecting ring chromosomes
83
Q

Specific chromosome structure probes:

A
  • Centromeric probes (CEP)

- Suitable for the detection of aneuploidy eg monosomies, trisomies etc

84
Q

Unique DNA sequence probes:

A
  • Locus specific indicators (LSI)
  • target specific genes
  • Useful for deletions, translocations, inversions
  • used in FISH eg dual fusion probes, break-apart probes
85
Q

TP53 LSI probe:

A
  • TP53 on both chromosome 7s are labelled orange, the centromeres of each chromosome are labelled green
  • in normal circumstances, the FISH should show two orange signals and two green signals
  • when P53 is deleted, there will only be one orange signal and two green signals, to indicate two chromosomes
86
Q

Dual colour, dual fusion translocation probes

A
  • Designed to detect gene fusions in recurring translocations
  • e.g. one part of a chromosome is labelled red, another part of a different chromosome is labelled green, if there is a translocation that results in a fusion gene, this area will appear yellow in FISH
87
Q

Dual colour, break-apart probes

A
  • two parts of the same chromosome are labelled differently (e.g. one green and one red)
  • if there is a translocation, these two labels will appear separate and distinct in FISH
  • if there is no abnormality, the red and green labels will be joined
88
Q

Advantages of FISH

A
  • very fast
  • high specificity and sensitivity
  • can use non dividing cells
  • don’t need good quality chromosomes
89
Q

Limitations of FISH

A
  • Data can be obtained only for the target chromosomes
  • FISH is not a good screening tool for AML or ALL
  • Only one or a few abnormalities can be assessed simultaneously (not used in complex cases)
90
Q

Myeloma high risk groups

A
  • t(4;14)IGH@-FGFR3,
  • t(14;16)IGH@-MAF
  • TP53 deletion
91
Q

Myeloma standard risk groups

A

The absence of high risk features & presence of hyperdiploidy 5,9,15

92
Q

t(4;14) abnormality

A

fusion of FGFR3-IGH@

93
Q

t(4;14) fusion of FGFR3-IGH@ genetic mechanism of action

A
  • overexpression of FGFR3 under the influence of IGH@
  • FGFR3 is involved in cell regulation and differentiation
  • overexpression leads to increased proliferation
  • high risk
94
Q

del(17) abnormality

A

deletion of tp53

95
Q

del(17) deletion of tp53 genetic mechanism of action:

A
  • TP53 deletion is hemizygous
  • Hyperdiploidy (extra copies): gene dosage effects, many deregulated genes
  • high risk
96
Q

5, 9, 15 hyperdiploidy has what risk?

A

standard

97
Q

translocations in variant APML case:

A

15q -> 22q -> 17q -> 15q

98
Q

prognosis of t(15;22;17)

A

t(15;17) has a favourable prognosis and this variant should not affect the prognosis

99
Q

Principle of mircoarrays

A
  • A collection of DNA spots attached to a solid surface
  • Spots are arrayed in rows and columns
  • Each DNA spot contains a specific DNA sequence -> probes -> used as hybridisation targets
  • These are detected and quantified by detection of fluorophore
  • Determination of the relative abundance of nucleic acid sequences in the target
100
Q

What are copy number variations

(CNVs)?

A
  • chromosomal deletions (loss of DNA)

- chromosomal duplications (gains of DNA)

101
Q

Types of DNA CNVs:

A 
Loss or gain of:
– Whole chromosome
– Several adjacent genes
– Single gene
– Exons (part of a gene)
102
Q

Methods for detecting DNA copy number variations

A
  • Karyotype
  • FISH (metaphase/interphase)
  • QF-PCR
  • DNA microarray
  • MLPA
  • NGS
103
Q

Types of microarrays:

A

Array CGH and SNP array

104
Q

Array CGH:

A
  • Patient DNA vs. normal reference control DNA

- DNA is fragmented -> fluorescently labelled -> competitively hybridised -> read with fluorescence scanner

105
Q

SNP array

A
  • Do not use a control reference DNA, instead, result is compared to averaged results for multiple normal samples
106
Q

Array CGH example/application:

A
  • Reference control DNA is labelled with Cy3 (green)
  • Patient test DNA is labelled is Cy5 (red)
  • hybridise these onto slide (array) which has probes
  • DNA competitvely hybridises -> produces fluorescence
  • looking for the fluorescence ratio between green an red
  • slide is put in scanner -> capture fluorescence signal -> quantify ratio of red and green

i.e. if patient (red) had a deletion of a part of the chromosome, there would be less red signal comparing to reference (green)

107
Q

How to detect CNVs:

A
  • Log R Ratio (LRR)

- B allele frequency (BAF)

108
Q

Log R Ratio (LRR)

A
  • Any deviations from zero for LRR is evidence for CNV.
109
Q

B allele frequency and Log R ratio interpretation

A
  • Normal (copy number=2) - LogR ratio 0
  • Deletion (copy number=1) -LogR ratio -0.5
  • Duplication (copy number=3) LogR ratio +0.3
110
Q

Interpretation of CNVs - consideration of size:

A

– General rule is that the larger the CNV the more likely it is pathogenic
– Not always true

111
Q

Databases to use when comparing CNV with internal and external databases

A

Databases to use:
– DGV
– DECIPHER
– ClinGen

112
Q

CNV Classifications:

A
  • pathogenic (or likely pathogenic)
  • uncertain
  • benign
113
Q

Microarray results - pathogenic CNV

A
  • Test parents for recurrence risk. Rule out balanced rearrangement.
  • Genetic counselling recommended.
114
Q

Microarray results of uncertain CNV

A
  • Testing parents may be helpful

- Genetic counselling may be appropriate

115
Q

Microarray results - benign CNV

A
  • Point mutations or balanced rearrangements not detected

- If specific disorder is suspected then test further

116
Q

What is Uniparental disomy UPD)?

A
  • Inheritance of two homologous chromosomes from one parent (e.g. two chromosomes only from dad and none from mum)
  • Heterodisomy: two different homologues from one parent (undetectable with microarray)
  • Isodisomy: two copies of the same homologue from one parent (picked up with microarray)
117
Q

Regions of homozygosity that are suggestive of UPD14:

A
  • Maternal UPD 14 (Temple Syndrome) -

- Paternal UPD 14 (Kagami-Ogata Syndrome)

118
Q

Characteristics of Maternal UPD 14 (Temple Syndrome)

A
  • Short stature,
  • low birth weight,
  • feeding difficulties
119
Q

Characteristics of Paternal UPD 14 (Kagami-Ogata Syndrome)

A
  • Dysmorphic facial features,
  • developmental delay,
  • feeding difficulties
120
Q

Confirming UPDs

A
  • SNP trio analysis

- MS-MLPA

121
Q

ROH diagnostic implications:

A

Uniparental disomy (UPD)

Identity by descent (IBD)

122
Q

ROH in consanguineous families:

A 
- the risk for autosomal recessive disease is directly proportional to the degree of
parental relationship (e.g. siblings are first degree relatives, have 25% expected homozygosity, half siblings are second degree relatives, have 12.5% expected homozygosity)
123
Q

Trisomy 21:

A
  • When comparing the control and the case in B allele frequency plot, there is a second band which is shifted to the right –> copy number gain/duplication
  • clinical features include: Poor immune function, developmental delay, intellectual disabilities
  • increased risk of: congenital heart disease, leukaemia, thyroid disorders
124
Q

Turner Syndrome (45,X):

A
  • female with only one x chromosome
  • when comparing the control and the case in the B allele frequency plot, the plot looks different to a typical female and has shifted to the left –> copy number loss/deletion
  • common abnormalities inlcude: Short stature, webbed neck, low-set ears,
125
Q

Human genetic diseases caused by loss or gain of whole chromosome

A
  • Trisomy 21 (Down syndrome)

- 45,X (Turner syndrome)

126
Q

What are LCRs?

A
  • Low copy repeat (LCR) sequences can cause DNA to misalign -> result in deletions or duplications
  • LCRs predispose region to genomic rearrangements by NAHRs
127
Q

What are NAHRs?

A
  • Non allelic homologous recombination
  • Misalignment and recombination between low copy repeats (LCR)
  • effect of deletions is more severe than that of duplication, so they are more commonly identified in patients
128
Q

Mechanisms of CNV formation

A
  • Non Allelic Homologous Recombination (NAHR)

- Non homologous end joining (NHEJ)/Replication based

129
Q

NAHR vs. NHEJ

A

NAHR:

  • Recurrent deletions/duplications
  • Clustered breakpoints
  • Low copy repeats (LCRs)

NHEJ:

  • Heterogeneous deletions/duplications
  • Scattered breakpoint
  • No LCRs
130
Q

DiGeogre syndrome (22q11 deletion) charcteristics:

A
  • CATCH
  • C: Cardiac defects
  • A: Abnormal facies
  • T: Thymic hypoplasia
  • C: Cleft Palate.
  • H: Hypocalcemia
131
Q

22q11.2 duplication syndrome

A
  • Same region as DiGeorge but milder than deletion

Features:
– mild to moderate mental retardation,
– growth retardation
– some abnormalities associated with Di-George

132
Q

Williams syndrome (7q11 deletion):

A

Features:

  • short nose, star pattern in iris
  • Developmental delay
133
Q

Prader Willi/ syndrome (15q11q13 deletion)

A
  • caused by paternal deletion

Features:

  • floppy at birth
  • develop obsession with eating and obesity
  • mental retardation
134
Q

Angleman syndrome (15q11q13 deletion)

A
  • caused by maternal deletion
  • frequent laughter and smiling
  • developmental delay, minimal use of words
135
Q

15q11q13 duplication syndrome:

A
  • duplications are usually maternal

Features:
– Autism
– Intellectual disability
– Seizures

136
Q

Microarray where there is a deletion and a duplication could be:

A
  • a translocation, but a microarray is unable to detect the structure of the chomrosome
  • in these cases, a karyotype will be used to determine if this is due to a translocation, or two separate events
  • in this event it is important to test parents - their chromosome structure may be normal but their children may have an unbalanced translocation
137
Q

Human genetic diseases cause by DNA copy number variations - microdeletions and microduplications of several adjacent genes:

A
  • Prader Willi/Angleman syndrome (15q11q13 deletion)
  • 15q11q13 duplication
  • DiGeogre syndrome (22q11 deletion)
    22q11 duplication
  • Williams syndrome (7q11 deletion)
138
Q

Charcot Marie Tooth Type 1A (Duplication of PMP22 gene on 17p12)

A
  • characterised by distal symmetrical muscle weakness
  • PMP22 is important in myelination of PNS
  • can be confirmed by microarray, FISH or MLPA
139
Q

Pros of microarray:

A
  • Whole genome analysis
  • Potentially quicker than karyotype
  • Some automation
140
Q

Limitations of microarray:

A
  • Unable to detect balanced rearrangements or small variants
  • Low level mosaicism can be missed (<10%)
  • Can be time consuming to analyse and report
141
Q

Why detection of CNVs from

NGS data is not a routine test:

A
  • Inconsistencies among different methods
  • Lack of good reference for CNVs
  • Difficult to differentiate between artefacts and true signal

Integrated Medical Science (2 decks)

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