MdCNV

Question 1

What were aspects of an intresting case of too many CNVS

Answer 1

De novo
Independent
large scale
tandem
CNVS
Inherited=constitutive (in the zygote so if you sample blood or skin you will find it)
Located across the genome
Frequently maternal origin
Phenotype of developmental disorders

Question 2

What was the scientific method

Answer 2

Observation: too many de novo constitutive CNVs
MdCNVs mutipke de novo CNVs
Hypothesis - there exists a mutator phenotype that raises the mutation frequency and increases the number of CNVs
Experiment 1437 individuals with 1 dnCNV
39 with 2 dnCNVs
1 individual with 3 dncnv
2 individuals with 4 and 7

Question 3

What is the MdnCNV criteria

Answer 3

more than 4CNVS and over 1000kb in length a proablity of occuring spontaneously is very rare so it not a spontaneous event

Question 4

What were the findings of the study

Answer 4

5 unrelated individuals met the MdnCNV criteria; these observations significantly exceed expectations of spontaneous independent origins for MdnCNVs supporting a mutator pheonotype hypthesis

Question 5

What detection was used to find the de novo CNV

Answer 5

Using aCGH genome hybridization where duplication shows eleveated signal intensity more sample DNA bound to the array

Question 6

Is the dnCNV in the proband observed in parents

Answer 6

NO so there is going to be elevated hybridization signal intensity in proband

Question 7

What observations were made from the MdnCNV profile and landscape

Answer 7

Across the genome
Maternal origin and Gains (CN3 and CN4)

Question 8

What doe these profile and landscapes look like

Answer 8

It is a graph where 0 is that there are no losses and above is a gain and below represents a loss and it is showing if it is coming from the maternal or paternal chromsome that doesn’t mean that it was caused in the maternal genome and passed down it just means the chromsome inherited from ther mother was affected

Question 9

What do MdnCNVs tend to be

Answer 9

Tandem duplications TD

Question 10

What is specefic about these CNVS that make them different

Answer 10

Too numerous to be spontaneous
Not restricted too a single chromosome not local
Across the genome landscape a global mechanism

Question 11

What does MdCNVs fit

Answer 11

A mutator phenotype phenomenon

Question 12

What do MdnCnvs tend to be

Answer 12

Longer legnth
Gains- Tandem duplications
Genome wide this larger length suggest a different mechansism

Question 13

What could be possible underlying mechanisms for CNV formation

Answer 13

Slippage at replication
NAHR = non-allelic homologous recombination
NHEJ non-homologous end joining
FoSTeS = Fork stalling and template switching
Retrotransposition

Question 14

What is slippage at replication

Answer 14

Polymerase can slip back and go agin which can form tandem duplication

Question 15

What is NAHR

Answer 15

A recombination even between low copy repeats that misalign, causing duplications or deletions

Question 16

What is low copy repeates

Answer 16

Long sequences with high similarity; they cause misalignment during meiosis, predisposing the region to CNVs

Question 17

What is NHEJ

Answer 17

A DNA repair mechanism that joins double-strand breaks without needing homology which can create complex CNVs

Question 18

What is FoSTeS/MMBIR

Answer 18

It is a replication based mechanism where the polymerase switches templates during replication, creating complicated rearrangements usualy ocuring when replication is out of control or during development and going too fast

Question 19

What is L1 retrotransposition

Answer 19

A process where a LINE-1 element copies itself through an RNA intermediate and inserts a new DNA copy into a new genomic location

Question 20

What is MMBIR

Answer 20

A replication based repair mechanism where the DNA polymerase switches templates using short microhomologus sequences, creating duplications, deletions, or complex CNVs

Question 21

What triggers MMBIR

Answer 21

A stalled or collapsed replication fork during DNA replication

Question 22

Explain how MMBIR might work

Answer 22

Okay so microhomeolgy is very short matching DNA sequences which usually appear in more than one place in the genome such as a sequence like AGCT and then there will be another region of AGCT so if the replication fork collaps DNA polymerase is going ot loose its spot and look for another spot it can bind to to start replicating
DNA is replicated again leading to duplications

Question 23

Can you tell the difference between paternal and maternal with MMBIR

Answer 23

Yes the short sequences differ between parents so paternal and maternal origins of strand switching events can be identifies

Question 24

What model does MDnCNVs fit

Answer 24

MMBIR

Question 25

Why would it not be the others

Answer 25

No L1 sequences NAHR could get deletions or duplications not always just duplications

Question 26

What would it mean if the chromsome was maternal or paternal or both

Answer 26

So if it is maternal that means it proably occured in oogenesit where if it is paternal it proably occured in speratgonesi if it is both then it woul dhave happened in the zygote

Question 27

What does constitutive mean

Answer 27

Also means that the phenomenon does not persist but is stopped early in development later occuring CNVs would be in certain and not all tissues meaning it is transient occurence of the mutator phenotype

Question 28

Talk about the proposed model for MD

Answer 28

So it starts with a faulty replication repair in the oogonium which will eventually develop to an occyte and there is a driver mutation in one of the chromsome that drives the mutator phenotype which is producing the red rna It is then lost in the First polar body and the sprem comes along creating an ootid and the second polar body but the RNA is still here DNA replication in two pronuclei Then zygote Early cleavage stage Then post maternal clearnce and the Rna is gone