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Neurogenetics Final With Complete Solutions Latest Update
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Neurogenetics Final With Complete Solutions LatestUpdate
Out of the ~300,000 rare variants that are found in each of our genomes, ~70 are
de novo variants. What are de novo variants? - correct answers Genetic alterations
that are present for the first time in one family member, not inherited from
parents
Which has the greatest potential to transmit ASD risk: common, rare, or de novo
variants. Why? Which generally has the smallest effect on phenotype? - correct
answers de novo, and then rare variants have greater potential to transmit ASD
risk due to natural selection, where as common variants are least likely
What is a simplex family?Why use simplex families in sequencing studies? - correct
answers A family in which only one individual has a disease, rather than a large
number of individuals with a disease (multiplex). It's a way to enrich your potential
variant pool with de novo variants.
Whole exome sequencing of simplex families has determined that there are more
de novo variants in coding regions in ASD cases compared to controls. - correct
answers Furthermore, the increased variants (SNVs or Indels) are not synonymous,
but instead likely gene disrupting variants such as frameshifts, indels, missense,
nonsense, splice site variants, etc.
Be able to look at unlabeled data in slide 11 and know which protein-truncating
variants are likely in genes that contribute to autism. - correct answers In controls,
,variants are randomly distributed across genes. In cases, variants accumulate in
genes that contribute to risk
How many statistically significant ASD-associated genes have been identified using
WES - correct answers To date, 102 statistically significant ASD-associated genes
have been identified using whole exome sequencing
By looking at the known function of these genes we can start to make some
hypotheses about the neurobiology of ASD. - correct answers Genes whose
protein products play a role in synaptic communication, and gene expression
regulation (e.g. chromatin modifiers and transcription factors) are the most
common.
Although exome sequencing has uncovered likely ASD risk genes, only 11% of
cases have one of these identified genes. So, what's causing ASD in the other 89%
of cases? - correct answers Maybe variants in non-coding regions... remember,
these are regions that are either not transcribed at all OR (more likely) are
transcribed, but not translated.
What do these noncoding regions of DNA do? - correct answers They are involved
in defining gene expression patterns...when and where (in which cell type) is a
gene going to be expressed.
Dr. Werling's research question - correct answers "Do de novomutation in
noncoding regions also contribute to ASD risk?"
, She has looked at 1,902 families WGS. At first it looked like cases had an increased
rate of de novo mutation as cases had more de novo
mutations than controls. But, before she could make this conclusion she needed to
correct for paternal age when the children were born. Why? - correct answers
Because older fathers pass on more de novo mutations to their children than
younger fathers because sperm are continuously produced throughout the male
life cycle, and accumulate mutations through multiple divisions
After correcting for paternal age this increase went away. What does this say
about the age of the autistic children's father (when the child was born)? - correct
answers They were older. So, more (56%) of autistic children in the simplex
collections were 2nd born...the youngest, and 44% of the autistic children were 1st
born...the oldest.
Dr. Werling ultimately identified ~70,000 de novo noncoding variants. How will she
determine if any of them contribute to ASD risk? - correct answers One way would
be to see if any given variant is found more often in cases than controls, but this is
actually incredibly unlikely as the number of de novo variants she's considering is
so small compared to the size of the genome queried. Indeed, none of them are
seen in more than 1 ASD case.
So how will she know if the variant is benign or contributing to the child's autism? -
correct answers If a variant is found in a coding region, researchers can make
predictions based on the genetic code...based on how the variant will affect the
encoded protein...but this isn't possible for noncoding variants.
One idea is that she can look to see if a variant occurs in a known genomic region,
i.e. in an enhancer, promoter, 5'UTR, intron, or 3'UTR. - correct answers However,
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