Of these, 7100 were non-synonymous, or premature stops, or small insertions or
deletions in the coding exons, suggesting that they could actually be deleterious.
And of these, at least 1100 were
novel, not present in databases of normal variance.
So you can see that, first starting out you have
an enormous number of variants that need to be assessed.
However, by applying a disease-based
approach, which is to assume that there was either autosomal
recessive or X-linked inheritance, the number of variants is filtered down
to only 136, and among those one
variant altered a conserved amino acid was predicted
to be damaging, was not present in a reference genome and was not
even gene in which deleterious mutations causing a different phenotype was known.
So the application of the mode of
inheritance to identifying this gene is very important.
Because you'll note that there are
over 7000 potentially damaging variants in genes.
1100 of them novel for which this child was a heterozygote.
On the other hand, by assuming that this was a
recessive or an X linked condition, as over here, there
are only 136 fit these, and of those only one
the gene called X-I-A-P, matched all the other criteria
including, non-conserved a gene that was
muted in other conditions, not in this inflammatory bowel etc.
And what's important about this discovery is that this
was now an indication for treatment that had not been
considered previously, and that was a bone marrow transplant, which
is indicated for individuals with a defect in this gene.
One can also do this, these sorts of studies in unrelated patients.
For example, suppose you have multiple unrelated
patients with the same disease, or unrelated trios.
Let's talk about the unrelated patients with the same disease first.
Here's an article published on the clinical use of whole-exome
sequencing for 250 consecutive patients
with undiagnosed diseases undergoing trio analysis.
[SOUND] Here's a trio.
Simply means an unaffected parent, another unaffected parent, and an affected child.
[SOUND] Now the mode of inheritance, in addition to dominant and
recessive, we can now add a third, which is new mutation.
Because by knowing the sequence in the parents, we can determine
whether a variant in the patient is not present in either parent.
And, for a devastating disease, it is often the case
that the disorder represents a new mutation in the child.
Here's an example representing a filtering scheme similar to what I
showed you before with the child with the inflammatory bowel disease.
You might start with whole genome sequencing, in which
case they'll be 4 million differences with the reference.
Or you may sta, you may start with whole exome sequencing
in which case you'll may have as many as 40,000 variants.