I need to understand the difference between complex disease and cancer in terms of variants detection. Can someone please explain briefly how detection of causal variants in cancer and complex diseases is different? Or how causal variants in cancer and complex diseases (is it only that we are considering germline mutations in complex disease ?) are different?
Dear,
In complex disease you do not have clear genotype-phenotype correlation. Certain SNVs residing in more than one gene in multiple chromosomes cumulatively play a role. Even when one of these mutations are present as germline, the patient might not have the phenotype. Therefore in a complex disease it is often assumed that multiple regions play a role in converging pathways. When I refer to complex disease I refer to a case where the phenotype is affected by more than 1 genetic alteration. For example, epilepsy is a complex disorder. Naturally in complex disorders, your primary targets are germline (it can be inherited or de novo).
In cancer, you generally speak about heterogeneity in means of genotype. A cell with a driver/predisposer mutation acquires many other mutations along the way and results in multiple subpopulations of cells with eventually messed up chromosomes. These driver/predisposer mutations are either acquired in somatic cells of the patient during his lifetime (sporadic) or present as germline (expected to be inherited). Therefore, you need to keep an eye on both germline and somatic acquired mutations.
Regards,
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Thank you, Ibrahim. Clear and succinct. I have another question: In case of complex disease, all we are concerned is about finding germline mutations, but in cancer it is about finding somatic by subtracting germline mutations. So what are the theoretical differences in terms of finding these mutations in each of complex disease and cancer?
Dear, I have not seen cases where a sporadic event enhances a complex disease state, so in case of complex disease expect multiple germline genetic alteration resulting in the patients phenotype. In these cases, you either can go genome wide association studies to use surrogate SNVs to track down genes playing role in the disease, or you can go whole genome sequencing for both patients and controls and then compare the results. You will be searching for a minimal common combination of SNVs(or other alterations) that exist in the patients but do not exist in the control.
In case of cancer, first you need to make sure that there is no predisposer mutation present germline, like in the case of BRCA. It can be that the parents are heterozygous but the child is homozygous for a tumor suppressor gene etc. If you do not find any of these and than you compare the mutations in the cancer tissue and the normal tissue. Are there any mutations that present in the cancer tissue that doesn't exist in the normal tissue? For example, in case of myeloproliferative leukemia (type of blood cancer), researchers compare buccal swab (inlining of your mouth) and the blood. If there are mutations in the DNA extracted from blood that do not exist in the buccal swab, then you concentrate on them. If you have a lot of patients and controls, your choice of sequencing is usually whole exome sequencing. Once you find your target, you need to confirm it via Sanger Sequencing. Once you confirm it, you need to make sure that it also exists in the RNA level by either RNA sequencing or RT-qPCR. The RT-qPCR will be a simpler and easier approach however in RNA sequencing you will have access to the overall expression levels and hence will have an idea how your mutation is affecting the whole cellular machinery. If you really wanna be rigorious than you need to make sure what you see in both DNA and RNA is also translated as functional protein. This should be done via in-vivo/in vitro functional studies and western blotting.
Regards,