Learnt Lessons
25/03/13 16:19 Filed in: GenomeWeb Daily Scan | HeLa cells;
Submitted by S. Pelech - Kinexus on Mon, 03/25/2013 - 23:30
It seems to be perfectly acceptable in society today for insurance companies and banking institutions to demand complete breakdowns on the health and financial situations about individual prospective clients. But getting DNA sequence information on individuals with respect to their single nucleotide polymorphisms (SNPs), even if they are long dead, well that's just too personal. The real catch is that we will not really be able to decipher the functional consequences of specific SNP's unless they can be correlated with a lot of phenotypic data. Only a few hundred mutations at best, out of around 60 million SNPs thought to exist in humans, can now be directly and strongly correlated with severe illnesses. Our real ignorance about how genome sequence data actually translates to specific phenotypes in reality provides the best privacy.
The UK government's plan to sequence the complete genomes of a 100,000 cancer patients over the next decade is, in my opinion, rather ill conceived beyond the high costs and diversion of limit resources from more productive avenues of cancer research. Gene mutation annotation initiatives, such as the Wellcome Trust Sanger Institute's COSMIC database, have already provided a wealth of gene mutations with linkages to different types of human cancers. Unfortunately, there is not much additional clinical or biochemical information provided with these mutations. I really doubt that many more new common cancer-associated mutations that are drivers as opposed to bystander mutations will be uncovered by many of the proposed massive genome-wide-sequencing studies. One of the characteristic properties of cancer cells is that they feature higher rates of mutations due to defective DNA repair from earlier mutations in the proteins that specifically monitor and carry out these repairs.
With hundreds of oncoproteins and tumour suppressor proteins already identified, it is becoming quite apparent that it is specific combinations of loss of function mutations in tumour suppressor genes and gain-of-function mutations in proto-oncogenes that result in progressive cancers. There may be millions, and perhaps billions of possible gene mutation combinations that will suffice to produce full blown cancer. In time, we will be able to identify many of the more frequent mutation combinations that cause cancer in individual patients and match this to the most appropriate drugs for their treatment. How soon this can be attained depends on how effectively cancer research is conducted.
To achieve this objective, so that people world-wide can receive more personalized medicine, families of cancer victims need to understand that they and everyone will benefit from the knowledge learned from their relatives' cancer cells. Tens of thousands of cancer researchers supported with public funding from governments and charitable donors, few of which have personally benefitted financially, have performed detailed biochemicals studies on hundreds of tumour cell lines obtained from cancer patients for over 50 years. HeLa cells are amongst the best characterized of these established cancer cell lines. It is a real shame that the HeLa cell genome sequence will not be broadly accessible to cancer researchers to build on the knowledge base.
The human genome sequences that would probably be the most useful for cancer research initially would be the US National Institutes of Health gold panel of 60 human tumour cell lines along with several hundred additional cancer cell lines that have been actively studied for several decades now. Most of these cell lines have a wealth of associated biochemical and phenotypic data, and can also be used in future studies to investigate the specific roles of intriguing mutations in a reproducible manner.
Link to the original blog post
It seems to be perfectly acceptable in society today for insurance companies and banking institutions to demand complete breakdowns on the health and financial situations about individual prospective clients. But getting DNA sequence information on individuals with respect to their single nucleotide polymorphisms (SNPs), even if they are long dead, well that's just too personal. The real catch is that we will not really be able to decipher the functional consequences of specific SNP's unless they can be correlated with a lot of phenotypic data. Only a few hundred mutations at best, out of around 60 million SNPs thought to exist in humans, can now be directly and strongly correlated with severe illnesses. Our real ignorance about how genome sequence data actually translates to specific phenotypes in reality provides the best privacy.
The UK government's plan to sequence the complete genomes of a 100,000 cancer patients over the next decade is, in my opinion, rather ill conceived beyond the high costs and diversion of limit resources from more productive avenues of cancer research. Gene mutation annotation initiatives, such as the Wellcome Trust Sanger Institute's COSMIC database, have already provided a wealth of gene mutations with linkages to different types of human cancers. Unfortunately, there is not much additional clinical or biochemical information provided with these mutations. I really doubt that many more new common cancer-associated mutations that are drivers as opposed to bystander mutations will be uncovered by many of the proposed massive genome-wide-sequencing studies. One of the characteristic properties of cancer cells is that they feature higher rates of mutations due to defective DNA repair from earlier mutations in the proteins that specifically monitor and carry out these repairs.
With hundreds of oncoproteins and tumour suppressor proteins already identified, it is becoming quite apparent that it is specific combinations of loss of function mutations in tumour suppressor genes and gain-of-function mutations in proto-oncogenes that result in progressive cancers. There may be millions, and perhaps billions of possible gene mutation combinations that will suffice to produce full blown cancer. In time, we will be able to identify many of the more frequent mutation combinations that cause cancer in individual patients and match this to the most appropriate drugs for their treatment. How soon this can be attained depends on how effectively cancer research is conducted.
To achieve this objective, so that people world-wide can receive more personalized medicine, families of cancer victims need to understand that they and everyone will benefit from the knowledge learned from their relatives' cancer cells. Tens of thousands of cancer researchers supported with public funding from governments and charitable donors, few of which have personally benefitted financially, have performed detailed biochemicals studies on hundreds of tumour cell lines obtained from cancer patients for over 50 years. HeLa cells are amongst the best characterized of these established cancer cell lines. It is a real shame that the HeLa cell genome sequence will not be broadly accessible to cancer researchers to build on the knowledge base.
The human genome sequences that would probably be the most useful for cancer research initially would be the US National Institutes of Health gold panel of 60 human tumour cell lines along with several hundred additional cancer cell lines that have been actively studied for several decades now. Most of these cell lines have a wealth of associated biochemical and phenotypic data, and can also be used in future studies to investigate the specific roles of intriguing mutations in a reproducible manner.
Link to the original blog post