6 replies to this topic

[ymc]

http://www.nytimes.c...?pagewanted=all

According to this NYT article, by sequencing the genome of your cancer cells and your normal cells and then make comparisons, you can find out exactly what type of cancer you have (cancers should be defined by their gene mutations instead of where they originate). Then if it happens that there is a drug that can target that specific mutation, then you can put cancer into remission as long as you keep taking that drug.

In the article, a medical researcher found that he had a certain type of leukemia. His colleagues found that his FLT3 gene has strange mutations and then they confirmed that it is indeed way overexpressed in his cancer cells. Then his colleagues found that a certain kidney cancer drug can inhibit FLT3. By taking this drug, the medical researcher's leukemia is in remission ever since.

I happen to have developed a pipeline to call mutations using publicly available software plus some of my custom programs. If you or your loved ones are interested in trying this, you can follow the following steps:

1. Find a service provider who is willing to do whole genome sequencing or exome sequencing (preferred because WGS will be too much data). For example, BGI is willing to do two sets of whole genome sequencing for US$10,000 and two sets of exome sequencing for US$4,000. Turn around time approximately two months.

2. Find a oncologist who is willing to extract the cancer cells and normal cells for you. Ideally he/she should also help you to follow up after receving the result of my analysis.

3. Send the sequences to me (ie the fastq files) and then I can analyze the data for you for free (may charge a fee if too many people are interested). Then I will send you back the suspected mutations.

4. Your oncologist should then check to see if certain gene is overexpressed. If you are lucky, there are some existing drugs that target your gene, then congratulations! Otherwise, keep the gene in mind and wait for drugs to develop or participate in current/future clinical trials.

If you are interested, you can PM me and we can discuss what to do.

Have a great day!

[ymc]

Oops... After reading the comment section of the article, people in the know said that genome sequencing revealed no mutations in the FLT3 gene for the medical researcher. They then did another round of RNA Sequencing (sequence all the RNAs expressed in the cancer cells and normal cells) to find FLT3 overexpressed. I don't have a pipeline for this now. But I understand the concept and should have no problem doing this.

For people who are interested, ideally you should do both exome sequencing and RNA sequencing. But if cost is a concern, you can do RNA sequencing first. If nothing abnormal is found, then you can try whole genome/exome sequencing.

I don't know the cost of RNA sequencing. I presume it should be similar to exome sequencing, ie US$4000 for two sets.

[ymc]

http://www.nytimes.c...ml?pagewanted=1

A failed case from the same series of reporting. I noticed that in this case, they didn't do RNA sequencing. To my surprise, even when they did the second round of sequencing after cancer recur, they still didn't do RNA sequencing. I think in cancer treatment, RNA sequencing is more important than DNA sequencing because:

1. Gene expression is closer to what's actually happening in our cells. Due to yet unclear mechanisms, different cells express genes differently. Just looking at the DNA sequence only won't tell us anything about what's going on in the cancer cell.
2. We still don't know the effect of the majority of DNA mutations. There are software to predict functions but they are still not useful now. I presume these software can improve when we know more about protein folding as well as promoter mechanisms.
3. Short read sequencing method is not good in finding structural variations (ie big insertion/deletion/translocation) in the genome. But cancer cells usually have large structural variations and they affect gene expression level greatly.

Edited by ymc, 12 July 2012 - 01:19 AM.

[ymc]

A comprehensive description of how this might work is detailed in a pilot study conducted by U of Michigan Medical School

https://docs.google....koA5pFmxwotE6gQ

[ymc]

View on Vimeo.

A great talk from a UCSF research on Targeted Cocktail Therapy. He thinks we are on the verge of curing cancer or making it a chronic disease like AIDS by using a cocktail of Targeted Therapy drugs.

[Multivitz]

Why not change the terrain of the cells so thier gene expression reflexs that terrain, a negative ion environment is healthy and helps elminate the cancer causes in the first place. The drug ultererd gene changes back after time anyway so whats the point lol. Gene therapy doesn't work thats why its taking many years to come to fruit. Just check the investment for projects that were on the cutting edge of the lunacy! Even cysticfibrosis can be cured and the condition was said to be genetic! As the patient gets better thier genes change expression! Better late than never?

[Multivitz]

Gene therapy, " we've nearly got the cure for you", "please, we had such a massive investments at the start to prove it was the best think to help humanity, give us a little longer please", " Oh by the way we've finally realised that the cell is controlled by it membrane, but we learnt alot of things with the money like, how to get a goat to make loads of silk, what genes to target bio weapons at, and loads of genes related to conditions that are curable but we keep telling everyone its just inside them, their weak ass genes, and only our drugs have the answer.....", " ANYONE who reputes our lies will be treated with a whole host of resistance from our brainwashed followers ", " we know you can remove a nucleus from a human cell and it keeps living normally for 3 months doing its job fine, responding fine, but.......", " all this comes from the same crowd who landed a man in a studio.....sorry I meant the moon, landed in the moon, doh, look, you know what I mean.....you don't?" Oh dear, that Mars probe looks fishy, and the ISS coverage was incredibly obvious, dismissed those as well. Dear oh dear. Come on, you wouldn't waste your time believing all this.......afraid you'll look silly in front of ya mum when you tell her your getting bulled by your self and some man said drink your own wee...     Start drinking from the fountain of youth , your urine turns the distilled water after a few days, you didn't know that did you. It only works on people who have had a comprehensive detox, but the next best thing is distilled water, natrually its -1 so it forms micro structures around membranes and binds to inorganic materials. Notice when left for days no hydrogen bubbles apear in it's container mmmm intresting. But NO I'm special thats how I feel, I want something that has taken LOADS of money to make, I want it CHEAP, its got to have a sexy name thats catchy, NO the cure has to work with just 1 pill, YES I don't mind some side effects as long as I can never comprehend the causes, I'm now begging for it please, please, is it better than the last one mmmmm tell me more, can my cat take it as a suppository....NO...I don't want it then, what else you got? Man.... I gotta go to my Doc's I think I've got a drug deficiency, my fugus needs feeding!