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A broken watch and deCode's test

Posted Oct 14 2008 12:01pm
I am posting today away from home. In case you didn't know, my family is a BRCA family and a wonderful lady who was hit with not one but 2 breast cancers and metastases just passed.

I am sad today. But even with that, I am bolstered by the amount of work being done in this field. Soon we will have tests which can identify risk for non BRCA breast cancer. But that day is not today.

Why? I just finished looking over some more of the SNPs which deCode is testing for....

rs1219648 the SNP associated with FGFR2 and Breast Cancer. Published in the "Highly respected" Nature Genetics!!!

1. Populations-1142 European/Caucasian with postmenopausal breast cancer
2. Penetrance- unk, but OR was 1.23 and for Hmz 1.79
3. Function- unk, but could be a splice site variation.
4. Prevalence- Not reported here.

There was another study in Jewish (Ashkenazi and Sephardic) and Arab women......about time
Here's why it gets confusing. They cover these SNPs as a haplotype study. What's a haplotype? A subset of SNPs that are linked together. In this case, the AAGT haplotype and the AAAC haplotype. The wildtype is GGAC.You see it turns out in the AAAC haplotype puts Sephardic women at increased risk for breast cancer, but not Ashkenazi Jews.It actually reduces risk in the Ashkenazi population!!! Huh?

I hope you see what I am getting at.

"Each of the genetic markers in this risk test have been replicated in between 5 and 30 different populations in studies bydeCODE genetics, theNational Cancer Institute, andUK Cancer Research."

Dr Gulcher's words, not mine.

That is just not true. Some of these SNPs are protective in some and risk creating in others. That data has NOT been replicated in truth. But, if you mean replicated in the same study........then you could stretch that to maybe 5 populations. But when you say population, do you mean the few hundred women from the US Multi-Ethnic Cohort that was lumped in with the Swedes? This is the frustration I have and why I startedHelixGene.

The days of silver tongued scientific shenanigans are over. I will personally read every study I can about each test and report turthfully and give clinical meaning to each study. I hope you willjoin me.

We have very few tools to assess risk properly in breast cancer care. But we should not put a tool in the chest which will not get the job done and that could result in improper guidance or significant medical misinformation. Clinical tools require much more refinement than one or 2 studies published in NEJM.

The Sherpa Says: Perlegen is also developing a breast cancer test. I hope they get the data before bringing a test to market. Here's a riddle, what does a broken watch and 2 of the SNPs from the deCode test have in common? Answer: They are both right, twice a day......
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