Topol on Genomics
Blog Address: http://blogs.medscape.com/topolongenomics
February 20, 2013

Key Issues in Genome Sequencing of Healthy Individuals

I briefly review 3 important articles that recently appeared, each touching on important controversies in the use of whole genome sequencing:

1. Should Healthy People Have Their Genomes Sequenced At This Time? Wall Street Journal, February 15, 2013.
2. A Genetic Code for Genius? Wall Street Journal, February 15, 2013.
3. Francke U, Djamco C, Kiefer AK, et al. Dealing with the unexpected: consumer responses to direct-access BRCA mutation testing. PeerJ. 2012;1:e8. DOI 10.7717/peerj.8

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Below is a transcript of Dr. Topol's post "Key Issues in Genome Sequencing of Healthy Individuals." We look forward to your feedback.

Welcome to another segment on genomic medicine. Today, I want to get in...

14 Comments
Posted By: Eric Topol  

January 9, 2013

Goodbye Amniocentesis, Hello Fetal Whole Genome Sequencing...Now What?

In this segment, I review the remarkable progress in the past 2 years for fetal DNA analysis through 4 major publications:

1. Lo YM, et al. Sci Transl Med. 2010 Dec 8;2(61):61ra91.

2. Kitzman JO, et al. Sci Transl Med. 2012 Jun 6;4(137):137ra76.

3. Fan HC, et al. Nature.2012 Jul 19;487(7407):320-324.

4. Wapner RJ, et al. N Engl J Me...

13 Comments
Posted By: Eric Topol  

December 14, 2012

Getting My Whole Genome Sequence

In this segment, I describe the experience of seeing the 3.3 million variants in my genome compared with the 3 billion bases in the reference human genome on my iPad via the 99-cent "My Genome" app. This comes after participating on the faculty at Illumina's inaugural "Understanding My Genome" conference and is of particular interest considering a review paper we just published on the role of p...

20 Comments
Posted By: Eric Topol  

November 25, 2012

A New, Major Rare Susceptibility Variant for Alzheimer's Disease

Two papers in the November 14, 2012, issue of the New England Journal of Medicine report on TREM2 varaints, and particularly R47H, which is linked to a 3-fold risk for Alzheimer's disease. Here, I discuss the implications of this new finding -- the first major one since the discovery of APOE4 for this condition -- with respect to both Alzheimer's disease and rare sequ...

2 Comments
Posted By: Eric Topol  

October 17, 2012

De Novo Mutations and the Implications for the Father's Biological Clock

Multiple papers recently published have documented links between de novo mutations and autism, schizophrenia, and intellectual disability. Here, I review the topic and raise some of the key questions on this issue going forward.

References:
- Kong A, et al. Rate of de novo mutations and the importance of father's age to disease risk. Nature. 2012;488:471-475.

3 Comments
Posted By: Eric Topol  

September 11, 2012

Decoding the Massive Dataset From the ENCODE Project

The Encyclopedia of DNA Elements (ENCODE) international study group published 35 papers on September 6-7, 2012, in Nature, Science, Genome Biology, and Genome Research. Here, I try to review the salient findings from that large body of work, with an emphasis on moving from genes to the genome, of appreciating long-range genome interactions, switches and circu...

4 Comments
Posted By: Eric Topol  

August 17, 2012

A Big Barrier to Cancer Genomic Sequencing

Recent studies, as well as a 3-part series in The New York Times, have highlighted the potential value of whole genome or exome sequencing to precisely guide therapy for patients with cancer. However, almost all samples today go into formalin fixe...

21 Comments
Posted By: Eric Topol  

July 12, 2012

Modifier Genes to Protect From Alzheimer's Disease, Serious Infection in Cystic Fibrosis

Two recent articles that use sequencing to find protective or modifier gene variants serve as great examples of advancing the understanding of the biology of these diseases....and may lead to new treatments, prevention.

References
- Jonsson T, et al. A mutation in APP protects against Alzheimer's disease and age-related cognitive decline. Nature. 2012 Jul 11. [Epub ahead o...

5 Comments
Posted By: Eric Topol  

June 10, 2012

Free Circulating DNA in the Blood to Provide Whole-Genome Sequence of a Fetus or Track Cancer

Two recent papers in Science Translational Medicine leverage remarkable information that can be derived from circulating free DNA in the blood. A group from Cambridge used targged-amplicon sequencing (TAM-Seq) to track speciic mutations in patients with ovarian and breast cancer, while a University of Washington group analyzed maternally derived fetal DNA from two parent-fetus trios to...

3 Comments
Posted By: Eric Topol  

May 14, 2012

Will Whole Genome Sequencing Predict Susceptibility to Illness?

A recent paper by a group from Johns Hopkins published in Science Translational Medicine evoked considerable interest with the disappointing results...what were they and what does this mean?

References:
- Roberts NJ, et al. The predictive capacity of personal genome sequencing. Sci Transl Med. 2012;4:133ra58
- Kohane I, Shendure J. What's a genome worth? ...

12 Comments
Posted By: Eric Topol  

 
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About This Blog

Disclosure: Eric J. Topol, MD, has disclosed he is on the scientific advisory board of Gilead Sciences and an advisor to Quest Diagnostics.

  • Eric Topol

    Director of the Scripps Translational Science Institute and Chief Academic Officer for Scripps Health. Professor of Genomics at The Scripps Research Institute and fully active clinically as a cardiologist at Scripps Clinic. Elected to the Institute of Medicine of the National Academy of Sciences, and voted the #1 Most Influential Physician Executive in the United States for 2012 in a poll conducted by Modern Healthcare. Author, Creative Destruction of Medicine.

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