Lower Cost DNA Sequencing

From physorg.com:

Being able to sequence a human genome for $1,000 or less (which is the price most insurance companies are willing to pay) could open a new era in personal medicine, making it possible to precisely diagnose the cause of many diseases and tailor drugs and treatment procedures to the genetic make-up of an individual.

“Despite the tremendous interest in using nanopores for sequencing DNA, it was unclear how, exactly, nanopores could be used to read the DNA sequence,” said U. of I. physics professor Aleksei Aksimentiev. “We now describe one such method.”

Aksimentiev and collaborators describe the method in a paper accepted for publication in the journal Nano Letters, and posted on the journal’s Web site.

“Through molecular dynamics simulations, we demonstrate that back-and-forth motion of a DNA molecule in a nanopore capacitor 1 nanometer in diameter produces an electrostatic fingerprint that can be used to read the genetic sequence,” said Aksimentiev, who also is a researcher at the Beckman Institute.

New technique could dramatically lower costs of DNA sequencing


Genes linked to suicidal thoughts with anti-depressant


Two gene variations appear frequently in depressed patients who contemplate killing themselves during treatment with a common antidepressant medication, a new study finds.

In the study, reports of suicidal thoughts occurred from 2 to 15 times as often in antidepressant-treated patients with the key gene variations as in patients without them, say psychiatrist Gonzalo Laje of the National Institute of Mental Health in Bethesda, Md., and his colleagues. Participants received citalopram, a widely prescribed antidepressant related to medications such as fluoxetine (Prozac).

The study identifies two crucial genes that contribute to the formation of cell receptors for glutamate, a chemical messenger in the brain that has been implicated in antidepressant effects. Variants of these genes apparently promote suicidal thinking only in depressed people taking antidepressants, the researchers conclude in the October American Journal of Psychiatry.

The researchers took samples of patients' blood and examined variations in the genetic code at 768 sites on 68 genes that possibly contribute to depression.

Further research may also yield a genetic test for the likelihood of antidepressant-treatment success, Weissman says. Only 25 percent of patients in Laje's study who developed suicidal thoughts recovered from depression while taking medication, compared with 42 percent of patients who reported no such thoughts.

Dangerous DNA: Genes linked to suicidal thoughts with med use: Science News Online, Oct. 6, 2007


As Personal Genomics Stands Poised to Go Mainstream, Researchers Urge Caution

In an article published in the upcoming issue of Science, University of Alberta researcher Tim Caulfield and co-authors highlight the need to proceed with caution when it comes to personal genomics projects that represent research milestones but are also fraught with ethical, social and clinical implications.

Scientists predict that within five years DNA sequencing technologies will be affordable enough that personal genomics will be integrated into routine clinical care. Companies are responding by offering their services for ancestry tracing, forensics, nutritional advice and reproductive assistance. It won’t be long before companies are able to offer Facebook-like social networking services centred around our genomes.

Caulfield and his colleagues pose these questions and warn that the routine generation of individual genome sequences will pose challenges to our health-care system. They argue that only clinically meaningful genomic test results should be integrated into medical decision-making—however, this will require clear standards, multidisciplinary collaboration and careful consideration of the ethical, social and clinical implications.

Newswise Medical News | As Personal Genomics Stands Poised to Go Mainstream, Researchers Urge Caution

Computer Program Traces Ancestry Using Anonymous DNA Samples

A group of computer scientists, mathematicians, and biologists from around the world have developed a computer algorithm that can help trace the genetic ancestry of thousands of individuals in minutes, without any prior knowledge of their background. The team’s findings will be published in the September 2007 edition of the journal PLoS Genetics.

Unlike previous computer programs of its kind that require prior knowledge of an individual’s ancestry and background, this new algorithm looks for specific DNA markers known as single nucleotide polymorphisms, or SNPs (pronounced snips), and needs nothing more than a DNA sample in the form of a simple cheek swab. The researchers used genetic data from previous studies to perform and confirm their research, including the new HapMap database, which is working to uncover and map variations in the human genome.

said Petros Drineas, the senior author of the study and assistant professor of computer science at Rensselaer Polytechnic Institute. “The program will be a valuable tool for understanding our genetic ancestry and targeting drugs and other medical treatments because it might be possible that these can affect people of different ancestry in very different ways.”

Although the human genome is 99 percent the same from human to human, it is that 1 percent that can have a major impact on our response to diseases, viruses, medications, and toxins. If researchers can uncover the minute genetic details that set each of us apart, biomedical research and treatments can be better customized for each individual, Drineas said.

Newswise Science News | Computer Program Traces Ancestry Using Anonymous DNA Samples



Genetic Link to Height


The findings, published in the September 2 advance online edition of Nature Genetics, stem from a large-scale effort led by scientists at the Broad Institute of Harvard and MIT, Children’s Hospital Boston, the University of Oxford and Peninsula Medical School, Exeter.

By analyzing DNA from nearly 35,000 people, the researchers zeroed in on a difference in the HMGA2 gene — a ‘C’ written in the DNA code instead of a ‘T’. Inheriting the ‘C’-containing copy of the gene often makes people taller: one copy can add about a half centimeter in height while two copies can add almost a full centimeter.

“Because height is a complex trait, involving a variety of genetic and non-genetic factors, it can teach us valuable lessons about the genetic framework of other complex traits — such as diabetes, cancer and other common human diseases.”said co-senior author Joel Hirschhorn, an associate member of the Broad Institute, a pediatric endocrinologist at Children’s Hospital Boston, and an associate professor of genetics at Harvard Medical School.

Nearly 90% of the variation in height among most human populations can be attributed to DNA. The remainder is due to environmental and lifestyle factors, such as nutrition.

After scrutinizing the initial data, the scientists identified a single letter change — known as a single nucleotide polymorphism or SNP — in the HMGA2 gene as the most promising result.
The genomic find, though, is not the only indication that HMGA2 affects height. Previous studies in mice and humans revealed that a handful of rare stature disorders result from severe mutations in the gene. Taken together, the findings provide strong evidence for a role for HMGA2 in height.

Newswise Science News | Genome Study Shines Light on Genetic Link to Height


Genomics and Insurance

Excerpt from conclusion:

Whatever the outcome of the privacy debate it seems clear that genomics will, in time, transform the insurance market every bit as much as it transforms the practice of medicine. The coming deluge of genetic information will force society to discuss openly the trade-offs, such as how to ration care, that have long been made in the shadows. It may even force the insurance industry to explain why it is allowed to discriminate on the basis of factors such as family medical history, pre-existing conditions and sex that are beyond the control of individuals.


Response by Dr. Jim Kaput of http://nutrigenomics.ucdavis.edu/

However this article does not address the limitations of the current
research on genetic testing and the fact that our lifestyles, and
particularly our nutrient intakes, alter our risk profiles.
Relying only on genetic
testing only, would not provide very accurate data for determining insurance
issues (the data is important, but only as a component, not as the only


Alcohol, Tobacco and Genetics

The researchers investigated the genomic factors underlying alcohol and tobacco use in a cohort of 120 families ...

The researchers used a dense map (three haplotypes per cM; r2>0.4), generated by merging 58000 SNPs (single nucleotide polymorphisms) and 437 microsatellite markers, to identify sex-specific and non-specific linked and associated areas.

Summary of Results
The researchers reported the following results:

using the information from the questionnaires, the researchers found sex differences in prevalence of alcohol (17.3% in females and 38.3% in males) and tobacco (22.2% in females and 28% in males) use

a common locus (an identifiable location on a chromosome) for alcohol and tobacco was found on chromosome (chr) 1. Also on chr 1, in an area believed to be involved with diastolic blood pressure (DBP), they found a locus for smoking.

on chr 3, in the area identified as being involved with pre-math stress DBP, they found a locus for alcohol

on chr 4, inside gene GRID2, researchers found linked and associated SNPs for smoking moreover they found associated SNPs inside these gene for alcohol in males

female-specific candidate SNPs were found inside the HTR2C gene for smoking.

Newswise Medical News | Alcohol, Tobacco and Genetics: "etiology "



Personal Genetics web site and information service startup. Founded by wife of google founder. Google is also an investor.

From the web page:
23andMe is a privately held company developing new ways to help you make sense of your own genetic information

Even though your body contains trillions of copies of your genome, you've likely never read any of it. Our goal is to connect you to the 23 paired volumes of your own genetic blueprint (plus your mitochondrial DNA), bringing you personal insight into ancestry, genealogy, and inherited traits. By connecting you to others, we can also help put your genome into the larger context of human commonality and diversity.

Toward this goal, we are building on recent advances in DNA analysis technologies to enable broad, secure, and private access to trustworthy and accurate individual genetic information. Combined with educational and scientific resources with which to interpret and understand it, your genome will soon become personal in a whole new way.

23andMe, Inc. - Home

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