Razib Khan One-stop-shopping for all of my content

June 28, 2018

Have your exome sequenced for $29.99

Filed under: DNA,Genetics,sales,science — Razib Khan @ 9:11 pm

Just a reminder that for the rest June Helix DNA kits with the cost of an Insitome app. Buy Regional Ancestry, Metabolism, or Neanderthal, and start your lifelong DNA journey with Helix for just $29.99! A great gift idea.

That means for the cost of an app Helix will sequence more 30 million markers in your genome. In contrast, rival genotyping companies only look at 500,000 to 1,000,000 markers.

Cost of use: FREE

The 30 million markers Helix sequences include your whole exome. The part of your genome which is involved in coding for proteins, and so impact your appearance and function. The Helix system also includes markers outside of the exome to further map your genome more effectively.

Insitome’s apps, whether it be Regional Ancestry, Metabolism, or Neanderthal are windows into the whole landscape of modern day personal genomics. Once Helix sequences you the data is banked for later use.

When new apps are developed on the Helix platform, your future purchases will only include the cost of the app! Entering the ecosystem now means that you will never have to pay the initial cost of the sequencing kit.

What are you waiting for? Get the Helix DNA kit and jump into the ecosystem now!

Have your exome sequenced for $29.99 was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

April 25, 2018

DNA, from genetics to genomics

Filed under: DNA,Genetics,Genomics,science — Razib Khan @ 11:59 am

In the early 1950s scientists established that the molecular structure of DNA was a double helix. The had discovered the physical substrate of heredity. With this discovery the field of molecular genetics was born (and eventually a Nobel Prize given!).

And yet we also know that Gregor Mendel discovered the laws of heredity, the “law of segregation” and the “law of independent assortment”, nearly a century before the discovery of DNA.

It was literally the product of a garden.

The mature field of genetics itself developed fifty years before the discovery of the structure of DNA, as a host of scientists stumbled upon Mendelian insights simultaneously. Most were biologists who worked with plants, flies, or even algebra — no need for a powerful microscope or structural models of molecules.

Though DNA has been the key to many of the discoveries of the past fifty years, it is important to remember that the field of genetics is predicated on an abstract understanding of how inheritance works across pedigrees, as opposed to the biophysical basis of that transmission. Before DNA, before chromosomes, what Mendel and his heirs understood is that inheritance occurs through a process where discrete units of heredity, “genes”, are passed down from generation to generation.

These genes usually come in two copies, ‘alleles,’ for many organisms.

Recessive expression patterns of a trait, where parents do not express a characteristic found in their offspring, becomes comprehensible when a Mendelian model is adopted. Prior to this many had an intuitive “blending” understanding of inheritance, where the characteristics of the parents mixed together to produce offspring. The ultimate problem with blending inheritance is that it had difficulty in explaining how variation persisted over time. A problem solved by the Mendelian insight that genetic variation never disappeared…it simply rearranged itself every generation!

Genetics was born on the backs of Drosophila

Between the reemergence of Mendelian thought around 1900 and the discovery of DNA in the 1950s much research occurred in the field of genetics. The Neo-Darwinian Synthesis built upon the mathematical foundations of population genetics, which took the Mendelian framework and formalized and extended them, to create a model of evolutionary biology for the 20th century. Medical geneticists began to understand the patterns of inheritance of rare diseases in humans with the aim of preventing illness. Those researchers working with fruit flies discovered many of the phenomena which define modern genetics, such as recombination. Finally, biochemists established that heredity and nucleic acids were intimately connected.

Just as an understanding of the discrete basis of inheritance in a Mendelian framework opened up the systematic scientific study of heredity, so the understanding of the double helical structure of DNA paved the way for the molecular revolution of the second half of the 20th century, and the genomic revolution of the 21st. An understanding of DNA as the mode of inheritance allowed for the development of techniques that traced transmission of variation at the level of genes themselves, as opposed to expressed traits.

Illumina sequencing machine

And while in the 20th century we spoke of genetics, and specific genes, today we speak of genomes and the whole set of genes organisms possess. That revolution can not be understood without the knowledge of DNA as the mode of inheritance. If classical Mendelian genetics is pattern recognition across pedigrees, 21st century genomics is a synthesis of classical genetics, post-DNA era biophysics, and cutting-edge computing. Genomics is as much engineering as it is science; and “big data” as much as information theory.

The understanding of DNA created the world where genetics transformed itself from an esoteric science of probabilities, to a mass market product of possibilities.

Classical genetics tells you that your relatedness to your brother or sister is expected to be 0.50. Modern genomics might tell you that your relatedness to your brother or sister is shared across 46.24% of your genome. A fuzzy probability becomes a crisp reality. As a science, genetics can be imagined without DNA. It was born and matured decades before we understood the importance of the double helix, but as a part of our lives, one can’t imagine genetics without DNA.

Learn more about where your traits for food tolerance fall on the spectrum and explore your Metabolism story today.

DNA, from genetics to genomics was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

April 10, 2012

DNA Replication

Filed under: Biology,DNA — Razib Khan @ 3:37 am

Most of you have probably seen this stylized graphic somewhere along the away (I think it was on PBS at some point). But it’s still cool….

May 2, 2011

Osama bin Laden and the DNA match

Filed under: DNA,Genetics,Genomics,Osama bin Laden — Razib Khan @ 4:10 pm

How they determine Osama bin Laden really is Osama bin Laden:

Once samples from all sources are in hand, analysts isolate a bit of DNA from each sample, make lots of copies of it, and then process the copies through a machine that analyzes genetic markers — DNA fingerprints — that have been passed down through a subject’s family. Typically, Bieber said, DNA tests examine around 15 of these markers.

It typically takes several hours to complete each step of the analysis process, Bieber said, though he noted that in high-profile cases like this one, law enforcement agencies might already have genetic profiles of the relatives available — which means they’d only have to complete one additional test.

I checked and it seems that there are paternity testing outfits that offer one day turnaround. So I guess it’s not implausible that they could have pulled this off. I assume they still use variable number tandem repeats for DNA profiling?

Update: Yeah, short tandem repeats.

July 8, 2010

To catch a predator: familial DNA

Filed under: crime,Culture,DNA,DNA fingerprinting — Razib Khan @ 9:51 pm

I already blogged this general issue, but the ‘grim sleeper’ murderer was caught because of a match of old samples with those of us his son. If I had to bet money I think this sort of result (California and Colorado are the two American states which have a system in place to allow for this) is going to allow for a push toward more widespread usage of the technique. It may be that we need to stop talking about privacy as if we can put off the inevitable future, and start talking about accuracy and precision with the data that is going to be easily available to authorities. By the way, I found this objection somewhat strange:

“I can imagine lots of African-American families would think it is not fair to put a disproportionate number of black families under permanent genetic surveillance,” said Jeffrey Rosen, a law professor at George Washington University who has written about this issue.

A disproportionate number of black families have relatives incarcerated. The American public does not seem particular worried about that. As I noted before, criminal behavior is not randomly distributed across families. Rather, there are distinct clusters, so familial genetic data is going to be more efficacious than you would expect if the commission of crime consisted of a sequence of independent events.

I have to add that worries about this technology strike me as a bit rich, in light of the fact that methods which are proven to be highly subjective and often inaccurate, such as fingerprinting and eyewitness identification, are accepted in the criminal justice system. I worry about what the state could do with DNA data if the state became malevolent, but despite its flaws it seems to me far preferable as a means of assessing evidence than some of the “tried & true” techniques. So let’s keep some perspective.

November 30, 2009

“Old Europe”

Filed under: DNA — Razib @ 9:43 pm

A Lost European Culture, Pulled From Obscurity:

The little-known culture is being rescued from obscurity in an exhibition, “The Lost World of Old Europe: the Danube Valley, 5000-3500 B.C.,” which opened last month at the Institute for the Study of the Ancient World at New York University. More than 250 artifacts from museums in Bulgaria, Moldova and Romania are on display for the first time in the United States. The show will run through April 25.

At its peak, around 4500 B.C., said David W. Anthony, the exhibition’s guest curator, “Old Europe was among the most sophisticated and technologically advanced places in the world” and was developing “many of the political, technological and ideological signs of civilization.”

The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World is a very interesting book. One of the problems with pre-literate civilizations is that they’re only accessible via archaeology, which is a field averse to system-building or theorizing. But it is likely from what we know of pre-literate cultures which Europeans encountered that lots of stuff happened. Perhaps ancient DNA will help resolve some of these questions, at least establishing whether peoples or just pots were on the move.

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