Author Topic: Gene typing, for free  (Read 4431 times)

Tom Bri

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Gene typing, for free
« on: September 19, 2016, 12:33:48 AM »
http://genesforgood.sph.umich.edu/

If you have considered getting your genes typed, for example for an ancestry match, this U of Michigan program will do what 23&Me charges $1000 for, but for free.
Free, except you have to spend a few hours answering their survey questions and taking an IQ test.

You answer the questions, they mail you a 'spit kit' which you spit into and mail back. A few weeks later you get your gene map.
I started the process about 2 weeks ago, and just mailed the spit kit back a few days ago.

MVal

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Re: Gene typing, for free
« Reply #1 on: September 19, 2016, 08:01:29 AM »
Wow, cool! Maybe I will try it.

CowboyAndIndian

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Re: Gene typing, for free
« Reply #2 on: September 19, 2016, 10:47:27 AM »
Thanks, just did the tests. Waiting for the spit kit.

nobodyspecial

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Re: Gene typing, for free
« Reply #3 on: September 21, 2016, 07:13:46 AM »

Dulcimina

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Re: Gene typing, for free
« Reply #4 on: September 21, 2016, 07:35:55 AM »
http://genesforgood.sph.umich.edu/

If you have considered getting your genes typed, for example for an ancestry match, this U of Michigan program will do what 23&Me charges $1000 for, but for free.
Free, except you have to spend a few hours answering their survey questions and taking an IQ test.

You answer the questions, they mail you a 'spit kit' which you spit into and mail back. A few weeks later you get your gene map.
I started the process about 2 weeks ago, and just mailed the spit kit back a few days ago.

I thought 23&me only charges $199.

Jack

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Re: Gene typing, for free
« Reply #5 on: September 21, 2016, 09:23:33 AM »
I've seen too much sci-fi (e.g. Gattaca) to be super enthusiastic about stuff like this.

nobodyspecial

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Re: Gene typing, for free
« Reply #6 on: September 21, 2016, 09:34:15 AM »
I've seen too much sci-fi (e.g. Gattaca) to be super enthusiastic about stuff like this.
I think the umich one is part of a study to identify a gene for believing conspiracy theories.

Guses

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Re: Gene typing, for free
« Reply #7 on: September 21, 2016, 09:59:51 AM »
They must use your gene data to build massive gene banks for identifying biomarkers and predictor genes. I would be fine with an arrangement like that.

Thanks for posting, I will see if I am eligible.

------------- Edit

Nope, not eligible. You need to live in the US.

« Last Edit: September 21, 2016, 10:09:06 AM by Guses »

nobodyspecial

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Re: Gene typing, for free
« Reply #8 on: September 21, 2016, 10:18:57 AM »
They must use your gene data to build massive gene banks for identifying biomarkers and predictor genes. I would be fine with an arrangement like that.

Nope, not eligible. You need to live in the US.
Ironically I think 23&me is only legal in Canada.

ps. I miss-read your post as predator genes. I thought homeland security is getting really paranoid of they are looking for invisible hidden aliens among us.

Guses

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Re: Gene typing, for free
« Reply #9 on: September 21, 2016, 11:20:50 AM »
They must use your gene data to build massive gene banks for identifying biomarkers and predictor genes. I would be fine with an arrangement like that.

Nope, not eligible. You need to live in the US.
Ironically I think 23&me is only legal in Canada.

ps. I miss-read your post as predator genes. I thought homeland security is getting really paranoid of they are looking for invisible hidden aliens among us.

Pfft. Good luck getting a DNA sample from a Predator that isn't already contaminated by ceramic. Even if you catch one, chances are it will blow itself up, goodbye sample!

That is besides the point though, everyone knows you need IR vision to spot a predator.

Tom Bri

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Re: Gene typing, for free
« Reply #10 on: September 21, 2016, 08:33:17 PM »
http://genesforgood.sph.umich.edu/

If you have considered getting your genes typed, for example for an ancestry match, this U of Michigan program will do what 23&Me charges $1000 for, but for free.
Free, except you have to spend a few hours answering their survey questions and taking an IQ test.

You answer the questions, they mail you a 'spit kit' which you spit into and mail back. A few weeks later you get your gene map.
I started the process about 2 weeks ago, and just mailed the spit kit back a few days ago.

I thought 23&me only charges $199.

If so, that is a huge drop in price from a year or two ago. Good news, but this is even cheaper, for what appears to be similar services.

By the way, I got notification that my spit kit is at the lab.

sol

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Re: Gene typing, for free
« Reply #11 on: September 21, 2016, 10:28:28 PM »
If so, that is a huge drop in price from a year or two ago.

How do you figure?  23andMe used to be $99, then there was this big uproar when they doubled the price to $199 last year.

Tom Bri

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Re: Gene typing, for free
« Reply #12 on: September 22, 2016, 01:05:25 AM »
If so, that is a huge drop in price from a year or two ago.

How do you figure?  23andMe used to be $99, then there was this big uproar when they doubled the price to $199 last year.

Because I don't closely follow the prices of services I don't use. Apparently my info is years out of date.

okobrien

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Re: Gene typing, for free
« Reply #13 on: December 10, 2016, 11:29:53 AM »
So after reading this thread to my wife, she decided to use genes for good to find out her genetic makeup.  She estimates that the surveys took over 5 hours to complete in total.  We got the results today to find...She is 100% European!  That is right, they don't go into any more detail than the specific continent your ancestors are from.  So after all that, I found out I married a white woman.  I would have never guessed.

sol

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Re: Gene typing, for free
« Reply #14 on: December 10, 2016, 02:32:45 PM »
We got the results today to find...She is 100% European!  That is right, they don't go into any more detail than the specific continent your ancestors are from.  So after all that, I found out I married a white woman.  I would have never guessed.

Well that kind of sucks. 

If it matters to you, the 23andme service gives you significantly more detail than that.  For example, I am also white but they told me that my gene markers suggest I am 40.1% northwestern European (broken down as 34.3 British and Irish, 13.6% French and German, 2.2% Scandanavian).  Also similar breakdowns for the southwestern and eastern European percentages, and a basically meaningless breakdowns for the 0.2 African and 0.2% Asian and Native American in my genome.

For each of those categories, they give you the sections of each chromosome that correspond with the identification.  So for example, my chromosome 9 is basically 100% British/Irish.  The only segments of my genome identified as African are on chromosomes 5 and 10.  They have a ton of information about how they make these identifications, including the sizes of the reference populations they use to make these determinations and maps that show you how strongly each identifier is associated with a particular geographic region.  You can easily spend days reading about yourself, if you're interested.  Some overview description of their methodology from their public website:  https://www.23andme.com/ancestry-composition-guide/

They also give you some information about your maternal and paternal heritage, but this stuff is much more powerful if you have other people in your family also use their service.  For example, they could tell me where my maternal and paternal haplogroups are from, which is basically where my paternal grandfather's paternal grandfather and my maternal grandmother's maternal grandmother are from.  Because I have a female cousin who has used their service, I also know where my paternal grandmother is from, since her mom inherited my grandmother's haplogroup.  But I have no genetic information about where my maternal grandfather is from, and I never will unless his son (my uncle) or his son's son (my cousin) signs up.

This stuff makes more sense with pictures, but basically you can only get reliable information about the origin of two different people in your ancestry, your father's unbroken line of sons and your mother's unbroken line of daughters.  My only biological child is a daughter, so that paternal line ends with me unless my little brother ever has a son.

There's a ton more info in there related to your physical self.  They can identify your hair color and eye color, for example, and a bunch of other random stuff like whether or not you appear to have the common mutations for things like lactose intolerance, a cleft chin, male pattern baldness, or freckles. 

The controversial stuff, though, for which they got into legal trouble, was identifying which markers you have that published research has correlated with specific health problems, like breast cancer, alzheimers, and parkinsons.  The FDA freaked when they learned that people were making health decisions for themselves based on their genetic makeup, without those genetic tests getting FDA approval as diagnostic tools. 

They used to give everyone a risk percentage, in the context of the overall risk percentage, for each disease.  So for example the average risk of prostate cancer in men is 17.8%, so if your markers suggest your personal risk is higher or lower than that, they would tell you your apparent risk percentage (the percentage of people with your genome who get prostate cancer) and the ratio of that percent to 17.8%, so you can see how much more/less likely than average you are.  All of this was provided with relative confidence levels links to the peer-reviewed journal articles describing the correlations for each marker, for people who really wanted to dig into the details. 

So for example, they're pretty certain I'm never going to develop a biological gluten intolerance.  Celiac disease is well studied, it has well known genetic markers, and I don't have any of them.  By contrast, they think there's a small chance that might have an elevated risk of male infertility, but the research isn't very conclusive on the correlations between the markers and actual infertility, and I don't have all the markers anyway.  For the record, I don't have celiac disease and I'm not infertile. 

The reason I got tested in the first place was that we were having a baby, and we have friends who inadvertently gave their children a crippling inherited genetic disorder because they had no idea they were both recessive carriers.  23andme is just one of many services that screen new parents, but this sort of testing is a relatively new thing.  They check for things like cystic fibrosis, BRCA, phenylketonuria, and Tay-Sachs.  That part, at least, I recommend for anyone considering reproducing. 

VladTheImpaler

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Re: Gene typing, for free
« Reply #15 on: December 10, 2016, 03:05:02 PM »
We got the results today to find...She is 100% European!  That is right, they don't go into any more detail than the specific continent your ancestors are from.  So after all that, I found out I married a white woman.  I would have never guessed.

Well that kind of sucks. 

If it matters to you, the 23andme service gives you significantly more detail than that.  For example, I am also white but they told me that my gene markers suggest I am 40.1% northwestern European (broken down as 34.3 British and Irish, 13.6% French and German, 2.2% Scandanavian).  Also similar breakdowns for the southwestern and eastern European percentages, and a basically meaningless breakdowns for the 0.2 African and 0.2% Asian and Native American in my genome.

For each of those categories, they give you the sections of each chromosome that correspond with the identification.  So for example, my chromosome 9 is basically 100% British/Irish.  The only segments of my genome identified as African are on chromosomes 5 and 10.  They have a ton of information about how they make these identifications, including the sizes of the reference populations they use to make these determinations and maps that show you how strongly each identifier is associated with a particular geographic region.  You can easily spend days reading about yourself, if you're interested.  Some overview description of their methodology from their public website:  https://www.23andme.com/ancestry-composition-guide/

They also give you some information about your maternal and paternal heritage, but this stuff is much more powerful if you have other people in your family also use their service.  For example, they could tell me where my maternal and paternal haplogroups are from, which is basically where my paternal grandfather's paternal grandfather and my maternal grandmother's maternal grandmother are from.  Because I have a female cousin who has used their service, I also know where my paternal grandmother is from, since her mom inherited my grandmother's haplogroup.  But I have no genetic information about where my maternal grandfather is from, and I never will unless his son (my uncle) or his son's son (my cousin) signs up.

This stuff makes more sense with pictures, but basically you can only get reliable information about the origin of two different people in your ancestry, your father's unbroken line of sons and your mother's unbroken line of daughters.  My only biological child is a daughter, so that paternal line ends with me unless my little brother ever has a son.

There's a ton more info in there related to your physical self.  They can identify your hair color and eye color, for example, and a bunch of other random stuff like whether or not you appear to have the common mutations for things like lactose intolerance, a cleft chin, male pattern baldness, or freckles. 

The controversial stuff, though, for which they got into legal trouble, was identifying which markers you have that published research has correlated with specific health problems, like breast cancer, alzheimers, and parkinsons.  The FDA freaked when they learned that people were making health decisions for themselves based on their genetic makeup, without those genetic tests getting FDA approval as diagnostic tools. 

They used to give everyone a risk percentage, in the context of the overall risk percentage, for each disease.  So for example the average risk of prostate cancer in men is 17.8%, so if your markers suggest your personal risk is higher or lower than that, they would tell you your apparent risk percentage (the percentage of people with your genome who get prostate cancer) and the ratio of that percent to 17.8%, so you can see how much more/less likely than average you are.  All of this was provided with relative confidence levels links to the peer-reviewed journal articles describing the correlations for each marker, for people who really wanted to dig into the details. 

So for example, they're pretty certain I'm never going to develop a biological gluten intolerance.  Celiac disease is well studied, it has well known genetic markers, and I don't have any of them.  By contrast, they think there's a small chance that might have an elevated risk of male infertility, but the research isn't very conclusive on the correlations between the markers and actual infertility, and I don't have all the markers anyway.  For the record, I don't have celiac disease and I'm not infertile. 

The reason I got tested in the first place was that we were having a baby, and we have friends who inadvertently gave their children a crippling inherited genetic disorder because they had no idea they were both recessive carriers.  23andme is just one of many services that screen new parents, but this sort of testing is a relatively new thing.  They check for things like cystic fibrosis, BRCA, phenylketonuria, and Tay-Sachs.  That part, at least, I recommend for anyone considering reproducing.

Upon obtaining a copy of Sol's DNA results I confirmed the conspiracy:
100% various LATINO

Caught ya again Sol!!

Roots&Wings

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Re: Gene typing, for free
« Reply #16 on: December 14, 2016, 05:46:59 AM »
So after reading this thread to my wife, she decided to use genes for good to find out her genetic makeup.  She estimates that the surveys took over 5 hours to complete in total.  We got the results today to find...She is 100% European!  That is right, they don't go into any more detail than the specific continent your ancestors are from.  So after all that, I found out I married a white woman.  I would have never guessed.

I also was pretty disappointed with the 100% European result. But wrote to Genes for Good asking about how to get more detailed ancestry results.

You can upload the 23andme file from your raw genetic data zip file to gedmatch.com (upload instructions here) to get detailed ancestry results for free. Overview of how to interpret your ancestry in gedmatch here. That's what I did. It was pretty interesting.

Also going to upload the raw genetic data and play around with Stanford's free Interpretome for the health indicators.

If anyone has other free resources, I'd be curious to know.
« Last Edit: December 14, 2016, 06:24:07 AM by step-in-time »

okobrien

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Re: Gene typing, for free
« Reply #17 on: December 15, 2016, 07:35:27 PM »
So after reading this thread to my wife, she decided to use genes for good to find out her genetic makeup.  She estimates that the surveys took over 5 hours to complete in total.  We got the results today to find...She is 100% European!  That is right, they don't go into any more detail than the specific continent your ancestors are from.  So after all that, I found out I married a white woman.  I would have never guessed.

I also was pretty disappointed with the 100% European result. But wrote to Genes for Good asking about how to get more detailed ancestry results.

You can upload the 23andme file from your raw genetic data zip file to gedmatch.com (upload instructions here) to get detailed ancestry results for free. Overview of how to interpret your ancestry in gedmatch here. That's what I did. It was pretty interesting.

Also going to upload the raw genetic data and play around with Stanford's free Interpretome for the health indicators.

If anyone has other free resources, I'd be curious to know.

This is great to know, Thanks!  I will share this with my wife and see what we get.

CowboyAndIndian

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Re: Gene typing, for free
« Reply #18 on: December 16, 2016, 06:26:57 AM »
[quote author=step-in-time link=topic=61620.msg1340430#msg1340430 date=1481719619
You can upload the 23andme file from your raw genetic data zip file to gedmatch.com (upload instructions here) to get detailed ancestry results for free. Overview of how to interpret your ancestry in gedmatch here. That's what I did. It was pretty interesting.

Also going to upload the raw genetic data and play around with Stanford's free Interpretome for the health indicators.
[/quote]

Does Genes for Good give the raw genetic data?

Roots&Wings

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Re: Gene typing, for free
« Reply #19 on: December 16, 2016, 07:44:13 AM »
Does Genes for Good give the raw genetic data?

Yep! You can download a massive 245 MB file with your raw genetic data.

The entire Genes for Good process, from completing the online health surveys (~5 hrs over 1 week), to receiving the spit kit, and their lab processing the results, for me took about 2.5 months. It wasn't fast :)
« Last Edit: December 16, 2016, 07:48:13 AM by step-in-time »

CowboyAndIndian

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Re: Gene typing, for free
« Reply #20 on: December 16, 2016, 07:50:55 AM »
Does Genes for Good give the raw genetic data?

Yep! You can download a massive 245 MB file with your raw genetic data.

The entire Genes for Good process, from completing the online health surveys (~5 hrs over 1 week), to receiving the spit kit, and their lab processing the results, for me took about 2.5 months. It wasn't fast :)

Thanks, I sent my spit kit in in early November and still have not got the results. Good to know the time line.

Roots&Wings

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Re: Gene typing, for free
« Reply #21 on: December 16, 2016, 08:03:44 AM »
^ Yeah, I sent my spit kit back in early Oct, and got the results last week.

Roots&Wings

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Re: Gene typing, for free
« Reply #22 on: December 16, 2016, 10:07:15 AM »
OK, I couldn't really figure out Stanford's Interpretome site at all for health or ancestry.

But, codegen.eu seems really comprehensive and userfriendly for health indicators. And gives you a full report of your genetic health indicators that you can view in Dashboard and Topics.

It takes the file: GFG7_filtered_unphased_genotypes_23amdMe.txt
I wasted about 15 minutes trying to upload the wrong file to Interpretome & Codegen!

Gedmatch.com (ancestry) takes the file: GFG7_filtered_imputed_genotypes_noY_noMT_23amdMe.txt

Would love to hear other tips or resources if anyone has some! What else can be done with raw genetic data?!