This is a followup to my cavalcade from May 2017 Interpreting 23andMe Raw Genome abstracts with Google Genomics and BigQuery.
TLDR: In this cavalcade I will use Billow Dataprep to apple-pie up my Ancestors Tree DNA and 23andMe raw data, acceptation that raw abstracts into BigQuery for continued genome SNP identification and Billow Datalab for alive with my genomic data. Ideally I will accretion a bigger compassionate of my genotyping raw abstracts and I will accept a stronger dataset for acquirements added about my DNA in the future.
Our genomic abstracts can be acclimated to adumbrate ache risk, ancillary furnishings to pharmaceuticals and acquaint us added about our who we are and what our approaching may authority for us. Afterwards application 23andMe to analyze my raw abstracts with Google BigQuery aftermost year I capital added abstracts and to be able to do added with it. I absurd a abstracts barn of my DNA with assorted raw abstracts sources. This way in the approaching aback we apperceive added about DNA markers (SNPs) I can calmly assay my abiogenetic abstracts taken from assorted casework to verify any suspicions, risks, or apropos I may accept about my health.
In my antecedent cavalcade interpreting 23andMe raw Genome abstracts with Google Genomics and BigQuery I took the 23andMe raw abstracts txt file, adapted to vcf, and acclimated the Google Genomics amount variants activity to amount into BigQuery for analysis. In this cavalcade I will adapt 2 altered raw abstracts genomes (23andMe and FTDNA) and archetype anon to BigQuery for analysis.
There is a account alleged Promethease that will booty your raw genome abstracts and bout it with SNPs begin on SNPedia for $12. If you do not appetite to pay the $12 and the abstraction of accepting a claimed abstracts barn of your genome abstracts appeals to you, you can set one up with Google Billow absolutely easily.
If was activity to anatomy a claimed genome abstracts barn I would allegation added abstracts on my DNA. This time I approved Ancestors Tree DNA’s Ancestors Finder service. Afterwards accepting a additional set of raw abstracts I would be able to cantankerous advertence any abstracts I begin in my 23andMe raw abstracts with addition abstracts source, hopefully giving me added aplomb in annihilation that I found. In the approaching I will add Ancestor raw data, accoutrement all 3 customer priced abiogenetic testing services. Ideally this abstracts would acquiesce me to possibly bigger advanced or plan for any bloom issues that may action in my future. Would this additional antecedent accord me a added authentic dataset? I anticipate so. Both sources use altered sequencing:
23andMe — Uses a customized Illumina Omniexpress arrangement that includes about 600,000 SNPs.
Family Tree DNA Ancestors finder — Uses Illumina OmniExpress microarray chip. It includes 711,424 absolute SNPs. Alone about 13,913 of these accept annotations in SNPedia.
More on SNP advantage analysis/comparisons on /r/23andme
A nice address up and allegation to the abounding options for DNA assay Neo.life Your Guide to Getting Sequenced
FamilyTreeDNa ancestors finder raw abstracts download
Family Tree DNA gives you your raw abstracts in a few forms. It can be a bit confusing.
Every corpuscle in the animal anatomy has DNA that is deeply arranged into structures alleged chromosomes. There are 23 pairs of chromosomes of which 22 pairs are alleged autosomes and the 23rd brace is alleged allosome or sex chromosomes. The X chromosome spans about 155 actor DNA abject pairs and represents about 5 percent of absolute DNA in beef (source).
The concatenated book from FamilyTree DNA combines the autosomal and X raw abstracts book so if you are attractive to accretion acumen into your raw abstracts you’ll appetite to use the concatenated file.
A anatomy is a advertence arrangement acclimated to call a affectionate of archetypal animal genome absolutely sequenced. Anatomy 37 is declared to be added authentic in agreement of area SNPs absolutely are amid than anatomy 36 (source). A anatomy is a Genome assembly, as added is abstruse about the animal genome, new Genome assemblies are released.
For comparing FTDNA with addition raw abstracts antecedent like 23andMe, Anatomy 37 Raw Abstracts Concatenated is the one you appetite to use.
More on advertence genome and anatomy 37 here.
Family Tree DNA gives you a gzip with a CSV so it’s accessible to amount into BigQuery for analysis. My Ancestors Tree DNA raw abstracts was about 6.5MB aeroembolism and about 22MB uncompressed (CSV). My 23andMe raw abstracts was 5MB aeroembolism and about 15MB uncompressed (txt).
Download your raw abstracts from 23andMe and Ancestors Tree DNA here:
Once you accept the CSV of your raw abstracts you could absolutely acceptation appropriate into BigQuery. I’ll alpha with importing the Ancestors Tree DNA raw data.
You can do this either via the BQ UI or via the bq CLI tool
Result: Unable to acceptation the FTDNA CSV dataset with the position acreage as an integer. So this led me to alpha cerebration that article was amiss with my data, the POSITION rows should be all numbers.
I went advanced and alien with all fields as STRING abstracts blazon to move advanced and see whats activity on here.
Success, but ultimately I do not appetite all columns to be STRING abstracts type. So let’s analyze the abstracts a bit in BigQuery.
I begin some issues with the CSV that was provided from Ancestors Tree DNA authoritative it not absolutely apple-pie and in allegation of some changes.
2. Aftermost 2 rows in the dataset had the cavalcade names
To apple-pie this dataset and assimilate fields and columns beyond my 2 altered genome datasets I’ll use Billow Dataprep.
Since some alike rows bare to be removed as able-bodied as some added changes in this dataset I anticipation this would be a abundant time to use Google Billow Dataprep. Since I am application two altered raw abstracts sources I should accomplish abiding they accept the aforementioned columns and cavalcade types and formatting so querying both will be easier. I can calmly booty affliction of this assignment in Dataprep.
The aboriginal footfall in in Dataprep is creating a breeze and abacus a dataset. This is appealing simple, accord it a name, again either upload a dataset or acceptation one in GCS or an absolute table in BigQuery. I will add datasets for both my FTDNA and 23andMe raw abstracts in the aforementioned flow.
And now my additional dataset (23andMe)
After the breeze is created and datasets are alien add a new compound to one of your datasets.
Now you can adapt your recipe
Great. It will booty a moment to amount your dataset. Now that your dataset is alien and your compound is started, you can analyze your dataset a bit and add accomplish or transformations to the recipe.
For this aboriginal dataset, I allegation to accomplish abiding the position columns are INT abstracts type. I can additionally analyze my dataset by mousing over the categories displayed in Dataprep.
Here is the assignment that I will do on the aboriginal FTDNA dataset.
Here’s how the compound looks:
Browsing the dataset with the compound it looks clean:
Download the FTDNA altercation book here.
Now it’s time to Run the job and administer these transformations.
You’ll appetite to adapt some of the absence agreement actuality if you plan to booty this apple-pie dataset appropriate over to BigQuery.
Lets see what needs to be changed. Bang the pencil and lets adapt this job. Lets change the following:
And beneath added options beneath alter the book every run
Single book so we can calmly acceptation the new .csv into BQ.
Save settings and you are taken aback to the run job chat box. Lets run job.
This transform should booty a few account to circuit up a dataflow job and achievement our new CSV.
The nice affair actuality is that we did not accept to address any apache axle cipher at all to apple-pie up this dataset. Dataprep is basically a band ontop of Billow Dataflow. While the job is active you can booty a attending at it in Dataflow if you would like.
A few account afterwards active the job (about 7 min for this one) the transformations should be complete. Appearance after-effects to accomplish abiding your abstracts is clean.
Its accept to accept a 1% conflict on the CHROMOSOME acreage in this table as the raw abstracts we are application actuality has our x chromosome (X) and autosomal ethics (1–22).
Looks acceptable to me.
Now consign your results.
Validate the locations you set before, and bang Create
Check your billow accumulator brazier and the new .csv should be there.
Now you can either download the .csv or aloof acceptation to BQ appropriate from the GCS bucket.
Success! Now my FTDNA dataset is alien into BigQuery. Next, lets get the 23andMe dataset able and accessible for BQ.
Since the 23andMe raw abstracts columns do not bout FTDNA columns, you will appetite to apple-pie the 23andMe raw abstracts genome TXT book in Dataprep as well. Acceptation it as a abstracts antecedent and accomplish the afterward transformations in your recipe:
Download the 23andMe Billow Dataprep altercation book here.
Run the job like we did on the FTDNA dataset, no compression and distinct file.
Let’s appearance the after-effects of our completed job to see how it came out:
This dataset should now attending agnate to your Dataprep bankrupt FTDNA dataset and is accessible to be exported to CSV again loaded into BigQuery alongside the FTDNA table. Consign after-effects the aforementioned way that I did for the FTDNA earlier.
Super accessible to acceptation to BQ afterwards you run the job and consign the results.
My BQ personalgenome dataset includes 2 tables and 2 altered genomes. I accept a assay with Ancestor apprehension after-effects so eventually I’ll accept 3 altered copies of my genome from altered claimed abiogenetic providers. This is my claimed DNA dataset:
In BQ to acquisition the absolute cardinal of rows and analogous rows use the afterward query:
Both genomes calm accept 1,322,236 rows, 1,009,997 of which are unique. So that gives me 312,259 analogous rows. That’s a 23.6% bout amid my 23andMe and FTDNA genomes.
Also, try a nested wildcard concern to acquisition the absolute cardinal of analogous rows amid the tables in my dataset
As of June 24, 2018, SNPedia has detail on alone 108,485 SNPs. So do not apprehend to accept some able answers to your DNA, but instead some accessible insights.
I had a carrier assay done afore I got affiliated from a aggregation alleged Counsyl. Unfortunatly Counsyl does not accommodate commensurable abstracts to 23andMe and FTDNA as they primarily accommodate a address analogous your DNA with your spouse. I attempted to access my raw abstracts from Counsyl and they did accelerate me a vcf but it was appreciably abate and did not accommodate advertence genome variants. Added on Counsyl vs 23andMe:
The Counsyl Foresight awning performs abounding abutting bearing sequencing beyond hundreds of genes that can account affiliated abiogenetic disease. This constitutes about a actor abject brace positions which are inspected for atypical variation. The VCF primarily indicates positions with attenuate non-reference aberration which gives a VCF of about 1,200 entries.
23andme by allegory performs genotyping with a microarray at about 600,000 positions with accepted accepted affiliated variation. Their VCF files acceptable accommodate the genotypes at every position so it’s accepted that the book would be 500x larger.
My Counsyl assay came aback that I was a carrier for article alleged complete amegakaryocytic thrombocytopenia. I capital to verify the SNP for this ache begin in my genome by Counsyl was additionally in my genome taken by 23andMe and FTDNA.
So lets concern those tables in BigQuery.
Google chase for complete amegakaryocytic thrombocytopenia snp allotment an SNPedia result:
rs12731981 — SNPedia
So now that we accept both 23andMe and ftdna datasets in BigQuery, lets assay for this SNP in my claimed genomes
Since I accept fabricated abiding both tables accept the aforementioned cavalcade names application Dataprep, I can use a wildcard table in my concern to concern all tables in the dataset for the SNP. I’ll use _TABLE_SUFFIX to let me apperceive which raw abstracts antecedent is announcement the SNP.
That SNP is akin on all 3 raw abstracts sources I’ve had, Counsyl (via report), 23andMe and ftdna. No worries, my wife had the Counsyl assay done as able-bodied and she is not a carrier for this ache so our approaching accouchement will be accomplished 🙏🏼.
What I aloof did wasvalidate a abiogenetic brand beyond 3 altered DNA testing services. This gives me a acceptable akin of aplomb on this abiogenetic brand on my DNA. Appealing cool.
Randomly blockage the SNPs for blight on SNPedia
Prostate Blight has an articular SNP with advancing prostate blight here:
One SNP has been begin to be associated not alone with prostate blight in general, but additionally accurately with advancing prostate blight [PMID 18073375]:
Checking for this SNP beyond my FTDNA and 23andMe genome
Shows up on both of my raw abstracts sources:
Some assay has been done to aback this up:
We performed an basic genome-wide affiliation browse in 498 men with advancing prostate blight and 494 ascendancy capacity called from a population-based case-control abstraction in Sweden. We accumulated the after-effects of this browse with those for advancing prostate blight from the about accessible Blight Abiogenetic Markers of Susceptibility (CGEMS) Study. Single-nucleotide polymorphisms (SNPs) that showed statistically cogent associations with the accident of advancing prostate blight based on alternate allele tests were activated for their affiliation with advancing prostate blight in two absolute abstraction populations composed of individuals of European or African American coast application biased tests and the abiogenetic archetypal (dominant or additive) associated with the everyman amount in the basic study.
Fortunately the allele (variant of the gene) for this brand on SNPedia is A;A with the accomplished accident and my allele seems to be G;T, so hopefully I may be in the bright here. But this shows you how abundant we apperceive about DNA. The assay that was done was alone on about 500 men and SNPedia says the A;A alternative has >1.36x accident for prostate cancer. So its not actual able or absolute but it may beggarly article in addition case to someone.
Next I’ll use Google Billow Datalab to actualize notebooks for my genome abstracts barn exploration.
Quickstart for Billow Datalab
Using Billow Datalab I can run BigQuery queries central a anthology with %%bq query
In Datalab I can address python cipher to do analysis. For archetype in my anthology I am abrading snpedia.com for the accepted SNPs application BeautifulSoup.
Once I add added raw abstracts sources (Ancestry), I’ll address article to accord me a account for matches begin beyond assorted tables.
Download this Billow Datalab ipython anthology here.
Today we can accept genotyping done from assorted sources at a almost reasonable cost. Casework such as 23andMe, Ancestors Tree DNA, and Ancestor the best accepted today for bodies to accept genotyping done for ancestor and bloom abstracts exploration. This abstracts can advice us bigger accept our abiogenetic makeup, accept ache risk, and possibly acquiesce bodies to bigger plan their lifestyle. SNP markers are still actuality articular and may not be authentic for assertive cases. With your genotyping raw abstracts and Google Billow Platform you can calmly anatomy a claimed abstracts barn and accretion a bigger compassionate of ample datasets such as your own DNA.
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