yfull-review

YFull review – What can you learn from your Y chromosome?

Rating based on our YFull review

7 Facts from our YFull review

  1. YFull location: Moscow, Russia
  2. Services: DNA data upload and interpretation of Y-DNA and mtDNA
  3. Reports: Y-DNA and mtDNA Interpretation
  4. Privacy: active sharing of aggregate customer data with third parties 
  5. Cost: $49 for Y-DNA analysis, additional $25 for mtDNA analysis
  6. Complementary services: Nebula Genomics ($299 for 30x whole genome sequencing, including Y-DNA and mtDNA)
  7. Alternatives: FamilyTreeDNA (Big Y test that includes an STR test and a SNP test)

YFull Introduction

This is a review of YFull, an upload site for Y chromosome and mitochondrial DNA sequencing data that provides advanced ancestry analysis.

Single nucleotide polymorphisms, or SNPs, are differences in DNA sequences at the level of individual base pairs. For example, when DNA sequences from two individuals differ at a single position or base, this is called an SNP. 

On the other hand, short tandem repeats, or STRs, are a series of repeated DNA sequences (A, T, C, or Gs) that differ between individuals. Identifying the number of repeats at specific areas of the genome can create a “DNA fingerprint”. This genomic fingerprint may be used to investigate an individual’s genetic genealogy. 

Together, SNPs and STRs are markers that can be inherited. The combination of such markers is known as a haplotype. There are different Y-DNA and mt-DNA tests for different haplotypes, which may assign individuals to a specific “haplogroup”. While Y-DNA tests can tell us more about paternal origins, mtDNA tests tell us about maternal origins. 

YFull was created in 2013 in Moscow, Russia with the specific purpose of interpreting Y-chromosome sequences. With this in mind, the service is not a DNA testing company. Rather, it is an analysis company that offers next-generation sequencing interpretation (for Y-DNA and mtDNA). Moreover, the company offers convenient visualization of DNA results and a detailed, public haplogroup tree so that you can compare your “path of mutations” with the “path of mutations” of other samples in YFull’s database. 

The original team consisted of Vadim Urasin, who has been an active participant of the DNA genealogical community since 2008. Other members of the original team include Vladimir Tagankin, the DNA database “semargl.me” developer, and Roman Sychev, a moderator on dna-forums.org. 

Want the most complete Y chromosome and mtDNA sequencing data to use with YFull? Nebula Genomics offers 30x Whole Genome Sequencing for just $299! Click here to learn more!

How to upload your data to YFull

Let’s start the YFull review with an overview of the service. 

A chart detailing which features are reported in NGS interpretation for VCF and BAM files.
A chart detailing which features are reported in NGS interpretation for VCF and BAM files.

To order a YFull test analysis, raw data from other genetic testing providers must be uploaded to YFull. Your raw data file can be from Nebula Genomics, FTDNA Big Y, Full Genomes Inc, YSEQ, Enlighten, Veritas Genetics, BGI, Novogene, 23mofang, Dante Labs, WeGene, or Yoogene. The data can be uploaded as a BAM file or VCF file. One caveat is that data extraction from VCF files will be incomplete (about 50-70% of data). Additionally, STR marker matches will not be reported should a VCF file be uploaded. Finally, YFull does not accept data in FASTQ format. Therefore, optimal results require the upload of a BAM file. A URL link must be provided to your raw data file using services, such as Dropbox or Google drive. 

Finally, Customers can create a username when placing an order. At the time of ordering, no payment is required. 

YFull order page.
YFull order page.

After several weeks, the results will be ready. At this time, a payment of $49 is requested through Paypal, Apple Pay, Cloud Payments, or credit card. One can also obtain mtDNA interpretation at an additional cost ($25).

A chart detailing which features are reported in NGS interpretation for mtDNA.
A chart detailing which features are reported in NGS interpretation for mtDNA.

Review of YFull Reporting

As mentioned previously, there are two types of Y-DNA mutations: SNPs and STRs. Both types of mutations are useful to probe for different reasons. YFull offers an analysis of both SNPs and STRs. 

YFull customer homepage.
YFull customer homepage.

According to YFull, there are 185,780 known SNPs and 780+ known STRs. There exist 1,482,319 novel variants that have not discovered before. 

List of known SNPs.
List of known SNPs.

The known SNP report shows the customer’s position on the Y-haplotree and the SNP results for all SNPs tested on the customer’s branch of the tree. Additional lists of SNPs are provided in adjacent tabs, highlighting “ambiguous” SNPs and no call SNPs (i.e. SNPs that were not determined during the process of genotyping a person’s DNA). 

YFull list of novel SNPs.
YFull list of novel SNPs.

A list of novel or private SNPs can also be viewed. These novel SNPs are stratified by quality (e.g. Best, Acceptable, Ambiguous, Low, One Reading). All private SNPs have a YFS prefix. The red checkmark next to some of these SNPs means that they can be verified through YSEQ. The G refers to the gene that this SNP is located within. 

Aligned sequencing reads.
Aligned sequencing reads.
List of indels.
List of indels.

The report also shows insertions and deletions (indels), which are positions in the sequence that have extra nucleotides. 

YFull close matches.
YFull close matches.

Moreover, one can access SNP matches, which are SNPs that are shared or assumed to be shared with other samples in YFull’s database, and can be traced back to a distant common ancestor. A customer’s sample will continue to be compared as the database is updated. If any of these private SNPs are later found to match new YFull samples, these SNPs will be given names in the Y-series

YFull search in a BAM file.
YFull search in a BAM file.

One can also observe individual SNPs to get more information, including the number of reads that overlap that SNP, reference sequences, and so forth. 

YFull SNP query feature.
YFull SNP query feature.

There is a useful feature to allow customers to query results by SNP name. 

We finish our review of YFull reporting with a look at the YReport feature.  YTree includes family tree DNA haplogroups and SNPs that are shared (Y-SNPs) in every haplogroup. YTree is based on public sample data, including the 1000 Genomes Project. YTree is updated almost every month based on submissions from haplogroup experts, ISOGG, and others. The list of SNPs from the root to the terminal haplogroup is sharable. 

YFull YTree.
YFull YTree.
YTree statistics.
YTree statistics.

One can also observe STR results (780 that are tested), matches, and variants.

YFull STR results.

Additional features include haplogroup age estimates are based on a 2015 study in which the authors outline an original method of selecting true mutations. If a customer’s raw data includes mtDNA sequencing, mtDNA haplogroups based on PhyloTree are listed. In March 2019, the platform introduced mtDNA analysis for an additional fee.

Other services include:

  • Statistics, such as BAM file size, mapped reads, length coverage, median depth coverage, and more (in the YReport)
  • CSV files (comma delimited files) for known SNPs, novel SNPs, and known STRs
  • The ability to browse raw data by position (genome builds hg19 or hg38)
  • My news: a chronological listing of changes to YTree since your YFull sample (upon updates)

You can take a tour of these features on YFull’s website. 

Review of YFull Privacy

The website’s privacy policy states that “YFull.com respects your privacy and will not disclose your personal information without your consent” unless required by law. The policy further states that “Aggregated Genetic and Self-Reported Information” may be disclosed to third parties.

This information is stripped of any identifying information that can be assigned to a specific individual. This collected information may also be published in peer-reviewed scientific journals

The personal information annex to the privacy policy states the variety of user data that is collected. This includes email address, ancestry information & raw genetics data, cookies, and IP address.

The YFull team has full access to this data. Partial access to certain data may be allowed by members of groups that the user has joined. 

Citizen science and academic researchers may also use this data. This occurs in instances where the user has given personal permission to participate in a study. YFull stores your data for as long as the website exists on a server. This server is located in a secure data center in Moscow, Russia.

Some information, such as email addresses, is stored on Google servers. You can delete your data and account at any time by navigating to the “settings” page. All samples associated with your account will be deleted and cannot be recovered if you delete your account. 

YFull Reviews

Several short reviews can be found on the company website. In addition, a few users have written blog posts detailing their experiences with the company’s services:

Review of YFull Pros and Cons

Pros

  1. You will not be charged for your upload until your results are ready, and the platform has no subscription fees.
  2. You can find additional information about your private variants. This includes the different names given to those variants and the regions of the Y-chromosome where those variants appear.
  3. You can compare the results across different NGS or whole-genome tests that you have taken.
  4. YFull Groups can display and compare all STRs (not just the first 111).
  5. You can find SNP matches in YFull Groups not only for your terminal SNP but for any named or unnamed variant.
  6. You can contact other people in your YFull Groups.
  7. Questionable SNPs or STRs from your NGS test can be verified at YSEQ and added to your test results.
  8. The platform is also equipped to support mtDNA sequencing interpretation.

Cons

  1. STR analysis is given less priority than SNP analysis and takes several weeks to complete, delaying the receipt of interpretation results.
  2. YTree is updated monthly whereas other services are updated weekly.

Nebula Genomics

We finish our YFull review, by looking at some comlementary products.

Want the most complete Y chromosome and mtDNA sequencing data to use with YFull? Nebula Genomics offers 30 Whole Genome Sequencing for just $299! Furthermore, our data can be imported into FamilyTreeDNA which also offers access to a large database of Y chromosome and mitochondrial DNA data. To learn more about the importance of sequencing Y-DNA and mtDNA more generally, check out this blog post

Did you like our YFull review? You can find more reviews here! This includes review of many other DNA upload sites like Genetic Genie (free) and Promethease ($12).

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