Saturday, 26 April 2014

A new BAM file analysis service from Full Genomes Corporation and a special offer on the FGC test

The following message is posted on behalf of Full Genomes Corporation:

Full Genomes Corporation (FGC) is announcing the official launch of a service to analyze BAM files from Family Tree DNA's Big Y product. The analysis is being launched at a price of $50 per kit. Recently, FGC had offered the Big Y analysis for a limited time, as a beta product, at no charge. FGC will continue to allow individuals to contribute their BAM files to the Full Genomes database without charge, so that their results may be used in kit cross-comparisons. The offering is designed to provide broader access to FGC's proprietary Y chromosome analysis services and to build FGC's database for purposes of kit comparisons.

The analysis will include the same reports as provided to customers of the Full Genomes sequencing product, with the exception of the mitochondrial DNA analysis, which will use the Yoruba reference sequence for Big Y kits. So, the analysis will consider Y-STRs and INDELs, in addition to Y-SNPs. To be clear, however, the results won't be able to achieve the same resolution as the Full Genomes sequencing product due to limitations with the underlying data from the Big Y test.

Interested individuals should first obtain access to their Big Y BAM file by contacting Family Tree DNA customer service. Those interested in ordering analysis can follow the instructions here to set up a Full Genomes account, make payment, and upload their BAM file; analysis will be performed in weekly batches. Those who are only interested in contributing their results to the Full Genomes comparison database may send the download link to, while also indicating their interest in donating their results and optionally providing a name (like FTDNA Kit Number) to associate with the results.

According to Dr. Greg Magoon, Y chromosome data analysis consultant for FGC, "I think the FGC analysis will address many of the needs that have been expressed by members of the genetic genealogy community who have been looking at Big Y results in recent weeks. In my view, the main strengths of the FGC analysis include its cross-kit comparisons and its SNP reliability classifications. We have put a lot of R&D into separating the wheat from the chaff to allow customers and researchers to quickly focus on the most reliable, phylogenetically-useful variants. I think the FGC analysis will help to significantly speed the interpretation of results and decrease the burden on busy genetic genealogists."

Separately, FGC is announcing a beta-stage referral program, which will provide customers with access to advanced analyses of their Full Genomes "next-gen" sequencing data. A Full Genomes customer who refers at least three other individuals to order the Full Genomes test will be entitled to a bleeding-edge, advanced analysis of their choosing. Potential analysis options include:
-Remapping of results to the newer, build 38 human genome reference sequence
-Remapping of results with a new and improved alignment algorithm/approach
-Y-STR analysis using a newer, larger STR database
-Phylogenetic analysis for portions of the Y tree
-Variant calling (SNPs and INDELs) for autosomal and X-chromosome data

Interested customers are advised to contact to supply documentation of referrals and to discuss custom analysis options.

Dr Magoon said: "From a research perspective, I'm very excited about the potential for the referral program to push the boundaries of Y-chromosome analysis. We've already been able to work with customers on a case-by-case basis to do some very interesting customized analyses with the Full Genomes results, including the identification of large duplications and deletions through copy-number variation (CNV) analysis."

Speaking about FGC's next-gen sequencing test, CEO Justin Loe said:  "The FGC Y chromosome product is the most comprehensive in the market today but it is also, as we recognize, expensive for many potential customers. Over the near term, we expect to be able to make this product more affordable. Additionally, with the advent of new sequencing technologies other products will also be offered."
In fact, in honor of DNA Day, Full Genomes is currently offering a limited-time discount of 20% off the normal price for their comprehensive Y chromosome sequencing test (using coupon code "FGCDNA").

Dr Magoon commented: "I think what we're seeing across genetic genealogy is that companies are finding a niche with products focused on particular areas. For example, 23andMe has been a pioneer in autosomal DNA. We have seen that BritainsDNA has been making great advances in developing innovative chip-based tests for Y chromosome (and other) markers. Family Tree DNA has established a leadership role in Y-STRs and in full mitochondrial DNA sequencing. YSEQ, with Dr. Thomas Krahn, is the world leader in developing Y chromosome marker tests using Sanger sequencing. I am very excited to see FGC working hard to establish a similar role here in the field of "next-gen" Y chromosome sequencing."

Related blog posts
- A confusion of SNPs

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