Full Genomes Corporation

From ISOGG Wiki
Jump to: navigation, search
Full Genomes Corporation
Type Inc.
Industry Genetic genealogy
Founded 2013
Founder(s) Justin Loe, Leon Kull, Paul Conroy, Abdullah Marafi
Headquarters Rockville, Maryland, USA
Area served International
Products Genome NGS Sequencing, Interpretation (SNPs, STRs, Phylogeny)
Website www.fullgenomes.com


Full Genomes Corporation was founded in 2013 to make next generation sequencing technology available for the DTC (direct to consumer) market focusing on the Y chromosome. The founders are well known citizen scientists and active in the genetic genealogy community. The headquarters are in Rockville, Maryland, in the USA.

Contents

Team

  • Justin Loe, MS, CEO
  • Leon Kull, Director Data Analysis
  • Greg Magoon, PhD, Y-chromosome Analytical Consultant

Y-DNA comprehensive sequencing

Up to April 2015 approximately 1,000 kits where sequenced or analyzed with registration of 35,000 novel SNPs at the time of the analysis. [1]

Y Elite 2.0

Introduced in May 2015.

  • $750
  • length coverage: 13.2+ megabases
  • read length: 250 bp, coverage 30x+
  • supplier: Omega Bioservices, 99% quality control success
  • replaces: Y Elite (100 bp BGI) and Y Prime (100 bp)
  • features: better SNP calling and better STR calling quality

Product history

Y Elite 1.0 (2013-2015): FGC introduced this service DTC (Direct To Consumer) in spring 2013. The test is known as the Y Elite. Key information (see also Y-DNA SNP testing chart):

  • $850 USD (introduced at $1,499, for early birds $1,299, later lowered to $1,250, $1,099, $999, $975, $850)
  • Sequencing is provided by the BGI in Hong Kong.
  • Raw data (BAM file): Read length 100 base pairs, coverage 50x, approximately 20-25 million bp are called from the ca. 58 million Y-chromosome bp (the centromere and the huge q12 region are not included), ca. 14 million bp with reliable mappings (high quality SNPs)[2][3]
  • SNP Report: approx. 1700 "usable" SNPs reported, check for known Y-SNPs, Y-DNA haplogroup assignment, Report of private (new) SNPs, in common haplogroups 25-40 private SNPs are found
  • YFull evaluation: confidence regions length averaged at 23 Mbp. With average mutation rate 0.82 ∙ 10^-9 per year per bp the resolution is 53 years per mutation (for comparison BigY has 10.31 Mbp and 118 years per mutation). [4]
  • Y-STR Report: 300+ Y chromosome STRs (Markers)
  • Approx. 99% coverage of the mtDNA sequence

Y Prime (2014-2015): was introduced in July 2014. Costs were $750 (originally priced at $625, $589 with an introductory price at launch of $599. Subsequently raised to $650).

BAM-file analysis

FGC for $50 provides an analysis of third party BAM files and provides the same interpretation results (SNP, STR) as mentioned above. For details see:

Whole genome tests

Over 20x: High-coverage

Introduced in summer 2014.

  • 30x, read depth averages around 20-30. Coverage seems to be well over 90% of the sequenceable genome, probably close to 95%.[5]
  • $1,850 USD (introduced at $1,800 for early birds)
  • Y chromosome data (YFull): Length coverage: 22,858,252 bp, Mean depth coverage:21.38X, Median depth coverage:12X [6]
  • Based on dbSNP 142 expected to cover over 100 million known variant sites (mostly SNPs) plus novel variants identified in the ~3 billion nucleotide sites in the human genome; ca. 4.7 million sites called with variation from the reference sequence. [7]
  • Data will be delivered by hard drive (100 gigabytes or more of raw data)

7x to 19x: Medium-coverage

Introduced in July 2015. No beta results yet available.

  • 10x coverage $675. Use order code: WGS-10x

up to 6x: Low-coverage

Introduced in July 2015. No beta results yet available.

  • 4x coverage $325. Use order code: WGS-4xcoverage. Expected similar to 1000 Genomes (4x and higher).
  • 2x coverage $225. Use order code: WGS-2xcoverage

Reviews

Privacy policy, terms and conditions

This information is not yet available on the homepage and was given by Justin Loe in the Facebook page in December 2013.

  • DNA: sent to BGI
  • Data: data is stored where analyses are performed and in our site
  • Data Access: not published, via website or direct delivery
  • IDs: BGI and/or others only receive anonymous ids, not names

External links

References

  1. Justin Allen Loe. eMail 2015-04-22 to Chris Rottensteiner and Debbie Kennett
  2. Justin Allen Loe. Message posted 2013-11-09 in Facebook group, https://www.facebook.com/groups/fullgenomesY/
  3. Greg Magoon comparison table, published in FGC Facebook group, http://i.imgur.com/Gq7jDrX.png
  4. ADAMOV, D., GURYANOV, V., KARZHAVIN, S., TAGANKIN, V., URASIN, V.. Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data. The Russian Journal of Genetic Genealogy (Русская версия), mar. 2015. Available at: http://rjgg.molgen.org/index.php/RJGGRE/article/view/151/175. Date accessed: 06 May. 2015.
  5. Feedback from a whole genome customer. June 2015. http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=89764&viewfull=1#post89764
  6. Sample FGC whole genome: (Y chromosome data from whole genome), July 2015. http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=94263&viewfull=1#post94263
  7. Greg Magoon about prototype results: "102.8 million variant sites with read depth ≥8, 106.5 million with at least one mapped read.", E-Mail Mar 23, 2015