Next generation sequencing
From ISOGG Wiki
Next generation sequencing (NGS, NextGenSeq) is a new method for sequencing genomes at high speed and at low cost. It is also known as second generation sequencing (SGS) or massively parallel sequencing (MPS). For genetic genealogy purposes NGS is used for the BIG Y test from Family Tree DNA and the Y Prime, Y-Elite and whole-genome sequencing tests from Full Genomes Corporation. The mitochondrial DNA full sequence test from FTDNA also uses next generation sequencing technology.
DTC DNA testing companies
Direct to consumer DNA testing using next generation sequencing availability:
WGS: whole genome
- Y-Elite (incl. mtDNA): Full Genomes Corporation
- Big Y: Family Tree DNA (available only with existing Y-DNA test)
- Naughton B. Oxford Nanopore in 2016. Boolean Biotech, 10 October 2016.
- Crane L. The future of DNA sequencing is already in the classroom . Columbia University Computer Science website, 25 January 2016.
- Wherper M. The $1000 genome arrives - for real this time. Forbes, 14 January 2014.
- Collins FS, Hamburg MA. First FDA authorization for next-generation sequencer. Perspective article, New England Journal of Medicine, 19 November 2013.
- Next Gen Seek - making sense of next-generation sequencing data
- 8 realities of the sequencing GWAS by Dan Koboldt, MassGenomics, 31 March 2014.
- Illumina destroy the opposition again - almost... by Mick Watson, Opiniomics, 14 January 2014.
- An introduction to next generation sequencing technology - Illumina guide
- Wikibook on Next Generation Sequencing
- Wikipedia article on DNA sequencing
- Systematic multi-sample analysis of the effect of sample type (blood vs. saliva) on variant calling in WGS A white paper from DNA Genotek and Severn Bridges Genomics]
- Next generation genomics: a world map of high-throughput sequencers
- A comparison of mappers
- Next generation sequencing for dummies A Powerpoint presentation by Andy Vierstraete, Department of Biology, Ghent University, June 2012
- GigaScience a journal sponsored by BGI
- I've received my Y-chromosome sequencing results - what now? by Thomas Krahn. The slides from Thomas Krahn's presentation at the Institute for Genetic Genealogy in August 2014.
- Genohub Find and order next generation sequencing services from top providers (link 10 WGS 20x)
- Combining SNPs, STRs, and genealogy to build a surname origins tree by Maurice Gleeson. A presentation given at the Family Tree DNA Group Administrators' Conference in Houston, Texas, in November 2015.
- Building a family tree with SNPs, STRs, and named people by Maurice Gleeson. A presentation given at Genetic Genealogy Ireland in October 2015.
- Surfing the SNP tsunami: NGS for genetic genealogists by John Cleary. A presentation given at Genetic Genealogy Ireland in October 2015.
- It's not just 'deep ancestry' - how NGS & Y-STR testing can further your research by John Cleary. A presentation given at Who Do You Think You Are? Live in April 2015.
- Video on how to sequence the human genome
- Jain M, Olsen HE, Paten B, Akeson M (2016). The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biology 17: 239.
- Goodwin S, McPherson JD, McCombie R (2016). Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics 17: 333-351.
- Muzzey D, Evans EA, Lieber C (2015). Understanding the basics of NGS: from mechanism to variant calling. Current Genetic Medicine Reports 3(4):158-165.
- Van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014). Ten years of next generation sequencing technology Trends in Genetics 2014 30(9): 418-426 (subscription required). An excellent review article.
- Robasky K, Lewis NE, Church G. The role of replicates for error mitigation in next-generation sequencing. Nature Reviews Genetics 2014; 15: 56–62 (subscription required).
- Lou DI, Hussman JA, McBee RM et al. High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proceedings of the National Academy of Sciences, published online before print 15 November 2013.
- Behjati S, Tarpey PS. What is next generation sequencing? Archives Dis Child Educ Pract Ed 2013; 98: 236-238.
- O'Rawe J, Jiang T, Sun G et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Medicine 2013 5: 28.
- Grada A, Weinbrecht K. Next-generation sequencing: methodology and application. Journal of Investigative Dermatology 2013: e11.
- Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. Journal of Applied Genetics 2011 Nov; 52(4): 413-35.
- Altman A, Weber P, Bader M et al. A beginners guide to SNP calling from high-throughput DNA sequencing data. Human Genetics 2012; 131:1541-1554 (subscription required).
- Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics 2011 12: 443-451 (June) (subscription required).
- Shendure J, Hanlee Ji (2008). Next-generation DNA sequencing. Nature Biotechnology 26, 1135 - 1145 (2008). A useful introductory review article.