Archive | Publications & Surveys RSS feed for this section

Next Generation Sequencing Market Trends

paper_02The GEN report by Enal Razvi, Ph.D. provides an overview of the current NGS field in terms of application areas and utilization patterns.

Some findings of the report:

    • The exponential growth of NGS-focused publications illustrates the expansion of NGS and its penetration info research.
    • 49% of next generation sequencing methods are used for basic research.
    • 29% of researchers are using NGS for comparative genome sequencing
    • 38% of research efforts are studying somatic mutation
      33% are studying mRNA expression via RNA-Seq

New kids on the show – who will be the winner?

Next Generation Sequencing is still a quite young market. Therefore we face the same situation every year: there is a lot of innovation going on in regard to new technologies, new instruments and other inventions. Amongst all these innovations GenomeWeb picked out the new platforms and asked in a survey about the expectancies in the market.

Instruments that were part of this survey are (at least in one of several questions):

  • Oxford Nanopore’s MinIon
  • Illumina’s X-Ten
  • Illuminas NextSeq 500
  • QIAGEN’s GeneReader
  • Life Technologies’ Ion Torrent PGM
  • Illumina HiSeq

Here are some of the results:

  • 35% of the participants say that the MinIon has the greatest impact on the sequencing community
  • 30% of the participtants will purchase most likely the NextSeq 500
  • Illumina HiSeq / MiSeq outperform the Ion Torrent Proton / PGM in data accuracy and throughput, the Ion Torrent instruments are better in respect of run time and instrument price

Read the complete survey here.

NGS Applications – get an insight…

paper_02

You want to know more about projects where your research colleagues used next generation sequencing?

Check out the Nature Reviews overview of interesting publications releated to different applications of next generation sequencing.

Whose genome has been sequenced? Aquila chrysaetos

de-novo-sequencingEvery day an unimaginable number of NGS data is generated. Anyhow the number of avian genomes that have been sequenced so far is still quite small (Doyle et al table 1). Doyle et. al added one more avian genome to this list – the “Golden Eagle” Aquila chrysaetos.

What was sequenced?

A male golden eagle (Aquila chrysaetos canadensis) captured in the southern Sierra Nevada.

Sequencing strategy: Whole genome sequencing

  1. Libraries & Sequencing: 1 channel 2x 100 bp SG paired-end sequencing and 1 channel 2x 100 bp mate-paired sequencing using the Illumina HiSeq platform
  2. Data output: 68.4 Gb of raw data (25.3 Gb from the SG and 43.1 Gb from the mate-pair library). Total genome size (incl mtDNA) ~ 1.28 Gbp. Overall genome coverage ~ 40x. Longest scaffold: 11,517,212 bp
  3. Results: The mtDNA genome is characterised by 13 protein-coding genes, 2 rRNAs and 23 tRNAs. The annotation produced a total of 16,571 predicted nuclear genes.

Besides the nuclear genome Doyle et al could also assemble the complete mitochondrial genome. Furthermore they found ~ 800,000 novel polymorphisms. These polymorphisms can now help to define markers that are involved in carnivory orother biological processes.

Read the complete publication here.

Whose Genome Has Been Sequenced? – Recent posts:

The next step after sequencing: Synthesis of a designer chromosome

Next generation sequencing allows deciphering genomes of any kind and size; But, what to do with all this information?

Now a group of scientists from the John Hopkins University in Baltimore around Jef Boeke and 79 other authors published that they have been able to synthesize one of the 16 chromosomes of the baker’s yeast. Instead of the natural 317,000 bases they have reduced the chromosome to 274,000 bases by leaving out what they regarded as redundant or not necessary to grow under cell culture conditions.

Yeast cells already today produce important substances in large fermenters. They are used for bio fuel production but also for the production of Artemisinin, a potent malaria drug.

By reducing the genome of such organisms, the perfect “factory” can be designed in the future that delivers high yield of the desired substance at a minimum cost and a minimum contamination with other undesired metabolic byproducts. The White Biotechnology is certainly a hope for our permanent growing population. A number of companies engaged in this field can be found here.

Illumina – smarter than Google

Technology Review‘s analysed the markets Energy, Biotech, Computing & Communications, Internet & Digital Media, and Transportation in search of the smartest company in 2013. The main criteria is to look for the company with the biggest impact on the industry, mainly driven by innovation. They put together a list of the 50 smartest companies

… and the winner is:  Illumina

Important other companies, everyone knows are well behind… – maybe also because reputation has no influence on the ranking. Here some examples:

  • Google  #3
  • Dropbox #6
  • Amazon #10
  • Siemens #24
  • IBM # 35

By the way: in last year’s ranking Illumina was not even on the list. But Complete Genomics (#11), Life Technologies (#27) and Roche (#34).

erfolg

 

 

Congratulations, Illumina!

There is more than one bottleneck in NGS

The blog on NGS perspectives published recently a great survey (sponsered by QIAGEN) about the biggest bottlenecks researchers face by using the NGS technology. 26% of the 924 participants voted for the complexity of the data analysis. And from my point of view the challenge with data analysis has just begun. Because the sequencers out there produce more and more data in a single run. So high-end software solutions are a prerequisite for further usage of these machines.

What is the primary sequencing work done in your lab?

QIAGEN Survey

 

Also interesting: one of the questions from the survey asked about the applications that everyone runs with the NGS-instruments. The answers show that more and more scientists use NGS for dedicated purposes, like to know more about the expressed genes in a sample or about the mutations and existence of specific genes or gene panels.

 

 

Visit NGS Perspectives to view or download the complete survey.

RAD-Seq Publications in 2013

RADSeqDear NGS-Expert Blog reader,

As 2013 draws to a close, I wanted to take a few minutes and bring you a some interesting statistics on current trends in RAD sequencing publications and highlight the increasing use of this technology in genomics research.

2013 RAD-Seq Publications in Review

Through November 2013, there have been 45 peer-reviewed scientific papers featuring RAD-Seq as a major component of the published work. This value represents a 135% increase from the number of manuscripts published in 2012 and a 400% increase over the last two years.

RAD continues to be used extensively across a broad spectrum of genetic systems to answer fundamental questions in biology. This year, approximately 70% of the published work focused on applications of RAD-Seq in animal systems, while plant genomics efforts comprise roughly a quarter of the published scientific activity.

Finally, here are the three most-cited Rad-Seq Papers from 2013 (as reported by Google Scholar)

  • Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing.
    Ogden R, Gharbi K, Mugue N, Martinsohn J, Senn H, Davey JW, Pourkazemi M,
    McEwing R, Eland C, Vidotto M, Sergeev A, Congiu L.  Mol Ecol. 2013
    Jun;22(11):3112-23.
    http://www.ncbi.nlm.nih.gov/pubmed/23473098
  • Genomic patterns of introgression in rainbow and westslope cutthroat trout
    illuminated by overlapping paired-end RAD sequencing. Hohenlohe PA, Day MD, Amish SJ, Miller MR, Kamps-Hughes N, Boyer MC, Muhlfeld CC, Allendorf FW, Johnson EA, Luikart G.  Mol Ecol.
    2013 Jun;22(11):3002-13.
    http://www.ncbi.nlm.nih.gov/pubmed/23432212
  • Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis). Gagnaire PA, Normandeau E, Pavey SA, Bernatchez L. . Mol Ecol.
    2013 Jun;22(11):3036-48.
    http://www.ncbi.nlm.nih.gov/pubmed/23181719

Best wishes for a safe holiday season.
Rick Nipper,
President, Floragenex

Whose genome has been sequenced? Nasuia deltocephalinicola

de-novo-sequencingThe human genome comprises more than 3 billion base pairs and builts up more than 20,000 protein coding genes. For genomes like this high-throughput sequencers, like the HiSeq 2000 are a revelation. In this article we talk about the smallest genome sequenced so far – here sequencing with the MiSeq is more than sufficient. The main role of this small symbiont (Nasuia deltocephalinicola) together with the symbiont Sulcia muelleri is to provide 10 essential amino acids to the pest insect Macrosteles quadrillineatus (Bennett et al).

What was sequenced?

10 phloem-feeding pest insects (Macrosteles quadrillineatus) including the obligate symbionts Nasuia deltocephalinicola & Sulcia muelleri.

Sequencing strategy: Whole genome sequencing

  1. Libraries & Sequencing: 2x 250 bp paired-end sequencing using the Illumina MiSeq platform
  2. Data output: 12,000 contigs (> 500 bp) including reads from the pest insect and Sulcia muelleri; MIRA and Velvet assembly revealed two large scaffolds for Nasuia (~102 kb & ~12 kb)
  3. Bioinformatics: Many tools have been used, including Velvet for inital read assembly; SOAP2 to map the symbion-derived reads to the Velvet contigs and MIRA for re-assembly of isolated symbiont reads

The biggest challenge with this genome mixture was definitely the bioinformatic analysis. During several cycles of mapping and assembly the reads that belong to one organism needs to be filtered out of the remaining reads. But this labour-intensive approach revealed the smallest bacterial genome yet sequenced (112 kb).

Read the complete publication here.

Whose Genome Has Been Sequenced? – Recent posts:

Whose genome has been sequenced? Thunnus orientalis

de-novo-sequencingTalking about sealife everyone knows how sharks or whales look like or how they behave. Sadly, I think little is known about tuna. Tuna is more or less only known as delicous meal. So it’s all the more pleasant to see that the recent de novo genome sequencing approach of Nakamuar et. al aim to learn more about the predatory behaviour of tuna and not about breeding or cultiviation (Nakamuar et. al). With this genome sequencing project of Thunnus orientalis the scientists could prove that tuna harbors some unique tactics to catch their prey.

What was sequenced?

The diploid genome of a wild-caught male Pacific bluefin tuna (T. orientalis) was sequenced.

Sequencing strategy: Whole genome sequencing

  1. Hybrid approach: Roche 454 GS FLX Titanium & Illumina GAIIx
  2. Libraries: Shotgun & paired-end libraries on Roche 454 & paired-end libraries on Illumina GAIIx
  3. Read output: 31.9 million 454 reads, including 4.9 million long paired-end reads (11.9x coverage) & 229.7 million Illumina paired-end reads (43x coverage)
  4. Data output: 192,169 contigs (> 500 bp) that could be assembled in 16,802 scaffolds (> 2 kb), totaling 740.3 Mb (= 92.5% of the estimated genome size (~ 800 Mb))
  5. Bioinformatics: Roche 454 read assembly with Newbler (Version 2.5) followed by mapping of the paired-end Illumina reads with Bowtie (Version 0.12.7).
    Note: 7,259 nucleotide mismatches & 312,851 short InDel’s could be eliminated by mapping the Illumina reads onto the scaffolds by bwa (Version 0.5.9)

Sequencing strategy: Transcriptome analysis

  1. Libraries & Sequencing: Normalized cDNA libraries have been sequenced with the Roche 454 FLX Titanium Instrument
  2. Read output: 3.8 million 454 reads
  3. Data output: 5,741 full-length cDNA sequences
  4. Bioinformatics:Assembly was performed using Newbler (Version 2.5)

From the sequencing strategy point of view this publication shows again that the hybrid approach of the Roche 454 long read technology and the Illumina short read technology is one of the most used techniques for de novo genome sequencing (Hybrid assemblies).

From a scientific point of view this publication could show that tuna hs the most RH2 paralogs among studied fishes and that three of these genes are mutated compared to the others. And according to Nakamuar et. al these changes might be responsible for the great feature of tuna to detect blue-green contrasts and therefore to be able to measure the distance to prey in the blue-pelagic ocean.

Read the complete publication here.

Whose Genome Has Been Sequenced? – Recent posts: