Tag Archives: Next generation sequencing

Are you a NGS expert?

Some months ago we asked you for how long you have been involved with next generation sequencing.

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Almost 200 people sent their feedback and gave us a very interesting insight in their experience with NGS. To take this into account, we want to further align our posts with the focus topics of our readers.

Feel free to send me your comments and suggestions to make ngs-expert.com even more valuable for you.

Why should I buy Illumina stock shares?

What is the impact for a company of winning an award? In case of Illumina you can cleary see it is about brand and market awareness. Only recently we reported about the award for Illumina of beeing the smartest company in 2013. Today we have a short interview for you that answers the question: why to buy stock shares for Illumina.

From my point of view the only risk of being a market leader in a highly dynamic area like next generation sequencing is, that you have a lot to loose. But Illumina is working on this. One example: only this year Illumina launched two new next generation sequencing instruments: the X-Ten for human whole genome sequencing and the Next500 – a mid-size sequencer that fills the gap between the HiSeq and the MiSeq. So let’s see what happens next…

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).

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Congratulations, Illumina!

Tumor Heterogeneity And The Underlying Genetics

Although this recorded seminar is promoted by Illumina, I still can recommend it as a very good talk about basic concepts on tumor heterogeneity and the underlying genetics. Kenneth Bloom, Chief Medical Officer at Clarient (GE Healthcare) and a pathologist, explains the needs for the application of NGS in clinical lab in a simple and very vivid manner. While watching this video I gained a better idea of the needs of a diagnostics lab and the challenges in developing a diagnostic NGS panel.

Next Generation Sequencing in Lung Cancer

Dr. Benjamin Levy (Head of Thoracic Medical Oncology, Division of Hematology-Oncology, Beth Israel Medical Center, Continuum Cancer Centers of New York and Assistant Professor of Medicine, Albert Einstein College of Medicine) is talking with Selma Schimmel about next generation sequencing in lung cancer.

The interview was filmed at the American Society of Clinical Oncology Annual Meeting in Chicago 2013.

Clinical Genomics Using NGS Approach

Video by Cambridge Healthtech about the impact of next generation sequencing on clinical genomics.

Nazneen Aziz of the College of American Pathologists and Konrad J. Karczewski of Stanford University are talking about analytical and bioinformatics standards, personal analysis, challenges and interpretation services.

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:

News From The World Of NGS

Pacific Bioscience’s instrument PacBio RS is known as the third generation sequencing technology. And again they proof their innovative character. During the course of the last couple of months two new chemistry packages have been released (XL & P4). And during the last couple of days two even more interesting news were spread:

1. Roche and PacBio’s signed an agreement for codeveloping diagnostic products for the PacBio RS instrument (Genome Web). From my point of view this is a huge signal. Roche, as an experienced player in the NGS market with its own sequencing instruments see’s a lot of potential in the SMRT technology. So the PacBio RS system obviously got out of the teething phase and will increase its importance in the NGS business in the coming months.

2. And also New England Biolabs a big player in the area of enzyme production, proteomics and drug discovery is using the PacBio RS to study bacterial methylomes and work on new reagents for 5-mc detection. And the CSO from NEB highlights that they have choosen “the PacBio system to study bacterial methylomes because of a unique feature of SMRT sequencing that enables the detection of base modifications through the system’s kinetics”. (Genome Web)

Beside the great news for Pacific Biosciences als Life Technologies or better Thermo Fisher signed a great deal with the Chinese Dx firm iGenomics to install 32 Ion Proton sequences in 2013 (Genome Web).

And clearly all developments focus on Molecular Diagnotics and Clinical Diagnostics. And to add the missing link in this news update also Illumina recently announced that they partner with G3 to identify novel biomarkers and pathways in cardiovascular disease.

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:

Running a NGS Company Is Profitable

A recent article in GEN (Genetic Engineering & Biotechnolgy News) ranked the 2012 salaries of the TOP 20 CEO’s of life sciences tools and technologies providers.

Amongst them: the CEO’s of PacificBiosciences, Illumina, Life Technologies:

Michael W. Hunkapiller, Ph.D. (PacBio) $2,177,002

Jay T. Flatley (Illumina)  $8,171,080

Gregory T. Lucier (LifeTech) $10,268,445

But although this is really impressive, it’s still not outrageous. Imagine being a 28-year old soccer player: you can earn 4times as much as G.T. Lucier … (Forbes)

The complete article can be found here.