Monthly Archives: January 2015

Illumina’s Latest Release: HiSeq 3000, 4000, NextSeq 550 and HiSeq X5

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HiSeq 3000, HiSeq 4000, HiSeq X Five, HiSeq X Ten

Illumina’s latest instrument release essentially comes down to more data/day.  Using the same patterned flow cell technology already in use with the HiSeq X Ten, The HiSeq 3000 has an output of 750 Gb or 2.5B PE150 reads in 3.5 days. The HiSeq 4000 has two flow cells, so twice the output: 1.5 Tb, 5B PE150 reads in 3.5 days. The NextSeq 550 combines the current NextSeq 500 with a microarray scanning system that fits right into the flow cell holder. The HiSeq X Five is less exciting; just half the number of instruments as the HiSeq X Ten.

If you don’t have the $10M budget for a HiSeq X Ten, you can purchase a HiSeq X Five and scale to the X Ten at a lower price/instrument: $1M/unit

Price Price/unit $/Genome* Consumables $/Gb
HiSeq X Five $6M $1.2M $1,425 $1,200 $10.6
HiSeq X Ten $10M $1M $1,000 $800 $7

*Price per 30X human genome according to Illumina. We’re not aware of any sequencing facility currently offering 30 human genomes for $1,000. On Genohub today, you can order a single whole human genome at 35X for $1,750.

Both the HiSeq X Five and Ten are still only “licensed” for human whole genomes [Update: Since this post was published in January 2015, Illumina now allows the sequencing of other large species on the HiSeq X Ten. For an up to date status on what is and what isn’t allowed on a HiSeq X, follow our HiSeq X Guide Page]. That basically means that while they can technically be used on non-human samples or transcriptomes, Illumina wants these focused on the WGS market (probably thinking about the BGI / Complete Genomic’s WGS instrument release this year).  Plus it gives them an excuse to release patterned flowed cells on more models, hence the HiSeq 3000/4000. Interestingly, Illumina is going to start bundling the TruSeq PCR-free and TruSeq Nano library prep kits (the only chemistry currently compatible with the X Five and X Ten) with X Five/Ten cluster reagents. At least for now, they don’t intend on doing this with the HiSeq series. Other news from this release:

HiSeq 3000/4000 do not have a rapid mode, high-output only. However PE150 reads only take 3.5 days

You can’t upgrade from a HiSeq 2500 (non-patterned flow cell) to a HiSeq 3000 or 4000 (patterned flow cells)

You can upgrade from the single flow cell HiSeq 3000 to dual flow cell HiSeq 4000

HiSeq 3000 yields >200 Gb/day, a 28% increase vs. HiSeq 2500 v4, yet the cost to purchase a HiSeq 3000 is the same as a HiSeq 2500. With two flow cells, the HiSeq 4000 yields twice as much data.

Sequencing Applications and Turnaround Time 

Exomes Transcriptomes 30X Genomes
HiSeq 3000 90 (2×75, <2 days) 50 (2×75, <2 days) 6 (2×150, 3.5 days)
HiSeq 4000 180 (2×75, <2 days) 100 (2×75, <2 days) 12 (2×150, 3.5 days)

So in the end, assuming sequencing facilities aren’t fed up with this break neck upgrade cycle and actually purchase these instruments, researchers can expect more data with faster turnaround times. We’ve already spoken to a few of our service providers who are considering upgrades to their HiSeq 1500/2000 instruments. As soon as these new instruments are available on Genohub, we’ll make an announcement [Update: they are all available, use our NGS Matching Engine for access to the latest Illumina instruments]. If you’d like to be the first to know send us an email at support@genohub.com. In the meantime, our providers offer services on the HiSeq 2500 v4, HiSeq X Ten, NextSeq 500 and HiSeq instruments (amongst many others).  You can order these services immediately and expect data delivery within the listed guaranteed turn around times. If you’re not sure what technology / instrument is right for you, just enter the number of reads or coverage you need and let our NGS Matching Engine identify the best service for you.  So what’s next? A little bird has told us patterned flow cells on the MiSeq !

TCR-Repertoire Sequencing Services

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TCR sequencing

The immune repertoire reflects the sum total of diverse B and T-cells in the circulatory system. The adaptive immune system drives immune response by these hypervariable molecules. The antigen specificity of each T-cell receptor (TCR) is determined by the complementarity-determining region: CDR3 of the beta receptor chain, formed by V, D and J gene regions. Examination of TCR diversity is important for understanding adaptive immunity and it’s function in diseases.  Next generation sequencing has become a powerful tool for measuring TCR diversity. Before samples can be sequenced a unique library preparation method must be performed to allow for reproducible and reliable results.

Girihlet, a newly formed biotech company in Brooklyn, NY is one of the first companies to offer TCR repertoire sequencing services and is the first to offer it on Genohub.com. We got in touch with Girihlet to learn more about this service offering and have posted our conversation with one of it’s co-founders, Dr. Ravi Sachidanandam. Ravi also holds a position as Assistant Professor on the faculty of  the Icahn School of Medicine at Mount Sinai, department of Oncological Sciences. He has published over 85 papers in the latest and most interesting areas of genomics, including small RNA, mRNA splicing, methylation and virology.

Genohub: Hi Ravi, we’re excited that you’ve joined Genohub.com and listed your services. We’re particularly interested in the TCR-repertoire sequencing services you have on Genohub.com. Not many service providers currently offer this service, how come?

Ravi: There are very few companies that offer this currently, and this is mostly because it’s a very challenging problem both experimentally and computationally. It may be easier to count all the dollar bills in circulation than to profile the diversity of the T Cell Receptors.

Genohub: Can you comment briefly on the ‘library prep’ approach to TCR profiling?

Ravi: Our library prep method is very unique, it is based on quantifying RNA, and in particular just the CDR3 regions while most of the other companies quantify DNA. This allows us to only quantify functional rearranged TCR locus. We also use universal primers for amplification and do not depend on previously known TCR regions, thereby accelerating discovery.  We have also compared our data to flow results and demonstrated good concordance.

Genohub: Inefficiencies during library prep and and sequencing can lead to severe bias generating artificial TCR diversity. Does your approach address this?

Ravi: The beauty of our approach is we use common primers to amplify the T cell receptor regions.  This ensures there is no bias during PCR, allowing for accurate sequencing. And since the accuracy and enrichment for the TCR mRNAs is >98%, we need very little total RNA and less sequencing depth reducing the overall cost of sequencing.

Genohub: How many sequencing reads or TCR sequences do you recommend for a single human sample? Our readers can use your recommendation directly on our project search page: https://genohub.com/shop-by-next-gen-sequencing-project/.

Ravi: Currently 10 million sequences of 150bp PE reads is enough to accurately and quantitatively capture most of the TCR diversity

Genohub: How do you handle under-expression?

Ravi: We keep track of low -expressed TCR transcripts as they are needed to understand the statistics of the distribution of the TCR repertoire. We provide these to the researchers, in case they might need to look for rare transcripts.

Genohub: Why is diversity of the immune repertoire important for health?

Ravi: The diversity is the key to the effectiveness of the TCR-repertoire.  The diversity reflects the ability of the immune system to fight infections.  

Genohub: Any comments on its use for vaccine development, autoimmune study, biomarker detection?

Ravi: We believe the TCR sequence can be easily monitored over time, thereby serving as a powerful biomarker to study the effects of vaccination, to determine if the vaccination was effective. It will also be useful in understanding the underlying cause of autoimmune reactions.

Genohub: Thanks for taking the time to discuss this exciting new method. Is there anything that you’d like to add?

Ravi: Girihlet is very excited to take this approach to the rest of scientific community and make a significant difference on how the TCR is sequenced currently and eventually have an impact on the practice of “precision medicine”. 

Genohub Projects Now Support Multiple Collaborators

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Most researchers using Genohub typically work in a team with other investigators and administrators. However, so far every Genohub user has been able to view and manage only the projects they directly started on Genohub.

We’re pleased to announce that effective immediately, you can add one or more collaborators to any of your Genohub projects, all the way from the project request stage until after your project is complete and the results are ready.

By quickly adding a collaborator to your project you can allow another member of your team to view the quotes and detailed project information. You may also give them permission to manage the project (e.g. post messages, accept quotes, attach files, etc.).

In addition to setting per-member permissions, you can also choose whether each member receives email notifications when there is activity on your project.

To add a collaborator, all you need is their email address:

Genohub Collaboration Tool

For instance you may want to share the instant Genohub quote on a particular service with the primary investigator on your team in order to get their approval. You may also want to give someone at your purchasing department access to the detailed pricing information on your project. Or you may want a colleague to manage the project and handle the communication with the service provider while you’re on vacation. This can all be done by simply adding these individuals as collaborators.

Please give it a try and feel free to reach out to us at support@genohub.com if you have any questions or feedback.