New products from Affymetrix for Gene Expression Analysis and Microbial and Human Genotyping

Monday, September 26, 2016 Christopher Krebs

This summer Affymetrix launched several new arrays that leverage the most up-to-date knowledge of genomes and transcriptomes and offer two new focused approaches to genomic medicine. While the array content is new, the sample prep requirements have not changed. Because of this, we can offer these products immediately. Moreover, if you’ve run Affy arrays in the past, your overall project costs will likely remain the same or, in some cases, may even be less.

The new arrays are:

Clariom-S

Clariom-D

Axiom Microbiome

Axiom Precision Medicine Research

 

Clariom-S & Clariom-D

Despite sounding like a popular allergy medicine, these two new arrays combine to give you either a “surface” or “deep” view of the transcriptome. The probes have been designed using annotation as current as April 2016 from the broadest set of databases yet. The surface-view or S arrays contain probes for > 20,000 well-annotated genes, while the deep-view or D arrays interrogate > 500,000 transcripts, including splice variants, rare RNA isoforms and long-noncoding RNA.

For those of you trying to decide between microarrays and RNA-seq, the new Clariom-D array will allow you to interrogate elements within the transcriptome, such as long-noncoding RNA and alternative splice variants that would otherwise require deep sequencing of your RNA-seq libraries. Click here to see how arrays compare to RNA-seq (EMI06543_3_Brochure_Array_or_Seq_0316_WEB.pdf).

Both types of Clariom arrays are available in single-sample cartridges. Clariom-S is also available in the 24-array plate format. In addition to human, the Clariom line extends to rat and mouse, as well.

 

Axiom Microbiome

The Axiom Microbiome Array provides the power to detect microbial content in complex samples across five domains. The array content includes probes to > 11,000 organisms and allows detection to species and strain levels, where available. Arrays are configured in 24- and 96-array plate formats. The Axiom Microbial Detection Analysis Software (MiDAS) is easy-to-use and available as a free download from the Affy website.

 

Axiom Precision Medicine Research (PMR)

Axiom PMR Arrays contain > 900,000 single nucleotide polymorphisms (SNPs), copy number variants (CNV), and insertion/deletion (indel) markers along with a genome-wide association studies (GWAS) imputation module covering all five major ancestral population groups for dense genotyping. Probes cover common and rare variants including markers of clinical relevance, pharmacogenomics, cancer variants and HLA alleles. Axiom HLA Analysis software provides improved imputation of HLA alleles in multi-ethnic populations. Comprehensive analysis support and marker customization capabilities are available with no minimum sample commitments.

For questions or more information about these or any Affymetrix services, contact Chris Krebs at ckrebs@umich.edu or our Affymetrix sales rep Peter Graf at Peter_Graf@Affymetrix.com.

Kickin’ the tires

Monday, April 4, 2016 Jeanne Geskes

We at the DNA Sequencing Core sometimes get the opportunity to give a new instrument a try before committing to a purchase.  Right now at the Core in the Illumina Sequencing group we are kickin’ the tires on a few pieces of equipment:

  • HTG Molecular’s EdgeSeq
  • Agilent’s TapeStation 4200
  • Illumina’s NeoPrep

HTG Molecular’s EdgeSeq

HTG's extraction free (no nucleic acid extraction!) chemistry allows us to make next generation sequencing libraries directly from cell lines, fixed or frozen tissue, plasma, serum, and PAXgene.  They have targeted panels for miRNA and messenger RNA (including a systems biology panel with 2,560 genes, an immuno-oncology panel, and a lymphoma panel). The EdgeSeq is on campus and available for projects. We will keep the demo unit until late May 2016. For more information please visit HTG’s website: https://www.htgmolecular.com/

If you have more questions or are interested in bringing a project to us during the demo period, please contact Jeanne Geskes at jgeskes@umich.edu or our local HTG representative Scott Wernersbach at swernersbach@htgmolecular.com

Agilent’s TapeStation 4200

With 2 Agilent Bioanalyzers and one TapeStation 2200 already pillars of the DNA SeqCore’s RNA and DNA QC, the 4200 offers the fastest throughput with the least hands on time. We have the demo unit here for a couple of weeks. It allows us to load 96 samples at a time and walk away. For more information please visit Agilent’s website: http://www.genomics.agilent.com/en/TapeStation-System/4200-TapeStation-I...

If you have more questions or are interested in the 4200, please contact Jeanne Geskes at jgeskes@umich.edu or our local Agilent representative Pakito Martinez at pakito.martinez@agilent.com

Illumina’s NeoPrep

Illumina’s NeoPrep is a next generation sequencing library prep robot.  Using digital microfluidics the NeoPrep offers a simultaneous library prep of 16 samples with very little hands on time. The DNA kit requires 100ng but offers on board hands free library prep, PCR, quantification and normalization. The RNA library prep requires as little as 25 ng. We have the demo unit for another few weeks. For more information please visit Illumina’s web site: http://www.illumina.com/systems/neoprep-library-system.html

If you have more questions or are interested in the NeoPrep, please contact Jeanne Geskes at jgeskes@umich.edu or our local Illumina representative Scott Evans at sevans@illumina.com.

Meet the UM DNA Sequencing Core!

Tuesday, January 5, 2016 Robert Lyons

I would like to introduce the Sequencing Core team, with whom I am very proud to work: yes, I know the rows are difficult to discern. (I will try to give hints.)

In the front row (left to right), is Craig Johnson (Biostatistician), Tyler Simonds (Affy Specialist), Angela Chidester (Illumina Seq Specialist), Tricia Tamsen (Illumina Seq Specialist), Tina Cartaciano (Affy Specialist) and Jeanne Geskes (Illumina Sequencing Manager, Assistant Director of Technology).

The second row shows David Erdody (DNA Isolation), Doug Warshow (Sample Clerk), Betsy Ketterer (Illumina Seq Tech, wearing a white jacket), David Sheltraw (Illumina Microarray Tech), Leigh Baker (Illumina Seq Tech), and Andrea Kuligowski (Sanger Seq Tech).

In the third row (again L->R) is Chris Krebs (Affymetrix and DNA Isolation Manager, in a dark red shirt), Barry McKay (Sample Clerk, grey beard), Jodi Atkins (Sanger Seq Tech, purple shirt) and Yang Pei (IT specialist, farthest right, in a dark shortsleeved shirt).

Our fourth row includes Kerim Yilmaz (IT/App development, wearing a bright blue shirt), Omer Kocaoglu (IT Manager), Susan Dagenais (Illumina Microarray Tech), Kathy Borysko (PacBio/Sanger Seq Tech), Melissa Coon (Illumina Seq Tech) and Suzanne Genik (Fragment Analysis Tech, light blue jacket).

The final row, in the back, has Robert Lyons (Core Director), Richard Conto (IT System Administrator), Connie Esposito (Manager, Sanger Seq and Assistant Diretor of Core Operations), Chris McHenry (PacBio Seq Tech) and Steven Kerwin (Sanger Seq Tech).

Not shown: Nick Gallagher (Affy Specialist), Ellen Pedersen (Sequenom Specialist) and Jeffrey Handt (Sample Clerk).

DNA Sequencing Core has new web interface!

Tuesday, January 5, 2016 Robert Lyons

Welcome to the new website of the  University of Michigan DNA Sequencing Core! We are shutting down our two previous websites, moving the useful content to this new site, and adding lots of new information and cool tools. For example, check out the menu pulldowns for either 'Platforms' or 'Services' (see above), which will give you a wonderful overview of our full line of services. Some of you may be unaware of our full list of service offerings! Our FAQ pages, too, are getting a big facelift in order to add support for everything we do (instead of being Sanger-centric as they were previously). Finally, I hope you enjoy the blog entries (such as this one) in which we make announcements about new developments, new instruments and new capabilities. Enjoy!   - Bob Lyons, Director