Frequently Asked Questions

Eureka Genotyping Solutions

Q: How many SNPs and how many samples?

A: The Eureka Genotyping Solution is suitable for querying tens to thousands of loci for hundreds to thousands of samples. Maximum capacity is sequencing platform dependent. Please contact us at: eurekag@affymetrix.com to discuss the details of your specific project to determine assay capacity based on sequencing platform.

Q: What sequencing platforms are compatible with the assay?

A: Eureka Genotyping Solutions is platform agnostic and is compatible with any Next Generation Sequencing platform. However current sample indices are only compatible with Illumina platforms. Please contact us at: eurekag@affymetrix.com for further details.

Q: How much DNA is required for the assay?

A: See the Sample Submission page.

Q: What applications can the Eureka Assay be used for?

A: The Eureka Assay enables broad profiling of single nucleotide polymorphisms (SNPs), copy number variations (CNVs), INDELs, Gene Expression and epigenetic events, such as methylation. The assay can be used to define presence or absence, or identify contamination.

Q: How does the assay work?

A: A probe triplet is used to interrogate each locus of interest. The probe triplet contains a unique interrogation portion, a common PCR primer and a barcode. Many triplets can be mixed in a probe blend. Following sample DNA and probe blend mixing and hybridization, a ligase is added to join any adjacent left and right probes. PCR amplification proceeds from sample indices containing primers that are unique to each sample, but contain the common PCR primer site. The PCR primers also contain sequences required for NGS data generation. Each usable sequence read contains a SNP and locus sequence and a sample index. Based on the sequences the reads are assigned to sample, allele and locus. The number of reads is analyzed to determine the probability of each genotype for a given sample and a given locus. Depending on the confidence levels of the genotype call established by the statistical model used, a genotype assignment is made.

Q: What types of data output will I get from the assay?

A: For every project, data can be reported back with a variety of information including sample, loci, allele A and B reads, probability of each genotype and the genotype call (AA, AB, BB or no call). See Sample Reports to see what the output looks like.

Q: Is the assay available as a product or a service?

A: The Eureka Genotyping Assay is only available as a service at this time. Please contact us at: eurekag@affymetrix.com for further details.

Q: Is the assay design fixed or flexible? In other words, can targets be easily added or removed from a design?

A: For a custom Eureka panel, probes can be added or removed. If you have specific questions regarding assay flexibility, please contact us at: eurekag@affymetrix.com for more information.

Samples for NGS

Q: Can you process low quantity DNA samples for NGS library preparation?

A: Yes, Affymetrix can prepare libraries and generate sequencing data from samples that have as little as 1 ng of purified DNA without a whole-genome amplification step; this helps reduce amplification bias before library preparation. Affymetrix cannot guarantee results with low sample quantity.

Q: Can you process low quantity RNA samples?

A: The requirements for RNA samples vary depending on the sample (enriched or not, intact or fragmented, etc). Please contact us at: eurekag@affymetrix.com for details.

Q: Should I submit ready-made libraries or use the Affymetrix library preparation service?

A: We prefer to work with Affymetrix prepared libraries. However, libraries prepared by customers with experience in library preparation can perform as well as Affymetrix prepared libraries. Please contact us at: eurekag@affymetrix.com for details.

Q: What should I do if my sample does not meet the Affymetrix quality requirements?

A: Affymetrix experts can recommend methods for sample purification. If the sample quality cannot be improved, we will attempt to generate libraries and sequence data from low quality samples at the customer’s express request. However, Affymetrix cannot guarantee sequencing results with poor quality samples.

Q: Do you accept samples from overseas?

A: Yes. Samples must be shipped and received frozen. Please contact us at: eurekag@affymetrix.com for shipping details and instructions.

Q: What is the turnaround time for a sequencing project?

A: The design of sequencing projects varies widely, and influences turnaround time. Library preparation at Affymetrix will add to the turnaround time, but tends to produce better overall results than customer-prepared libraries. Please contact us at: eurekag@affymetrix.com for details.

Q: I made my libraries with Nextera – can you make sequence data?

A: Yes. Whenever supplying ready-made libraries, you are required to specify the library prep method used and the primer sequences at the time of sample submission. Sequence data generation costs usually increase with Nextera libraries.

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