DNAprint Genomics (DNAG)

[sam1933]

SERVICES AVAILABLE



1. Custom SNP Panel Development

For groups requiring single-run or routine screening of customer-defined SNP panels, Ellipsis offers complete panel development, optimization and validation, rapid turnaround and custom data reporting. Custom SNP panels can be developed for a variety of species screening applications using either of our technology platforms.

2. Custom Regional Fine Mapping and Candidate Gene Analysis

For customers looking to perform more refined SNP studies, Ellipsis offers a library of mapped, annotated SNPs, many pre-validated, for development of customer-defined SNP analysis. This library includes over a million human SNPs that can be used alone or in combination with a client’s proprietary SNP markers.

3. Focused Pre-validated panels for Human and Mouse Studies

Using our Illumina GoldenGate Technology, we can offer the following pre-validated SNP panels:

a. Human Linkage IV Panel
This panel is ideal for detecting linkage to a human disease or trait. It includes over 6,000 SNPs selected for high information content and high minor allele frequency in major human populations. All SNPs in the panel are validated for physical and genetic map positions and are evenly distributed across the genome, with an average spacing of 482 kb (0.64 cM).


b. Mouse Linkage Panels
These panels are ideal for for obtaining genome-wide genetic data to identify mouse quantitative trait loci (QTLs), and map candidate genes. Two panels are available:

Mouse Low Density (LD) Linkage Panel (377 loci) This panel has been optimized for application to N2 and F2 mouse genetics crosses. These crosses can be used for mapping quantitative trait loci.

Mouse Medium Density (MD) Linkage Panel (1449 loci) This panel has been provides greater resolution than the Mouse Low Density Linkage Panel. It has been optimized for various mapping applications including characterization of transgenic, congenic and knockout animals, and genetic mapping in advanced intercross mouse lines.

c. Human Major Histocompatability Complex (MHC) Panels
These panels are ideal for examining susceptibility to a wide variety of inflammatory diseases linked to the MHC gene cluster. Two complementary panels of either exon-centric SNPs (1,200 SNPs within 10 kb of MHC coding regions), or mapping SNPs (1,250 SNPs with average spacing of 3.8 kb), can be used separately or combined into a dense mapping set with an average SNP spacing of 2 kb across the entire MHC region.

d. Cancer SNP panel
This panel is ideal for candidate gene-based association studies in Cancer. The panel consists of 1421 SNPs derived from over 400 Cancer-related genes. The SNPs were chosen from the National Cancer Institute’s SNP500Cancer Database.

e. ANCESTRYbyDNA™ 2.5 (available through DNAPrint)
This panel surveys 176 Ancestry Informative Markers (AIMs) to provide an inference of genetic ancestry or heritage. The AIMs were carefully selected from large-scale screens of the human genome, and are characterized by sequences of DNA that are more prevalent in people from one continent than another. Using complex statistical algorithms, the test can determine with confidence to which of the major bio-geographical ancestry groups, Sub -Saharan African, European, East Asian or Native American, a person belongs, as well as the relative percentages in cases of admixed peoples. It represents a great tool for population stratification, and is of interest to those individuals or groups wishing to gain a greater understanding of their ancestry and lineage.

f. EURODNA 1.0 (available through DNAPrint)
This panel is similar to ANCESTRYbyDNA™ 2.5 but focuses on European sub-ancestry. EURODNA 1.0 breaks the European ancestry into 4 groups, reporting individuals’ percentages for each: Northwestern European, Southeastern European, Middle Eastern and South Asian.



4. Genome-wide panels (Standard and Custom)

a. Standard Panels
The following Standard Genotyping BeadChips are offered on our Illumina platform, using Illumina’s Infinium technology. Each panel is ideal for whole-genome association studies and LOH/copy number analysis.



Human-1 Genotyping BeadChip

over 100,000 validated SNP markers
markers selected using a gene-centric approach
most of the SNPs are within exons or within 10 kb of transcripts
HumanHap300 Genotyping BeadChip
over 317,000 tag SNPs derived from Phase I HapMap data
high density of tag SNPs within 10 kb of transcripts
high density of tag SNPs in evolutionarily conserved regions
high density of tag SNPs across MHC region
HumanHap550 Genotyping BeadChip
over 550,000 SNPs
contains content of HumanHap300 BeadChip PLUS an additional 240,000 tag SNPs
additional content provides coverage in regions of lower LD, mitochondrial and Y chromosome SNPs, and SNPs in copy number polymorphism regions
HumanHap650Y Genotyping BeadChip
over 650,000 SNPs
contains content of HumanHap550 BeadChip PLUS an additional 100,000 tag SNPs in the Yoruba population


b. Custom Panels
Clients can use Illumina’s Infinium technology to customize between 7,600 to 121,600 bead types (1 – 2 bead types required per SNP). Beadchips can consist entirely of customized SNPs panels, or custom content can be added to standard panels.

For clients working in non-human species or those studying proprietary/non-public SNPs, Ellipsis offers affordable, complete SNP assay development and genotyping services. Ellipsis has experience in a variety of challenging genomes such as potato, in addition to more traditional standard model organisms and agricultural animal species. With fully automated SNP assay design, Ellipsis can offer cost-effective custom services.

5. Gene Expression Services

In addition to SNP genotyping, our Illumina platform provides a robust system for assaying gene expression. Expression BeadChips are available to assay genome wide expression profiles for human, mouse and rat, on standardized or custom panels. This system is economical, provides greater throughput, and requires less input RNA than comparable current technologies. Illumina has also developed a system to assay partially degraded RNA, such as that from formalin-fixed, paraffin-embedded samples. Both standard and custom panels are available for this assay. Please contact us for more information.

6. Other Services

Ellipsis also provides DNA purification services from blood samples (tubes or FTA cards) or buccal swabs, for those seeking more upstream support in their genotyping studies. Ellipsis will also work with clients on an individual basis to provide other services as needed. Please contact us at [e-mail], or fill out the request form for further information.