1. Axiom®
Genome-Wide CHB 1 & CHB 2 Array Plate Set
The highest coverage of rare and common variants for association studies in Han Chinese populations
Highlights
n 1.2 million SNPs selected from GWAS in Han
Chinese populations
n Comprehensive genotype-tested SNPs including
maximized rare and common allele coverage
n Focus on SNPs with strong disease associations
and functional relevance
n Cost- and analysis-efficient design using only highly
informative CHB markers to avoid redundancy
n Fully automatable with quick assay turnaround time
n Low running costs enable highly powered studies
n Flexible, automation-friendly data analysis software
for simplified data management
Array design/SNP selection
All of the content for Axiom®
Genome-Wide (GW) CHB 1
& CHB 2 Array Plate Set was selected from Axiom®
Genomic
Database, which contains genotype-tested markers derived
from various public sources, including the International HapMap
Project, the Single Nucleotide Polymorphism Database (dbSNP),
and the 1000 Genomes Project. Each marker was tested
extensively to ensure robust detection of the minor allele
with stringent performance criteria in the Axiom®
Assay.
Our genotype testing program gives us uniquely detailed
data on population-specific linkage disequilibrium and
haplotypes. This allows us to be highly efficient when selecting
tagging SNPs for high genomic coverage. By avoiding marker
redundancy and uninformative markers, we minimize the
numbers of SNPs needed to achieve genomic coverage.
SNPs were selected to provide maximum genome-wide
coverage including: chromosomes X and Y, mitochondrial
SNPs, cSNPs (coding SNPs), and indels (see Table 1).
Also included on the array are SNPs within functionally
relevant coding and untranslated regions (UTR) including
markers for ADME and disease-associated SNPs. SNPs
were selected from disease annotation databases such as
Gene Ontology (GO) for the cardiovascular system, Sanger
Cancer Gene Census, PharmaADME, SNPs within the Major
Histocompatibility Complex (MHC) region on chromosome
6, and SNPs originating from the National Human Genome
Research Institute (NHGRI) Catalog of Published Genome-
Wide Association Studies (see Table 1).
Comprehensive genomic coverage
The 1.2 million SNPs in Axiom Genome-Wide CHB 1 & CHB 2
Array Plate Set were chosen to deliver comprehensive coverage
of rare and common alleles in Han Chinese populations.
Axiom®
Genome-Wide (GW) CHB 1 Array Plate was designed
for high genomic coverage of common alleles, while Axiom®
Genome-wide (GW) CHB 2 Array Plate focuses on rare variants.
Axiom GW CHB 2 Array Plate was specifically designed to
supplement the content of the Axiom GW CHB 1 Array Plate.
This complementary nature is shown in Table 2.
Data Sheet
Table 1: Breakdown of SNPs by biological relevance.
Biological category
No. SNPs
Axiom
GW CHB 1
Array Plate
No. SNPs
Axiom GW
CHB 1 & CHB 2
Array Plate Set
cSNPs-nonsynonymous 4,225 10,560
cSNPs-synonymous 3,243 8,422
Splicing and UTR 7,641 20,538
Chromosome X 12,545 36,841
Chromosome Y 1,613 2,460
Indels 3,112 3,826
Mitochondrial 217 304
ADME 3,723 7,886
Genic 277,429 552,684
Inflammation and
immunity pathways
4,387 12,009
MHC 1,873 4,229
Cardiovascular N/A 14,293
NHGRI
disease-associated
2,114 2,424
Sanger Cancer
Gene Census
N/A 16,781
Total SNPs 640,674 1,282,446
