Human660W-Quad v1 DNA Analysis BeadChip Kits

System: iScan, BeadStation, BeadArray Reader, HiScanSQ
Technology: BeadArray
Assay: Infinium DNA Analysis Assay
Applications: Cytogenetic Analysis, Whole-Genome Genotyping and Copy Number Analysis
Species: Human
Contents: Each kit contains 4-96 BeadChips, along with reagents for amplifying, fragmenting, hybridizing, labeling, and detecting 16-384 whole-genome genotyping samples

The Human660W-Quad BeadChip offers comprehensive genomic coverage across many populations and the majority of known variation in regions of the genome, based on HapMap release 24 data. The broad, evenly spaced whole-genome marker set provides high genomic coverage for powerful genome-wide association studies. The entire panel of nearly 660,000 markers provides exceptional identification of known and novel structural variants.

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System Description


The Human660W-Quad BeadChip was built on the HumanHap550 BeadChip. For powerful CNV and cytogenetic analysis, the dense backbone content is combined with an additional 100,000 markers that are highly informative for analyzing common CNV regions. These markers specifically target regions of common copy number variation that were recurrently identified in a high-density screen for CNVs that occur in two or more HapMap samples.

These BeadChips were developed in collaboration with researchers at The Centre for Applied Genomics, Hospital for Sick Children, Toronto, the Wellcome Trust Sanger Institute, and Harvard Medical School/Brigham and Women's Hospital.

  • The convenient quad-sample format enables simultaneous processing of four samples at a time, increasing sample throughput and decreasing experimental variability
  • The Human660W-Quad BeadChip offers the ability to assay limited sample resources, down to 200 ng DNA per sample
  • Process samples using the single-tube, PCR-free Infinium HD Assay
  • Add up to 60,800 SNPs of choice with the semi-custom Human550-Quad+ BeadChip

2010 GWAS Roadmap

Illumina's freely accessible iControlDB is an online database of genotype and phenotype data from individuals on all ILMN’s GWAS arrays that can be used as controls for association or imputation studies.

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Specification

Learn more about how this product is used.




Comprehensive Coverage
of high-value regions:
               
BeadChip Human660w-Quad v1
Number of Markers
per Sample		 657,366
Number of Samples
per BeadChip		 4
DNA Input Requirement
(per sample)		 200 ng
Genomic Coverage  
CEU (Mean /
Median / r2 > 0.8)		 0.92 / 1.0 / 0.87
CHB+JPT 0.92 / 1.0 / 0.85
YRI 0.74 / 0.87 / 0.56
Minor Allele Frequency*  
CEU (Mean /
Median / r2 > 0.8)		 0.24 / 0.23
CHB+JPT 0.21 / 0.20
YRI 0.22 / 0.21
Spacing (kb)  
(Mean / Median) 4.42 / 2.3
90th %ile Largest Gap 18.6
Marker Categories  
Markers Within 10 kb
of a RefSeq Gene		 332,756
Non-Synonymous SNPs 10,051
MHC† / ADME‡ / Indel SNPs 3,177 / 8,440 / 0
Sex Chromosome
(X / Y PAR Loci)		 16,509 / 44 / 15
Mitochondrial SNPs 135


*Based on HapMap rel 24 for HumanCytoSNP-12 and Human660W-Quad, and rel 23 for Human1M-Duo.

**Based on RefSeq and Ensembl databases.

†As defined by de Bakker, 2006

‡Within 10 kb of 333 known ADME-related genes.
 




Contents of the Human660W-Quad DNA Analysis BeadChip Kits:
Catalog Number
WG-311-1501
WG-311-1502
WG-311-1503
WG-311-1504
Number of Samples
16
48
96
384
Number of BeadChips
4
12
24
96
Ship at -65° to -85°C. Store at RT.
Multi-Sample Amplification 1 Mix (MA1)
2.3 ml
2.3 ml
4.6 ml (2 x 2.3 ml)
18.4 ml (8 x 2.3 ml)
Ship at -65° to -85°C. Store at -15° to -25°C.
Multi-Sample Amplification 2 Mix (MA2)
3.9 ml
3.9 ml
7.8 ml (2 x 3.9 ml)
31.2 ml (8 x 3.9 ml)
Multi-Sample Amplification Master Mix (MSM)
4.2 ml
4.2 ml
8.4 ml (2 x 4.2 ml)
33.6 ml (8 x 4.2 ml)
Fragmentation Solution (FRG)
3 ml
3 ml
6 ml (2 x 3 ml)
24 ml (8 x 3 ml)
XStain BeadChip Solution 1 (XC1)
2 ml
6 ml (3 x 2 ml)
12 ml (6 x 2 ml)
48 ml (24 x 2 ml)
XStain BeadChip Solution 2 (XC2)
2 ml
6 ml (3 x 2 ml)
12 ml (6 x 2 ml)
48 ml (24 x 2 ml)
Two-Color Extension Master Mix (TEM)
1 ml
3 ml (3 x 1 ml)
6 ml (6 x 1 ml)
24 ml (24 x 1 ml)
Anti-Stain Two-Color Master Mix (ATM)
2.3 ml
6.9 ml (3 x 2.3 ml)
13.8 ml (6 x 2.3 ml)
55.2 ml (24 x 2.3 ml)
Superior Two-Color Master Mix (STM)
3.3 ml
9.9 ml (3 x 3.3 ml)
19.8 ml (6 x 3.3 ml)
72.9 ml (24 x 3.3 ml)
Resuspension, Hybridization,
and Wash Solution (RA1)
55 ml
55 ml
55 ml
180 ml
XStain BeadChip Solution 4 (XCa)
29 ml
29 ml
29 ml
116 ml (4 x 29 ml)
Spacing (kb)
Precipitation Solution (PA1)
4.0 ml
7 ml
14 ml (2 x 7 ml)
45 ml
Marker Categories
Humidifying Buffer (PB2)
80 ml
12 ml (3 x 4 ml)
24 ml (6 x 4 ml)
60 ml
Hybridization Preparation Buffer (PB1)
80 ml
1.9 L (2 x 950 ml)
3.8 L (4 x 950 ml)
11.4 L (12 x 950 ml)
XStain BeadChip Solution 3 (XC3)
80 ml
240 ml
240 ml
960 ml (4 x 240 ml)

Applications

Whole-Genome Genotyping and Copy Number Variation Analysis

Genome-wide association studies (GWAS) map genetic variation across human populations to identify variants associated with human disease. Infinium HD BeadChips offer GWAS researchers the flexibility to profile samples with up to 5 million markers in high-throughput format, and deliver dense genome-wide coverage with the most up-to-date content available from the scientific community. Strategically selected probes provide sensitive copy number variation analysis and target high-value regions of the genome associated with disease.

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Cytogenetic Analysis

Structural variability is a substantial source of genetic varia­tion that has a major influence on phenotypic variation. Cytogenetic analysis allows researchers to profile chromosomal aberrations such as amplifications, deletions, rearrangements, point mutations, copy number changes, and copy-neutral loss of heterozygosity (LOH) events.

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