In the previous article “Understanding These Chips to Master Genotyping in No Time,” the Tech Guru introduced the top two companies in the genotyping market and their respective products. Today, we continue to share with you the 11 chips you shouldn’t miss when it comes to genotyping!
1
Star Products
Located in California, USA, Affymetrix is a leading chip manufacturer internationally. Affymetrix’s GeneChip biological chip detection system is a complete detection platform composed of high-density GeneChip chips, reagents, hybridization and scanning instruments, data processing, and analysis tools. It is the world’s first chip system approved for in vitro diagnostics by the EU and the US FDA. The chips that support the GeneChip Scanner 3000 7G instrument are commonly known as card-type chips (each chip processes only one sample).
The following star chips are products of the chip industry giant Affymetrix, which are currently in use at BGI.
Figure 1: Affymetrix GeneTitan High-Throughput Chip Plate and GeneChip Card-Type Chip
NO.1 Genome-Wide Human SNP Array 6.0
Manufacturer: Affymetrix
Chip Features: The Genome-Wide Human SNP Array 6.0 chip uniquely contains over 1.8 million genetic variation markers, including single nucleotide polymorphisms (SNPs) and copy number variations (CNVs).
Table 1: Specifications of the Genome-Wide Human SNP Array 6.0 Chip
|
Number of SNPs on the chip |
906,600 |
|
Number of non-polymorphic probes for copy number detection |
946,000 |
|
Starting DNA amount |
500ng |
|
Average detection rate (0.1) |
＞99% |
|
Average minor allele frequency (MAF) |
HapMap Caucasian 19.6% |
|
HapMap Asian 18.2% |
|
|
HapMap African 20.6% |
NO.2 OncoScan™ FFPE Chip and OncoScan™ CNV FFPE Chip
Manufacturer: Affymetrix
Chip Features:
■ Requires very little starting sample amount, with results obtained quickly—48 hours from 80ng FFPE-derived DNA to results;
■ One analysis, multiple data—whole genome copy number analysis, detection of ≤10MB loss of heterozygosity (LOH) in the genome, and detection of key acquired mutations;
■ Detection of copy number changes with as low as 25% abnormal cell chimerism, while linear copy number detection can go as high as 50 copies;
■ High resolution copy number detection (50 – 125kb) in key cancer genes;
■ Rapid analysis—copy number information for hundreds of samples can be analyzed in minutes;
■ The OncoScan FFPE chip includes a panel for acquired mutations covering 74 mutations in 9 genes (BRAF, KRAS, EGFR, IDH 1, IDH 2, PTEN, PIK3CA, NRAS, TP53);
■ The new OncoScan CNV FFPE kit reduces the detection of 74 mutation sites in the OncoScan FFPE kit, with the remaining design fully consistent with the OncoScan FFPE kit, offering a more economical price that meets the needs of CNV detection in translational medicine and clinical diagnostics.
The OncoScan™ chip utilizes Molecular Inversion Probe (MIP) technology, a mature technique for analyzing copy number changes, loss of heterozygosity, and detecting acquired mutations. Studies have shown that this chip has been validated in various aspects, performing excellently on highly degraded DNA—such as that from tumor samples preserved in formalin-fixed paraffin-embedded (FFPE) specimens from various periods; or samples with very low starting DNA amounts, making this chip a necessary choice for cancer clinical research.
NO.3 CytoScan™ HD Chip
Manufacturer: Affymetrix
Chip Features:
■ The highest density genetics chip in the industry—capable of detecting over 2.7 million biological markers;
■ Approximately 750,000 SNP probes with over 99% genotyping accuracy;
■ Approximately 2 million copy number probes, all screened through genetic quantitative effect detection;
■ Product tested on 3,500 samples before market launch;
■ For CNV detection, CytoScan™ HD has the best gene coverage in the industry;
■ Covers >36,000 RefSeq genes with an average marker length of 880 bases;
■ Increases coverage for cancer-related and genetic disease-related genes;
■ Fully covers all genes recognized by the International Society for Cytogenetics (ISCA), cancer-related genes, OMIM genes on the X chromosome, etc.;
■ Simple operation process: from genome to results takes only 2.5 days;
■ Only 7.5 hours of manual operation;
■ Unique human genome scaffold design;
■ Supports the widest variety of sample types;
■ Supports common sample types such as amniotic fluid, buccal epithelial cells, blood, fresh frozen tissues, abortion products, and cultured cells.
Table 2: Specifications of the CytoScan™ HD Chip
|
Copy Number Analysis Markers |
|
|
Total Number of Copy Number Markers |
2,696,550 |
|
Number of Non-Polymorphic Markers |
1,953,246 |
|
Number of SNP Markers |
743,304 |
|
Average Marker Interval (bp) |
|
|
Within Genes (All Below Genes) |
880 |
|
ISCA Genes |
384 |
|
Cancer Genes |
553 |
|
OMIM Morbid Genes |
659 |
|
X Chromosome OMIM Morbid Genes |
486 |
|
RefSeq Genes |
880 |
|
Between Genes (Non-Gene Scaffold) |
1,737 |
|
Total (Gene and Non-Gene Scaffold) |
1,148 |
|
Percentage of Covered Genes (25 Markers/100kb) |
|
|
ISCA Genes (340) |
100% |
|
Cancer Genes (526) |
100% |
|
OMIM Morbid Genes (2,640) |
98% |
|
X Chromosome OMIM Morbid Genes (177) |
100% |
|
RefSeq Genes (36,121) |
96% |
NO.4 CytoScan™ 750k Chip
Manufacturer: Affymetrix
Chip Features:
■ Whole genome coverage, focusing on cytogenetics-related regions, cost-effective and efficient;
■ 750,000 probes for copy number analysis;
■ 200,000 SNP probes, accuracy > 99%;
■ 550,000 unique, non-polymorphic probes;
■ All probes are selected from CytoScan™ HD and have been validated; the workflow is identical to that of CytoScan™ HD.
NO.5 CytoScan™ Optima Chip
Manufacturer: Affymetrix
Chip Features:
The probes of the CytoScan™ Optima Array are selected based on the experience from the CytoScan™ HD Array, totaling 315,608 probes, covering controls, copy number (CN), and single nucleotide polymorphism (SNP) probes. This includes 180,180 CN and 148,450 SNP markers, evenly distributed across the genome, with a focus on 396 prenatal-related gene regions. By combining SNP and non-polymorphic probes, this chip can be applied to CNV detection in prenatal and miscarriage samples, detection of allele imbalance, identification of neutral copy number variations (AOH/LOH), and determination of the occurrence of chromosomal unbalanced translocations.
2
Classic Products
Currently, gene testing companies in the domestic market are emerging like mushrooms after rain. Many companies consider directly using chips targeted at the Chinese population during product development. Both Affymetrix and Illumina have relevant products, and here is the information on two classic chips.
NO.6 Axiom® Genome-Wide CHB 1 & CHB 2
Manufacturer: Affymetrix
Chip Features:
■ Nearly 1.3 million SNP markers, achieving the highest coverage for the Chinese population in the market;
■ Fully validated SNP markers, maximizing coverage of rare and common alleles;
■ Focused on SNPs closely related to diseases and functional relevance;
■ Economically efficient design, selecting only markers related to the Chinese population to avoid redundancy;
■ Fully automated for high throughput;
■ Achieves high sample volume research at low costs;
■ Flexible, automated data analysis software to simplify data processing.
Figure 2: Illumina’s Chinese-8 Chip
NO.7 HumanOmniZhongHua-8 Beadchip (Chinese-8 Chip)
Manufacturer: Illumina
Chip Features:
■ Covers about 81% of common variants (MAF≥5%) and 60% of rare variants (MAF≥2.5%) in the Chinese population;
■ Obtains the latest content from the well-established Infinium HD analysis based on the 1000 Genomes Project;
■ Suitable for genome-wide association studies (GWAS) in the Chinese population.
Table 3: Chip Parameters
|
Chip Name |
Axiom® Genome-Wide CHB 1 & CHB 2 |
HumanOmniZhongHua-8 Beadchip |
|
Number of Loci |
1,280K |
900K |
|
Population Coverage (CHB+JPT) |
(MAF > 5%): 84% (MAF > 2%): 78% |
(MAF > 5%): 81% (MAF > 2.5%): 60% |
|
Samples per Chip |
96 |
8 |
|
Instrument Used |
GeneTitan |
iScan |
Note:
Affymetrix’s CHB chip requires 96 samples to be run simultaneously, which can be challenging to gather. If the sample amount is less than 96, or not a multiple of 96, then the Chinese-8 chip would be more suitable.
If the sample volume is large, the CHB chip can handle a larger throughput, reducing errors between manual or instrument batches, leading to better experimental reproducibility.
3
New Products
The following products are all new chips released in 2016, quickly establishing their presence in the chip market with distinct features and special advantages.
NO.8 Axiom® Precision Medicine Research Array
Manufacturer: Affymetrix
Chip Features:
This newly launched genotyping chip for precision medicine research targets global populations. Developed over several years by international precision medicine research teams, the marker information covers over 25 ethnicities globally, mixing markers from the 1000 Genomes Project with the smallest allele frequency ranges. Clinical relevant markers were selected from public databases, including ClinVar, CPIC, PharmaGKB, and PharmaADME.
Currently, this chip is directly priced on the Affymetrix website at just $29/sample, which is considered very affordable in the chip industry, with no quantity limit (minimum order of one chip for 96 samples).
NO.9-11 Infiniumm® Global Screening Array (GSA)
Coincidentally, Illumina also launched a chip covering world populations in 2016, also referencing data from the 1000 Genomes Project, collectively referred to as the Infiniumm® Global Screening Array (GSA) chip. However, it is composed of the following three chips, allowing researchers to select the appropriate chip based on their research objectives.
Product Names:
NO.9 Infinium Multi-Ethnic Global BeadChip (for global populations)
NO.10 Infinium Multi-Ethnic AMR/AFR BeadChip (for African ancestry Americans)
NO.11 Infinium Multi-Ethnic EUR/EAS/SAS BeadChip (for Europeans/East Asians/South Asians)
Manufacturer: Illumina
Chip Features:
Table 4: Excerpt of Infiniumm® Global Screening Array (GSA) Chip Features
This concludes the introduction to the genotyping special issue. If you have any questions, feel free to leave a message for the Tech Guru! You can also call our customer service hotline: 400-706-6615, where a professional and enthusiastic customer service representative will assist you.
Written by: Xu Xiaoling
Edited by: Marketing Department
Product images sourced from various brand official websites
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