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Getting SNPpy With It The GT Guide to Genotyping Technologies


Getting SNPpy With It

The GT Guide to Genotyping Technologies

There might be 10 million SNPs, but will it take 45 companies’ tools to find them?

by Adrienne Burke


Michael Boyce-Jacino, chief technology officer for Orchid BioSciences, says the SNP-technology field is “early in its exploding phase” right now. No argument here. For the tables on the following pages, Genome Technology tracked down 21 purveyors of SNP technologies and a score of others offering SNP data and services.

We’ll acknowledge right up front: Our list is our best effort, but it’s probably not exhaustive. Also, between press time and magazine delivery it’s likely that more SNP discovery methods and services will be launched. SNP detection is a booming business.

Its dawn was a little more than 10 years ago, according to Boyce-Jacino, who was there to greet it. That was when a team at Molecular Tool in Baltimore, charged with determining the parentage of 50,000 thoroughbred foals for the Jockey Club of America, developed a single-base primer extension strategy to find genetic markers on the horses’ genomic DNA. In 1992, when he and Molecular Tool founder Philip Goelet sought NIH funding to use that technology to build a “single nucleotide polymorphism” map of the human genome, Boyce-Jacino believes they coined the term.

But NIH wasn’t impressed. Their proposal was rejected and it wasn’t until microsatellite researchers such as Eric Lander, Ken Buetow, and Avarinda Chakravarty saw how SNPs could help them complete linkage studies that polymorphisms really caught on, Boyce-Jacino says.

Since then, growth has gone out of sight. In 1992, Molecular Tool, which has since been acquired by Orchid, was first to submit data — 200 SNPs it had identified by fragment resequencing in the human genome databases — to dbSNP. By 1995, Boyce-Jacino says the scientific community had identified some 40,000 candidate SNPs in silico. Today, more than 3 million SNPs have been cataloged by the industry at large.

Depending how you do the math, there could be as many as 10 million SNPs in the human population. Identifying, scoring, and linking them all to disease or drug response is a gargantuan job, to be sure.

But can it really support a market of several dozen genotyping technology vendors? Boyce-Jacino thinks not. “There’s definitely not room for all these companies. We’ll start to see a consolidation,” he predicts. “You’ll have five or six purveyors of SNPs, and a few dominant tool makers.”

How will they shake out? Drug makers will likely determine that. On behalf of the SNP Consortium last year, PricewaterhouseCoopers grilled 20 drug discovery and development executives for their thoughts on SNPs. Most reported that their companies were not prepared to fully utilize genotyping information in drug discovery efforts, and many didn’t anticipate that such data would affect commercial drug development for at least another 10 years. The pharma folks said public perception, regulatory issues, and healthcare providers and payers would be obstacles to the full utilization of genotyping technology in drug development.

But the two biggest obstacles they cited were lack of a proof of concept and cost. At between $0.40 and $1.51 per SNP, and with the ability to process only 10,000 or 100,000 per day, genotyping has been deemed cost prohibitive by some drug companies.

Some vendors boast that their technology can process SNPs at a cost of .50 cents each or that it requires just 5 nanograms of DNA per assay. But many of those surveyed by the SNP Consortium are waiting for costs to get down to a penny per SNP, and 64 percent of them said they need technologies that use one nanogram or less of DNA per assay.

What might be even worse news for SNP technology vendors, but encouraging to the companies listed at left, is that most of those 20 execs didn’t view genotyping as a job for their staff. Instead, they said they would outsource the chore. Let’s see what our table looks like a year from now.

Genotyping Tools Galore

Looking to Score SNPs? Choose Your Weapon

Affymetrix Flexible GeneChip Array Uses nucleic acid hybridization to parse as many as 2,000 individual reaction products from complex pooled mixtures. Allows user to create and implement hybridization-based assays of own design. Five arrays $1,250 D 40,000 genotypes per day
Affymetrix GeneChip HuSNP Mapping Assay Probe array offers highly parallel interrogation of nearly 1,500 SNPs covering all 22 autosomes and the X chromosome in a single experiment. Five arrays $3,200 D 40,000 genotypes per day
Amersham Pharmacia Biotech MegaBACE Genotyping System Genotyping on either 48- or 96-capillary systems uses multiple injection method, allowing up to 12 SNPs to be serially injected into the same matrix within each capillary. SNP Profiler is fully automated software to support genotyping application. Genetic Profiler software supports microsatellite genotyping and other fragment analysis. D DNA Sciences 48 capillaries score 7,680 SNPs per day; 96 capillaries score 15,360 SNPs per day
Amersham Pharmacia Biotech SNiPer High-throughput SNP scoring system utilizes Rolling Circle Amplification to score SNPs from genomic DNA. D Oxagen, Riken University, University of Washington 50,000 genotypes per day
Applied Biosystems GeneMapper/LinkMaper Linkmapper, developed with Genomica, and the ABI Prism GeneMapper High Performance Genotyping Software, provide allele calling functionality, quality checking, genetic-data management, and analysis capabilities in one integrated system. $15,000 D D
Applied Biosystems TaqMan Gene Expression Reagents TaqMan probe and two sequence-detection primers for each gene transcript. D NCI D
Applied Biosystems ABI Prism SnaPshot Multiplex Kit Product for high-throughput SNP validation and low to medium SNP screening on electrophoresis system for production scale DNA analysis. ABI 3700: $300,000 SnaPshot: D Celera, DeCode, NCI, Sanger Centre, Whitehead Institute D
CuraGen SNP Calling Integrates Curagen''s genomic technologies, including expression and proteomics technologies, to identify and characterize SNPs. Coding SNPs are then associated with disease genes and validated with a human clinical population. Available via partnership, not off-the-shelf Bayer D
CyGene TPA (Triplex Protection Assay) Non-PCR-based method to detect and characterize specific nucleic acid sequences by formation of stable triplex nucleic acid structures via the hybridization of target-specific probes. Anticipated cost: $1.50 per scored SNP Vaporware Launch expected 2001 1,000 SNPs scored per 8-hour day
Illumina BeadArray Platform Ultra high-throughput genotyping platform under development with Applied Biosystems for year-end release will employ Illumina''s optical fiber bundle arrays, which contain microscopic beads coated with particular molecules and bind to matching molecules in a sample. D Vaporware 1,000 SNPs scored per minute: in 96-well plate format with 2,000 SNPs per bundle, 192,000 SNPs could be analyzed in one experiment in just over three hours
Intergen Amplifluor SNPs Genotyping System Exclusive dual fluorophore, closed-tube format to genotype SNPs. Assay development: $250 for 100 reactions High throughput screening: $495 for 500 reactions Centers for Disease Control and Prevention, Molecular Devices, National Institutes of Health, University of Birmingham, University of Virginia HTP capability depends on instrument
Li-Cor SAGA GT Genotyping System An infrared flourescent system composed of hardware, reagents, and software that completely automates microsatellite analysis. $65,000 D Up to 540 multiplexed sample lanes per 8-hour day; as many as 10 multiplexed loci per sample lane
Lynx Megatype Genomic DNAs from affected and control samples are pooled, and new SNPs are identified within population being analyzed. Designed to identify SNPs that are most likely to be associated with the disease or trait phenotype in the affected samples by identifying SNPs that are significantly under or over represented in affected versus control samples. D Early access: Genomics Collaborative, Oxagen, Aventis Crop Sciences Full commercial launch planned 2001 Equivalent of 200 million genotypes per experiment
Molecular Devices SNP Genotyping Using High Efficiency Fluorescence Polarization (HEFP) Fluorescence Polarization-based genotyping system capable of interfacing with various biologies for interrogating SNPs. $80,000+ depending on configuration and throughput of instrument Incyte Genomics, Whitehead Institute/MIT, Washington University, among others Ranging from thousands to tens of thousands of assay points per operating day
Motorola Code Link Bioarray system includes bioarrays, instrumentation, reagents, and software. The bioarrays being tested at the Mayo Clinic include the p450 arrays with more than 75 SNPs from the p450 family. D In beta at Mayo Clinic D
Nanogen Nanochip System A 99-site electronically powered microarray with loader and reader. DNA and RNA are moved and concentrated by controlling the current at each test site. Uses low conductivity buffer to control hybridizaton parameters. $150,000 for instrument, $150 per chip Mayo Clinic, National Cancer Institute, Aventis Pharmaceuticals, Egea Biosciences Multiple SNPs for a single sample or multiple samples for a single SNP
Orchid SNP-IT Single-base primer extension technology that isolates and interrogates a specific SNP utilizing a two-phase approach of hybridization followed by polymerase-mediated extension to accurately determine genotype information. Flexibility of the technology enables applications on a variety of instrumentation platforms and read-out formats. D Licensed by Applied Biosystems, Amersham Pharmacia Biotech, Perkin Elmer D
Orchid SNPstream 25K and SNPware 384 reagent kits System including hardware, software, assay development, and custom reagent kits for high-throughput genotyping applications. Instrument technology in conjunction with Beckman Coulter. Customized per customer specs Bristol-Myers Squibb, GlaxoSmithKline, DNAPrint Genomics Scores up to 25,000 SNPs per day
Orchid SNPcode Custom Kits Array format genotyping kits for use with Affymetrix GeneFlex chips and systems. Customized per user specs Exelixis Allows customization and analysis of more than 100 different SNPs simultaneously
Orchid SNPstream 5K and SNPware reagent kits Bead array format genotyping system including hardware, software and reagent kits for medium-throughput applications. Instrument and bead technology in conjunction with Luminex. D Vaporware Launch planned in 2001 Will be able to score approximately 5,000 SNPs per day
Orchid SNPware 96 Complete consumable reagent kits for simple, lower throughput applications using a conventional plate reader or visual interpretation of genotype results. D Vaporware Launch planned in 2001 Will be for lower-throughput in the 1,000 SNPs per day range
Promega READIT SNP Genotyping System Method for detecting presence or absence of particular DNA alleles Adaptable to variety of instrument formats depending on desired batch size, throughput, and budget. $25,000 - $100,000 depending on instrumentation In beta at unnamed research centers 700 samples per 8-hour day
Pyrosequencing PSQ 96 System Moderate to ultra high-throughput DNA analysis based on the company''s ''sequencing by synthesis'' technology, an enzymatic cascade reaction that creates a light flash when bases match. Sequencing systems include ink-jet cartridge instrument, computer, software, reagent kit. Complete system with software and startup kit: $89,000 AstraZeneca, Glaxo SmithKline, Curagen, DZGenes, NIH, Bayer, Harvard Medical School, and others 4,500 SNPs scored per 8-hour period
Pyrosequencing PTP (Preferred Technology Program) High-throughput SNP analysis system based on 384 well microplates and the ‘sequencing by synthesis’ technology. In addition to software and reagent kits, PTP includes sample preparation robotics for a fully automated operation. D Wallenberg Consortium North Scores up to 100,000 SNPs per day
Qiagen Masscode System Permits simultaneous pooled analysis of 15 SNPs per well using less than 5 ng genomic DNA. Agilent single quadrupole mass-spec-based detection system capitalizes on novel, photocleavable low molecular weight Masscode tags. Universally optimized assay relies on incorporation of Masscode-tagged oligonucleotides with allele-specific discrimination. Dedicated software converts mass spectra raw data into statistically based genotype calls. Agilent 1100 LC/MSD and related Masscode components: approx. $150,000 University of Washington School of Pharmacy, Daiichi Pure Chemical SNPs scored in 8-hour period per mass spec: >40,000
Sequenom Mass Array Enables large-scale SNP analysis and improves upon mass spectrometry. Analyzes a molecule directly, without the need for labels or tags. Approx. $395,000 Sanger Centre, Whitehead Institute, NIH, NCI, Hitachi, Gemini Genomics, USDA, Genetics Institute, and Genaissance Pharmacaeuticals, and others 50,000 SNP assays per day
ThermoHybaid DASH (Dynamic Allele Specific Hybridization) SNP scoring instrument available with 2 different SNP scoring technologies and dedicated software suites. McSNP assay combines classic approach for allele discrimination with melting curve analysis. DASH assay uses a strepavidin-coated plate for dynamic allele specific hybridization. Both include automated software scoring suites with experimental design tools. $44,500 for instrument with a cost per test of $0.12-$0.50 D Up to 10,000 SNPs per day
Third Wave Invader assay Detects specific sequences by using structure-specific Cleavase enzymes to cleave a complex formed by the hybridization of overlapping oligonucleotide probes. Uses signal amplification system and works on genomic DNA in concentrations below 5 ng per well or reaction. Flexible in a variety of formats including microtiter plates. D Novartis, Applera, Pfizer, SmithKline Beecham, BML, Specialty Laboratories, Sanger Centre, NIH, University of Minnesota, Stanford University, Imperial College, Wellcome Trust/University of Cambridge Automation dependent, up to 100,000 SNPs per day
Variagenics NuCleave Genotyping/Haplotyping Platform Proprietary technology that uses Bruker Daltonics mass spectrometry to measure DNA fragments produced by chemical cleavage at points where it has inserted synthesized nucleotide analogs. Can score both strands at the same time. Technology offered as part of broader collaboration (Variagenics Impact Program) or to clinical laboratories involved in genotyping for clinical trials. Waters supplies reagent kits. D Covance D
Visible Genetics OpenGene system System includes automated DNA sequencers that analyze 400 bases in about 30 minutes and software for sequence analysis. System suited to clinical as well as research applications. From $40,000 to $60,000 depending on options GlaxoSmithKline 24,000 bases per day



Free Score: Public SNP databases

ALFRED — 213 polymorphisms

CGAP Genome Annotation Initiative —
16,000 SNPs, 6,825 validated

The SNP Consortium Database —
1,106,042 SNPs, 856,666 available

Human Gene Mutation Database — 21,591 mutations

Human SNP Database — 3,358 SNPs

HGBase — 62,907 SNPs

db SNP — 2,558,364 SNPs

CEPH Genotype Database —
2,966,800 genotypes, 1,494 confirmed SNPs


Don’t Want to DIY? Companies performing SNP services


DNA Sciences



Lark Technologies


Orchid BioSciences






SNP Sellers: Private purveyors of SNP data


Celera Genomics

DNA Print

DeCode Genetics

G enomics Collaborative/NetGenics

Gemini Genomics

Incyte Genomics

Orchid BioSciences



The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.