What ParAllele Bioscience does

ParAllele BioScience was a venture-backed genetics tools company founded in October 2001 by a team of scientists from the Stanford Genome Technology Center. The company developed proprietary Molecular Inversion Probe (MIP) and Mismatch Repair Detection (MRD) technologies for highly multiplexed SNP discovery and genotyping, protected by an exclusive license to Stanford's US Patent 6,858,412. Its commercial product line — marketed under the MegAllele brand — comprised genotyping reagent kits in 3K, 5K, and 10K SNP configurations, application-specific panels (10K and 20K non-synonymous cSNP panels, a Human Immune-Inflammation panel, and a DME-T drug metabolism and transport panel), and full-service genotyping offerings. The biochemistry was designed for integration with Affymetrix GeneChip Tag Arrays and the GeneChip Scanner 3000 via TrueTag universal molecular tags.

The company served three primary customer segments: pharmaceutical companies (Merck, Roche, Novartis, Genaissance) for drug target and biomarker discovery, academic research centers (Baylor College of Medicine, Cambridge University, University of Southern California, University of Iowa) for large-scale disease association studies, and government research institutes, most notably as a participant in the NIH-funded International HapMap Project. Revenue was generated through three streams: professional genotyping and discovery services delivered directly to pharma and academic customers, one-time sales of MegAllele reagent kits distributed globally through Affymetrix's commercial channel, and licensing of proprietary SNPs and technologies to partners.

ParAllele raised approximately $28.5 million across disclosed rounds — Series A from Abingworth, Versant, and Index Ventures in October 2001; a $22.5 million Series B led by Mohr Davidow Ventures in September 2003; and a $6 million follow-on in April 2005 — before signing an agreement to be acquired by Affymetrix on May 31, 2005.

Name

ParAllele Bioscience

Legal name

ParAllele BioScience Inc.

Website

https://parallelebio.com

Company type

Private

Founded year

2001

Operating status

Acquired

Headcount range

1–10 employees

Short description

ParAllele BioScience, founded in 2001 and acquired by Affymetrix in 2005, developed Molecular Inversion Probe technology for highly multiplexed SNP genotyping and discovery, serving pharmaceutical, academic, and government genomics researchers via reagent kits and services.

Ownership category

akta.pro rank

Product category

Genetic Research Tools & Services

NAICS

Research and Development in Biotechnology (except Nanobiotechnology) (541714), Scientific Research and Development Services (5417), Analytical Laboratory Instrument Manufacturing (334516)

SIC

Services-Commercial Physical & Biological Research (8731), Laboratory Analytical Instruments (3826)

akta.pro primary industry

Genotyping Platforms & Services (SNP arrays, GBS, sequencing) (AFABALAE)

akta.pro secondary industries

Molecular Biology & Genomics Instruments (PCR/qPCR, Sequencing, Microarrays) (HLAGAIAF), Genomic & Multi-Omic Biomarkers (NGS panels, transcriptomics, proteomics, metabolomics) (HLAAAMAJ)

Keywords

• SNP genotyping
• Molecular inversion probes
• Genetic variation discovery
• Pharmacogenomics research
• High multiplex assays

Headquarters

HQ city

Waltham

HQ country

United States

HQ region

North America

Offices1 record

Markets served

GTM type

B2B

Offering type

Services

Cost components

Personnel, Technology or R&D, Operations, Marketing or Sales

Revenue model

1. Genotyping Services: Full-service genotyping offerings where ParAllele performs highly multiplexed SNP discovery and genotyping, provides data analysis, and delivers comprehensive genetic study results to pharmaceutical and academic partners.
2. MegAllele Genotyping Products: Sale of genotyping reagent kits (MegAllele products) including custom panels of 3,000-5,000 SNPs and standard panels up to 10,000 pre-selected SNPs. Products designed for use with Affymetrix GeneChip Tag Arrays and instrumentation.
3. Technology Licensing: Licensing of proprietary SNPs and technologies to pharmaceutical and biotech partners. ParAllele licensed over 400 proprietary SNPs from Genaissance and developed co-marketing arrangements.

Pricing tiers

Go-to-market motion2 records

Distribution channels2 records

Marketing channels3 records

Core offering

ParAllele BioScience developed and sold the MegAllele line of highly multiplexed SNP genotyping reagent kits (3K, 5K, and 10K custom and standard SNP panels) and complementary full-service genotyping offerings and Discovery Partnerships. The offerings were built on proprietary Molecular Inversion Probe (MIP) technology and related platforms to enable pharmaceutical and academic customers to perform comprehensive genetic variation studies in single-tube reactions. MegAllele products were designed to integrate with Affymetrix GeneChip instruments and arrays.

Product overview

ParAllele BioScience provides a comprehensive genetic discovery platform centered on the MegAllele product line for SNP genotyping and discovery. The core offerings include MegAllele Genotyping Kits (available in 3K, 5K, and 10K SNP configurations) and specialized application-specific panels such as the 10K/20K cSNP (non-synonymous) panels, the Human Immune-Inflammation panel, and the DME-T (drug metabolism and transport) panel. These products are complemented by full-service genotyping offerings and Discovery Partnerships. The technology stack is built on three proprietary platforms: Molecular Inversion Probe (MIP) technology for highly multiplexed SNP genotyping, Mismatch Repair Detection (MRD) technology for comprehensive SNP discovery, and TrueTag technology for universal microarray-based detection. The MegAllele kits are designed to integrate with Affymetrix GeneChip platforms, specifically the Scanner 3000 and Tag Arrays.

Differentiator

Problem solved

Functional benefit

Brands

• MegAllele: Next-generation genotyping technology and product line that enables comprehensive SNP genotyping studies. Includes genotyping reagent kits, software, and assay panels for use with Affymetrix GeneChip arrays.
• Molecular Inversion Probe (MIP)
• Mismatch Repair Detection (MRD)
• TrueTag Technology
• Lab in a Tube

Products and services

• MegAllele Genotyping Kits Next-generation genotyping kits that comprehensively and accurately score thousands to tens of thousands of targeted SNPs per DNA sample in a single assay, using optimized TrueTag universal molecular tags for detection on Affymetrix GeneChip platforms. Available in 3K, 5K, and 10K SNP configurations.
• MegAllele 10K cSNP Kit Highly multiplexed assay of 10,000 amino-acid-changing SNPs enabling affordable whole genome studies based on direct detection of disease alleles rather than reliance on linkage disequilibrium.
• MegAllele 20K Non-Synonymous SNP Panel Expanded assay panel of 20,000 fully validated non-synonymous SNPs representing more than 10,000 human genes with SNPs that code for amino acid changes, offering cost-effective whole genome analysis potential.
• MegAllele Human Immune-Inflammation Genotyping Panel Application-specific SNP genotyping panel covering approximately 8,000 SNPs from over 1,000 candidate genes related to the genetics of immunity and inflammation, supporting studies in autoimmune and infectious diseases.
• MegAllele DME-T Assay Panel Assay panel providing full coverage of genetic variation for more than 160 genes involved in drug metabolism and transport pathways, incorporating approximately 1,500 SNPs including proprietary variants from Genaissance.
• ParAllele Discovery Partnerships Comprehensive genetic discovery services combining ParAllele's MIP and MRD technologies with genetic and statistical expertise for optimal study design and data analysis, enabling comprehensive discovery and scoring of genetic variation in cohorts for pharmaceutical and academic partners.
• MegAllele Genotyping Services Full-service genotyping offering in which researchers can submit samples for analysis using custom-designed or standard assay panels at multiple SNP densities, with ParAllele performing highly multiplexed genotyping and delivering data analysis.

Quantifiable outcome

• Up to 10,000-20,000 SNPs genotyped in single assay
• +3 more outcomes

Named customers10 records

Segments4 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Integration3 records

Feature4 records

Partnerships

Twelve partnerships are on record, tiered major, core and supporting.

• University of Southern CaliforniamajorStrategic or Co-development Partner · 27 April 2005Collaboration to discover genes associated with Lupus using Immune-Inflammation panel. Dr. Chaim Oscar Jacob leads study covering over 5 million genotypes - largest childhood onset Lupus trial of its kind.
• Genaissance PharmaceuticalsmajorStrategic or Co-development Partner · 5 April 2005License and co-marketing agreement. ParAllele licensed over 400 proprietary SNPs from Genaissance for MegAllele DME-T assay panel covering 160+ genes involved in drug metabolism and transport. Genaissance offers panel in GLP-compliant environment for clinical applications.
• University of IowamajorStrategic or Co-development Partner · 28 March 2005Collaboration with University of Iowa Cell Biology and Functional Genomics Laboratory, UI Department of Ophthalmology, and UI Center for Macular Degeneration to discover genes responsible for age-related macular degeneration (AMD). Led by Gregory Hageman, Ph.D.
• NovartiscoreStrategic or Co-development Partner · 5 October 2004Collaboration to discover genetic variations associated with coronary artery disease. ParAllele uses Mismatch Repair Detection technology to discover novel SNPs in candidate genes selected by Novartis. Results will be used for biomarker identification and new drug target prioritization.
• Cambridge UniversitymajorStrategic or Co-development Partner · 20 July 2004Large-scale genetic study of type 1 diabetes with Prof. John Todd's team at Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory. Uses 10,000 non-synonymous SNPs to compare genotypes between 1,000 diabetic and 1,000 control samples.
• AffymetrixcoreChannel Partner/ Reseller/ Distributor · 19 May 2004Non-exclusive distribution and marketing agreement. Affymetrix distributes ParAllele's MegAllele genotyping reagents for use with GeneChip arrays. ParAllele designs assays and manufactures reagent kits and software while Affymetrix markets integrated products with its arrays and instrumentation. Expanded from year-long R&D collaboration.
• National Cancer Institute (NCI)majorStrategic or Co-development Partner · 12 May 2004NCI became early access customer for MegAllele SNP genotyping platform. ParAllele supplies MegAllele reagent kits, software, and configured instrumentation to Laboratory of Genomic Diversity at NCI-Frederick for disease-mapping in admixed populations.
• RochecoreStrategic or Co-development Partner · 1 September 2003Demonstrated new approach for discovering disease-associated genes in type 2 diabetes. Used proprietary MRD SNP discovery technology to identify common and rare SNPs among functional regions. Study uncovered several new genetic risk factors for diabetes and confirmed known genetic risk factors. Among largest studies of its kind performed.
• MerckcoreStrategic or Co-development Partner · 9 July 2003Collaboration on SNP genotyping study using ParAllele's lab-in-a-tube technology. ParAllele develops assays, performs highly multiplexed genotyping, provides data analysis, and develops platform extensions. Second collaboration announced in May 2004 for SNP discovery to discover genetic variations impacting disease susceptibility and drug response.
• Affymetrix (GeneChip Tag Arrays Supply)coreTechnology or Integration · 18 March 2003Three-year non-exclusive agreement for Affymetrix to supply GeneChip Tag Arrays for use with ParAllele's lab-in-a-tube assay technology. Arrays used in ParAllele's commercial genotyping service business and pharmaceutical collaborations.
• Baylor College of MedicinecoreStrategic or Co-development Partner · 29 October 2002Selected by NIH as part of $37M HapMap Project grant. Baylor uses ParAllele's MIP technology to discover haplotypes shared among human populations. ParAllele's technology produces tens of thousands of probes over two years, resulting in tens of millions of genotypes. Subsequent collaboration on cardiovascular genetics (July 2003) and flu vaccine response study.
• SeraCare Life SciencessupportingStrategic or Co-development PartnerAgreement allows ParAllele to provide DNA samples with genotyping services. SeraCare (acquiring Genomics Collaborative assets) provides DNA repository enabling timely replication of genetic discoveries and extension to other populations.

Scale indicators5 records

Recent moves9 records

Expansion highlights6 records

Direct peers

• Nanogen: Electronically addressable microarray platform provider for SNP genotyping and molecular diagnostics; overlapped with ParAllele in providing multiplexed genotyping solutions to pharma and clinical labs.
• Sequenom: Mass spectrometry-based SNP genotyping company (MassARRAY) that competed directly with ParAllele for pharma and academic high-throughput genotyping projects in the 2003-2005 timeframe.
• Illumina: Developer of microarray and bead-based genotyping platforms (BeadArray, GoldenGate, Infinium) that competed head-to-head with ParAllele's MegAllele assays in pharma and academic SNP-genotyping workflows during the same era.
• Third Wave Technologies: Molecular diagnostics and SNP genotyping company (Invader chemistry) competing for clinical and research genotyping programs; comparable in customer base and assay multiplexing approach.
• Perlegen Sciences: High-density oligonucleotide array-based genotyping company that, like ParAllele, partnered with Affymetrix and competed for large-scale pharma and government population-genetics projects.
• Orchid BioSciences: SNP genotyping services and chemistry provider (SNPstream, GenePaint) serving pharma, academic, and government customers with highly multiplexed assays, overlapping directly with ParAllele's discovery partnership offering.

Broad incumbents

• Affymetrix: Microarray platform incumbent whose GeneChip Tag Arrays and Scanner 3000 were the read-out hardware for ParAllele's MegAllele kits; Affymetrix was both ParAllele's exclusive distribution partner and eventual acquirer.
• Applied Biosystems: Major life-science instruments provider (TaqMan assays, SNPlex) offering competing SNP genotyping chemistries and the dominant qPCR/sequencing instrumentation used in pharma discovery labs during ParAllele's commercial window.
• Roche Diagnostics: Was both a ParAllele customer (Type 2 diabetes study) and a broader competitor/partner via its AmpliChip and diagnostics platforms in the pharma genotyping space.

Emerging players

• deCODE Genetics: Population-genomics company performing large-scale disease association studies; overlapped with ParAllele's pharma customer profile and represented a potential alternative model for genetic discovery partnerships.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks6 records

Key highlights7 records

Customer concentration

Revenue estimate

Valuation estimate

Number of profiles

Profiles12 records

Funding overview

Funding rounds3 records

Investors4 records

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M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about ParAllele Bioscience