Features Partner Sites Information LinkXpress hp
Sign In
Advertise with Us

Download Mobile App




Classification Software for Discovery of Biomarker Patterns

By Biotechdaily staff writers
Posted on 14 Apr 2004
Multivariate classification software helps scientists discover multiprotein biomarker patterns that result in assays with high predictive accuracy.

The latest version of Biomarker Patterns Software (BPS) 5.0 is a Windows-based package for supervised classification of SELDI (surface-enhanced laser desorption/ionization) mass spectral data sets derived from the ProteinChip platform of Ciphergen Biosystems, Inc. More...
(Fremont, CA, USA). Ciphergen collaborated with Salford Systems (San Diego, CA, USA) to create BPS by modifying and enhancing Salford's existing CART technology. Salford's expertise in the Classification and Regression Tree procedure is well established. Ciphergen has exclusive rights to this software in the field of proteomics.

A major new component of BPS 5.0 allows intelligent feature selection using functionality from Salford's TreeNet algorithm, which embodies multiple additive regression trees (MART). The methodology is based on CART but with adaptations designed to extract the most reliable information from the data set.

TreeNet builds a large number of small trees, each designed to help correct the errors of its predecessors. This new feature avoids the potential problem of "overfitted data,” a condition that occurs when many data points are analyzed against a relatively small sample set, a situation frequently encountered in the early phases of a discovery project, when a relatively small number of samples may be available. By allowing a more focused analysis on the variables that really matter, there is a notable payoff from preselecting variables.

"This is the first time these technologies have been combined in this way, and putting such a powerful but easy-to-use software tool in the hands of a large universe of clinical researchers and biologists holds the potential to discover and create break-through, multibiomarker diagnostic assays,” stated Dan Steinberg, president and CEO of Salford Systems.

Recently, Ciphergen was issued a U.S. patent on a method for finding protein patterns in mass spectrometry data using the classification and regression tree algorithm to identify diagnostic patterns of proteins derived from any type of mass spectrometry data. This method is used in Ciphergen's SELDI ProteinChip Biomarker System for biomarker discovery, validation, and assay development.

Salford Systems provides state-of-the-art mining and business intelligence software and consultation services. Its software is being successfully used in all aspects of complecx data analysis, including predictive modeling and segmentation.

"Biomarker Patterns Software is the only commercially available clinical proteomics software that addresses both discovery of protein multi-markers and their translation to assays with high predictive accuracy,” said Martin Verhoef, president of Ciphergen's Biosystems Division.

Ciphergen's ProteinChip Systems enable protein discovery, characterization, identification, and assay development to provide researchers with predictive, multimarker assay capabilities and a better understanding of biologic function at the protein level.




Related Links:
Ciphergen

New
Gold Member
Serological Pipets
INTEGRA Serological Pipets
3-Part Differential Hematology Analyzer
Swelab Alfa Plus Sampler
New
Hemodynamic System Monitor
OptoMonitor
New
Silver Member
Quality Control Material
NATtrol Chlamydia trachomatis Positive Control
Read the full article by registering today, it's FREE! It's Free!
Register now for FREE to LabMedica.com and get access to news and events that shape the world of Clinical Laboratory Medicine.
  • Free digital version edition of LabMedica International sent by email on regular basis
  • Free print version of LabMedica International magazine (available only outside USA and Canada).
  • Free and unlimited access to back issues of LabMedica International in digital format
  • Free LabMedica International Newsletter sent every week containing the latest news
  • Free breaking news sent via email
  • Free access to Events Calendar
  • Free access to LinkXpress new product services
  • REGISTRATION IS FREE AND EASY!
Click here to Register








Channels

Molecular Diagnostics

view channel
Image: The ONC IN-CYT platform leverages cross indication biomarker cyto-signatures (Photo courtesy of OraLiva)

AI-Powered Cytology Tool Detects Early Signs of Oral Cancer

Each year, 54,000 Americans are diagnosed with oral cancer, yet only 28% of cases are identified at an early stage, when the five-year survival rate exceeds 85%. Most diagnoses occur in later stages, when... Read more

Hematology

view channel
Image: The microfluidic device for passive separation of platelet-rich plasma from whole blood (Photo courtesy of University of the Basque Country)

Portable and Disposable Device Obtains Platelet-Rich Plasma Without Complex Equipment

Platelet-rich plasma (PRP) plays a crucial role in regenerative medicine due to its ability to accelerate healing and repair tissue. However, obtaining PRP traditionally requires expensive centrifugation... Read more

Immunology

view channel
Image: PD-1 protein blockade is the standard treatment for advanced melanoma among the different types of immunotherapy (Photo courtesy of 123RF)

Precision Tool Predicts Immunotherapy Treatment Failure in Melanoma Patients

Melanoma, though accounting for only about 4% of skin tumors, is the deadliest form of skin cancer due to its high potential to metastasize. While immunotherapy, especially PD-1 protein blockade, has revolutionized... Read more

Pathology

view channel
Image: Researchers have developed a novel method to analyze tumor growth rates (Photo courtesy of Adobe Stock)

Novel Method To Analyze Tumor Growth Rates Helps Tracks Progression Between Diagnosis and Surgery

Patients diagnosed with breast cancer often worry about how quickly their tumors grow while they wait for surgery, and whether delays in treatment might allow the disease to spread beyond the point of cure.... Read more
Copyright © 2000-2025 Globetech Media. All rights reserved.