Feeds:
Posts
Comments

Posts Tagged ‘Cancer Genetics’


     


SomaticSeq: An Ensemble Approach with Machine Learning to Detect Cancer Variants

June 16 at 1pm EDT Register for this Webinar |  View All Webinars

Accurate detection of somatic mutations has proven to be challenging in cancer NGS analysis, due to tumor heterogeneity and cross-contamination between tumor and matched normal samples. Oftentimes, a somatic caller that performs well for one tumor may not for another.

In this webinar we will introduce SomaticSeq, a tool within the Bina Genomic Management Solution (Bina GMS) designed to boost the accuracy of somatic mutation detection with a machine learning approach. You will learn:

  • Benchmarking of leading somatic callers, namely MuTect, SomaticSniper, VarScan2, JointSNVMix2, and VarDict
  • Integration of such tools and how accuracy is achieved using a machine learning classifier that incorporates over 70 features with SomaticSeq
  • Accuracy validation including results from the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, in which Bina placed 1st in indel calling and 2nd in SNV calling in stage 5
  • Creation of a new SomaticSeq classifier utilizing your own dataset
  • Review of the somatic workflow within the Bina Genomic Management Solution

Speakers:

Li Tai Fang

Li Tai Fang
Sr. Bioinformatics Scientist
Bina Technologies, Part of
Roche Sequencing

Anoop Grewal

Anoop Grewal
Product Marketing Manager
Bina Technologies, Part of
Roche Sequencing

<Read full speaker bios here>

Cost: No cost!

Schedule conflict? Register now and you’ll receive a copy of the recording.

This webinar is compliments of: 

Bio-ITWorld.com/Bio-IT-Webinars

Read Full Post »


Reporter: Aviva Lev-Ari, PhD, RN

 

Mayo Launches OncoSpire with Cancer Genetics; Opens Exome Service for Rare Diseases, Advanced Cancer

May 29, 2013

The Mayo Clinic is continuing its push into clinical sequencing with several new initiatives. Recently, it announced that it has teamed up with Cancer Genetics to form a commercial entity dedicated to developing products to better diagnose cancer, guide treatment, and predict outcomes. Additionally, the center has now opened a whole-exome sequencing service for patients with unknown diseases or advanced cancer, Gianrico Farrugia, who heads Mayo’s Center for Individualized Medicine, told Clinical Sequencing News.

It has also launched a clinical trial involving next-gen sequencing of patients with castration-resistant prostate cancer, called Prostate Cancer Medically Optimized Genome-Enhanced Therapy, or PROMOTE. The goal is to use sequencing technologies to identify treatment options for prostate cancer patients.

In addition, in April, it launched its first next-generation sequencing panel for hereditary colorectal cancer, and it has around 26 additional panels in the pipeline, Farrugia said.

OncoSpire Genomics

The Mayo/Cancer Genetics entity, dubbed OncoSpire Genomics, will be based in Rochester, Minn. It will focus on cancer biomarker discovery, around which tests can be developed to diagnose cancer, guide treatment, predict drug response and resistance, and predict outcomes.

“We felt that this was an opportunity for us to create a new company that would allow Mayo’s expertise to be partnered with outside resources to accelerate the process of bringing new biomarkers out for our patients,” Farrugia said.

The venture will leverage Mayo Clinic’s clinical expertise and next-generation sequencing resources with Cancer Genetics’ “commercial acumen” and operating capital, Panna Sharma, Cancer Genetics’ CEO, told CSN.

Initially, OncoSpire will focus on hematological and urogenital cancers. A board composed of both Mayo and Cancer Genetics employees will choose the projects, which will be carried out by Mayo staff, Farrugia said. The Mayo has one of the “best clinically annotated biobanks,” he said, and “the ability to use that is key.”

The initial board of governors consists of six members, three Mayo Clinic appointees and three Cancer Genetics appointees. Farrugia is on the board along with Scott Beck, administrator of the Mayo’s Center for Individualized Medicine, and Kathy Bates, director of business development for Mayo’s Medical Laboratories. The three representatives from Cancer Genetics are Sharma, Founder and Chairman of the Board Raju Chaganti, and John Pappajohn, a member of the firm’s board of directors.

Sequencing will initially be done at Mayo, but Farrugia said that the team has not yet decided if that will be its long-term plan.

Sharma added that more details about the products and commercial timeline would be provided at an analyst day conference that will be held in Rochester in the next month or two.

WES Service

Separately, the Mayo has launched a whole-exome sequencing service for patients with unknown diseases and advanced cancer.

For this service, Mayo has been contracting sequencing to Baylor College of Medicine and Foundation Medicine, but plans to do more in-house sequencing by the end of year when its pipeline is CLIA certified. The center is working with Silicon Valley Biosystems to develop that clinical sequencing pipeline (CSN 1/23/2013).

The exome service has been available since September, said Farrugia, but Mayo has only recently begun advertising for it. Around 30 to 35 patients have gone through the pipeline thus far.

The diagnostic rate is about 40 percent for the cancer patients and slightly higher for the diagnostic odyssey patients, said Farrugia, but those “numbers are too small to attach too much significance to them,” he said.

The Mayo Clinic works with patients’ insurance companies to obtain reimbursement for the services, which often will include targeted sequencing as well as whole-exome sequencing, and the average out-of-pocket expense ranges between $7,000 and $11,000, depending on the patient’s condition and what the service entails, said Farrugia.

For instance, the service for cancer patients can include obtaining a new tissue sample, sequencing both normal and tumor samples, and sometimes doing both targeted sequencing for a quicker turnaround and exome sequencing, Farrugia said.

As such, the total price charged for the cancer service can be much higher than what is charged for patients with a rare disease, sometimes approaching $30,000, Farrugia said, although prices vary.

Because of all these variables, Farrugia said there isn’t a list price for the service. “We’re really tailoring it to the patient and what we think they can best benefit from,” he said.

Turnaround time is still too long, he said, about one to two months, which he said will be reduced when the center’s clinical sequencing pipeline becomes CLIA certified and more can be done in-house.

Additionally, every patient that receives clinical sequencing also has the option of participating in research, said Farrugia. If the patient consents to research sequencing, that is done at the Mayo Clinic, while the clinical sequencing is outsourced. However, he said that is a temporary model until Mayo’s clinical exome pipeline is CLIA certified and has New York state approval.

The center also offers patients a choice in terms of which incidental findings to receive from the sequencing. Typically, patients with advanced cancer just want to hear about anything that’s actionable, while the conversation with patients and families with diagnostic odysseys is longer and more complicated, he said.

Like other labs offering clinical sequencing, Mayo has decided to diverge from recommendations recently published by the American College of Medical Genetics and Genomics, which say that providers should always return pathogenic variants from a list of 57 genes related to 24 disorders (CSN 5/8/2013).

The recommendations, which were released in March, have sparked a debate in the field as to how best to deal with incidental findings, and a number of groups have written publications both in support of and disagreeing with the recommendations (CSN 5/22/2013).

Farrugia said that Mayo has also written a formal response to ACMG, which he said would be published in an upcoming journal, detailing where it agrees and where it disagrees with the recommendations.

Monica Heger tracks trends in next-generation sequencing for research and clinical applications for GenomeWeb’s In Sequenceand Clinical Sequencing News. E-mail Monica Heger or follow her GenomeWeb Twitter accounts at @InSequence and@ClinSeqNews.

Related Stories

http://www.genomeweb.com/sequencing/mayo-launches-oncospire-cancer-genetics-opens-exome-service-rare-diseases-advanc?hq_e=el&hq_m=1586418&hq_l=8&hq_v=e1df6f3681

 

Read Full Post »