The Data Insights team at Roche Sequencing Solutions attended the Curating the Clinical Genome meeting in Hinxton, UK this year. The conference was a great opportunity to hear from individuals actively involved in use of genetics in the clinic and leading initiatives to define and improve the state-of-the-art for the field.
The Food and Drug Administration (FDA) recently launched a second precisionFDA Challenge to engage the genomics community in improving algorithms used for next-generation sequencing (NGS) analysis. This “Truth Challenge” aims to evaluate software pipelines for analyzing whole human genome sequencing datasets by comparing resulting variant calls against a new known truth that is not publically available at the time of submission.
The Bina Bioinformatics team is excited to tell you about our latest research in genetic variation analysis at ISMB 2016 this upcoming weekend in Orlando, Florida. Our Bioinformatics Scientist, Mohammad Sahraeian, will be presenting several significant enhancements made to a previously published, integrative structural variation (SV) caller, MetaSV. Recent enhancements have shown improvements in accuracy and speed at detecting more structural variations types, such as insertions, deletions, inversions and duplications, over the original tool. To learn more about this work, be sure to bookmark and check out the following poster presentation on Sunday afternoon:
Roche Sequencing Solutions is excited to welcome you to the Festival of Genomics at the Boston Convention Center from June 27th - 29th. Come by booth #232 to learn what we have in store for an end-to-end NGS workflow, from sample prep to informatics analysis.
Time & Date:
REGISTER TO JOIN US on Thursday June 16, 2016, 10 am PT // 1 pm ET.
SOMATICSEQ: AN ENSEMBLE APPROACH WITH MACHINE LEARNING TO DETECT SOMATIC MUTATION DETECTION
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.
Details on Vardict, a new variant caller, have been published recently in Nucleic Acids Research by authors, Zhongwu Lai and Jonathan Dry, among others from AstraZeneca . The current version of the Bina Read Alignment Variant Calling and Expression software module for secondary analysis includes Vardict, along with five other tools, for calling SNVs or indels from tumor-normal pairs. As the article demonstrates, VarDict has multiple strengths that extend our capabilities in variant calling beyond what was available before its release. Notably, the algorithm is particularly good at detecting indels. It also handles ultra-deep sequenced samples, which have become more common of late, and supports variant calling in tumor-only samples (in addition to tumor-vs-normal calling).
Topics: DREAM Challenge Results, Somatic Mutation Detection, Tumor-Normal, Webinar, Bina RAVE, SomaticSeq, AstraZeneca, Sequencing, VarScan, JointSNVMix, SomaticIndelDetector, VarDict, MuTect, SomaticSniper
At the beginning of the year, we launched the Bina Science section on our website to showcase open source algorithms and peer reviewed journal articles that our team has produced. We are excited to announce the latest addition to our website, the Bina Library. We invite you to explore white papers and poster presentations, watch webinars and case study videos, and learn more about how our products can help you advance genomic discoveries. Simply choose the media type or topic at the top of the page to get started with discovering what we have in our library.
In the keynote presentation of this month’s Bio-IT World Conference and Expo, Dr. Heidi Rehm, Chief Laboratory Director at Partners Healthcare Personalized Medicine, emphasized the need to publicly share genetic variant information to advance patient care. She candidly told the story where her lab at Partners Healthcare reported the result of a genetic test for a fetus at risk for Noonan syndrome as “pathogenic”, only to find out later that there was conflicting evidence and the gene mutation should not be ruled as pathogenic in certain ethnic groups. When she contacted the physician to present the new finding, she was told that the parents had terminated the pregnancy.
At Bina, we employ various variant standardization methods to improve variant annotation performance. Previously we’ve shared how the Bina AAiM software applies variant normalization and its impact. In this post, we’ll show another method that we use.
Pancreatic Neuroendocrine Tumors (PNETs) are a rare but clinically important form of cancer. Because many PNETs grow silently and are therefore frequently diagnosed at a late stage, approximately 65% of patients present with unresectable or metastatic disease. As a result, these patients have a poor prognosis and a median survival time of 24 months with limited treatment options.