Daily Archives: February 13, 2013

Public release date: 12-Feb-2013 [ | E-mail | Share ]

Contact: Sumrina Yousufzai syousufzai@plos.org 415-568-3164 Public Library of Science

A new form of genetic testing of the bacteria that causes tuberculosis can provide better information on TB transmission and also trace TB outbreaks more accurately than the current standard test, according to a study from Germany published in this week's PLOS Medicine.

A team of researchers led by Stefan Niemann from Forschungszentrum Borstel, Molecular Mycobacteriology, compared the results of the two types of tests on 86 M. tuberculosis isolates from a TB outbreak in the German states of Hamburg and Schleswig-Holstein between 1997 and 2010, in which 2301 people were diseased in the study period.

They found that the new test (whole genome sequencing) provided more accurate information on clustering and longitudinal spread of the pathogen than the standard test (classical genotyping). Importantly, whole genome sequencing revealed that first outbreak isolates were falsely clustered by classical genotyping and do not belong to one recent transmission chain.

By using whole genome sequencing, the authors estimated that the genetic material of M. tuberculosis evolved at a rate at 0.4 mutations per genome per year, suggesting that the bacterium grows in its natural host (infected people) with a doubling time of 22 hours, or 400 generations per year. This finding about the evolution of M. tuberculosis indicates how information from whole genome sequencing can be used to help trace future outbreaks.

Importantly, as the costs of whole genome sequencing are declining, this test could soon become the standard method for identifying transmission patterns and rates of infectious disease outbreaks.

The authors say: "Our study demonstrates that whole genome sequencing-based typing provides epidemiologically relevant resolution of large, longitudinal [Mycobacterium tuberculosis] outbreaks much more efficiently than classical genotyping."

They continue: "We envision that [whole genome sequencing] progressive effective implementation will be accelerated by the continuously decreasing sequencing costs, broader distribution of so-called bench top genome sequencers, and upcoming bioinformatics developments to facilitate quick and relevant interpretation of the resulting data in public health and medical contexts."

###

View post:
Whole genome sequencing better at tracing TB outbreaks than standard test

BALTIMORE, Feb. 12, 2013 /PRNewswire/ --Exemplar LIMS has been selected as the primary lab management and electronic lab notebook (ELN) solution for NY Genome Center's laboratory operations. Sapio's LIMS system will initially track next generation sequencing workflows from the Illumina family of sequencers from request through analysis. Support for additional next gen sequencers will be added as needed.

Sapio's LIMS software will be deployed on Apple iPads using Exemplar LIMS for Tablets solution. This enables lab technicians to take the LIMS with them as they move around the laboratory, improving LIMS usability and lab technician efficiency. NY Genome Center will also be utilizing Exemplar's Materials Management capabilities for detailed tracking of reagent usage. NYGC will ultimately be processing samples for both research and clinical applications via a CLIA certified laboratory. Sapio's experience with implementing best practices for both research and clinical labs will accelerate the LIMS implementation in support of these NYGC objectives.

"The team at New York Genome Center has been impressed with the flexibility and scalability of Sapio's offerings," commented NYGC President & Scientific Director Robert B. Darnell, MD, PhD. "With Sapio we found an entrepreneurial partner that understands how important customer service and collaboration are to NYGC. We look forward to working with Sapio to design a solution for the genome center of the future."

"The leadership at NYGC has recognized the importance of next generation sequencing technology for both research and clinical applications and has assembled a top-notch team from top to bottom. We are both honored and enthused to be supporting the NYGC objectives with the ultimate goal of curing diseases," said Kevin Cramer, VP at Sapio Sciences. "We look forward to working with the NYGC team towards creating a world-class lab operation as they scale to be one of the largest NGS facilities in the North America."

For more information or to schedule a product demonstration, visit http://www.SapioSciences.com.

About Sapio Sciences Llc

Sapio Sciences is a leading provider of LIMS and Data Management software, enabling scientists to manage samples, protocols, assay data and clinical trials.With extensive expertise in genomics/NGS labs, Exemplar LIMS breaks new ground in its breadth of functionality and ease of configuration. With built-in Sample Management, Electronic Lab Notebook (ELN), scientific data management (SDMS) and integrated analytics, Exemplar LIMS addresses the full life cycle of samples from receipt to processing and analysis. Sapio will continue to lead in ease of use and breadth of functionality across its product line, enablingorganizations toreduce costs while increasing productivity and efficiencyof both laboratories and researchers alike.

About New York Genome Center

Founded in August 2010, the New York Genome Center (NYGC) is an independent, non-profit organization leveraging the collaborative resources of leading academic medical centers, research universities, and commercial organizations. Our vision is to transform medical research and clinical care in New York through the creation of one of the largest genomics research facilities in North America, integrating sequencing, bioinformatics, and data management. For more information, visit http://www.nygenome.org

Read more:
New York Genome Institute Selects Exemplar LIMS to Manage Next Gen Sequencing Labs