ORLANDO, USA, Oct 17, 2017/ PRNewswire/

Strand NGS now supports large scale RNA- and small-RNA-Seq and Unique Molecular Identifiers (UMIs) for DNA-, RNA-, and small-RNA-Seq.

Strand Life Sciences announced the latest version release of its bioinformatics flagship product, Strand NGS, at the Annual Meeting of the American Society of Human Genetics today. Two major themes in Strand NGS v3.1 address recent challenges in next generation sequencing (NGS).

The first theme is large-scale RNA-Seq data analysis. Current cross-cohort RNA- and small-RNA-Seq studies span tens of replicates and batches across hundreds of samples, sometimes conducted across several different institutions. For such studies, Strand NGS v3.1 includes confounding variable analysis to eliminate technical effects, including batch effects; the t-SNE plot; profile and heat-map plots of gene-body coverage; and several other notable visual enhancements.

The second new feature is support for Unique Molecular Identifiers, or UMIs, for DNA-, RNA- and small-RNA-Seq. UMI support in Strand NGS is end-to-end, spanning alignment to variant calling in DNA-Seq, and alignment to quantification in RNA- and small-RNA-Seq. The Bioo Scientific, Qiagen, and Rubicon UMI protocols are natively supported, and an intuitive interface allows the specification of custom UMI protocols.

“For liquid biopsies and low-grade FFPE samples, UMI support in DNA-Seq enables the detection of somatic variants at low concentrations. In RNA-Seq, large-scale and UMI support can be used in single-cell-based studies that reveal tumor-cell heterogeneity, even at low concentrations”, says Dr. Vamsi Veeramachaneni, Chief Scientific Officer, Strand Life Sciences.

“At Strand, we are continuously working towards improving the accuracy and efficiency of NGS data analysis. Customers can look forward to Strand NGS becoming available on the cloud in the near future”, says Dr. Ramesh Hariharan, Chief Executive Officer, Strand Life Sciences.

Visit Strand Life Sciences at ASHG booth #1017 to know more about Strand NGS v3.1 and other products and service offerings from Strand Life Sciences. Click here to access detailed agenda and v3.1 release notes.

About Strand Life Sciences

Strand Life Sciences is a premier life science informatics innovation company. Founded in 2000, Strand is a leader in technology innovations for healthcare using genomics. By enhancing sequence-based diagnostics and clinical genomic data interpretation using a strong foundation of computational, scientific, and medical expertise, Strand is bringing individualized medicine to the world. To know more, visit www.strandls.com

Address of the bookmark: http://www.strand-ngs.com/strand-announce-strandngss-v31

The webinar will highlight some of the interesting case studies wherein multi-gene testing with NGS was helpful in arriving at a confirmatory as well as differential diagnosis, even for complex clinical conditions. With robust bioinformatic analysis, we were able to detect few complex variations in few cases which a conventional test had missed. Some of those cases will also be discussed.

Session 1: 9 am CET, 18 Apr 2018
Session 2: 8 am CET, 18 Apr 2018 
To attend, register here: http://www.strand-ngs.com/webinar_registration

About Speaker: Dr. Aparna Ganapathy is Senior scientist- Clinical Diagnostics at Strand Life Sciences. She has over 8 years of experience in human genetics and molecular biology. She received her Ph.D. in Human Molecular Genetics from Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore. At Strand Life Sciences, she is involved in the interpretation and clinical reporting of the genetic disorders. The focus of these genetic tests is to provide accurate and rapid clinical diagnosis for various inherited disorders.

Source: http://www.eurekalert.org/pub_releases/2014-05/esoh-pco052914.php

Research Area:
Analysis of Next Generation sequence data in cancer
Methods for analysis of structural variation in cancer genomes
Next Generation sequencing in malaria
Computational comparative genomics
Sensitive genomic sequence search techniques using hidden Markov models
Tasmanian devil facial tumour disease

Link @ http://www.wehi.edu.au/faculty_members/dr_tony_papenfuss

The importance of transcriptional control has been explored in a burgeoning line of research over several decades; nevertheless, we are still far from having a complete picture of the regulatory mechanisms of genes and non-coding RNAs, and their influences on different phenotypes and disease states of a cell. Recent shifts towards large-scale analyses of transcriptional regulation on a sequence and epigenetic level are at the forefront of research, mainly due to sequencing technology advancements and a deeper understanding of the fundamental regulatory processes involved.

Arriving at a better understanding of the influence of specific parts of the overall regulatory machinery on disease states is a high priority of the group’s research agenda.

We are seeking an enthusiastic student to join the group as a PhD student. Applicants must have a BSc(Hons) or MSc degree in a relevant discipline and a willingness to learn and apply new techniques and work in a team. Both local and international students are encouraged to apply.

The studentship covers all university fees and an annual tax-exempt stipend of NZ$22,000 for three years.

Sebastian Schmeier recently joined Massey University and started his own research group in Auckland, New Zealand, a city regularly ranked one of the most livable in the world. This is your chance to experience the amazing Auckland lifestyle and the excitement of joining a young new science team, while staying connected to world class scientific networks.

To apply for the post, please send a cover letter stating your interest in the position and why you think you would be a good candidate, a Curriculum Vitae, a copy of your academic transcript, a sample of your written scientific work, and the names of three referees. Applications will be accepted until the position is filled.

Enquiries and applications to Sebastian Schmeier (s.schmeier@massey.ac.nz).

The evolutionary connections between organisms are represented graphically through phylogenetic trees. Due to the fact that evolution takes place over long periods of time that cannot be observed directly, biologists must reconstruct phylogenies by inferring the evolutionary relationships among present-day organisms. 
Application of the techniques that make this possible can be seen in the very limited field of human genetics, such as the ever more popular use of genetic testing to determine a child's paternity, as well as the emergence of a new branch of criminal forensics focused on genetic evidence.
The effect on traditional scientific classification schemes in the biological sciences has been dramatic as well. Work that was once immensely labor- and materials-intensive can now be done quickly and easily, leading to yet another source of information becoming available for systematic and taxonomic appraisal. This particular kind of data has become so popular that taxonomical schemes based solely on molecular data may be encountered. Proponents even claim that taxonomy was previously based on morphology alone, which of course is utter fable.

For additional information on phylogenetics, see list of Phylogenetics Resources on the Internet.

Phylogeny and Reconstructing Phylogenetic Trees: http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html
the CBRG and Department of Statistics Phylogeny tutorial: http://www.compbio.ox.ac.uk/tutorials/phylogeny/
TUTORIAL: PHYLOGENETIC ANALYSIS USING PARSIMONY:http://home.cc.umanitoba.ca/~psgendb/GDE/phylogeny/parsimony/phylip.parsimony.html

PHYLIP: http://www.umanitoba.ca/afs/plant_science/psgendb/doc/Phylip/main.html
An Introduction to Molecular Phylogeny: http://bibiserv.techfak.uni-bielefeld.de/gcb04/tutorials/hoef-emden/GCB04Tut.pdf

How to make a phylogenetic tree: http://www.hiv.lanl.gov/content/sequence/TUTORIALS/TREE_TUTORIAL/Treetutorial.html
Phylogenetic Trees: http://cnx.org/content/m11052/latest/
Phylogeny by Ron Shamir: http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf
Introduction to Phylogeny: http://www.utm.edu/departments/cens/biology/rirwin/391/391Phylog.htm
Lecturer notes on Phylogeny: http://www.sbc.su.se/~bens/course_material/phylocourse1/lecture2.pdf
Principles and Practice of Phylogenetic Systematics:http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes.htm

Inferring phylogenetic trees: http://www.cis.hut.fi/Opinnot/T-61.6070/slides2008/pres_6070.pdf

Lecture Notes

Chapter 1 - The Diversity, Classification, and Evolution of Vertebrates:http://academic.emporia.edu/mooredwi/nathist/chap1.htm

Algorithms for Phylogenetic Reconstructions:http://lectures.molgen.mpg.de/Algorithmische_Bioinformatik_WS0405/phylogeny_script.pdf

Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. For more detail : http://www.phylogeny.fr/version2_cgi/index.cgi

A Brief Tutorial on Phylogenetics
http://bioss.ac.uk/~dirk/talks/tutorial_phylogenetics.pdf

A Brief Tutorial on Phylogenetics Human Rabbit Chicken
http://bioss.ac.uk/~dirk/talks/psnup_tutorial_phylogenetics.pdf

Phylogenetic Tree Computation Tutorial Overview
http://pga.lbl.gov/Workshop/April2002/lectures/Olken.pdf

MrBayes: A program for the Bayesian inference of phylogeny
http://golab.unl.edu/teaching/SBseminar/manual.pdf

Web sites providing software for the construction of phylogenetic trees

• BioEdit

• Coelocanth-Fish Out of Time

• Computational Biochemistry Research Group

• Digital Taxonomy

• Hennig 86

• Hyperclean from Bioinformatics Solutions, Inc.

• Memorial University of Newfoundland

• Mr. Bayes

• NONA

• Oxford University Evolutionary Biology Group

• Paleobiology Database

• PAUP

• Phylip Homepage

• Poy

• Sinauer Associates

• TNT-Tree Analysis Using New Technology

• Tree Base

• Treefinder

• Tree-Puzzle

• Tree View-Taxonomy and Systematics Group at Glasgow

• Washington University-List of Phylogeny Software

Genomics England will play a key role in building on the UK’s long track record as leader in medical science advances to push the boundaries by unlocking the power of DNA data. The UK will become the first ever country to introduce this technology in its mainstream health system – leading the global race for better tests, better drugs and above all better, more personalised care.

http://www.genomicsengland.co.uk/100k-genome-project/

http://www.interpretomics.co/