Sentences with phrase «deep sequencing»

This type of deep sequencing lets researchers search for minor variants in a virus that can acquire mutations and ultimately take over.

RNA sequencing from whole blood will be performed by processing the RNA and performing deep sequencing.

We assayed (1) the absolute number of 16S rRNA gene copies and (2) overall community structure queried by deep sequencing of 16S rRNA gene tags.

SNP analysis of deep sequencing reads corresponding to the XMRV genomes of 22Rv1 (A) and LNCaP (B), as well as the mitochondrial genomes of these two cell lines (C) was performed.

For his post-doctoral project with David Conway, Alfred studied Gambian P. falciparum isolates using deep sequencing data to investigate signatures of balancing selection, with the aim of identifying new targets for functional and immunological investigation.

Amplified libraries were size - selected on a 2 % agarose gel at approximately 350 bp average length and then sent to an outside company (Elim Biopharmaceuticals, Hayward, CA) for deep sequencing on an Illumina Genome Analyzer IIx (Illumina, San Diego, CA).

Captured libraries then underwent deep sequencing on the Illumina platform, achieving a median of 590-fold coverage for each site.

To find a solution to this, Marcel Martin at Bioinformatics Long - term Support (WABI) at SciLifeLab, in collaboration with the group of Gunilla Karlsson Hedestam at Karolinska Institutet, has developed a practical, computational technique, IgDiscover, that enables rapid production of individualized V gene databases following deep sequencing of expressed antibody repertoires.

Targeted Deep Sequencing Reveals Clinically Relevant Subclonal IgHV Rearrangements in Chronic Lymphocytic Leukemia

To determine whether the growth advantage conferred by X4 - ZFNs treatment in the presence of X4 - and R5X4 - HIV resulted from a survival advantage of CXCR4 disrupted cells, we performed flow cytometry at various time points post infection as well as deep sequencing of the X4 - ZFNs target site on HIV - infected and uninfected cultures.

Age - related variations in DNA methylation were analyzed by deep sequencing technology, which revealed distinct patterns, with gains in methylation in older individuals occurring at genomic sites that were unmethylated in young individuals, and vice versa.

BIOHM's Gut Report will show consumers exactly which microorganisms are in their gut through our DNA deep sequencing analysis of your microbiome (your body's native eco-system made of microorganisms).

When these errors are corrected on the basis of redundant deep sequencing coverage, the final consensus sequences of VP35, VP42, and VP62 are identical to each other and to the 22Rv1 consensus sequence, including a previously described natural polymorphism (A → G) at position 790 [23], [38].

The new deep sequencing methods allow data to be acquired much more efficiently and inexpensively, but optimal methods are less well developed (for some recent work in this area see [8, 14, 26]-RRB-.

The results also demonstrate the value of PrimerID sequencing to provide a high - resolution view of all the mutations present in a given viral population — something that conventional deep sequencing approaches can not do as accurately or efficiently.

In such circumstances, ultra-rapid deep sequencing will be «extremely useful,» he said.

New deep sequencing methods provide a convenient platform for characterizing the composition of the human microbiota [4, 7, 8, 13, 15 — 19].

Deep sequencing validation revealed some interesting allele frequency patterns for validated mutations:

From a total of 10,896,742 raw deep sequencing reads, 40,844 reads were mapped to the 22Rv1 - associated XMRV genome (Fig. 5, «LNCaP (from 2003)»), and the resulting consensus assembly was found to be identical to 22Rv1 - associated XMRV (Fig. 6, «LNCaP (from 2003, consensus)»).

Grant 1592: Investigation into the Genetics of Scottie Cramp: Sequencing of Associated Chromosomal Regions Dr. Natasha J Olby, VetMB PhD Project Goal: Following up on previous research funded by CHF, the goal of this project is to use deep sequencing techniques to identify genetic mutations associated with Scottie Cramp.

«Our combined analysis of cell - free DNA and white blood cell DNA allows for identification of tumor DNA with much higher sensitivity, and deep sequencing also helps us find those rare tumor DNA fragments.»

«To address this problem we combined single - cell sequencing with targeted single - molecule deep sequencing.

To thoroughly characterize mammoth - specific genes and their functions, Lynch and his colleagues deep sequenced the genomes of two woolly mammoths and three Asian elephants — the closest living relative of the mammoth.

They then comprehensively analyzed the changes in the whole genome and epigenome using next generation deep sequencing.

In addition, disruption frequency in cultures treated with X4 - ZFNs as determined by deep sequencing remained remarkably stable between 32 — 33 % from day 5 to day 26 post-transduction in the absence of HIV, which suggests that simultaneous disruption of ccr5 and cxcr4 does not adversely affect cell growth.

«Without deep sequencing and careful analysis, we never would have been able to detect and identify the forces at work and it will be exciting to discover if these insights extend to other microbial communities,» Bhaya noted.

The poor apparent coverage was the result of high sequence divergence of the TMAdV genome from SAdV - 18, which hindered the identification of most of the 16,524 actual deep sequencing reads derived from TMAdV (Fig. 2B, red).

The Ag1000G project is using whole genome deep sequencing to provide a high - resolution view of genetic variation in natural populations of A. gambiae.

LabPMM's FLT3 ITD MRD test is an NGS - based targeted deep sequencing assay that can be used to detect ITDs ranging from 9 bp to > 126 bp in size.

Deep sequenced mRNAs and small noncoding RNAs from 16 brain regions of chimpanzees and rhesus macaques, and compared to the complementary human BrainSpan dataset.

For example, by deep sequencing bacterial DNAs from diseased and healthy subjects, the inventors propose that features associated with certain microbiome compositional and / or functional features (e.g., the amount of certain bacteria and / or bacterial sequences corresponding to certain genetic pathways) can be used to predict the presence or absence of an autoimmune condition.

Highlights of Relevant Experience: Managed matrix team of U.S. and U.K. scientists in first ever large - scale use of US DNA TAP Store integrated liquid handling capabilities to support deep sequencing technology project to generate data for genetic rare variants and for potential asset realignment with project delivery of more than 12,000 samples prepared under extremely tight time lines for GlaxoSmithKline.

To facilitate whole - genome sequencing of TMAdV, we prepared amplified cDNA / DNA libraries for deep sequencing from lung tissue and a lung swab sample from 2 different monkeys using previously published protocols [23], [52].

Infant T cell repertoire analysis combines quantitative PCR to determine relative frequency of T cell receptor chain families with deep sequencing (LINK TO URI GSC) of the CDR3 region to evaluate clonal diversity within each family.