Accel-NGS® 2S DNA Library Kits
Vasculogenic mimicry in small cell lung cancer
Nat Commun. 2016 Nov 9;7:13322.
Small cell lung cancer (SCLC) is characterized by prevalent circulating tumour cells (CTCs), early metastasis and poor prognosis. We show that SCLC patients (37/38) have rare CTC subpopulations co-expressing vascular endothelial-cadherin (VE-cadherin)…. more »
A comparative study of ChIP-seq sequencing library preparation methods
BMC Genomics (2016) 17:816.
ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo “library preparation” to enable subsequent high-throughput sequencing…. more »
Cell cycle progression in Caulobacter requires a nucleoid-associated protein with high AT sequence recognition
Proc Natl Acad Sci U S A. 2016 Sep 19. pii: 201612579.
In all organisms, morphological and functional diversity is the product of cell type-specific genetic programs. Asymmetric cell division in Caulobacter yields daughter cells that differ functionally due to the differential read-out of their genomes…. more »
Distinct sub-clonal tumour responses to therapy revealed by circulating cell-free DNA
Ann Oncol (2016). doi: 10.1093/annonc/mdw278. First published online: August 8, 2016.
The application of precision medicine in oncology requires in-depth characterisation of a patient’s tumours and the dynamics of their responses to treatment. We used next generation sequencing of circulating cell-free DNA to monitor the response of a KIT p.L576P-mutant metastatic vaginal mucosal melanoma to sequential targeted, immuno- and chemotherapy…. more »
Digital sorting of pure cell populations enables unambiguous genetic analysis of heterogeneous formalin-fixed paraffin-embedded tumors by next generation sequencing
Sci Rep. 2016 Feb 11;6:20944. doi: 10.1038/srep20944.
Precision medicine in oncology requires an accurate characterization of a tumor molecular profile for patient stratification. Though targeted deep sequencing is an effective tool to detect the presence of somatic sequence variants, a significant number of patient specimens do not meet the requirements needed for routine clinical application… more »
Application of sequencing, liquid biopsies, and patient-derived xenografts for personalized medicine in melanoma
Cancer Discov. 2016 Mar;6(3):286-99. doi: 10.1158/2159-8290. CD-15- 1336. Epub 2015 Dec 29.
Targeted therapies and immunotherapies have transformed melanoma care, extending median survival from ∼9 to over 25 months, but nevertheless most patients still die of their disease. The aim of precision medicine is to tailor care for individual patients and improve outcomes… more »
Genome sequence of Klebsiella pneumoniae urinary tract isolate Top52
Genome Announc. 2(4):e00668-14. doi:10.1128/genomeA.00668-14.
Klebsiella pneumoniae is a significant cause of nosocomial infections, including ventilator-associated pneumonias and catheter-associated urinary tract infections. K. pneumoniae strain TOP52 #1721 (Top52) was isolated from a woman presenting with acute cystitis and subsequently characterized using various murine models of infection… more »
Genome sequence of Klebsiella pneumoniae respiratory isolate IA565
Genome Announc. 2(5):e00896-14. doi:10.1128/genomeA.00896-14.
Klebsiella pneumoniae is a clinically significant opportunistic bacterial pathogen as well as a normal member of the human microbiota. K. pneumoniae strain IA565 was isolated from a tracheal aspirate at the University of Iowa Hospitals and Clinics… more »
Risk stratification of Barrett’s oesophagus using a non-endoscopic sampling method coupled with a biomarker panel: a cohort study
Lancet. 2016, Nov 10; doi: 10.1016/S2468-1253(16)30118-2.
FFPE-extracted DNA was quantified by PCR with primers specific to ALU115 repetitive elements (appendix 1, p 1). At least 10-25 ng quantified DNA was used for library preparation with TP53 Accel-Amplicon comprehensive panel (Swift Biosciences, Ann Arbor, MI, US)…more »
Newborn screening quality assurance program for CFTR mutation detection and gene sequencing to identify Cystic Fibrosis
Journal of Inborn Errors of Metabolism & Screening. 2016, Volume 4:1-11.
All newborn screening laboratories in the United States and many worldwide screen for cystic fibrosis. Most laboratories use a second-tier genotyping assay to identify a panel of mutations in the CF transmembrane regulator (CFTR) gene… more »
Accel-NGS Methyl-Seq DNA Library Kits
Detecting DNA methylation using the Oxford Nanopore Technologies MinION sequencer
bioRxiv. doi: http://dx.doi.org/10.1101/047142, Epub 2016 Apr 4.
Nanopore sequencing instruments measure the change in electric current caused by DNA transiting through the pore. In experimental and prototype nanopore sequencing devices it has been shown that the electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine…. more »
Accel-NGS 1S DNA Library Kits
Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology
FEMS Microbiol Lett. 2016 Mar;363(6). pii: fnw027. doi: 10.1093/femsle/fnw027. Epub 2016 Feb 5.
Single-stranded DNA (ssDNA) phages are profoundly different from tailed phages in many aspects including the nature and size of their genome, virion size and morphology, mutation rate, involvement in horizontal gene transfer, infection dynamics and cell lysis mechanisms. Despite the importance of ssDNA phages as molecular biology tools and model systems, the environmental distribution and ecological roles of these phages have been largely unexplored… more »
GATA2 deficiency in children and adults with severe pulmonary alveolar proteinosis and hematologic disorders
BMC Pulm Med. 2015 Aug 12;15:87. doi: 10.1186/s12890-015-0083-2.
The majority of cases with severe pulmonary alveolar proteinosis (PAP) are caused by auto-antibodies against GM-CSF. A multitude of genetic and exogenous causes are responsible for few other cases… more »
Unique synteny and alternate splicing of the chitin synthases in closely related heliothine moths
Gene. 2015 Dec 10;574(1):121-39. doi: 10.1016/j.gene.2015.08.001. Epub 2015 Aug 5.
Chitin is an extracellular biopolymer that contributes to the cuticular structural matrix in arthropods. As a consequence of its rigid structure, the chitinous cuticle must be shed and replaced to accommodate growth… more »
Complete mitochondrial genome of Muricea crassa and Muricea purpurea (Anthozoa: Octocorallia) from the eastern tropical Pacific
bioRxiv. doi: http://dx.doi.org/10.1101/042945.
We sequenced the complete mitogenomes of two eastern tropical Pacific gorgonians, Muricea crassa and Muricea purpurea, using NGS technologies. The assembled mi- togenomes of M. crassa and M. purpurea were 19,586 bp and 19,358 bp in length, with a GC-content ranging from 36.0% to 36.1%, respectively… more »
Genome Sequences of Campylobacter jejuni 81-176 Variants with Enhanced Fitness Relative to the Parental Strain in the Chicken Gastrointestinal Tract
Genome Announc. 2(1):e00006-14. doi:10.1128/genomeA.00006-14.
Campylobacter jejuni is a major cause of food-borne infections in the United States due to its ability to asymptomatically colonize the gastrointestinal tracts of chickens. Using competition assays with parental C. jejuni 81-176, variants with consistently improved fitness in chicken ceca relative to the parental strain were identified and sequenced… more »