Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing

Fusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment. Fusion gene partner choice and breakpoint-position promiscuity restricts diagnostic detection, even for known and recurrent configurations. Here, we develop FUDGE (FUsion Detection from Gene Enrichment) to accurately and impartially identify fusions. FUDGE couples target-selected and strand-specific CRISPR-Cas9 activity for fusion gene driver enrichment - without prior knowledge of fusion partner or breakpoint-location - to long read nanopore sequencing with the bioinformatics pipeline NanoFG. FUDGE has flexible target-loci choices and enables multiplexed enrichment for simultaneous analysis of several genes in multiple samples in one sequencing run. We observe on-average 665 fold breakpoint-site enrichment and identify nucleotide resolution fusion breakpoints within 2 days. The assay identifies cancer cell line and tumor sample fusions irrespective of partner gene or breakpoint-position. FUDGE is a rapid and versatile fusion detection assay for diagnostic pan-cancer fusion detection

Generation of entangled coherent states via cross phase modulation in a double electromagnetically induced transparency regime

The generation of an entangled coherent state is one of the most important ingredients of quantum information processing using coherent states. Recently, numerous schemes to achieve this task have been proposed. In order to generate travelling-wave entangled coherent states, cross phase modulation, optimized by optical Kerr effect enhancement in a dense medium in an electromagnetically induced transparency (EIT) regime, seems to be very promising. In this scenario, we propose a fully quantized model of a double-EIT scheme recently proposed [D. Petrosyan and G. Kurizki, {\sl Phys. Rev. A} {\bf 65}, 33833 (2002)]: the quantization step is performed adopting a fully Hamiltonian approach. This allows us to write effective equations of motion for two interacting quantum fields of light that show how the dynamics of one field depends on the photon-number operator of the other. The preparation of a Schr\"odinger cat state, which is a superposition of two distinct coherent states, is briefly exposed. This is based on non-linear interaction via double-EIT of two light fields (initially prepared in coherent states) and on a detection step performed using a $50:50$ beam splitter and two photodetectors. In order to show the entanglement of a generated entangled coherent state, we suggest to measure the joint quadrature variance of the field. We show that the entangled coherent states satisfy the sufficient condition for entanglement based on quadrature variance measurement. We also show how robust our scheme is against a low detection efficiency of homodyne detectors.Comment: 15 pages, 9 figures; extensively revised version; added Section

Measurement of the νe and total 8B solar neutrino fluxes with the Sudbury Neutrino Observatory phase-III data set

This paper details the solar neutrino analysis of the 385.17-day phase-III data set acquired by the Sudbury Neutrino Observatory (SNO). An array of 3He proportional counters was installed in the heavy-water target to measure precisely the rate of neutrino-deuteron neutral-current interactions. This technique to determine the total active 8B solar neutrino flux was largely independent of the methods employed in previous phases. The total flux of active neutrinos was measured to be 5.54-0.31+0.33(stat.)-0.34+0.36(syst.)×106 cm-2 s-1, consistent with previous measurements and standard solar models. A global analysis of solar and reactor neutrino mixing parameters yielded the best-fit values of Δm2=7.59-0.21+0.19×10 -5eV2 and θ=34.4-1.2+1.3degrees