SARS-CoV-2 genomic surveillance using rapid point of care COVID-19 antigen tests at public test sites in California.

California's SARS-CoV-2 genomic surveillance program (California COVIDNet) developed whole genomic sequencing (WGS) capability from positive COVID-19 antigen tests to maintain genomic surveillance from public test sites. Over 4-months, COVIDNet sourced specimens from positive COVID-19 antigen tests from 142 California public test sites in 43 counties. Successful WGS was defined as at least 83% reference coverage with a minimum 20x genomic read depth.

UShER-TB: Scalable, Comprehensive, Accessible Phylogenomic Analysis of .

, the bacterium responsible for the Tuberculosis (TB) disease, remains a leading global infectious disease killer, and genomic epidemiology is essential for understanding its transmission dynamics. Computational limitations prevent comprehensive phylogenetic analysis of the publicly available genomes. Here, we create UShER-TB, a comprehensive pipeline for scalable phylogenomic MTB analysis.

Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance.

Introduction: The SARS-CoV-2 pandemic represented a formidable scientific and technological challenge to public health due to its rapid spread and evolution. To meet these challenges and to characterize the virus over time, the State of California established the California SARS-CoV-2 Whole Genome Sequencing (WGS) Initiative, or "California COVIDNet". This initiative constituted an unprecedented multi-sector collaborative effort to achieve large-scale genomic surveillance of SARS-CoV-2 across California to monitor the spread of variants within the state, to detect new and emerging variants, and to characterize outbreaks in congregate, workplace, and other settings.

Closed Genome Sequence of Clostridium botulinum Strain IBCA10-7060 Type Bh.

Clostridium botulinum strain IBCA10-7060 was isolated from a stool specimen from an infant botulism patient and is the only Clostridium botulinum strain known that produces botulinum toxin type H. We present here its 4.09-Mbp closed genome sequence.

Unique -mer sequences for validating cancer-related substitution, insertion and deletion mutations.

Cancer genome sequencing has led to important discoveries such as the identification of cancer genes. However, challenges remain in the analysis of cancer genome sequencing. One significant issue is that mutations identified by multiple variant callers are frequently discordant even when using the same genome sequencing data.

High density mechanical energy storage with carbon nanothread bundle.

The excellent mechanical properties of carbon nanofibers bring promise for energy-related applications. Through in silico studies and continuum elasticity theory, here we show that the ultra-thin carbon nanothreads-based bundles exhibit a high mechanical energy storage density. Specifically, the gravimetric energy density is found to decrease with the number of filaments, with torsion and tension as the two dominant contributors.

Whole genome analysis identifies the association of TP53 genomic deletions with lower survival in Stage III colorectal cancer.

DNA copy number aberrations (CNA) are frequently observed in colorectal cancers (CRC). There is an urgent need for CNA-based biomarkers in clinics,. n For Stage III CRC, if combined with imaging or pathologic evidence, these markers promise more precise care.

Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2.

HepG2 is one of the most widely used human cancer cell lines in biomedical research and one of the main cell lines of ENCODE. Although the functional genomic and epigenomic characteristics of HepG2 are extensively studied, its genome sequence has never been comprehensively analyzed and higher order genomic structural features are largely unknown. The high degree of aneuploidy in HepG2 renders traditional genome variant analysis methods challenging and partially ineffective.

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562.

K562 is widely used in biomedical research. It is one of three tier-one cell lines of ENCODE and also most commonly used for large-scale CRISPR/Cas9 screens. Although its functional genomic and epigenomic characteristics have been extensively studied, its genome sequence and genomic structural features have never been comprehensively analyzed.

Vinylene and benzo[][1,2,5]thiadiazole: effect of the π-spacer unit on the properties of bis(2-oxoindolin-3-ylidene)-benzodifuran-dione containing polymers for n-channel organic field-effect transistors.

Two polymers based on (3,7)-3,7-bis(2-oxoindolin-3-ylidene)benzo[1,2-:4,5-']difuran-2,6(3,7)-dione (BIBDF) coupled with ()-2-(2-(thiophen-2-yl)vinyl)thiophene (TVT) or dithienylbenzothiadiazole (TBT), namely PBIBDF-TVT and PBIBDF-TBT were synthesized the Stille coupling reaction. The effect of benzothiadiazole or vinylene-π spacer of the copolymers on optical properties, energy levels, electronic device performance and microstructure were studied. It was found that PBIBDF-TBT based OFET devices, annealed at 180 °C, showed better performance with the highest electron mobility of 2.

Tuning the Amount of Oxygen Vacancies in Sputter-Deposited SnO films for Enhancing the Performance of Perovskite Solar Cells.

This work demonstrates the effect of oxygen vacancies in SnO thin films on the performance of perovskite solar cells. Various SnO films with different amounts of oxygen vacancies were deposited by sputtering at different substrate temperatures (25-300 °C). The transmittance of the films decreased from 82 to 66 % with increasing deposition temperature from 25 to 300 °C.

Identification of large rearrangements in cancer genomes with barcode linked reads.

Large genomic rearrangements involve inversions, deletions and other structural changes that span Megabase segments of the human genome. This category of genetic aberration is the cause of many hereditary genetic disorders and contributes to pathogenesis of diseases like cancer. We developed a new algorithm called ZoomX for analysing barcode-linked sequence reads-these sequences can be traced to individual high molecular weight DNA molecules (>50 kb).

Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy.

Genomic instability is a frequently occurring feature of cancer that involves large-scale structural alterations. These somatic changes in chromosome structure include duplication of entire chromosome arms and aneuploidy where chromosomes are duplicated beyond normal diploid content. However, the accurate determination of aneuploidy events in cancer genomes is a challenge.

Molecular Engineering Strategy for High Efficiency Fullerene-Free Organic Solar Cells Using Conjugated 1,8-Naphthalimide and Fluorenone Building Blocks.

We designed, synthesized, and characterized a series of novel electron deficient small molecule nonfullerene acceptors based on 1,8-naphthalimide (NAI) and 9-fluorenone (FN) with different branched alkyl chains using various techniques. These molecules are based on an acceptor-donor-acceptor-donor-acceptor (A1-D-A2-D-A1) molecular design configuration with NAI as the end-capping acceptor (A1), FN as electron-withdrawing central (A2) group, and thiophene ring as a donor (D) unit. These materials are named as NAI-FN-NAI (BO) and NAI-FN-NAI (HD) where BO and HD represent butyloctyl and hexyldecyl alkyl groups, respectively.

A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.

We present SWAN, a statistical framework for robust detection of genomic structural variants in next-generation sequencing data and an analysis of mid-range size insertion and deletions (<10 Kb) for whole genome analysis and DNA mixtures. To identify these mid-range size events, SWAN collectively uses information from read-pair, read-depth and one end mapped reads through statistical likelihoods based on Poisson field models. SWAN also uses soft-clip/split read remapping to supplement the likelihood analysis and determine variant boundaries.

From brittle to ductile: a structure dependent ductility of diamond nanothread.

As a potential building block for the next generation of devices/multifunctional materials that are spreading in almost every technology sector, one-dimensional (1D) carbon nanomaterial has received intensive research interests. Recently, a new ultra-thin diamond nanothread (DNT) has joined this palette, which is a 1D structure with poly-benzene sections connected by Stone-Wales (SW) transformation defects. Using large-scale molecular dynamics simulations, we found that this sp(3) bonded DNT can transition from brittle to ductile behaviour by varying the length of the poly-benzene sections, suggesting that DNT possesses entirely different mechanical responses than other 1D carbon allotropes.

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.

Haplotyping of human chromosomes is a prerequisite for cataloguing the full repertoire of genetic variation. We present a microfluidics-based, linked-read sequencing technology that can phase and haplotype germline and cancer genomes using nanograms of input DNA. This high-throughput platform prepares barcoded libraries for short-read sequencing and computationally reconstructs long-range haplotype and structural variant information.

Emergence of Hemagglutinin Mutations During the Course of Influenza Infection.

Influenza remains a significant cause of disease mortality. The ongoing threat of influenza infection is partly attributable to the emergence of new mutations in the influenza genome. Among the influenza viral gene products, the hemagglutinin (HA) glycoprotein plays a critical role in influenza pathogenesis, is the target for vaccines and accumulates new mutations that may alter the efficacy of immunization.

Tuning the resonance properties of 2D carbon nanotube networks towards a mechanical resonator.

The capabilities of the mechanical resonator-based nanosensors in detecting ultra-small mass or force shifts have driven a continuing exploration of the palette of nanomaterials for such application purposes. Based on large-scale molecular dynamics simulations, we have assessed the applicability of a new class of carbon nanomaterials for nanoresonator usage, i.e.

Allele-specific copy number profiling by next-generation DNA sequencing.

The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. We describe a new method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normals.

Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer.

Background: Gastric cancer is the second-leading cause of global cancer deaths, with metastatic disease representing the primary cause of mortality. To identify candidate drivers involved in oncogenesis and tumor evolution, we conduct an extensive genome sequencing analysis of metastatic progression in a diffuse gastric cancer. This involves a comparison between a primary tumor from a hereditary diffuse gastric cancer syndrome proband and its recurrence as an ovarian metastasis.

A programmable method for massively parallel targeted sequencing.

We have developed a targeted resequencing approach referred to as Oligonucleotide-Selective Sequencing. In this study, we report a series of significant improvements and novel applications of this method whereby the surface of a sequencing flow cell is modified in situ to capture specific genomic regions of interest from a sample and then sequenced. These improvements include a fully automated targeted sequencing platform through the use of a standard Illumina cBot fluidics station.

RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing.

Background: Rare single nucleotide variants play an important role in genetic diversity and heterogeneity of specific human disease. For example, an individual clinical sample can harbor rare mutations at minor frequencies. Genetic diversity within an individual clinical sample is oftentimes reflected in rare mutations.