RESUMEN
The need to accurately identify the complete structural variation profile of genomes is becoming increasingly evident. In contrast to reference-based methods like sequencing or comparative methods like aCGH, optical mapping is a de novo assembly-based method that enables better realization of true genomic structure. It allows for independently detecting balanced and unbalanced structural variants (SVs) from separate alleles and for discovering de novo events. Here we show how Bionano Genome Mapping creates de novo assemblies from native and intact, megabase-scale DNA molecules and uses those assemblies to detect a wide range of structural variants.
Asunto(s)
Alelos , Mapeo Cromosómico/métodos , Variación Genética , Genoma Humano , Análisis de Secuencia de ADN/métodos , HumanosRESUMEN
Application of optical mapping based on BioNano Genomics Irys(®) technology ( http://www.bionanogenomics.com/ ) is growing rapidly since its debut in November 2012. The technology can be used to facilitate genome sequence assembly and analysis of genome structural variations. We describe here the detailed protocol that we used to generate a whole genome BioNano map for Aegilops tauschii, the D genome progenitor of hexaploid wheat (Triticum aestivum). We are using the whole genome BioNano map to validate sequence assembly based on the next-generation sequencing, order sequence scaffolds, and ultimately build pseudomolecules for the genome.
Asunto(s)
Mapeo Cromosómico/métodos , Genoma de Planta , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Nanotecnología/métodos , Análisis de Secuencia de ADN/métodos , Triticum/genética , Óptica y FotónicaRESUMEN
The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a large, diverse set of sequencing data for seven human genomes; five are current or candidate NIST Reference Materials. The pilot genome, NA12878, has been released as NIST RM 8398. We also describe data from two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry. The data come from 12 technologies: BioNano Genomics, Complete Genomics paired-end and LFR, Ion Proton exome, Oxford Nanopore, Pacific Biosciences, SOLiD, 10X Genomics GemCode WGS, and Illumina exome and WGS paired-end, mate-pair, and synthetic long reads. Cell lines, DNA, and data from these individuals are publicly available. Therefore, we expect these data to be useful for revealing novel information about the human genome and improving sequencing technologies, SNP, indel, and structural variant calling, and de novo assembly.
Asunto(s)
Benchmarking , Genoma Humano , Exoma , Genómica , Humanos , Mutación INDELRESUMEN
The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug's basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, using both long and short read technologies. A RNA-seq time course across all five developmental stages and male and female adults generated 36,985 coding and noncoding gene models. The most pronounced change in gene expression during the life cycle occurs after feeding on human blood and included genes from the Wolbachia endosymbiont, which shows a simultaneous and coordinated host/commensal response to haematophagous activity. These data provide a rich genetic resource for mapping activity and density of C. lectularius across human hosts and cities, which can help track, manage and control bed bug infestations.
Asunto(s)
Chinches/genética , Regulación del Desarrollo de la Expresión Génica , Estadios del Ciclo de Vida/genética , Animales , Sangre , Mapeo Cromosómico , Ingestión de Alimentos , Femenino , Perfilación de la Expresión Génica , Humanos , Masculino , Modelos Moleculares , Filogenia , Análisis de Secuencia de ARNRESUMEN
Today's biobanks must work to take full advantage of collected samples, while maximizing sample quality and minimizing costs to sustain operations for a long period of time. This is a tall order that will require collaboration and compromise for both end-users and collection sites. This article discusses the efforts of the Génome Québec-Centre Hospitalier Affilié Universitaire Régional de Chicoutimi Biobank to fractionate blood samples for the simultaneous preservation of plasma and DNA-containing layers while minimizing resources required for shipping and transport. This article also describes methods for successful reproducible application of the plasma-depleted blood sample to GenPlates (GenVault, Carlsbad, CA).