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

308

301

Although massively parallel sequencing approaches have been widely used to study genomic variation, simple alignment of short reads to a reference genome cannot be used to investigate the full range of structural variation and phased diploid architecture, which are important for precision medicine. By contrast, the single-molecule real-time (SMRT) sequencing platform produces long reads that can resolve repetitive structures effectively. We integrated this technology with several other sequencing approaches to construct a high-quality

Section: Bac_168-g09mentioning

confidence: 75%

“…Sequencing library preparation using the GemCode platform. Sample indexing and partition barcoded libraries were prepared using GemCode Gel Bead and Library Kit (10× Genomics) 4 . Sequencing was conducted with Illumina Hiseq2500 to generate linked reads.…”

Section: Methodsmentioning

confidence: 99%

De novo assembly and phasing of a Korean human genome

Seo

Rhie

Kim

et al. 2016

308

301

“…First, we used droplet-based massively-parallel single-cell RNA-Seq 8 ( Methods ) to profile EpCAM + epithelial cells from the small intestine of C57BL/6 wild-type and Lgr5-GFP knock-in mice 1 (Fig. 1a).…”

Section: Resultsmentioning

confidence: 99%

A single-cell survey of the small intestinal epithelium

Haber

Biton

Rogel

et al. 2017

1,346

115

1,694

Intestinal epithelial cells (IECs) absorb nutrients, respond to microbes, provide barrier function and help coordinate immune responses. We profiled 53,193 individual epithelial cells from mouse small intestine and organoids, and characterized novel subtypes and their gene signatures. We showed unexpected diversity of hormone-secreting enteroendocrine cells and constructed their novel taxonomy. We distinguished between two tuft cell subtypes, one of which expresses the epithelial cytokine TSLP and CD45 (Ptprc), the pan-immune marker not previously associated with non-hematopoietic cells. We also characterized how cell-intrinsic states and cell proportions respond to bacterial and helminth infections. Salmonella infection caused an increase in Paneth cells and enterocytes abundance, and broad activation of an antimicrobial program. In contrast, Heligmosomoides polygyrus caused an expansion of goblet and tuft cell populations. Our survey highlights new markers and programs, associates sensory molecules to cell types, and uncovers principles of gut homeostasis and response to pathogens.

“…increase in scaffold N50 was achieved 42 . Linked-read technology has been used to generate contiguous 40-200 kb blocks of genomic variants in the correct order (phased) from trio DNA (collected from a mother, father and child), a cancer cell line and a primary tumour 43 . Inheritance patterns of genomic deletions and gene rearrangements were defined, and haplotype analyses found copy number variation in a mutation in a cancer-driver gene.…”

Section: Methods For Linking Sequences In Genome Assemblymentioning

confidence: 99%

“…Multiplexed primer-based assay technologies have the potential to deconvolve the sequencing read data to count and map haplotype assemblies in several lines 86 . Complementary approaches such as linked-read 43 sequencing and long-read sequencing 35 also show promise for the large-scale genetic analyses of populations in genomics-led breeding strategies.…”

Section: Crop Breeding As a Dna-assembly Problemmentioning

confidence: 99%

Genomic innovation for crop improvement

Bevan

Uauy

Wulff

et al. 2017

331

240

Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genome structure and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access to the large and complex genomes of crops and their wild relatives. Sequencing of wild crop relatives is identifying a wide spectrum of genetic variation, permitting the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems. In the twentieth century, famines caused by political crises, mismanagement of food production or genocide killed an estimated 70 million people and were second only to war as the greatest manmade cause of death 1 . The father of the Green Revolution, Norman Borlaug, summarized the importance of crops: "Without food, people perish, social and political organizations disintegrate, and civilizations collapse. " For thousands of years, people have dedicated considerable resources to securing food supplies; for example, grain supplies to ancient Rome were secured through an extensive network of long-distance transport, and the distribution of grain was coordinated and subsidized by the cura annonae ('care for the grain supply'), an important figure who contributed to the maintenance of political unity and power.During the past 10,000 years, a period known as the Holocene, Earth's environment has been unusually stable. This probably facilitated the domestication of crops from wild species, resulting in steadily improved yields and adaptation to new agricultural areas. The production of food is now carried out on a vast scale, with 38% of Earth's surface dedicated to agriculture 2 . This increased production is having a pervasive influence on ecosystems worldwide: nitrogen production for agriculture accounts for 1.2% of global energy consumption 3 ; photosynthesis can no longer maintain stable levels of atmospheric carbon dioxide; and food production consumes around 70% of freshwater supplies. The modelling of crop responses to increases in temperature predicts that there will be a considerable reduction in the yield of rice, an important crop around the world 4 . Climate change could also alter the dynamics of crop pathogenic agents by altering the range of vectors and by compromising the immune response of crops 5 .Crop production must therefore adapt to more variable environments and the substantial impact it has on the environment needs to be reduced. Productivity must also increase at a much greater rate than in the past to meet the needs of Earth's growing population 6 . Genetic improvements in crop performance continue to be crucial for increasing crop productivity, but current rates of improvement are unable to meet the demands of sustainability and food security 7 . Plant genomics has a central role in the improvement of crops, includi...