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May 1, 2019

Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population.

The central goal of medical genomics is to understand the inherited basis of sequence variation that underlies human physiology, evolution, and disease. Functional association studies currently ignore millions of bases that span each centromeric region and acrocentric short arm. These regions are enriched in long arrays of tandem repeats, or satellite DNAs, that are known to vary extensively in copy number and repeat structure in the human population. Satellite sequence variation in the human genome is often so large that it is detected cytogenetically, yet due to the lack of a reference assembly and informatics tools to measure this variability,…

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May 1, 2019

Next-Generation Sequencing and Emerging Technologies.

Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively…

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May 1, 2019

Long-read sequencing reveals a 4.4 kb tandem repeat region in the mitogenome of Echinococcus granulosus (sensu stricto) genotype G1.

Echinococcus tapeworms cause a severe helminthic zoonosis called echinococcosis. The genus comprises various species and genotypes, of which E. granulosus (sensu stricto) represents a significant global public health and socioeconomic burden. Mitochondrial (mt) genomes have provided useful genetic markers to explore the nature and extent of genetic diversity within Echinococcus and have underpinned phylogenetic and population structure analyses of this genus. Our recent work indicated a sequence gap (>?1 kb) in the mt genomes of E. granulosus genotype G1, which could not be determined by PCR-based Sanger sequencing. The aim of the present study was to define the complete mt genome,…

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May 1, 2019

Structural variants in 3000 rice genomes.

Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual SV calls that grouped into 1.5 million allelic variants. We found enrichment of long SVs in promoters and an excess of shorter variants in 5' UTRs. Across the rice genomes, we identified regions of high SV frequency enriched in stress response genes. We demonstrated how SVs may help in finding causative variants in genome-wide association analysis. These new insights…

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May 1, 2019

Paragraph: A graph-based structural variant genotyper for short-read sequence data

Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, a fast and accurate genotyper that models SVs using sequence graphs and SV annotations produced by a range of methods and technologies. We demonstrate the accuracy of Paragraph on whole genome sequence data from a control sample with both short and long read sequencing data available, and then apply it at scale to a cohort of 100 samples of diverse ancestry sequenced with short-reads. Comparative analyses indicate that Paragraph has better accuracy than…

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April 23, 2019

Application Brief: Whole genome sequencing for de novo assembly – Best Practices

Single Molecule, Real-Time (SMRT) Sequencing on the Sequel II System enables easy and affordable generation of high-quality de novo assemblies of even the most complex genomes. With megabase-size contig N50s, consensus accuracies >99.99%, and tools for phasing haplotypes you can capture undetected SNVs, fully intact genes, and regulatory regions embedded in complex structures that fragmented draft genomes often miss.

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April 23, 2019

Application Brief: Structural variant detection using whole genome sequencing – Best Practices

With the Sequel II System powered by Single Molecule, Real-Time (SMRT) Sequencing technology and SMRT Link v7.0, you can affordably and effectively detect structural variants (SVs), copy number variants, and large indels ranging in size from tens to thousands of base pairs. PacBio long-read whole genome sequencing comprehensively resolves variants in an individual with high precision and recall. For population genetics and pedigree studies, joint calling powers rapid discovery of common variants within a sample cohort.

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April 23, 2019

Application Brief: Variant detection using whole genome sequencing with HiFi reads – Best Practices

With highly accurate long reads (HiFi reads) from the Sequel II System, powered by Single Molecule, Real-Time (SMRT) Sequencing technology, you can comprehensively detect variants in a human genome. HiFi reads provide high precision and recall for single nucleotide variants (SNVs), indels, structural variants (SVs), and copy number variants (CNVs), including in difficult-to-map repetitive regions.

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April 1, 2019

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (

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April 1, 2019

The role of genomic structural variation in the genetic improvement of polyploid crops

Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between multiple gene and sequence copies, and in genetic mapping, hindering use of genomic data for genetics and breeding. Polyploid genomes may also be more prone to containing structural variation, such as loss of gene copies or sequences (presence–absence variation) and the presence of genes or sequences in multiple copies (copy-number variation). Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation, we propose…

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April 1, 2019

Discovery of tandem and interspersed segmental duplications using high throughput sequencing.

Several algorithms have been developed that use high throughput sequencing technology to characterize structural variations. Most of the existing approaches focus on detecting relatively simple types of SVs such as insertions, deletions, and short inversions. In fact, complex SVs are of crucial importance and several have been associated with genomic disorders. To better understand the contribution of complex SVs to human disease, we need new algorithms to accurately discover and genotype such variants. Additionally, due to similar sequencing signatures, inverted duplications or gene conversion events that include inverted segmental duplications are often characterized as simple inversions, likewise, duplications and gene…

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April 1, 2019

Long-read sequencing identified intronic repeat expansions in SAMD12 from Chinese pedigrees affected with familial cortical myoclonic tremor with epilepsy.

The locus for familial cortical myoclonic tremor with epilepsy (FCMTE) has long been mapped to 8q24 in linkage studies, but the causative mutations remain unclear. Recently, expansions of intronic TTTCA and TTTTA repeat motifs within SAMD12 were found to be involved in the pathogenesis of FCMTE in Japanese pedigrees. We aim to identify the causative mutations of FCMTE in Chinese pedigrees.We performed genetic linkage analysis by microsatellite markers in a five-generation Chinese pedigree with 55 members. We also used array-comparative genomic hybridisation (CGH) and next-generation sequencing (NGS) technologies (whole-exome sequencing, capture region deep sequencing and whole-genome sequencing) to identify the…

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April 1, 2019

Critical length in long read resequencing

Long read sequencing has a substantial advantage for structural variant discovery and phasing of variants compared to short-read technologies, but the required and optimal read length has not been assessed. In this work, we used simulated long reads and evaluated structural variant discovery and variant phasing using current best practice bioinformatics methods. We determined that optimal discovery of structural variants from human genomes can be obtained with reads of minimally 15 kbp. Haplotyping genes entirely only reaches its optimum from reads of 100 kbp. These findings are important for the design of future long read sequencing projects.

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