DNA sequencing articles within Nature Communications

Featured

  • Article
    | Open Access

    It remains challenging to characterise somatic copy number alterations (SCNAs) in tumors and the surrounding tissues with spatial and single-cell resolution. Here, the authors develop the scCUTseq approach to characterise SCNAs from single cells in multi-region prostate cancer samples and identify pseudo-diploid cells and subclones.

    • Ning Zhang
    • , Luuk Harbers
    •  & Nicola Crosetto

  • Article
    | Open Access

    Copy number variants (CNV) are shown to contribute to the etiology of various genetic disorders. Here, authors present ECOLE, a deep learning-based somatic and germline CNV caller for WES data. Utilising a variant of the transformer architecture, the model is trained to call CNVs per exon.

    • Berk Mandiracioglu
    • , Furkan Ozden
    •  & A. Ercument Cicek

  • Article
    | Open Access

    Here the authors introduce a new method to study DNA in single cells by long-read sequencing. Their method gives a more complete view of the genomic structure of individual cells and allows to study genetic differences at the single-cell level.

    • Joanna Hård
    • , Jeff E. Mold
    •  & Adam Ameur

  • Article
    | Open Access

    Acorales is sister to all other monocots and contains only one family with just one genus, Acorus. Here, the authors assemble the genome of the diploid Ac. gramineus and the tetraploid Ac. calamus, reconstruct an ancestral monocot karyotype and gene toolkit, and discuss the origin and evolution of the two species and other monocots.

    • Liang Ma
    • , Ke-Wei Liu
    •  & Zhong-Jian Liu

  • Article
    | Open Access

    Monocots are one of the most diverse and dominant clades of flowering plants. Here, the authors assemble the genome of Acorus gramineus, confirm its phylogenetic position as sister to the rest of monocots and reveal the absence of tau (τ) whole-genome duplication observed in the majority of monocot clades.

    • Xing Guo
    • , Fang Wang
    •  & Huan Liu

  • Article
    | Open Access

    Here, the authors provide an exome study of hand grip strength, a proxy of generalized muscle strength. They identify six exome-wide significant genes, with links to disease, and additivity of rare and common genetic variant effects on muscle strength.

    • Yunfeng Huang
    • , Dora Bodnar
    •  & Heiko Runz

  • Article
    | Open Access

    Li-Fraumeni syndrome (LFS) is associated with pathogenic germline TP53 variants and predisposes patients to cancer; understanding the evolution and drivers of LFS-related tumours remains crucial. Here, the authors analyse 22 LFS tumours using whole-genome sequencing and reconstruct the evolution and timing of somatic driver alterations.

    • Nicholas Light
    • , Mehdi Layeghifard
    •  & Adam Shlien

  • Article
    | Open Access

    The interplay between histone modifications and DNA methylation plays a crucial role in establishing and maintaining the epigenomic landscape. Here, the authors develop a nanopore sequencing based method for mapping histone modifications and DNA methylation from native, long, single DNA molecules.

    • Xue Yue
    • , Zhiyuan Xie
    •  & Yimeng Yin

  • Article
    | Open Access

    Most genetic association studies have been done on single nucleotide polymorphisms and small indels, while other types of variants have been less studied. Here, the authors use whole genome sequencing in a diverse population to identify and provide experimental evidence for associations between structural variants and blood-cell traits.

    • Marsha M. Wheeler
    • , Adrienne M. Stilp
    •  & Alex P. Reiner

  • Article
    | Open Access

    Consensus sequence-based methods for self-correction of long-read sequencing data are affected by biases that can mask true variants characterizing little-covered or low-frequency haplotypes. Here, to address this issue, the authors develop a variation graph-based method for performing haplotype-aware self-correction of long reads.

    • Xiao Luo
    • , Xiongbin Kang
    •  & Alexander Schönhuth

  • Article
    | Open Access

    Long-read sequencing technologies are useful for the multifaceted task of characterising somatic mutations, including structural variants, in cancers. Here, the authors combine short and long read sequencing for the phasing analysis, which enables them to resolve the chromosomal backgrounds of somatic mutations in Japanese non-small cell lung cancers.

    • Yoshitaka Sakamoto
    • , Shuhei Miyake
    •  & Ayako Suzuki

  • Article
    | Open Access

    Common variants have been discovered to be associated with Alopecia Areata; however, rare variants have been less well studied. Here, the authors use whole-exome sequencing to identify associated rare variants in the hair keratin gene KRT82. Further, they find that individuals with Alopecia Areata have reduced expression of KRT82 in the skin and hair follicle.

    • Stephanie O. Erjavec
    • , Sahar Gelfman
    •  & Angela M. Christiano

  • Article
    | Open Access

    Germline de novo mutations can impact individual fitness, but their role in human male infertility is understudied. Trio-based exome sequencing identifies many new candidate genes affecting male fertility, including an essential regulator of male germ cell pre-mRNA splicing.

    • M. S. Oud
    • , R. M. Smits
    •  & J. A. Veltman

  • Article
    | Open Access

    Obtaining accurate variant calls from multiple displacement amplified single cell DNA sequencing data needs dedicated models that account for amplification bias and copy errors. Here, the authors describe ProSolo, a model for calling single nucleotide variants with control over the false discovery rate.

    • David Lähnemann
    • , Johannes Köster
    •  & Alexander Schönhuth

  • Article
    | Open Access

    The Lake Malawi cichlid fishes are an example of extreme vertebrate radiation; however, there is very little sequence divergence among the species. Here the authors present a comparative genome-wide methylome study to suggest DNA methylation played a major role in the extensive phenotypic diversity amongst these fishes.

    • Grégoire Vernaz
    • , Milan Malinsky
    •  & Eric A. Miska

  • Article
    | Open Access

    Despite being a common congenital facial anomaly, the genetic etiology of craniofacial microsomia (CFM) is not well understood. Here, the authors use exome and genome sequencing of 146 individuals with CFM to identify haploinsufficient variants in SF3B2 as a prevalent underlying cause.

    • Andrew T. Timberlake
    • , Casey Griffin
    •  & Daniela V. Luquetti

  • Article
    | Open Access

    Mobile element insertions (MEIs) are a source of repetitive genetic variation and can lead to genetic disorders. Here the authors use Cas9-targeted nanopore sequencing to efficiently saturate enrichment for known and non-reference MEIs.

    • Torrin L. McDonald
    • , Weichen Zhou
    •  & Alan P. Boyle

  • Article
    | Open Access

    Several existing algorithms predict the methylation of DNA using Nanopore sequencing signals, but it is unclear how they compare in performance. Here, the authors benchmark the performance of several such tools, and propose METEORE, a consensus tool that improves prediction accuracy.

    • Zaka Wing-Sze Yuen
    • , Akanksha Srivastava
    •  & Eduardo Eyras

  • Article
    | Open Access

    Sequencing and mapping of long repetitive regions can be challenging due to technical difficulties in sequencing and assembly of the sequence data. Here authors report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe to reveal highly polymorphic and hot spots for genome variation features.

    • Yusuke Oizumi
    • , Takuto Kaji
    •  & Junko Kanoh

  • Article
    | Open Access

    The detection of aberrations in circulating tumour DNA represents a non-invasive method to survey the oncogenes and tumour suppressors that are modified within a patient’s cancer. Here, the authors analysed more than 10,000 patients using a targeted sequencing panel and report on the frequencies of the mutations that they found.

    • Yongliang Zhang
    • , Yu Yao
    •  & Qiang Zeng

  • Article
    | Open Access

    Working with cancer genomes from multiple projects can increase investigative power, but quality of sequences can vary. Here, the authors present a framework for comparing whole genome sequencing quality to help researchers guide downstream analyses and exclude poor quality samples.

    • Justin P. Whalley
    • , Ivo Buchhalter
    •  & Ivo G. Gut

  • Article
    | Open Access

    The molecular basis of the clinically important MAM blood group antigen present in most humans is unknown. We identify EMP3 as its encoding gene, establishing MAM as a new blood group system, and demonstrate the role of EMP3 in erythropoiesis through its interaction with the signalling molecule CD44.

    • Nicole Thornton
    • , Vanja Karamatic Crew
    •  & David J. Anstee

  • Article
    | Open Access

    DNA is an attractive digital data storing medium due to high information density and longevity. Here the authors use millions of sequences to investigate inherent biases in DNA synthesis and PCR amplification.

    • Yuan-Jyue Chen
    • , Christopher N. Takahashi
    •  & Karin Strauss

  • Article
    | Open Access

    Structural variants (SVs) contribute to the genetic architecture of many brain-related disorders. Here, the authors integrate SV calls from genome sequencing (n = 755) with RNA-seq data (n = 629) from post-mortem dorsal lateral prefrontal cortex to annotate the gene regulatory effects of SVs in the human brain and their potential to contribute to disease.

    • Lide Han
    • , Xuefang Zhao
    •  & Douglas M. Ruderfer

  • Article
    | Open Access

    The complexity of structural variation (SV) and short tandem repeats (STRs) makes it necessary to apply different calling and filtering strategies to sequencing datasets. Here, Jakubosky et al. report a comprehensive SV and STR callset from whole-genome sequencing of 477 individuals from iPSCORE and HipSci using five algorithms.

    • David Jakubosky
    • , Erin N. Smith
    •  & Kelly A. Frazer

  • Article
    | Open Access

    Most human protein-coding genes are expressed as multiple isoforms. Here the authors present ORF Capture-seq that uses cloned ORFs as probes to capture and sequence full length transcript sequences. This enables highly sensitive characterization of eukaryotic transcriptomes.

    • Gloria M. Sheynkman
    • , Katharine S. Tuttle
    •  & Marc Vidal

  • Article
    | Open Access

    Common variants identified by large-scale genomewide association studies cannot account fully account for the heritability of schizophrenia (SCZ). Here, the authors report high-coverage whole-genome sequencing of 1162 SCZ cases and 936 controls and explore the contribution of different types of variants to SCZ.

    • Matthew Halvorsen
    • , Ruth Huh
    •  & Jin P. Szatkiewicz

  • Article
    | Open Access

    Non-canonical HLA-bound peptides from presumed non-coding regions are potential targets for cancer immunotherapy, but their discovery remains challenging. Here, the authors integrate exome sequencing, transcriptomics, ribosome profiling, and immunopeptidomics to identify tumor-specific non-canonical HLA-bound peptides.

    • Chloe Chong
    • , Markus Müller
    •  & Michal Bassani-Sternberg

  • Article
    | Open Access

    Little is known about the genetics of sclerosing stromal tumor of the ovary, a rare type of sex cord-stromal tumor. Here, the authors use sequencing strategies to show that in a cohort of 26 tumor samples 65% carry a FHL2-GLI2 fusion gene and demonstrate in vitro that the fusion gene has oncogenic properties.

    • Sarah H. Kim
    • , Arnaud Da Cruz Paula
    •  & Britta Weigelt

  • Article
    | Open Access

    Birch pitch is thought to have been used in prehistoric times as hafting material or antiseptic and tooth imprints suggest that it was chewed. Here, the authors report a 5,700 year-old piece of chewed birch pitch from Denmark from which they successfully recovered a complete ancient human genome and oral microbiome DNA.

    • Theis Z. T. Jensen
    • , Jonas Niemann
    •  & Hannes Schroeder

Browse broader subjects

Browse DNA sequencing across other nature.com journals