PaperPlayer biorxiv genomics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.234765v1?rss=1

Authors: Huang, M., Zhang, Z., Zhang, N. R.

Abstract:

Confounding variation, such as batch effects, are a pervasive issue in single-cell RNA sequencing experiments. While methods exist for aligning cells across batches, it is yet unclear how to correct for other types of confounding variation which may be observed at the subject level, such as age and sex, and at the cell level, such as library size and other measures of cell quality. On the specific problem of batch alignment, many questions still persist despite recent advances: Existing methods can effectively align batches in low-dimensional representations of cells, yet their effectiveness in aligning the original gene expression matrices is unclear. Nor is it clear how batch correction can be performed alongside data denoising, the former treating technical biases due to experimental stratification while the latter treating technical variation due inherently to the random sampling that occurs during library construction and sequencing. Here, we propose SAVERCAT, a method for dimension reduction and denoising of single-cell gene expression data that can flexibly adjust for arbitrary observed covariates. We benchmark SAVERCAT against existing single-cell batch correction methods and show that while it matches the best of the field in low-dimensional cell alignment, it significantly improves upon existing methods on the task of batch correction in the high-dimensional expression matrix. We also demonstrate the ability of SAVERCAT to effectively integrate batch correction and denoising through a data down-sampling experiment. Finally, we apply SAVERCAT to a single cell study of Alzheimer's disease where batch is confounded with the contrast of interest, and demonstrate how adjusting for covariates other than batch allows for more interpretable analysis.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.234682v1?rss=1

Authors: Zhao, Z., Elsik, C. G., Hibbard, B. E., Shelby, K. S.

Abstract:

Alternative splicing increases the transcriptome diversity in eukaryotes. In insects, alternative splicing may causes resistance to pesticides and Bt toxins. The alternative splicing in western corn rootworm (Diabrotica virgifera virgifera LeConte) has not been studied. To investigate its alternative splicing pattern and relation to Bt resistance, we carried out single-molecule real-time (SMRT) transcript sequencing and Iso-seq analysis on resistant, eCry3.1Ab-selected and susceptible, unselected, western corn rootworm neonate midguts which fed on seedling maize with and without eCry3.1Ab for 12 and 24 hours. We present transcriptome-wide alternative splicing patterns of western corn rootworm midgut in response to feeding on eCry3.1Ab-expressing corn using a comprehensive approach that combines both RNA-seq and SMRT transcript sequencing techniques. We found that 67.73% of multi-exon genes are alternatively spliced, which is consistent with the high transposable element content of the genome. One of the alternative splicing events we identified was a novel peritrophic matrix protein with two alternative splicing isoforms. Analysis of differential exon usage between resistant and susceptible colonies showed that in eCry3.1Ab-resistant western corn rootworm, expression of one isoform was significantly higher than in the susceptible colony, while no significant differences between colonies were observed with the other isoform. Our results provide the first survey of alternative splicing in western corn rootworm and suggest that the observed alternatively spliced isoforms of peritrophic matrix protein may be associated with eCry3.1Ab resistance in western corn rootworm.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.233726v1?rss=1

Authors: Athanasouli, M., Witte, H., Weiler, C., Loschko, T., Eberhardt, G., Sommer, R. J., Rödelsperger, C.

Abstract:

Background: Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics. Results: Here, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-to-one orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths and screens for atypical domain combinations and species-specific orphan genes resulted in 4,221 candidate genes that were subject to community-based curation. Corrections for 2,851 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%. Conclusions: Our work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.04.236703v1?rss=1

Authors: Sesia, M., Bates, S., Candes, E., Marchini, J., Sabatti, C.

Abstract:

This paper proposes a novel statistical method to address population structure in genome-wide association studies while controlling the false discovery rate, which overcomes some limitations of existing approaches. Our solution accounts for linkage disequilibrium and diverse ancestries by combining conditional testing via knockoffs with hidden Markov models from state-of-the-art phasing methods. Furthermore, we account for familial relatedness by describing the joint distribution of haplotypes sharing long identical-by-descent segments with a generalized hidden Markov model. Extensive simulations affirm the validity of this method, while applications to UK Biobank phenotypes yield many more discoveries compared to BOLT-LMM, most of which are confirmed by the Japan Biobank and FinnGen data.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.04.236653v1?rss=1

Authors: Hassan, S. S., Attrish, D., Ghosh, S., Pal Choudhury, P., Roy, B.

Abstract:

One of the most important proteins for COVID-19 pathogenesis in SARS-CoV2 is the ORF3a protein which is the largest accessory protein among others accessory proteins coded by coronavirus genome. The major roles of the protein include virulence, infectivity, ion channel activity, morphogenesis and virus release. The coronavirus, SARS-CoV2 is continuously evolving naturally and thereby the encoded proteins are also mutating rapidly. Therefore, critical study of mutations in ORF3a is certainty important from the pathogenetic perspective. Here, a sum of 175 various non-synonymous mutations in the ORF3a protein of SARS-CoV2 are identified and their corresponding effects in structural stability and functions of the protein ORF3a are studied. Broadly three different classes of mutations, such as neutral, disease and mixed (neutral and disease) type mutations were observed. Consecutive mutations in some ORF3a proteins are established based on timeline of detection of mutations. Considering the amino acid compositions over the ORF3a primary protein sequences, twenty clusters are detected based on K-means clustering method. Our findings on 175 novel mutations of ORF3a proteins will extend our knowledge of ORF3a, a vital accessory protein in SARS-CoV2, which would assist to enlighten on the pathogenicity of this life-threatening COVID-19.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.04.235952v1?rss=1

Authors: Gabrielaite, M., Norskov-Lauritsen, N., Nielsen, F. C., Johansen, H. K., Marvig, R. L.

Abstract:

Achromobacter species are increasingly being detected in patients with cystic fibrosis (CF), and this emerging pathogen has been associated with antibiotic resistance and more severe disease outcomes. Nonetheless, little is known about the extent of transmission and genetic adaptation in Achromobacter infections. We sequenced the genomes of 101 clinical isolates of Achromobacter collected from 51 patients with CF-the largest longitudinal dataset to-date. We performed a comprehensive pathogenomic analysis to identify pathogen population structure, within-host adaptation, mutational signatures, patient-to-patient transmission events, and associated genetic variation with antibiotic resistance phenotypes. We found that the population of Achromobacter isolates was composed of five different species where A. xylosoxidans accounted for 52% of the infections. Most patients were infected by unique Achromobacter clone types; nonetheless, patient-to-patient transmission events identified by shared clone types were observed in 35% (N=18) of patients. We found that the same regulatory and inorganic ion transport genes were frequently mutated in persisting clone types within and between species indicating convergent genetic adaptation. Genome-wide association study (GWAS) of six antibiotic resistance phenotypes revealed that the majority of associated genes were involved in transcription and inorganic ion transport. Overall, we provide insight into pathogenomics of chronic Achromobacter infections and show the relevance of whole genome sequencing of clinical isolates. Our findings on evolution and genetic adaptation can facilitate the understanding of disease progression, inform antibiotic treatment, and identify patient-to-patient transmission.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.04.234153v1?rss=1

Authors: Ghanchi, N. K., Masood, K. I., Nasir, A., Khan, W., Abidi, S. H., Shahid, S., Mahmood, S. F., Kanji, A. R., Razzak, S. A., Ansar, Z., Islam, N., Dharejo, M. B., Hasan, Z., Hasan, R.

Abstract:

Objectives: Pakistan has a high infectious disease burden with about 265,000 reported cases of COVID-19. We investigated the genomic diversity of SARS-CoV-2 strains and present the first data on viruses circulating in the country. Methods: We performed whole-genome sequencing and data analysis of SARS-CoV-2 eleven strains isolated in March and May. Results: Strains from travelers clustered with those from China, Saudi Arabia, India, USA and Australia. Five of eight SARS-CoV-2 strains were GH clade with Spike glycoprotein D614G, Ns3 gene Q57H, and RNA dependent RNA polymerase (RdRp) P4715L mutations. Two were S (ORF8 L84S and N S202N) and three were L clade and one was an I clade strain. One GH and one L strain each displayed Orf1ab L3606F indicating further evolutionary transitions. Conclusions: This data reveals SARS-CoV-2 strains of L, G, S and I have been circulating in Pakistan from March, at the start of the pandemic. It indicates viral diversity regarding infection in this populous region. Continuing molecular genomic surveillance of SARS-CoV-2 in the context of disease severity will be important to understand virus transmission patterns and host related determinants of COVID-19 in Pakistan.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.04.236893v1?rss=1

Authors: Bull, R. A., Adikari, T., Hammond, J. M., Stevanovski, I., Ferguson, J. M., Beukers, A. G., Naing, Z., Yeang, M., Verich, A., Gamaarachichi, H., Kim, K. W., Luciani, F., Stelzer-Braid, S., Eden, J.-S., Rawlinson, W. D., van Hal, S. J., Deveson, I. W.

Abstract:

Viral whole-genome sequencing (WGS) provides critical insight into the transmission and evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. To address this, we performed viral WGS with ONT and Illumina platforms on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls, enabling rigorous evaluation of analytical performance. Despite the elevated error rates observed in ONT sequencing reads, highly accurate consensus-level sequence determination was achieved, with single nucleotide variants (SNVs) detected at >99% sensitivity and >98% precision above a minimum ~60-fold coverage depth, thereby ensuring suitability for SARS-CoV-2 genome analysis. ONT sequencing also identified a surprising diversity of structural variation within SARS-CoV-2 specimens that were supported by evidence from short-read sequencing on matched samples. However, ONT sequencing failed to accurately detect short indels and variants at low read-count frequencies. This systematic evaluation of analytical performance for SARS-CoV-2 WGS will facilitate widespread adoption of ONT sequencing within local, national and international COVID-19 public health initiatives.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.04.235655v1?rss=1

Authors: Schede, H. H., Schneider, C. G., Stergiadou, J., Borm, L. E., Ranjak, A., Yamawaki, T. M., David, F. P. A., Lonnerberg, P., Laurent, G., Tosches, M. A., Codeluppi, S., La Manno, G.

Abstract:

Genomics techniques are currently being adapted to provide spatially resolved omics profiling. However, the adaptation of each new method typically requires the setup of specific detection strategies or specialized instrumentation. A generic approach to spatially resolve different types of high throughput data is missing. Here, we describe an imaging-free framework to localize high throughput readouts within a tissue by combining compressive sampling and image reconstruction. We implemented this framework to transform a low-input RNA sequencing protocol into an imaging-free spatial transcriptomics technique (STRP-seq) and validated this method with a transcriptome profiling of the murine brain. To verify the broad applicability of STRP-seq, we applied the technique on the brain of the Australian bearded dragon Pogona vitticeps. Our results reveal the molecular anatomy of the telencephalon of this lizard, providing evidence for a marked regionalization of the reptilian pallium and subpallium. Overall, the proposed framework constitutes a new approach that allows upgrading in a generic fashion conventional genomic assays to spatially resolved techniques.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.235226v1?rss=1

Authors: Sakurai-Yageta, M., Kumada, K., Gocho, C., Makino, S., Uruno, A., Tadaka, S., Motoike, I. N., Kimura, M., Ito, S., Otsuki, A., Narita, A., Kudo, H., Aoki, Y., Danjoh, I., Yasuda, J., Kawame, H., Minegishi, N., Koshiba, S., Fuse, N., Tamiya, G., Yamamoto, M., Kinoshita, K.

Abstract:

Background: Increasing the power of genome-wide association studies in diverse populations is important for understanding the genetic determinants of disease risks, and large-scale genotype data are collected by genome cohort and biobank projects all over the world. In particular, ethnic-specific SNP arrays are becoming more important because the use of universal SNP arrays has some limitations in terms of cost-effectiveness and throughput. As part of the Tohoku Medical Megabank Project, which integrates prospective genome cohorts into a biobank, we have been developing a series of Japonica Arrays for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population. Results: We designed a novel version of the SNP Array for the Japanese population, called Japonica Array NEO, comprising a total of 666,883 SNPs, including tag SNPs of autosomes and X chromosome with pseudoautosomal regions, SNPs of Y chromosome and mitochondria, and known disease risk SNPs. Among them, 654,246 tag SNPs were selected from an expanded reference panel of 3,552 Japanese using pairwise r2 of linkage disequilibrium measures. Moreover, 28,298 SNPs were included for the evaluation of previously identified disease risk SNPs from the literature and databases, and those present in the Japanese population were extracted using the reference panel. The imputation performance of Japonica Array NEO was assessed by genotyping 286 Japanese samples. We found that the imputation quality r2 and INFO score in the minor allele frequency bin >2.5%-5% were >0.9 and >0.8, respectively, and >12 million markers were imputed with an INFO score >0.8. After verification, Japonica Arrays were used to efficiently genotype cohort participants from the sample selection to perform a quality assessment of the raw data; approximately 130,000 genotyping data of >150,000 participants has already been obtained. Conclusions: Japonica Array NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores for this population and further identifying disease risk alleles among individuals of East Asian ancestry.

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