A Survey on Monochromatic Connections of Graphs

Li, Xueliang; Wu, Di

doi:10.20429/tag.2017.000104

Cited by 15 publications

(13 citation statements)

References 25 publications

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“…Fastq files were realigned using BWA-MEM. 73 Files were then sorted with samtools 74 , duplicates were marked with Picard, and base recalibration was performed with GATK, using known polymorphisms downloaded from the following locations: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz and https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/GATK/All_20180418.vcf.gz.…”

Section: Methodsmentioning

confidence: 99%

Griffin: Framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA

Doebley

Liao

et al. 2021

Preprint

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Cell-free DNA (cfDNA) has the potential to inform tumor subtype classification and help guide clinical precision oncology. Here we developed Griffin, a new method for profiling nucleosome protection and accessibility from cfDNA to study the phenotype of tumors using as low as 0.1x coverage whole genome sequencing (WGS) data. Griffin employs a novel GC correction procedure tailored to variable cfDNA fragment sizes, which improves the prediction of chromatin accessibility. Griffin achieved excellent performance for detecting tumor cfDNA in early-stage cancer patients (AUC=0.96). Next, we applied Griffin for the first demonstration of estrogen receptor (ER) subtyping in metastatic breast cancer from cfDNA. We analyzed 254 samples from 139 patients and predicted ER subtype with high performance (AUC=0.89), leading to insights about tumor heterogeneity. In summary, Griffin is a framework for accurate clinical subtyping and can be generalizable to other cancer types for precision oncology applications.

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Section: Methodsmentioning

confidence: 99%

Griffin: Framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA

Doebley

Liao

et al. 2021

Preprint

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“…In summary, the reads were mapped against cannabis reference genome (cs10 v. 2.0; GenBank Accession No. GCA_900626175.2; Hurgobin et al ., 2020) using BWA-MEM (Li, 2013). The nucleotide variants were called using Platypus (Rimmer et al ., 2014).…”

Section: Methodsmentioning

confidence: 99%

Accumulation of somatic mutations leads to genetic mosaicism in Cannabis

Adamek

Torkamaneh

Jones

2021

Preprint

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Cannabis is typically propagated using stem cuttings taken from mother plants to produce genetically uniform propagules. However, producers anecdotally report that clonal lines deteriorate over time and eventually produce clones with less vigour and lower cannabinoid levels than the original mother plant. While the cause of this deterioration has not been investigated, one potential contributor is the accumulation of somatic mutations within the plant. To test this, we used deep sequencing of whole genomes (>50x depth of coverage) to compare the variability within an individual Cannabis sativa cv. Honey Banana plant sampled at the bottom, middle and top. Overall, we called over 6 million sequence variants based on a published reference genome (SNPs, MNPs, and indels) and found that that the top had the most by a sizable amount. We compared the variants among the samples and uncovered that nearly 600K (34%) were unique to the top while the bottom only contained 148K (12%) and middle with 77K (9%) unique variants. Bioinformatics tools were used to identify high impact mutations in critical cannabinoid/terpene biosynthesis pathways. While none were identified, some contained more than double the average level of nucleotide diversity (π) in or near the gene, including OLS, CBDAS, HMGR2 and CsTPS9FN. The first two genes code for essential enzymes required for the cannabinoid pathway while the other two are involved in the terpene pathways, demonstrating that mutations were accumulating within these pathways and could influence their function. Overall, these data identified a measurable number of intra-plant genetic diversity that could impact the long-term genetic fidelity of clonal lines and potentially contribute to the observed decline in vigour and cannabinoid content.

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“…7 . 17 [57] with default parameters and the relative alignment file was converted to a binary alignment map (BAM) file using SAMtools v1 . 9 [58].…”

Section: Methodsmentioning

confidence: 99%

ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections

Marcolungo

Beltrami

Esposti

et al. 2021

Preprint

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We report Accurate SARS-CoV-2 genome Reconstruction (ACoRE), an amplicon-based viral genome sequencing workflow for the complete and accurate reconstruction of SARS-CoV-2 sequences from clinical samples, including suboptimal ones that would usually be excluded even if unique and irreplaceable. We demonstrated the utility of the approach by achieving complete genome reconstruction and the identification of false-positive variants in >170 clinical samples, thus avoiding the generation of inaccurate and/or incomplete sequences. Most importantly, ACoRE was crucial to identify the correct viral strain responsible of a relapse case, that would be otherwise mis-classified as a re-infection due to missing or incorrect variant identification by a standard workflow.

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A Survey on Monochromatic Connections of Graphs

Cited by 15 publications

References 25 publications

Griffin: Framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA

Griffin: Framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA

Accumulation of somatic mutations leads to genetic mosaicism in Cannabis

ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections

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