Next-Generation Whole Genome Sequencing of Dengue Virus

In September 2018, a child who had returned from Somalia to Germany presented with cutaneous diphtheria by toxigenic Corynebacterium diphtheriae biovar mitis. The child’s sibling had superinfected insect bites harbouring also toxigenic C. diphtheriae. Next generation sequencing (NGS) revealed the same strain in both patients suggesting very recent human-to-human transmission. Epidemiological and NGS data suggest that the two cutaneous diphtheria cases constitute the first outbreak by toxigenic C. diphtheriae in Germany since the 1980s.

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A67 Use of next-generation whole-genome sequencing to understand drug-resistant Mycobacterium tuberculosis in Botswana

Virus Evolution ◽

10.1093/ve/vey010.066 ◽

2018 ◽

Vol 4 (suppl_1) ◽

Author(s):

T Iketleng ◽

T Mogashoa ◽

B Mbeha ◽

L Letsibogo ◽

J Makhema ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Drug Resistant ◽

Next Generation

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Comparison of targeted next-generation sequencing for whole-genome sequencing of Hantaan orthohantavirus in Apodemus agrarius lung tissues

Scientific Reports ◽

10.1038/s41598-019-53043-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 5

Author(s):

Jin Sun No ◽

Won-Keun Kim ◽

Seungchan Cho ◽

Seung-Ho Lee ◽

Jeong-Ah Kim ◽

...

Keyword(s):

Next Generation Sequencing ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Clinical Samples ◽

Whole Genome ◽

Target Enrichment ◽

Next Generation ◽

Apodemus Agrarius ◽

Target Capture ◽

Generation Sequencing

Abstract Orthohantaviruses, negative-sense single-strand tripartite RNA viruses, are a global public health threat. In humans, orthohantavirus infection causes hemorrhagic fever with renal syndrome or hantavirus cardiopulmonary syndrome. Whole-genome sequencing of the virus helps in identification and characterization of emerging or re-emerging viruses. Next-generation sequencing (NGS) is a potent method to sequence the viral genome, using molecular enrichment methods, from clinical specimens containing low virus titers. Hence, a comparative study on the target enrichment NGS methods is required for whole-genome sequencing of orthohantavirus in clinical samples. In this study, we used the sequence-independent, single-primer amplification, target capture, and amplicon NGS for whole-genome sequencing of Hantaan orthohantavirus (HTNV) from rodent specimens. We analyzed the coverage of the HTNV genome based on the viral RNA copy number, which is quantified by real-time quantitative PCR. Target capture and amplicon NGS demonstrated a high coverage rate of HTNV in Apodemus agrarius lung tissues containing up to 103–104 copies/μL of HTNV RNA. Furthermore, the amplicon NGS showed a 10-fold (102 copies/μL) higher sensitivity than the target capture NGS. This report provides useful insights into target enrichment NGS for whole-genome sequencing of orthohantaviruses without cultivating the viruses.

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Understanding the genomic underpinnings of metastatic chromophobe renal cell carcinoma.

Journal of Clinical Oncology ◽

10.1200/jco.2016.34.2_suppl.513 ◽

2016 ◽

Vol 34 (2_suppl) ◽

pp. 513-513 ◽

Cited By ~ 1

Author(s):

Jozefina Casuscelli ◽

Patricia Wang ◽

Almedina Redzematovic ◽

William Lee ◽

Venkatraman E. Seshan ◽

...

Keyword(s):

Renal Cell Carcinoma ◽

Cell Carcinoma ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Renal Cell ◽

Chromophobe Renal Cell Carcinoma ◽

Whole Genome ◽

Next Generation ◽

Metastatic Tumors ◽

Histologic Subtype

513 Background: Chromophobe renal cell carcinoma (chRCC) is the third most common histologic subtype of kidney cancer. While most of these tumors have an indolent behavior, 7% of patients with chRCC develop metastases, with no currently available standard of care. The Cancer Genome Atlas characterized chRCC, highlighting pathognomonic single copy chromosomal losses of 1, 2, 6, 10, 13 and 17, as well as a minimal mutation burden distinguishing it from all other cancer types. However, only 15% of the analyzed patients had advanced disease. We analyzed metastatic chRCC to further characterize these tumors and elucidate mechanisms leading to aggressive disease using a variety of next generation and whole genome sequencing. Methods: Our cohort of metastatic chRCC consisted of 40 patients with available clinical and pathologic data. Whole genome sequencing (WGS) was performed on 6 patients (4 primary tumors and 2 metastases), 42 additional samples from 33 patients were analyzed using targeted next-generation sequencing (MSK-IMPACT). Notably, we were able to collect and analyze matched primary and metastatic tumors from 7 patients. As control cohort 27 non-metastatic chRCC tumors were sequenced with MSK-IMPACT. Copy number patterns were computed with OncoSNP seq and FACETS. Results: The most commonly mutated genes in the aggressive chRCC tumors were TP53 and PTEN (WGS: TP53 67 %, PTEN 33%; MSK-IMPACT: TP53 61%, PTEN 27%). No other genes were mutated frequently. Primary tumor samples of chRCC did show the typical pattern of chromosomal losses in 1, 2, 6, 10, 13 and 17. Interestingly, these canonical losses could not be detected in the metastases even when accounting for tumor purity. Conclusions: TP53 and PTEN mutations are highly enriched in both primary and metastatic tumors of aggressive chRCC compared to the non-aggressive tumors and likely play a critical role in disease progression. More intriguingly, the observation of differential copy numbers in matched primary and metastatic tumors suggest whole genome or whole chromosome events in these samples. We are currently employing different bioinformatic and cytogenetic platforms to validate our novel hypothesis of chromosomal events as driver for metastatic development in chRCC.

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Detection of identity by descent using next-generation whole genome sequencing data

BMC Bioinformatics ◽

10.1186/1471-2105-13-121 ◽

2012 ◽

Vol 13 (1) ◽

Cited By ~ 13

Author(s):

Shu-Yi Su ◽

Jay Kasberger ◽

Sergio Baranzini ◽

William Byerley ◽

Wilson Liao ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Next Generation ◽

Sequencing Data ◽

Identity By Descent

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Rapid whole genome sequencing of Miyazaki-Bali/2007 Pteropine orthoreovirus by modified rolling circular amplification with adaptor ligation – next generation sequencing

Scientific Reports ◽

10.1038/srep16517 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 7

Author(s):

Harpal Singh ◽

Tomoki Yoshikawa ◽

Takeshi Kobayashi ◽

Shuetsu Fukushi ◽

Hideki Tani ◽

...

Keyword(s):

Next Generation Sequencing ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Next Generation ◽

Generation Sequencing

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Next generation whole genome sequencing of Plasmodium falciparum using NextSeq500 technology in India

10.1101/068676 ◽

2016 ◽

Author(s):

Alassane Mbengue ◽

Pragya Namdev ◽

Tarkeshwar Kumar ◽

Kasturi Haldar ◽

Souvik Bhattacharjee

Keyword(s):

Plasmodium Falciparum ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Immune Evasion ◽

Malaria Elimination ◽

Protozoan Parasite ◽

Amplicon Sequencing ◽

Whole Genome ◽

Next Generation ◽

New Genes

AbstractPlasmodium falciparum is a protozoan parasite that causes the deadliest form of human malaria. Although, malaria burdens worldwide have decreased substantially over the last decade (WHO, 2014), genetic variation and adaptation by parasite strains against drugs and vaccines present significant challenges for the elimination of malaria (Ariey et al., 2014; Neafsey et al., 2015). India has formally launched a malaria elimination campaign (NVBDCP, 2016). Therefore, early in-country detection of drug resistance and/or immune evasion will be important for the program. Presently, the majority of surveillance methods in India detect a limited number of known polymorphisms (Campino et al., 2011; Chatterjee et al., 2016; Daniels et al., 2008; Mishra et al., 2015; Neafsey et al., 2012; Neafsey et al., 2008). A recently reported amplicon sequencing method enables targeted re-sequencing of a panel of genes (Rao et al., 2016). However, the capacity to identify new genes of resistance/immune evasion by whole genome sequencing (WGS) through next generation sequencing (NGS) in India, has remained elusive. Here we report the first WGS of P. falciparum strain performed by Eurofins Genomics India Pvt. Ltd at its Bengaluru division within 40 days of sample submission. Our data establish that timely, commercial WGS through NGS in India can be applied to P. falciparum to greatly empower the malaria elimination agenda in India.

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Genomic analysis of Korean patients with advanced prostate cancer by use of a comprehensive next-generation sequencing panel and low-coverage, whole-genome sequencing

Investigative and Clinical Urology ◽

10.4111/icu.2019.60.4.227 ◽

2019 ◽

Vol 60 (4) ◽

pp. 227

Author(s):

Minyong Kang ◽

Eunhae Cho ◽

Jahyun Jang ◽

Junnam Lee ◽

Youngjoo Jeon ◽

...

Keyword(s):

Prostate Cancer ◽

Next Generation Sequencing ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Advanced Prostate Cancer ◽

Genomic Analysis ◽

Whole Genome ◽

Next Generation ◽

Low Coverage ◽

Generation Sequencing

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Assessment of Metagenomic MinION and Illumina sequencing as an approach for the recovery of whole genome sequences of chikungunya and dengue viruses directly from clinical samples

10.1101/355560 ◽

2018 ◽

Cited By ~ 2

Author(s):

Liana E. Kafetzopoulou ◽

Kyriakos Efthymiadis ◽

Kuiama Lewandowski ◽

Ant Crook ◽

Dan Carter ◽

...

Keyword(s):

Dengue Virus ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Illumina Miseq ◽

Clinical Samples ◽

Whole Genome ◽

Metagenomic Sequencing ◽

Front Line ◽

Genome Sequences ◽

Oxford Nanopore

AbstractThe recent global emergence and re-emergence of arboviruses has caused significant human disease. Common vectors, symptoms and geographical distribution make differential diagnosis both important and challenging. We performed metagenomic sequencing using both the Illumina MiSeq and the portable Oxford Nanopore MinION to study the feasibility of whole genome sequencing from clinical samples containing chikungunya or dengue virus, two of the most important arboviruses. Direct metagenomic sequencing of nucleic acid extracts from serum and plasma without viral enrichment allowed for virus and coinfection identification, subtype determination and in the majority of cases elucidated complete or near-complete genomes adequate for phylogenetic analysis. This work demonstrates that metagenomic whole genome sequencing is feasible for over 90% and 80% of chikungunya and dengue virus PCR-positive patient samples respectively. It confirms the feasibility of field metagenomic sequencing for these and likely other RNA viruses, highlighting the applicability of this approach to front-line public health.

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