B Chromosomes in the Drosophila Genus

Our current knowledge of B chromosome biology has been augmented by an increase in the number and diversity of species observed to carry B chromosomes as well as the use of next-generation sequencing for B chromosome genomic analysis. Within the genus Drosophila, B chromosomes have been observed in a handful of species, but recently they were discovered in a single laboratory stock of Drosophila melanogaster. In this paper, we review the B chromosomes that have been identified within the Drosophila genus and pay special attention to those recently found in D. melanogaster. These newly-discovered B chromosomes have centromeres, telomeres, and a number of simple satellite repeats. They also appear to be entirely heterochromatic since next-generation sequencing of isolated B chromosomes did not detect sequences associated with known genic regions. We also summarize what effects the B chromosomes have been found to have on the A chromosomes. Lastly, we highlight some of the outstanding questions regarding B chromosome biology and discuss how studying B chromosomes in Drosophila melanogaster, which is a versatile model system with a wealth of genetic and genomic tools, may advance our understanding of the B chromosome’s unique biology.

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Next-Generation Sequencing in Acute Lymphoblastic Leukemia

International Journal of Molecular Sciences ◽

10.3390/ijms20122929 ◽

2019 ◽

Vol 20 (12) ◽

pp. 2929 ◽

Cited By ~ 17

Author(s):

Nicoletta Coccaro ◽

Luisa Anelli ◽

Antonella Zagaria ◽

Giorgina Specchia ◽

Francesco Albano

Keyword(s):

Next Generation Sequencing ◽

Acute Lymphoblastic Leukemia ◽

Residual Disease ◽

Age Of Onset ◽

Lymphoblastic Leukemia ◽

Genomic Analysis ◽

Next Generation ◽

Acute Leukemias ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias, and features different outcomes depending on the age of onset. Improvements in ALL genomic analysis achieved thanks to the implementation of next-generation sequencing (NGS) have led to the recent discovery of several novel molecular entities and to a deeper understanding of the existing ones. The purpose of our review is to report the most recent discoveries obtained by NGS studies for ALL diagnosis, risk stratification, and treatment planning. We also report the first efforts at NGS use for minimal residual disease (MRD) assessment, and early studies on the application of third generation sequencing in cancer research. Lastly, we consider the need for the integration of NGS analyses in clinical practice for genomic patients profiling from the personalized medicine perspective.

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Final report of ENGAGE ‐ Establishing Next Generation sequencing Ability for Genomic analysis in Europe

EFSA Supporting Publications ◽

10.2903/sp.efsa.2018.en-1431 ◽

2018 ◽

Vol 15 (6) ◽

Cited By ~ 8

Author(s):

Rene S. Hendriksen ◽

Susanne Karlsmose Pedersen ◽

Pimlapas Leekitcharoenphon ◽

Burkhard Malorny ◽

Maria Borowiak ◽

...

Keyword(s):

Next Generation Sequencing ◽

Genomic Analysis ◽

Final Report ◽

Next Generation ◽

Generation Sequencing

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How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes

Genes ◽

10.3390/genes8110294 ◽

2017 ◽

Vol 8 (11) ◽

pp. 294 ◽

Cited By ~ 21

Author(s):

Alevtina Ruban ◽

Thomas Schmutzer ◽

Uwe Scholz ◽

Andreas Houben

Keyword(s):

Next Generation Sequencing ◽

B Chromosomes ◽

Next Generation ◽

Sequence Composition ◽

Generation Sequencing

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Classical Genetics Meets Next-Generation Sequencing: Uncovering a Genome-Wide Recombination Map in Drosophila melanogaster

PLoS Genetics ◽

10.1371/journal.pgen.1003024 ◽

2012 ◽

Vol 8 (10) ◽

pp. e1003024 ◽

Cited By ~ 1

Author(s):

Nadia D. Singh

Keyword(s):

Drosophila Melanogaster ◽

Next Generation Sequencing ◽

Next Generation ◽

Genome Wide ◽

A Genome ◽

Generation Sequencing ◽

Classical Genetics

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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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Case Report: Metagenomics Next-Generation Sequencing Can Help Define the Best Therapeutic Strategy for Brain Abscesses Caused by Oral Pathogens

Frontiers in Medicine ◽

10.3389/fmed.2021.644130 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zhonghui Ma ◽

Su Yan ◽

Haoxin Dong ◽

Huifen Wang ◽

Yonggang Luo ◽

...

Keyword(s):

Next Generation Sequencing ◽

Brain Abscess ◽

Genomic Analysis ◽

Critical Factor ◽

Oral Microbiome ◽

Next Generation ◽

Gram Staining ◽

Brain Abscesses ◽

Generation Sequencing

Brain abscesses are associated with an increased long-term risk of new seizures and increased mortality within several years after infection. Common microorganisms that cause brain abscesses include bacteria, fungi, and mycoplasma. We report a 75-year-old man with a brain abscess caused by Prevotella denticola, an oral pathogen. Based on the clinical condition, we suspected that the patient had a blood-borne brain abscess, and he received antibiotics and systemic supportive treatment. The patient developed shock for the second time after negative Gram-staining results. Metagenomics next-generation sequencing showed one strain from the oral microbiome, confirming our hypothesis, and targeted antibiotic treatment was administered quickly. Thus, we report a case in which genomic analysis was the critical factor in determining the best antimicrobial therapy for administration.

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Somatic Variation as an Incidental Finding in the Pediatric Next Generation Sequencing Era

Molecular Case Studies ◽

10.1101/mcs.a006135 ◽

2021 ◽

pp. mcs.a006135

Author(s):

Marilena Melas ◽

Mariam T Mathew ◽

Mari Mori ◽

Vijayakumar Jayaraman ◽

Sarah A Wilson ◽

...

Keyword(s):

Next Generation Sequencing ◽

De Novo ◽

Tissue Sample ◽

Incidental Finding ◽

Pediatric Population ◽

Genomic Analysis ◽

Juvenile Myelomonocytic Leukemia ◽

Next Generation ◽

Somatic Variation ◽

Generation Sequencing

The methodologic approach used in next-generation sequencing (NGS) affords a high depth of coverage in genomic analysis. Inherent in the nature of genomic testing, there exists potential for identifying genomic findings that are incidental or secondary to the indication for clinical testing, with the frequency dependent on the breadth of analysis and the tissue sample under study. The interpretation and management of clinically meaningful incidental genomic findings is a pressing issue particularly in the pediatric population. Our study describes a 16-month old male who presented with Dandy-Walker malformation, metopic craniosynostosis and developmental delay. Clinical exome sequencing (ES) trio analysis revealed the presence of two variants in the proband. The first was a de novo variant in the PPP2R1A gene (c.773G>A, p.Arg258His), which is associated with autosomal dominant (AD) intellectual disability, accounting for the proband's clinical phenotype. The second was a recurrent hotspot variant in the CBL gene (c.1111T>C, p.Tyr371His), which was present at a variant allele fraction of 11%, consistent with somatic variation in the peripheral blood sample. Germline pathogenic variants in CBL are associated with AD Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia (JMML). Molecular analyses using a different tissue source, buccal epithelial cells, suggest that the CBL alteration may represent a clonal population of cells restricted to leukocytes. This report highlights the laboratory methodologic and interpretative processes and clinical considerations in the setting of acquired variation detected during clinical ES in a pediatric patient.

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CBX2-dependent transcriptional landscape: implications for human sex development and its defects

Scientific Reports ◽

10.1038/s41598-019-53006-7 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Patrick Sproll ◽

Wassim Eid ◽

Anna Biason-Lauber

Keyword(s):

Next Generation Sequencing ◽

Rna Sequencing ◽

Current Knowledge ◽

Next Generation ◽

Steroidogenic Factor 1 ◽

Sex Development ◽

New Genes ◽

Differences Of Sex Development ◽

Generation Sequencing ◽

Transcriptional Landscape

Abstract Sex development, a complex and indispensable process in all vertebrates, has still not been completely elucidated, although new genes involved in sex development are constantly being discovered and characterized. Chromobox Homolog 2 (CBX2) is one of these new additions and has been identified through a 46,XY girl with double heterozygous variants on CBX2.1, causing Differences of Sex Development (DSD). The mutated CBX2.1 failed to adequately regulate downstream targets important for sex development in humans, specifically steroidogenic factor 1 (NR5A1/SF1). To better place CBX2.1 in the human sex developmental cascade, we performed siRNA and CBX2.1 overexpression experiments and created a complete CRISPR/Cas9-CBX2 knockout in Sertoli-like cells. Furthermore, we deployed Next Generation Sequencing techniques, RNA-Sequencing and DamID-Sequencing, to identify new potential CBX2.1 downstream genes. The combination of these two next generation techniques enabled us to identify genes that are both bound and regulated by CBX2.1. This allowed us not only to expand our current knowledge about the influence of CBX2.1 in human sex development, but also to advance our insight in the mechanisms governing one of the most important decisions during embryonal development, the commitment to either female or male gonads.

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