scholarly journals Using human sequencing to guide craniofacial research

2018 ◽  
Author(s):  
Ryan P. Liegel ◽  
Erin Finnerty ◽  
Lauren Ward ◽  
Andrew DiStasio ◽  
Robert B. Hufnagel ◽  
...  
Keyword(s):  
Genetic Research ◽  
Genomic Analysis ◽  
Index Patient ◽  
Causal Variant ◽  
Craniofacial Development ◽  
Technological Innovations ◽  
Craniofacial Anomalies ◽  
Sequencing Studies ◽  
Craniofacial Syndrome ◽  
Rapid Generation

ABSTRACTA recent convergence of technological innovations has re-energized the ability to apply genetics to research in human craniofacial development. Next-generation exome and whole genome sequencing have dropped in price significantly making it relatively trivial to sequence and analyze patients and families with congenital craniofacial anomalies. A concurrent revolution in genome editing with the use of the CRISPR-Cas9 system enables the rapid generation of animal models, including mouse, which can precisely recapitulate human variants. Here we summarize the choices currently available to the research community. We illustrate this approach with the study of a family with a novel craniofacial syndrome with dominant inheritance pattern. The genomic analysis suggest a causal variant in AMOTL1 which we modeled in mice. We also made a novel deletion allele of Amotl1. Our results indicate that Amotl1 is not required in the mouse for survival to weaning. Mice carrying the variant identified in the human sequencing studies, however, do not survive to weaning in normal ratios. The cause of death is not understood for these mice complicating our conclusions about the pathogenicity in the index patient. Thus, we highlight some of the powerful opportunities and confounding factors confronting current craniofacial genetic research.

scholarly journals Nucleolin loss-of-function leads to aberrant FGF signaling and craniofacial anomalies

2021 ◽  
Author(s):  
Soma Dash ◽  
Paul Trainor
Keyword(s):  
Ribosome Biogenesis ◽  
Craniofacial Development ◽  
Rrna Synthesis ◽  
Growth Factor Signaling ◽  
Craniofacial Anomalies ◽  
Fgf Signaling ◽  
Loss Of Function ◽  
Tissue Specific ◽  
Rrna Transcription ◽  
Exogenous Addition

rRNA transcription and ribosome biogenesis are global processes required for growth and proliferation of all cells, yet perturbation of these processes in vertebrates leads to tissue-specific defects termed ribosomopathies. Mutations in rRNA transcription and processing proteins often lead to craniofacial anomalies, however the cellular and molecular reasons for this are poorly understood. Therefore, we examined the function of the most abundant nucleolar phosphoprotein, Nucleolin (Ncl), in vertebrate development. We discovered that Nucleolin is dynamically expressed during embryonic development with high enrichment in the craniofacial tissues. Consistent with this pattern of expression, ncl homozygous mutant (ncl-/-) zebrafish present with craniofacial anomalies such as mandibulofacial hypoplasia. We observe that ncl-/- mutants exhibit decreased rRNA synthesis and p53-dependent neuroepithelial cell death. In addition, the half-life of fgf8a mRNA is reduced in ncl-/- mutants, which perturbs Fgf signaling, resulting in misregulation of Sox9a mediated chondrogenesis and Runx2 mediated osteogenesis. Exogenous addition of human recombinant FGF8 to the mutant zebrafish significantly rescues the cranioskeletal phenotype, suggesting that Nucleolin regulates osteochondroprogenitor differentiation during craniofacial development by post-transcriptionally regulating Fgf signaling. Our work has therefore uncovered a novel tissue-specific function for Nucleolin in rRNA transcription and growth factor signaling during embryonic craniofacial development.

scholarly journals The Drosophila Genome Nexus: a population genomic resource of 605 Drosophila melanogaster genomes, including 197 genomes from a single ancestral range population

2014 ◽  
Author(s):  
Justin Lack ◽  
Charis Cardeno ◽  
Marc Crepeau ◽  
William Taylor ◽  
Russ Corbett-Detig ◽  
...  
Keyword(s):  
Population Genomics ◽  
Demographic History ◽  
Genetic Research ◽  
Genomic Analysis ◽  
Data Sets ◽  
Large Sample Size ◽  
Drosophila Genome ◽  
High Genetic Diversity ◽  
Population Genomic ◽  
Variant Detection

Hundreds of wild-derived D. melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach, and settled on an assembly strategy that utilizes two alignment programs and incorporates both SNPs and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets (previous DPGP releases and the DGRP freeze 2.0), and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 605 consistently aligned genomes, and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets.

scholarly journals Methylation profiling reveals novel molecular classes of rhabdomyosarcoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael R. Clay ◽  
Anand Patel ◽  
Quynh Tran ◽  
Dale J. Hedges ◽  
Ti-Cheng Chang ◽  
...  
Keyword(s):  
Copy Number ◽  
Soft Tissue Sarcomas ◽  
Genomic Analysis ◽  
Adult Type ◽  
Histologic Subtype ◽  
Sequencing Studies ◽  
Poor Outcomes ◽  
Aggressive Clinical Course ◽  
Age Range ◽  
Methylation Profiling

AbstractRhabdomyosarcomas (RMS) represent a family of aggressive soft tissue sarcomas that present in both children and adults. Pathologic risk stratification for RMS has been based on histologic subtype, with poor outcomes observed in alveolar rhabdomyosarcoma (ARMS) and the adult-type pleomorphic rhabdomyosarcoma (PRMS) compared to embryonal rhabdomyosarcoma (ERMS). Genomic sequencing studies have expanded the spectrum of RMS, with several new molecularly defined entities, including fusion-driven spindle cell/sclerosing rhabdomyosarcoma (SC/SRMS) and MYOD1-mutant SC/SRMS. Comprehensive genomic analysis has previously defined the mutational and copy number spectrum for the more common ERMS and ARMS and revealed corresponding methylation signatures. Comparatively, less is known about epigenetic correlates for the rare SC/SRMS or PRMS histologic subtypes. Herein, we present exome and RNA sequencing, copy number analysis, and methylation profiling of the largest cohort of molecularly characterized RMS samples to date. In addition to ARMS and ERMS, we identify two novel methylation subtypes, one having SC/SRMS histology and defined by MYOD1 p. L122R mutations and the other matching adult-type PRMS. Selected tumors from adolescent patients grouped with the PRMS methylation class, expanding the age range of these rare tumors. Limited follow-up data suggest that pediatric tumors with MYOD1-mutations are associated with an aggressive clinical course.

The developing role of pharmacogenetics in psychiatry

1999 ◽  
Vol 11 (2) ◽  
pp. 77-79
Author(s):  
D.J. Touw
Keyword(s):  
Drug Treatment ◽  
Large Scale ◽  
Genetic Research ◽  
Biological Response ◽  
Genomic Analysis ◽  
Normal Activity ◽  
Genetic Alterations ◽  
The Body ◽  
Target Drug ◽  
Drug Receptor

A great interindividual variability exists in biological response to drugs. This variability is partly attributable to pharmacodynamic factors (drug - receptor interactions) and partly to pharmacokinetic factors. Drugs can be eliminated from the body by renal clearance, metabolism or both. Although every tissue has some ability to metabolise xenobiotics like drugs, the liver is the principal organ of biotransformation. Major metabolising enzymes are the cytochrome-P450 mono-oxygenases, epoxide hydrolase, glucuronosyl-transferase, acetyl-transferase, sulfo-transferase and xanthine oxidase. Some of these enzymes display in a subset of subjects a ‘normal’ activity and in another subset of subjects a reduced or a greatly increased activity. This altered activity may be genetically determined and is then called genetic polymorphism. Clinically relevant metabolic differences traditionally have been defined by their genotypie expression such as ‘poor’ and ‘extensive’ metaboliser. The recent developments of powerful methods for DNA (or genomic) analysis portends a revolutionary expansion of our understanding of physiology as well as pathology. Pharmacogenetics is the study of genetic variation underlying differential response to drugs. Genotyping may become a useful tool in optimising drug treatment. Another part of the genetic research is directed towards the discovery of genetic alterations leading to diseases. Once identified, these genetic alterations can become targets for drug treatment (e.g. gene therapy). Pharmaco-genomics applies the large-scale systematic approaches of genomics to speed the discovery of drug response markers, whether they act at the level of the drug target, drug metabolism or disease pathway. Table I gives some examples of genetic alterations that are identified together with their effects. Some of these examples will be briefly discussed here.

scholarly journals Pan-sarcoma genomic analysis of KMT2A rearrangements reveals distinct subtypes defined by YAP1–KMT2A–YAP1 and VIM–KMT2A fusions

2020 ◽  
Vol 33 (11) ◽  
pp. 2307-2317 ◽  
Author(s):  
Lucas R. Massoth ◽  
Yin P. Hung ◽  
Valentina Nardi ◽  
G. Petur Nielsen ◽  
Robert P. Hasserjian ◽  
...  
Keyword(s):  
Soft Tissue ◽  
Rna Sequencing ◽  
Soft Tissue Sarcomas ◽  
Genomic Analysis ◽  
Index Patient ◽  
Genetic Alterations ◽  
Next Generation ◽  
Sclerosing Epithelioid Fibrosarcoma ◽  
Molecular Features ◽  
Histologic Subtypes

Abstract Sarcomas are driven by diverse pathogenic mechanisms, including gene rearrangements in a subset of cases. Rare soft tissue sarcomas containing KMT2A fusions have recently been reported, characterized by a predilection for young adults, sclerosing epithelioid fibrosarcoma-like morphology, and an often aggressive course. Nonetheless, clinicopathologic and molecular descriptions of KMT2A-rearranged sarcomas remain limited. In this study, we identified by targeted next-generation RNA sequencing an index patient with KMT2A fusion-positive soft tissue sarcoma. In addition, we systematically searched for KMT2A structural variants in a comprehensive genomic profiling database of 14,680 sarcomas interrogated by targeted next-generation DNA and/or RNA sequencing. We characterized the clinicopathologic and molecular features of KMT2A fusion-positive sarcomas, including KMT2A breakpoints, rearrangement partners, and concurrent genetic alterations. Collectively, we identified a cohort of 34 sarcomas with KMT2A fusions (0.2%), and YAP1 was the predominant partner (n = 16 [47%]). Notably, a complex rearrangement with YAP1 consistent with YAP1–KMT2A–YAP1 fusion was detected in most cases, with preservation of KMT2A CxxC-binding domain in the YAP1–KMT2A–YAP1 fusion and concurrent deletions of corresponding exons in KMT2A. The tumors often affected younger adults (age 20–66 [median 40] years) and histologically showed variably monomorphic epithelioid-to-spindle shaped cells embedded in a dense collagenous stroma. Ultrastructural evidence of fibroblastic differentiation was noted in one tumor examined. Our cohort also included two sarcomas with VIM–KMT2A fusions, each harboring concurrent mutations in CTNNB1, SMARCB1, and ARID1A and characterized histologically by sheets of spindle-to-round blue cells. The remaining 16 KMT2A-rearranged sarcomas in our cohort exhibited diverse histologic subtypes, each with unique novel fusion partners. In summary, KMT2A-fusion-positive sarcomas most commonly exhibit sclerosing epithelioid fibrosarcoma-like morphology and complex YAP1–KMT2A–YAP1 fusions. Cases also include rare spindle-to-round cell sarcomas with VIM–KMT2A fusions and tumors of diverse histologic subtypes with unique KMT2A fusions to non-YAP1 non-VIM partners.

scholarly journals Genomic Context and Mechanisms of the ACVR1 Mutation in Fibrodysplasia Ossificans Progressiva

Biomedicines ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 154
Author(s):  
Roberto Ravazzolo ◽  
Renata Bocciardi
Keyword(s):  
Genetic Research ◽  
Genomic Analysis ◽  
Basic Research ◽  
Genomic Region ◽  
Fibrodysplasia Ossificans Progressiva ◽  
Causative Mutation ◽  
Single Mutation ◽  
Genetic Modifiers ◽  
Genomic Context ◽  
Cis Acting

Basic research in Fibrodysplasia Ossificans Progressiva (FOP) was carried out in the various fields involved in the disease pathophysiology and was important for designing therapeutic approaches, some of which were already developed as ongoing or planned clinical trials. Genetic research was fundamental in identifying the FOP causative mutation, and the astonishing progress in technologies for genomic analysis, coupled to related computational methods, now make possible further research in this field. We present here a review of molecular and cellular factors which could explain why a single mutation, the R206H in the ACVR1 gene, is absolutely prevalent in FOP patients. We also address the mechanisms by which FOP expressivity could be modulated by cis-acting variants in the ACVR1 genomic region in human chromosome 2q. Finally, we also discuss the general issue of genetic modifiers in FOP.

scholarly journals Atypical Genotypes for Canine Agouti Signaling Protein Suggest Novel Chromosomal Rearrangement

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 739 ◽  
Author(s):  
Dayna L. Dreger ◽  
Heidi Anderson ◽  
Jonas Donner ◽  
Jessica A. Clark ◽  
Arlene Dykstra ◽  
...  
Keyword(s):  
Additional Data ◽  
Coat Color ◽  
Genetic Research ◽  
Causal Variant ◽  
Signaling Protein ◽  
Testing Laboratories ◽  
Basic Color ◽  
Commercial Testing ◽  
Potential Impact ◽  
Variant Identification

Canine coat color is a readily observed phenotype of great interest to dog enthusiasts; it is also an excellent avenue to explore the mechanisms of genetics and inheritance. As such, multiple commercial testing laboratories include basic color alleles in their popular screening panels, allowing for the creation of genotyped datasets at a scale not before appreciated in canine genetic research. These vast datasets have revealed rare genotype anomalies that encourage further exploration of color and pattern inheritance. We previously reported the simultaneous presence of greater than two allele variants at the Agouti Signaling Protein (ASIP) locus in a commercial genotype cohort of 11,790 canids. Here we present additional data to characterize the occurrence of anomalous ASIP genotypes. We document the detection of combinations of three or four ASIP allele variants in 17 dog breeds and Dingoes, at within-breed frequencies of 1.32–63.34%. We analyze the potential impact on phenotype that these allele combinations present, and propose mechanisms that could account for the findings, including: gene recombination, duplication, and incorrect causal variant identification. These findings speak to the accuracy of industry-wide protocols for commercial ASIP genotyping and imply that ASIP should be analyzed via haplotype, rather than using only the existing allele hierarchy, in the future.

scholarly journals Dynamic regulation and requirement for ribosomal RNA transcription during mammalian development

2021 ◽  
Author(s):  
Karla Terrazas Falcon ◽  
Kristin Watt ◽  
Soma Dash ◽  
Annita Achilleos ◽  
Emma Moore ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Ribosome Biogenesis ◽  
Protein Translation ◽  
Craniofacial Development ◽  
Rrna Synthesis ◽  
Craniofacial Anomalies ◽  
Congenital Diseases ◽  
Tissue Specific ◽  
Rrna Transcription ◽  
Pol I

Ribosomal RNA (rRNA) transcription by RNA Polymerase I (Pol I) is a critical rate-limiting step in ribosome biogenesis, which is essential for cell survival. Despite its global function, disruptions in ribosome biogenesis cause tissue-specific birth defects called ribosomopathies which frequently affect craniofacial development. Here, we present a cellular and molecular mechanism to explain the susceptibility of craniofacial development to disruptions in Pol I transcription. We show that Pol I subunits are highly expressed in the neuroepithelium and neural crest cells (NCC), which generate most of the craniofacial skeleton. High expression of Pol I subunits sustains elevated rRNA transcription in NCC progenitors, which supports their high tissue-specific levels of protein translation, but also makes NCC particulalry sensitive to rRNA synthesis defects. Underpinning these findings, NCC-specific deletion of Pol I subunits Polr1a, Polr1c, and associated factor Tcof1 in mice cell-autonomously diminishes rRNA synthesis, which causes an imbalance between rRNA and ribosomal proteins. This leads to increased ribosomal protein binding to Mdm2 and concomitantly diminished Mdm2 binding to p53. Consequently, p53 protein accumulates, resulting in NCC apoptosis and craniofacial anomalies. Furthermore, compound mutations in Pol I subunits and associated factors specifically exacerbates the craniofacial anomalies characteristic of the ribosomopathies Treacher Collins Syndrome and Acrofacial Dysostosis Cincinnati Type. Our novel results therefore demonstrate the dynamic spatiotemporal requirement for rRNA transcription during mammalian cranial NCC development and corresponding tissue-specific threshold sensitivities to disruptions in rRNA transcription in the pathogenesis of craniofacial congenital diseases.

scholarly journals Genomes of the “Candidatus Actinomarinales” Order: Highly Streamlined Marine Epipelagic Actinobacteria

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
pp. e01041-20
Author(s):  
Mario López-Pérez ◽  
Jose M. Haro-Moreno ◽  
Jaime Iranzo ◽  
Francisco Rodriguez-Valera
Keyword(s):  
Genomic Analysis ◽  
Gene Families ◽  
Genomic Diversity ◽  
Small Cells ◽  
Chemical Transformations ◽  
Sources Of Information ◽  
Depth Analysis ◽  
Sequencing Studies ◽  
Flexible Genome ◽  
Epipelagic Zone

ABSTRACT“Candidatus Actinomarinales” was defined as a subclass of exclusively marine Actinobacteria with small cells and genomes. We have collected all the available genomes in databases to assess the diversity included in this group and analyzed it by comparative genomics. We have found the equivalent of five genera and 18 genomospecies. They have genome reduction parameters equal to those of freshwater actinobacterial “Candidatus Nanopelagicales” or marine alphaproteobacterial Pelagibacterales. Genome recruitment shows that they are found only in the photic zone and mainly in surface waters, with only one genus that is found preferentially at or below the deep chlorophyll maximum. “Ca. Actinomarinales” show a highly conserved core genome (80% of the gene families conserved for the whole order) with a saturation of genomic diversity of the flexible genome at the genomospecies level. We found only a flexible genomic island preserved throughout the order; it is related to the sugar decoration of the envelope and uses several tRNAs as hot spots to increase its genomic diversity. Populations had a discrete level of sequence diversity similar to other marine microbes but drastically different from the much higher levels found for Pelagibacterales. Genomic analysis suggests that they are all aerobic photoheterotrophs with one type 1 rhodopsin and a heliorhodopsin. Like other actinobacteria, they possess the F420 coenzyme biosynthesis pathway, and its lower reduction potential could provide access to an increased range of redox chemical transformations. Last, sequence analysis revealed the first “Ca. Actinomarinales” phages, including a prophage, with metaviromic islands related to sialic acid cleavage.IMPORTANCE Microbiology is in a new age in which sequence databases are primary sources of information about many microbes. However, in-depth analysis of environmental genomes thus retrieved is essential to substantiate the new knowledge. Here, we study 182 genomes belonging to the only known exclusively marine pelagic group of the phylum Actinobacteria. The aquatic branch of this phylum is largely known from environmental sequencing studies (single-amplified genomes [SAGs] and metagenome-assembled genomes [MAGs]), and we have collected and analyzed the available information present in databases about the “Ca. Actinomarinales.” They are among the most streamlined microbes to live in the epipelagic zone of the ocean, and their study is critical to obtain a proper view of the diversity of Actinobacteria and their role in aquatic ecosystems.

scholarly journals seqr: a web-based analysis and collaboration tool for rare disease genomics

2021 ◽  
Author(s):  
Lynn Pais ◽  
Hana Snow ◽  
Ben Weisburd ◽  
Shifa Zhang ◽  
Samantha Baxter ◽  
...  
Keyword(s):  
Open Source ◽  
Rare Disease ◽  
Research Collaboration ◽  
Low Cost ◽  
Genomic Analysis ◽  
Disease Diagnosis ◽  
Causal Variant ◽  
Monogenic Disease ◽  
Disease Genes ◽  
Web Based

Exome and genome sequencing have become the tools of choice for rare disease diagnosis, leading to large amounts of data available for analyses. To identify causal variants in these datasets, powerful filtering and decision support tools that can be efficiently used by clinicians and researchers are required. To address this need, we developed seqr - an open source, web-based tool for family-based monogenic disease analysis that allows researchers to work collaboratively to search and annotate genomic callsets. To date, seqr is being used in several research pipelines and one clinical diagnostic lab. In our own experience through the Broad Institute Center for Mendelian Genomics, seqr has enabled analyses of over 10,000 families, supporting the diagnosis of more than 3,800 individuals with rare disease and discovery of over 300 novel disease genes. Here we describe a framework for genomic analysis in rare disease that leverages seqr's capabilities for variant filtration, annotation, and causal variant identification, as well as support for research collaboration and data sharing. The seqr platform is available as open source software, allowing low-cost participation in rare disease research, and a community effort to support diagnosis and gene discovery in rare disease.

Sign in / Sign up

Export Citation Format

Share Document