Narrowing and genomic annotation of the commonly deleted region of the 5q− syndrome

Blood ◽  
2002 ◽  
Vol 99 (12) ◽  
pp. 4638-4641 ◽  
Author(s):  
Jacqueline Boultwood ◽  
Carrie Fidler ◽  
Amanda J. Strickson ◽  
Fiona Watkins ◽  
Susana Gama ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Gene Prediction ◽  
The Novel ◽  
Gene Prediction Program ◽  
Hematopoietic Stem ◽  
Prediction Program ◽  
Genomic Annotation ◽  
Cd34 Cells ◽  
The Common ◽  
Complete Genomic

The 5q− syndrome is the most distinct of the myelodysplastic syndromes, and the molecular basis for this disorder remains unknown. We describe the narrowing of the common deleted region (CDR) of the 5q− syndrome to the approximately 1.5-megabases interval at 5q32 flanked by D5S413 and theGLRA1 gene. The Ensembl gene prediction program has been used for the complete genomic annotation of the CDR. The CDR is gene rich and contains 24 known genes and 16 novel (predicted) genes. Of 40 genes in the CDR, 33 are expressed in CD34+ cells and, therefore, represent candidate genes since they are expressed within the hematopoietic stem/progenitor cell compartment. A number of the genes assigned to the CDR represent good candidates for the 5q− syndrome, including MEGF1, G3BP, and several of the novel gene predictions. These data now afford a comprehensive mutational/expression analysis of all candidate genes assigned to the CDR.

scholarly journals ASPic-GeneID: A Lightweight Pipeline for Gene Prediction and Alternative Isoforms Detection

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Tyler Alioto ◽  
Ernesto Picardi ◽  
Roderic Guigó ◽  
Graziano Pesole
Keyword(s):  
Ab Initio ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Gene Prediction Program ◽  
C Elegans ◽  
Prediction Program ◽  
First Pass ◽  
Main Components ◽  
Genome Projects ◽  
Alternative Isoforms

New genomes are being sequenced at an increasingly rapid rate, far outpacing the rate at which manual gene annotation can be performed. Automated genome annotation is thus necessitated by this growth in genome projects; however, full-fledged annotation systems are usually home-grown and customized to a particular genome. There is thus a renewed need for accurateab initiogene prediction methods. However, it is apparent that fullyab initiomethods fall short of the required level of sensitivity and specificity for a quality annotation. Evidence in the form of expressed sequences gives the single biggest improvement in accuracy when used to inform gene predictions. Here, we present a lightweight pipeline for first-pass gene prediction on newly sequenced genomes. The two main components are ASPic, a program that derives highly accurate, albeit not necessarily complete, EST-based transcript annotations from EST alignments, and GeneID, a standard gene prediction program, which we have modified to take as evidence intron annotations. The introns output by ASPic CDS predictions is given to GeneID to constrain the exon-chaining process and produce predictions consistent with the underlying EST alignments. The pipeline was successfully tested on the entireC. elegansgenome and the 44 ENCODE human pilot regions.

scholarly journals Genome resources of four distinct pathogenic races within Fusarium oxysporum f. sp. vasinfectum that cause vascular wilt disease of cotton

2020 ◽  
Author(s):  
Subodh K Srivastava ◽  
Kurt Zeller ◽  
James H Sobieraj ◽  
Mark K Nakhla
Keyword(s):  
Fusarium Oxysporum ◽  
Gene Prediction ◽  
Whole Genome Sequence ◽  
Vascular Wilt ◽  
Gene Prediction Program ◽  
Public Health Agencies ◽  
Prediction Program ◽  
Methods Development ◽  
Pathogenic Races ◽  
And Control

Whole Genome Sequence (WGS) based identifications are being increasingly used by regulatory and public health agencies to facilitate the detection, investigation, and control of pathogens and pests. Fusarium oxysporum f. sp. vasinfectum (FOV) is a significant vascular wilt pathogen of cultivated cotton, and consists of several pathogenic races that are not each other’s closest phylogenetic relatives. We have developed WGS assemblies for isolates of race 1 (FOV1), race 4 (FOV4), race 5 (FOV5), and race 8 (FOV8) using a combination of Nanopore (MinION) and Illumina sequencing technology (Mi-Seq). This resulted in assembled contigs with more than 100X coverage for each of the FOV races and estimated genome sizes of FOV1 52 Mb, FOV4 68 Mb, FOV5 68 Mb and FOV8 55 Mb. The AUGUSTUS gene prediction program predicted 16,263 genes in FOV1, 20,259 genes in FOV4, 20,375 genes in FOV5 and 16,615 genes in FOV8. We were able to identify 525 genes unique to FOV1, 570 unique to FOV4, 1242 unique to FOV5 and 383 unique to FOV8. We expect that these findings will help in comparative genomics, and in the identification of unique genes as candidate targets for diagnostic marker and methods development to permit rapid differentiation of FOV subgroups.

Hoechst dye efflux reveals a novel CD7+CD34− lymphoid progenitor in human umbilical cord blood

Blood ◽  
2000 ◽  
Vol 96 (6) ◽  
pp. 2125-2133 ◽  
Author(s):  
Robert W. Storms ◽  
Margaret A. Goodell ◽  
Alan Fisher ◽  
Richard C. Mulligan ◽  
Clay Smith
Keyword(s):  
Stem Cells ◽  
Cord Blood ◽  
Umbilical Cord ◽  
Umbilical Cord Blood ◽  
Large Population ◽  
Lymphoid Cells ◽  
Human Umbilical Cord Blood ◽  
Human Umbilical Cord ◽  
Hematopoietic Stem ◽  
Cd34 Cells

Abstract A novel Hoechst 33342 dye efflux assay was recently developed that identifies a population of hematopoietic cells termed side population (SP) cells. In the bone marrow of multiple species, including mice and primates, the SP is composed primarily of CD34−cells, yet has many of the functional properties of hematopoietic stem cells (HSCs). This report characterizes SP cells from human umbilical cord blood (UCB). The SP in unfractionated UCB was enriched for CD34+ cells but also contained a large population of CD34− cells, many of which were mature lymphocytes. SP cells isolated from UCB that had been depleted of lineage-committed cells (Lin− UCB) contained CD34+ and CD34− cells in approximately equivalent proportions. Similar to previous descriptions of human HSCs, the CD34+Lin− SP cells were CD38dimHLA-DRdimThy-1dimCD45RA−CD71−and were enriched for myelo-erythroid precursors. In contrast, the CD34−Lin− SP cells were CD38−HLA-DR−Thy-1−CD71−and failed to generate myelo-erythroid progeny in vitro. The majority of these cells were CD7+CD11b+CD45RA+, as might be expected of early lymphoid cells, but did not express other lymphoid markers. The CD7+CD34−Lin− UCB SP cells did not proliferate in simple suspension cultures but did differentiate into natural killer cells when cultured on stroma with various cytokines. In conclusion, the human Lin− UCB SP contains both CD34+ multipotential stem cells and a novel CD7+CD34−Lin− lymphoid progenitor. This observation adds to the growing body of evidence that CD34− progenitors exist in humans.

scholarly journals High Integrity and Fidelity of Long-Term Cryopreserved Umbilical Cord Blood for Transplantation

2021 ◽  
Vol 10 (2) ◽  
pp. 293
Author(s):  
Gee-Hye Kim ◽  
Jihye Kwak ◽  
Sung Hee Kim ◽  
Hee Jung Kim ◽  
Hye Kyung Hong ◽  
...  
Keyword(s):  
Stem Cell ◽  
Cord Blood ◽  
Umbilical Cord ◽  
Umbilical Cord Blood ◽  
Clinical Applications ◽  
Hematopoietic Stem ◽  
Cd34 Cells ◽  
Hsc Transplantation

Umbilical cord blood (UCB) is used as a source of donor cells for hematopoietic stem cell (HSC) transplantation. The success of transplantation is dependent on the quality of cord blood (CB) units for maximizing the chance of engraftment. Improved outcomes following transplantation are associated with certain factors of cryopreserved CB units: total volume and total nucleated cell (TNC) count, mononuclear cell (MNC) count, and CD34+ cell count. The role of the storage period of CB units in determining the viability and counts of cells is less clear and is related to the quality of cryopreserved CB units. Herein, we demonstrate the recovery of viable TNCs and CD34+ cells, as well as the MNC viability in 20-year-old cryopreserved CB units in a CB bank (MEDIPOST Co., Ltd., Seongnam-si, Gyeonggi-do, Korea). In addition, cell populations in CB units were evaluated for future clinical applications. The stable recovery rate of the viability of cryopreserved CB that had been stored for up to 20 years suggested the possibility of uses of the long-term cryopreservation of CB units. Similar relationships were observed in the recovery of TNCs and CD34+ cells in units of cryopreserved and fresh CB. The high-viability recovery of long-term cryopreserved CB suggests that successful hematopoietic stem cell (HSC) transplantation and other clinical applications, which are suitable for treating incurable diseases, may be performed regardless of long-term storage.

Discovery of the novel HLA‐C *06:195 allele in a Singaporean unrelated hematopoietic stem cell donor

HLA ◽  
2021 ◽  
Author(s):  
Louise Cho ◽  
Zi‐Jing Seng ◽  
Nezih Cereb ◽  
Py‐Yu Lin ◽  
Kuo‐Liang Yang
Keyword(s):  
Stem Cell ◽  
Hematopoietic Stem Cell ◽  
The Novel ◽  
Hematopoietic Stem ◽  
Cell Donor

scholarly journals Targeted sequencing and integrative analysis to prioritize candidate genes in neurodevelopmental disorders

2021 ◽  
Author(s):  
Yi Zhang ◽  
Tao Wang ◽  
Yan Wang ◽  
Kun Xia ◽  
Jinchen Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Neurodevelopmental Disorders ◽  
De Novo ◽  
Genetic Data ◽  
Chinese Patients ◽  
The Novel ◽  
Mutational Spectrum ◽  
Functional Variants ◽  
Public Data ◽  
Chromosomal Genes

AbstractNeurodevelopmental disorders (NDDs) are a group of diseases characterized by high heterogeneity and frequently co-occurring symptoms. The mutational spectrum in patients with NDDs is largely incomplete. Here, we sequenced 547 genes from 1102 patients with NDDs and validated 1271 potential functional variants, including 108 de novo variants (DNVs) in 78 autosomal genes and seven inherited hemizygous variants in six X chromosomal genes. Notably, 36 of these 78 genes are the first to be reported in Chinese patients with NDDs. By integrating our genetic data with public data, we prioritized 212 NDD candidate genes with FDR < 0.1, including 17 novel genes. The novel candidate genes interacted or were co-expressed with known candidate genes, forming a functional network involved in known pathways. We highlighted MSL2, which carried two de novo protein-truncating variants (p.L192Vfs*3 and p.S486Ifs*11) and was frequently connected with known candidate genes. This study provides the mutational spectrum of NDDs in China and prioritizes 212 NDD candidate genes for further functional validation and genetic counseling.

CD26 expression on donor harvest as a risk predictive biomarker for developing Graft-versus-Host Disease post-Allogeneic Hematopoietic Stem Cell Transplantation: A tenyear followup study

2021 ◽  
pp. 1-12
Author(s):  
Sachin Punatar ◽  
Shruti Kandekar ◽  
Navin Khattry ◽  
Anant Gokarn ◽  
Kumar Prabhash ◽  
...  
Keyword(s):  
Stem Cell ◽  
Hematopoietic Stem Cell Transplantation ◽  
Stem Cell Transplantation ◽  
Clinical Outcomes ◽  
Graft Versus Host Disease ◽  
Transplant Recipients ◽  
Hematopoietic Stem ◽  
Graft Versus Host ◽  
Cd34 Cells ◽  
Cd26 Expression

BACKGROUND: Allogeneic hematopoietic stem cell transplantation (ASCT) is the preferred treatment option for patients with several hematologic disorders and immunodeficiency syndromes. Graft versus host disease (GVHD) is an immune mediated post-transplant complication which has a major impact on long term transplant outcomes. OBJECTIVE: Current efforts are focused on identification of new markers that serve as potential predictors of GVHD and other post-transplant clinical outcomes. METHODS: This study includes donor harvests collected from twenty-three allogeneic donors during period 2008–2009 and respective transplant recipients followed for clinical outcomes till March 2019. Percent CD26+ and CD34+ cells in donor harvest were analyzed using flow cytometry. Percent expression and infused dose of CD26+ and CD34+ cells were evaluated for association with various clinical outcomes. RESULTS: Total 23 healthy donors 28 years (13 males), and transplant recipients with median age 24 years (17 males) formed the study cohort. The diagnosis included malignant (n= 13) and non-malignant (n= 10) disorders. Median CD34brCD45lo HSC expression was 057% (IQR 024–103) while median CD26 expression was 1964% (IQR 896–3356) of all nucleated cells. CD26 expression was associated with donor age (P= 0.37). CD26 percent expression correlated with WBC engraftment (P= 0.015) and with acute GVHD (P= 0.023) whereas infused CD26 cell dose correlated with WBC engraftment (P= 0.004) and risk of CMV reactivation (P= 0.020). There was no statistically significant correlation of either CD26 expression or cell dose with chronic GVHD, EFS or OS.

scholarly journals Isolation of small, primitive human hematopoietic stem cells: distribution of cell surface cytokine receptors and growth in SCID-Hu mice

Blood ◽  
1995 ◽  
Vol 86 (2) ◽  
pp. 512-523 ◽  
Author(s):  
JE Wagner ◽  
D Collins ◽  
S Fuller ◽  
LR Schain ◽  
AE Berson ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Surface ◽  
Cell Population ◽  
Size Fraction ◽  
Cell Surface Antigens ◽  
Inhibitory Protein ◽  
Hematopoietic Stem ◽  
Cd34 Cells ◽  
Cell Fractions

Human CD34+ cells were subfractionated into three size classes using counterflow centrifugal elutriation followed by immunoadsorption to polystyrene cell separation devices. The three CD34+ cell fractions (Fr), Fr 25/29, Fr 33/37, and Fr RO, had mean sizes of 8.5, 9.3 and 13.5 microns, respectively. The majority of cells in the large Fr RO CD34+ cell population expressed the committed stage antigens CD33, CD19, CD38, or HLA-DR and contained the majority of granulocyte- macrophage colony-forming units (CFU-GM), burst-forming units-erythroid (BFU-E), and CFU-mixed lineage (GEMM). In contrast, the small Fr 25/29 CD34+ cells were devoid of committed cell surface antigens and lacked colony-forming activity. When seeded to allogeneic stroma, Fr RO CD34+ cells produced few CFU-GM at week 5, whereas cells from the Fr 25/29 CD34+ cell population showed a 30- to 55-fold expansion of myeloid progenitors at this same time point. Furthermore, CD34+ cells from each size fraction supported ontogeny of T cells in human thymus/liver grafts in severe combined immunodeficient (SCID) mice. Upon cell cycle analyses, greater than 97% of the Fr 25/29 CD34+ cells were in G0/G1 phase, whereas greater proportions of the two larger CD34+ cell fractions were in active cell cycle. Binding of the cytokines interleukin (IL)-1 alpha, IL-3, IL-6, stem cell factor (SCF), macrophage inhibitory protein (MIP)-1 alpha, granulocyte colony- stimulating factor (G-CSF), and granulocyte-macrophage (GM)-CSF to these CD34+ cell populations was also analyzed by flow cytometry. As compared with the larger CD34+ cell fractions, cells in the small Fr 25/29 CD34+ cell population possessed the highest numbers of receptors for SCF, MIP1 alpha, and IL-1 alpha. Collectively, these results indicate that the Fr 25/29 CD34+ cell is a very primitive, quiescent progenitor cell population possessing a high number of receptors for SCF and MIP1 alpha and capable of yielding both myeloid and lymphoid lineages when placed in appropriate in vitro or in vivo culture conditions.

Fielding and Richardson

PMLA ◽  
1966 ◽  
Vol 81 (5) ◽  
pp. 381-388
Author(s):  
William Park
Keyword(s):  
Twentieth Century ◽  
Eighteenth Century ◽  
Human Nature ◽  
General Type ◽  
Common Ground ◽  
The Other ◽  
The Novel ◽  
Tom Jones ◽  
The Common ◽  
The One

But the Discovery [of when to laugh and when to cry] was reserved for this Age, and there are two Authors now living in this Metropolis, who have found out the Art, and both brother Biographers, the one of Tom Jones, and the other of Clarissa.author of Charlotte SummersRather than discuss the differences which separate Fielding and Richardson, I propose to survey the common ground which they share with each other and with other novelists of the 1740's and 50's. In other words I am suggesting that these two masters, their contemporaries, and followers have made use of the same materials and that as a result the English novels of the mid-eighteenth century may be regarded as a distinct historic version of a general type of literature. Most readers, it seems to me, do not make this distinction. They either think that the novel is always the same, or they believe that one particular group of novels, such as those written in the early twentieth century, is the form itself. In my opinion, however, we should think of the novel as we do of the drama. No one kind of drama, such as Elizabethan comedy or Restoration comedy, is the drama itself; instead, each is a particular manifestation of the general type. Each kind bears some relationship to the others, but at the same time each has its own identity, which we usually call its conventions. By conventions I mean not only stock characters, situations, and themes, but also notions and assumptions about the novel, human nature, society, and the cosmos itself. If we compare one kind of novel to another without first considering the conventions of each, we are likely to make the same mistake that Thomas Rymer did when he blamed Shakespeare for not conforming to the canons of classical French drama.

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