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result(s) for
"Appleby, Alex. What"
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Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features
by
Appleby, Niamh
,
Jennings, Daisy
,
Strefford, Jonathan C.
in
631/208/212
,
692/699/1541/1990/283/1895
,
Agriculture
2022
The value of genome-wide over targeted driver analyses for predicting clinical outcomes of cancer patients is debated. Here, we report the whole-genome sequencing of 485 chronic lymphocytic leukemia patients enrolled in clinical trials as part of the United Kingdom’s 100,000 Genomes Project. We identify an extended catalog of recurrent coding and noncoding genetic mutations that represents a source for future studies and provide the most complete high-resolution map of structural variants, copy number changes and global genome features including telomere length, mutational signatures and genomic complexity. We demonstrate the relationship of these features with clinical outcome and show that integration of 186 distinct recurrent genomic alterations defines five genomic subgroups that associate with response to therapy, refining conventional outcome prediction. While requiring independent validation, our findings highlight the potential of whole-genome sequencing to inform future risk stratification in chronic lymphocytic leukemia.
Whole-genome sequencing of chronic lymphocytic leukemia from 485 patients identifies putative coding and noncoding drivers of disease. Genomically defined subgroups show distinct clinical and biological characteristics.
Journal Article
A haplotype-resolved, chromosome-scale genome for Malus domestica Borkh. ‘WA 38’
2024
Genome sequencing for agriculturally important Rosaceous crops has made rapid progress both in completeness and annotation quality. Whole genome sequence and annotation give breeders, researchers, and growers information about cultivar-specific traits such as fruit quality and disease resistance, and inform strategies to enhance postharvest storage. Here we present a haplotype-phased, chromosomal-level genome of Malus domestica, ‘WA 38’, a new apple cultivar released to market in 2017 as Cosmic Crisp®. Using both short and long-read sequencing data with a k-mer-based approach, chromosomes originating from each parent were assembled and segregated. This is the first pome fruit genome fully phased into parental haplotypes in which chromosomes from each parent are identified and separated into their unique, respective haplomes. The two haplome assemblies, ‘Honeycrisp’ originated HapA and ‘Enterprise’ originated HapB, are about 650 Megabases each, and both have a BUSCO score of 98.7% complete. A total of 53,028 and 54,235 genes were annotated from HapA and HapB, respectively. Additionally, we provide genome-scale comparisons to ‘Gala’, ‘Honeycrisp’, and other relevant cultivars highlighting major differences in genome structure and gene family circumscription. This assembly and annotation was done in collaboration with the American Campus Tree Genomes project that includes ‘WA 38’ (Washington State University), ‘d’Anjou’ pear (Auburn University), and many more. To ensure transparency, reproducibility, and applicability for any genome project, our genome assembly and annotation workflow is recorded in detail and shared under a public GitLab repository. All software is containerized, offering a simple implementation of the workflow.
Journal Article
Measurement of matter–antimatter differences in beauty baryon decays
2017
Differences in the behaviour of matter and antimatter have been observed in
K
and
B
meson decays, but not yet in any baryon decay. Such differences are associated with the non-invariance of fundamental interactions under the combined charge-conjugation and parity transformations, known as
CP
violation. Here, using data from the LHCb experiment at the Large Hadron Collider, we search for
CP
-violating asymmetries in the decay angle distributions of
Λ
b
0
baryons decaying to
pπ
−
π
+
π
−
and
pπ
−
K
+
K
−
final states. These four-body hadronic decays are a promising place to search for sources of
CP
violation both within and beyond the standard model of particle physics. We find evidence for
CP
violation in
Λ
b
0
to
pπ
−
π
+
π
−
decays with a statistical significance corresponding to 3.3 standard deviations including systematic uncertainties. This represents the first evidence for
CP
violation in the baryon sector.
CP
violation has deep implications for particle physics and cosmology. Previously observed only in meson decays, signs of
CP
violation have now been spotted in baryon decays by analysing the proton–proton collision data from the LHCb detector.
Journal Article
Measurement of the CKM angle γ from a combination of LHCb results
by
Fohl, K.
,
Jurik, N.
,
Wicht, J.
in
Classical and Quantum Gravitation
,
Compatibility
,
Confidence intervals
2016
A
bstract
A combination of measurements sensitive to the CKM angle γ from LHCb is performed. The inputs are from analyses of time-integrated
B
+
→
DK
+
,
B
0
→
DK
∗0
,
B
0
→
DK
+
π
−
and
B
+
→
DK
+
π
+
π
−
tree-level decays. In addition, results from a time-dependent analysis of
B
s
0
→
D
s
∓
K
±
decays are included. The combination yields
γ
= (72. 2
− 7.3
+ 6.8
)
°
, where the uncertainty includes systematic effects. The 95.5% confidence level interval is determined to be γ ∈ [55
.
9
,
85
.
2]°. A second combination is investigated, also including measurements from
B
+
→
D
π
+
and
B
+
→
D
π
+
π
−
π
+
decays, which yields compatible results.
Journal Article
Effect of coronary flow on intracoronary alteplase: a prespecified analysis from a randomised trial
by
McCartney, Peter
,
Wragg, Andrew
,
Fox, Keith A A
in
acute myocardial infarction
,
Angioplasty
,
Blood clots
2021
ObjectivesPersistently impaired culprit artery flow (
Journal Article
Functional connectivity associations with markers of disease progression in GRN mutation carriers
2024
Background Autosomal dominant progranulin (GRN) mutations are a common genetic cause of frontotemporal lobar degeneration. Though clinical trials for GRN‐related therapies are underway, there is an unmet need for biomarkers that can predict symptom onset and track disease progression. We previously showed that presymptomatic GRN carriers exhibit thalamocortical hyperconnectivity that increases with age when they are presumably closer to symptom onset. However, whether hyperconnectivity arises concomitantly with markers of neurodegeneration remains unclear. Method Utilizing T1 and task‐free functional magnetic resonance imaging (tf‐fMRI) from 49 presymptomatic and 26 symptomatic GRN mutation carriers, we determined the relationships between functional connectivity as measured by voxel‐wise whole brain degree and GRN‐relevant markers of disease progression, which included plasma neurofilament light chain (NfL) concentrations, CSF complement C1q and C3b protein levels, grey matter atrophy, and OCD symptom severity. Result NfL concentrations were associated with frontotemporoparietal and thalamic hyperconnectivity in presymptomatic GRN carriers and extensive regions of atrophy in symptomatic carriers. Complement levels were associated with regions of hyperconnectivity, but not gray matter, in symptomatic carriers. Presymptomatic carriers with thalamic hyperconnectivity tended to have lower grey matter volume in bilateral insula and left lateral parietal cortex, which are among regions that deteriorate in GRN‐FTD. OCD symptom severity was associated with hypoconnectivity across all GRN carriers. Conclusion In presymptomatic carriers, the co‐occurrence of hyperconnectivity, high NfL, and low gray matter suggests that tf‐fMRI hyperconnectivity may portend the onset of the neurodegenerative phase. These findings point toward hyperconnectivity as an indicator of approaching symptomatic onset.
Journal Article
Basic Science and Pathogenesis
by
McFall, David
,
Häkkinen, Suvi
,
Pasquini, Lorenzo
in
Adult
,
Atrophy - pathology
,
Biomarkers - blood
2024
Autosomal dominant progranulin (GRN) mutations are a common genetic cause of frontotemporal lobar degeneration. Though clinical trials for GRN-related therapies are underway, there is an unmet need for biomarkers that can predict symptom onset and track disease progression. We previously showed that presymptomatic GRN carriers exhibit thalamocortical hyperconnectivity that increases with age when they are presumably closer to symptom onset. However, whether hyperconnectivity arises concomitantly with markers of neurodegeneration remains unclear.
Utilizing T1 and task-free functional magnetic resonance imaging (tf-fMRI) from 49 presymptomatic and 26 symptomatic GRN mutation carriers, we determined the relationships between functional connectivity as measured by voxel-wise whole brain degree and GRN-relevant markers of disease progression, which included plasma neurofilament light chain (NfL) concentrations, CSF complement C1q and C3b protein levels, grey matter atrophy, and OCD symptom severity.
NfL concentrations were associated with frontotemporoparietal and thalamic hyperconnectivity in presymptomatic GRN carriers and extensive regions of atrophy in symptomatic carriers. Complement levels were associated with regions of hyperconnectivity, but not gray matter, in symptomatic carriers. Presymptomatic carriers with thalamic hyperconnectivity tended to have lower grey matter volume in bilateral insula and left lateral parietal cortex, which are among regions that deteriorate in GRN-FTD. OCD symptom severity was associated with hypoconnectivity across all GRN carriers.
In presymptomatic carriers, the co-occurrence of hyperconnectivity, high NfL, and low gray matter suggests that tf-fMRI hyperconnectivity may portend the onset of the neurodegenerative phase. These findings point toward hyperconnectivity as an indicator of approaching symptomatic onset.
Journal Article
Diagnosis and management of bile acid diarrhoea: a survey of UK expert opinion and practice
2020
ObjectiveBile acid diarrhoea (BAD), which includes bile acid malabsorption, causes a variety of digestive symptoms. Diagnostic rates and management vary considerably. We conducted a survey of current practice to review expert opinion and provide guidance on diagnosis and management.Design/methodAn online survey was conducted of clinical members of the UK Bile Acid Related Diarrhoea Network, who had all published research on BAD (n=21). Most were National Health Service consultants who had diagnosed over 50 patients with the condition.ResultsThe preferred terminology was to use BAD, with primary and secondary to classify causes. A wide range of presenting symptoms and associated conditions were recognised. SeHCAT (tauroselcholic acid) was the preferred diagnostic test, and 50% of respondents thought general practitioners should have access to this. Patients who met the Rome IV diagnostic criteria for functional diarrhoea, irritable bowel syndrome (IBS) with predominant diarrhoea or postcholecystectomy diarrhoea were usually investigated by SeHCAT, which was used sometimes in other types of IBS. Treatment with a bile acid sequestrant was offered to patients with low SeHCAT values, with expected response rates >70% in the most severe. Colestyramine was the usual sequestrant, starting between 2 g and 8 g daily; colesevelam was an alternative. In patients who had an incomplete response, increasing the dose, changing to an alternative sequestrant, use of loperamide and a low fat diet were suggested. Recommendations for follow-up and to improve the overall patient experience were made.ConclusionThis expert survey indicates current best practice in the diagnosis and management of BAD.
Journal Article
The Reuven Ramaty High-Energy Solar Spectroscopic Imager (RHESSI)
2002
Issue Title: Topical Issue: The Reuven Ramaty High-Energy Solar Spectroscopic Imager (RHESSI) - Mission Description and Early Results RHESSI is the sixth in the NASA line of Small Explorer (SMEX) missions and the first managed in the Principal Investigator mode, where the PI is responsible for all aspects of the mission except the launch vehicle. RHESSI is designed to investigate particle acceleration and energy release in solar flares, through imaging and spectroscopy of hard X-ray/gamma-ray continua emitted by energetic electrons, and of gamma-ray lines produced by energetic ions. The single instrument consists of an imager, made up of nine bi-grid rotating modulation collimators (RMCs), in front of a spectrometer with nine cryogenically-cooled germanium detectors (GeDs), one behind each RMC. It provides the first high-resolution hard X-ray imaging spectroscopy, the first high-resolution gamma-ray line spectroscopy, and the first imaging above 100 keV including the first imaging of gamma-ray lines. The spatial resolution is as fine as 2.3 arc sec with a full-Sun (1°) field of view, and the spectral resolution is 1-10 keV FWHM over the energy range from soft X-rays (3 keV) to gamma-rays (17 MeV). An automated shutter system allows a wide dynamic range (>10^sup 7^) of flare intensities to be handled without instrument saturation. Data for every photon is stored in a solid-state memory and telemetered to the ground, thus allowing for versatile data analysis keyed to specific science objectives. The spin-stabilized (15 rpm) spacecraft is Sun-pointing to within 0.2° and operates autonomously. RHESSI was launched on 5 February 2002, into a nearly circular, 38° inclination, 600-km altitude orbit and began observations a week later. The mission is operated from Berkeley using a dedicated 11-m antenna for telemetry reception and command uplinks. All data and analysis software are made freely and immediately available to the scientific community.[PUBLICATION ABSTRACT]
Journal Article
Differential Expression of SOX4 and SOX11 in Medulloblastoma
by
Chan, Wai-In
,
Scotting, Paul J.
,
Appleby, Vanessa J.
in
Biological and medical sciences
,
Biomarkers, Tumor
,
Cerebellar Neoplasms - classification
2002
Primitive neuroectodermal tumors (PNETs) are composed of immature neuronal precursor cells and sometimes more mature neuronal cell types. Medulloblastomas, occuring in the cerebellum, represent the most common PNET and are broadly classified into two subgroups: classical and desmoplastic. Desmoplastic medulloblastomas exhibit a slightly better prognosis than classical medulloblastomas. However, there are currently no good molecular markers available to distinguish clinical outcome and similar treatment is used for most patients with associated complications. It has been shown that neoplastic cells in these tumors recapitulate stages in maturation of normal human neuroblasts; therefore, embryological studies of the earliest events in the development of the cerebellum may provide useful information about the molecular behavior of the tumor. Transcription factors such as Sox proteins involved in neural development may also play a role in the etiology of brain tumors. Sox4 in particular has been implicated in the biology of several other types of cancer. We have studied the expression of Sox4, and the closely related Sox11 gene, in medulloblastomas. Sox4 and Sox11 were strongly expressed in most classical medulloblastomas but only weakly in desmoplastic medulloblastomas. The expression profile of these two genes in developing cerebellum was also analyzed. Our results suggest that strong Sox4 and Sox11 expression in classical medulloblastomas reflects their maturation-dependent expression during normal cerebellum development, and that they may therefore provide markers to divide tumors into clinically relevant subgroups.
Journal Article
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