مجال
التميز
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تميز دراسي وبحثي + إبداع علمي (ماجستير ودكتواره)
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البحوث المنشورة
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البحث (1):
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عنوان البحث:
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PP066:
No association between human papillomavirus infection and oral verrucous
lesions
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رابط البحث:
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Click here
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تاريخ النشر:
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موجز عن البحث:
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Purpose
Verrucous
carcinoma (VC) is a low grade, non-metastasising, slow-growing variant of
squamous cell carcinoma (SCC). The aetiology of VC is unknown, and the role
of human papillomavirus (HPV) as a causative factor remains contentious. This
dubiety can be attributed to varied detection procedures and difficulties in
defining ‘gold-standard’ histological criteria for diagnosing verrucous
lesions including VC, Verrucous hyperplasia (VH), and proliferative verrucous
leukoplakia (PVL). The rarity of these lesions also makes them difficult to
study and investigate, so most previous studies have been made on small
numbers of cases. The aim of this study is to analyse oral verrucous lesions
(including VC, VH, and PVL cases) for the presence of HPV subtype genomes.
Materials
and methods
We
used a recently developed and validated method, ‘next generation sequencing’
for the detection of HPV sequences, subtypes, and viral loads from nanogram
DNA quantities isolated from formalin-fixed paraffin-embedded tissue. In this
present study, we identified a total of 62 oral verrucous cases: 49 OVCs, 12
OVHs, and one PVL. DNA was extracted from all samples and libraries were
prepared followed by sequencing at coverage between 2.5% and 13%. Genomic
copy number karyograms were produced and all samples were analysed for the
presence of all HPV subtypes and for other known human viral genome
sequences.
Results
HPV
sequences were not detected in 61 verrucous cases out of 62 total cases. An
HPV type 16 sequence was detected in only one OVH sample [2.24 viral genomes
per cell].
Conclusions
We
confirm that NGS can be used as a precise method for detection of HPV
subtypes and loads, and provide genomic copy number karyograms for FFPE
verrucous samples in a single test. Furthermore, Our results demonstrate
conclusively that HPV involvement is unlikely to be a feature in oral
verrucous lesions, nor are any other common human viruses implicated.
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البحث ( 2):
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عنوان البحث:
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Next-Generation Sequencing
Analysis for Detecting Human Papillomavirus in Oral Verrucous Carcinoma.
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رابط إلى البحث:
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Click here
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تاريخ النشر:
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01/07/2014
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موجز عن البحث:
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Objective
The etiology of oral verrucous carcinoma is
unknown, and human papillomavirus ‘involvement’ remains contentious. The
uncertainty can be attributed to varied detection procedures and difficulties
in defining ‘gold-standard’ histologic criteria for diagnosing ‘verrucous’
lesions. Their paucity also hampers investigation. We aimed to analyze oral
verrucous lesions for human papillomavirus (HPV) subtype genomes.
Study Design
We used next-generation sequencing for the
detection of papillomavirus sequences, identifying subtypes and computing
viral loads. We identified a total of 78 oral verrucous cases (62 carcinomas
and 16 hyperplasias). DNA was extracted from all and sequenced at coverage
between 2.5% and 13%.
Results
An HPV-16 sequence was detected in 1
carcinoma and 1 hyperplasia, and an HPV-2 sequence was detected in 1
carcinoma out of the 78 cases, with viral loads of 2.24, 8.16, and 0.33 viral
genomes per cell, respectively.
Conclusions
Our results indicate no
conclusive human papillomavirus involvement in oral verrucous carcinoma or
hyperplasia.
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عنوان البحث:
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Next-Generation Sequencing
Analysis for Detecting Human Papillomavirus in Oral Verrucous Carcinoma.
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المؤتمرات العلمية:
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المؤتمر (1):
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عنوان المؤتمر:
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the 4th World Congress of the International
Academy of Oral Oncology in
2013
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تاريخ الإنعقاد:
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15 May
2013
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بلد
ومكان الإنعقاد:
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Greece
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طبيعة المشاركة:
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Poster
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عنوان المشاركة
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No
association between human papillomavirus infection and oral verrucous lesions
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ملخص المشاركة
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Purpose:
Verrucous carcinoma (VC) is a low grade, non-metastasising, slow-growing
variant of squamous cell carcinoma (SCC). The aetiology of VC is unknown, and
the role of human papillomavirus (HPV) as a causative factor remains
contentious. This dubiety can be attributed to varied detection procedures
and difficulties in defining ‘gold-standard’ histological criteria for
diagnosing verrucous lesions including VC, Verrucous hyperplasia (VH), and
proliferative verrucous leukoplakia (PVL). The rarity of these lesions also
makes them difficult to study and investigate, so most previous studies have
been made on small numbers of cases. The aim of this study is to analyse oral
verrucous lesions (including VC, VH, and PVL cases) for the presence of HPV
subtype genomes.
Materials
and methods: We used a recently developed and validated method, ‘next
generation sequencing’ for the detection of HPV sequences, subtypes, and
viral loads from nanogram DNA quantities isolated from formalin-fixed
paraffin-embedded tissue. In this present study, we identified a total of 62
oral verrucous cases: 49 OVCs, 12 OVHs, and one PVL. DNA was extracted from
all samples and libraries were prepared followed by sequencing at coverage
between 2.5% and 13%. Genomic copy number karyograms were produced and all
samples were analysed for the presence of all HPV subtypes and for other
known human viral genome sequences.
Results:
HPV sequences were not detected in 61 verrucous cases out of 62 total cases.
An HPV type 16 sequence was detected in only one OVH sample [2.24 viral
genomes per cell].
Conclusions:
We confirm that NGS can be used as a precise method for detection of HPV
subtypes and loads, and provide genomic copy number karyograms for FFPE
verrucous samples in a single test. Furthermore, Our results demonstrate
conclusively that HPV involvement is unlikely to be a feature in oral
verrucous lesions, nor are any other common human viruses implicated.
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المؤتمر (2):
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عنوان المؤتمر:
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The 7th Saudi
Students Conference in the UK
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تاريخ الإنعقاد:
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01-02 February 2014
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بلد
ومكان الإنعقاد:
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Edinburgh,
UK
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طبيعة المشاركة:
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Poster
presentation
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عنوان المشاركة
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Next
Generation Sequencing (NGS): a powerful tool providing new
insights into the genomic landscape of Oral Verrucous Carcinomas
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ملخص المشاركة
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Background:
Oral
verrucous carcinoma (OVC) is a low grade variant of oral squamous cell
carcinoma (OSCC). The aetiology of OVC is unknown, and the suggested role of
human papillomavirus (HPV) as a causative factor remains contentious.
Distinguishing OVC from OSCC is a common problem for pathologists due to the
poorly defined diagnostic criteria. The rarity of these lesions also makes
them difficult to investigate, so most previous studies have been made on
small numbers of cases. The aim of this study is to use NGS copy number (CN)
analysis to identify the genomic characteristic features of oral verrucous
lesions, including OVC, and oral verrucous hyperplasia (OVH), and compare
them with OSCCs, and to analyse those lesions for the presence of HPV.
Methods:
We
identified a total of 62 oral verrucous cases: 49 OVCs, and 13 OVHs. DNA was
extracted from all FFPE samples and sequenced at a coverage between 2.5% and
13%. Genomic CN karyograms were produced and compared between OVH, OVC and
OSCC samples. All samples were analysed for the presence of HPV subtypes and
for all known human viruses.
Results:
Visual
inspection of the 62 patient’s CN karyograms demonstrated regions of gain and
loss along the whole genome in OVC cases. Gain and loss features were
minimally found in OVH cases. The analysis of CN aberrations across the
entire OVCs data set revealed lower chromosomal instability features in OVCs
when compared to OSCCs. An HPV-16 sequence was detected in one OVH, and an
HPV-2 was detected in one OVC out of the 62 cases.
Conclusion:
We
confirm that NGS can be used as a powerful method for detection of HPV
subtypes and loads, and provide CN karyograms for FFPE verrucous samples in a
single test. Our results indicate that there is no HPV involvement in oral
verrucous lesions.
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المؤتمر (3):
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عنوان المؤتمر:
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The
Cold Spring Harbor Laboratory Meeting, The Biology of Genomes.
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تاريخ الإنعقاد:
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6-10 May 2014
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مكان
الإنعقاد:
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USA, cold spring harbor laboratory
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طبيعة المشاركة:
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Poster presentation
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عنوان المشاركة:
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Background:
Oral verrucous carcinoma (OVC) is
categorised as a low-grade variant of oral squamous cell carcinoma (OSCC).
The aetiology of OVC is unknown, and the suggested role of human
papillomavirus (HPV) as a causative factor remains contentious.
Distinguishing OVC from OSCC is a common problem for pathologists due to the
poorly defined diagnostic criteria. The rarity of these lesions also makes
them difficult to investigate, so most previous studies have been made on
small numbers of cases. The aim of this study is to use NGS copy number (CN)
analysis to identify the genomic characteristic features of oral verrucous
lesions, including OVC, and oral verrucous hyperplasia (OVH), a possible
precursor of OVC, and compare them with classical OSCCs, and to analyse those
lesions for the presence of HPV.
Methods:
We identified a total of 57 OVCs, 16 OVHs,
and 45 OSCC cases. DNA was extracted from all FFPE samples and sequenced at a
coverage between 2.5% and 13%. Genomic CN karyograms were produced and
compared between OVH, OVC and OSCC samples. All samples were analysed for the
presence of HPV subtypes and for all known human viruses.
Results:
Visual inspection of patient’s CN
karyograms revealed that genomic signatures usually associated with OSCCs
were completely absent in oral verrucous lesions. Gains of chromosome arms
7q, 16q and 17q were detected in OVCs at a frequency of ~50%, suggesting that
these CN alterations may be involved in the development of OVC.
Interestingly, losses were detected more frequently in OSCCs than OVCs,
suggesting that these CN alterations may be related to the more
aggressiveness behavior of OSCC tumours. Significant CN alterations in the
OVH group were present in OVCs. An HPV-16 sequence was detected in one OVH
and one OVC, and an HPV-2 sequence was detected in one OVC out of the 73 verrucous
cases with viral loads of 2.24, 8.16 and 0.33 viral genomes per cell
respectively.
Conclusion:
A previous study conducted by
our group have shown that NGS can be used as a powerful method for detection
of HPV subtypes and loads, and provide CN karyograms for FFPE samples in a
single test. To the best of our knowledge, this is the first study to use NGS
CN analysis and viral detection method on oral verrucous lesions. Although
the WHO describes OVC as a variant of classical OSCC, our CN results suggest
that it is a distinct entity. Nonetheless, and despite the verrucous
appearance, which is suggestive of viral aetiology, our results indicate that
there is no HPV involvement in oral verrucous lesions. We demonstrate that CN
analysis could contribute to differential diagnosis of oral verrucous lesions
and classical OSCCs using routine biopsy specimens.
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جوائز التكريم:
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الجائزة (1):
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مسمى الجائزة:
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first place prize for
poster presentation in medical science
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الجهة المانحة:
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7th
SIC organising committee
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تاريخ منح الجائزة:
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01/02/2014
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مجال التكريم:
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Medical Sciences
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