Recent advances in next-generation sequencing (NGS) technologies have enabled large-scale genome projects and new applications. Several sequencing platforms are now available from companies like Life Technologies and Illumina. These technologies have been applied to projects like the 1000 Genomes Project and The Cancer Genome Atlas to discover rare variants. NGS is also being used for diagnostic exome sequencing, HIV forensics, and human microbiome studies. Emerging technologies aim to further decrease costs while maintaining high throughput and accuracy.
NGS technologies - platforms and applicationsAGRF_Ltd
AGRF in conjunction with EMBL Australia recently organised a workshop at Monash University Clayton. This workshop was targeted at beginners and biologists who are new to analysing Next-Gen Sequencing data. The workshop also aimed to provide users with a snapshot of bioinformatics and data analysis tips on how to begin to analyse project data. Next Gen Sequencing Platforms and Applications was presented by AGRF Next Gen Manager, Mr. Matt Tinning.
Presented: 1st August 2012
NGS technologies - platforms and applicationsAGRF_Ltd
AGRF in conjunction with EMBL Australia recently organised a workshop at Monash University Clayton. This workshop was targeted at beginners and biologists who are new to analysing Next-Gen Sequencing data. The workshop also aimed to provide users with a snapshot of bioinformatics and data analysis tips on how to begin to analyse project data. Next Gen Sequencing Platforms and Applications was presented by AGRF Next Gen Manager, Mr. Matt Tinning.
Presented: 1st August 2012
The Spanish tobacco tax loopholes and their consequencesUCT ICO
Ángel López-Nicolás
Grupo de Investigación en Economía, Políticas Públicas y Salud, Universidad Politécnica de Cartagena
Belén Cobacho
Centre de Recerca en Economia i Salut, Universitat Pompeu Fabra
Esteve Fernández
Institut Català d’Oncologia
ICO-WHO Symposium 2012
This is a short presentation about company formation in Lithuania. For more information, please visit www.companyformationlithuania.com.
You can always reach us at office@bridgewest.eu or find us on www.bridgewest.eu for consulting services.
There is nowadays a growing need for sensing devices offering rapid and portable analytical functionality in real-time as well as massively parallel capabilities with very high sensitivity at the molecular level. Such devices are essential to facilitate research and foster advances in fields such as drug discovery, proteomics, medical diagnostics, systems biology or environmental monitoring.
In this context, an ideal solution is an ion-sensitive field-effect transistor sensor platform based on silicon nanowires to be integrated in a CMOS architecture. Indeed, in addition to the expected high sensitivity and superior signal quality, such nanowire sensors could be mass manufactured at reasonable costs, and readily integrated into electronic diagnostic devices to facilitate bed-site diagnostics and personalized medicine. Moreover, their small size makes them ideal candidates for future implanted sensing devices. While promising biosensing experiments based on silicon nanowire field-effect transistors have been reported, real-life applications still require improved control, together with a detailed understanding of the basic sensing mechanisms. For instance, it is crucial to optimize the geometry of the wire, a still rather unexplored aspect up to now, as well as its surface functionalization or its selectivity to the targeted analytes.
This project seeks to develop a modular, scalable and integrateable sensor platform for the electronic detection of analytes in solution. The idea is to integrate silicon nanowire field-effect transistors as a sensor array and combine them with state-of-the-art microfabricated interface electronics as well as with microfluidic channels for liquid handling. Such sensors have the potential to be mass manufactured at reasonable costs, allowing their integration as the active sensor part in electronic point-of-care diagnostic devices to facilitate, for instance, bed-side diagnostics and personalized medicine. Another important field is systems biology, where many substances need to be quantitatively detected in parallel at very low concentrations: in these situations, the platform being developed fulfills the requirements ideally and will have a strong impact and provide new insights, e.g. into the metabolic processes of cells, organisms or organs.
The Spanish tobacco tax loopholes and their consequencesUCT ICO
Ángel López-Nicolás
Grupo de Investigación en Economía, Políticas Públicas y Salud, Universidad Politécnica de Cartagena
Belén Cobacho
Centre de Recerca en Economia i Salut, Universitat Pompeu Fabra
Esteve Fernández
Institut Català d’Oncologia
ICO-WHO Symposium 2012
This is a short presentation about company formation in Lithuania. For more information, please visit www.companyformationlithuania.com.
You can always reach us at office@bridgewest.eu or find us on www.bridgewest.eu for consulting services.
There is nowadays a growing need for sensing devices offering rapid and portable analytical functionality in real-time as well as massively parallel capabilities with very high sensitivity at the molecular level. Such devices are essential to facilitate research and foster advances in fields such as drug discovery, proteomics, medical diagnostics, systems biology or environmental monitoring.
In this context, an ideal solution is an ion-sensitive field-effect transistor sensor platform based on silicon nanowires to be integrated in a CMOS architecture. Indeed, in addition to the expected high sensitivity and superior signal quality, such nanowire sensors could be mass manufactured at reasonable costs, and readily integrated into electronic diagnostic devices to facilitate bed-site diagnostics and personalized medicine. Moreover, their small size makes them ideal candidates for future implanted sensing devices. While promising biosensing experiments based on silicon nanowire field-effect transistors have been reported, real-life applications still require improved control, together with a detailed understanding of the basic sensing mechanisms. For instance, it is crucial to optimize the geometry of the wire, a still rather unexplored aspect up to now, as well as its surface functionalization or its selectivity to the targeted analytes.
This project seeks to develop a modular, scalable and integrateable sensor platform for the electronic detection of analytes in solution. The idea is to integrate silicon nanowire field-effect transistors as a sensor array and combine them with state-of-the-art microfabricated interface electronics as well as with microfluidic channels for liquid handling. Such sensors have the potential to be mass manufactured at reasonable costs, allowing their integration as the active sensor part in electronic point-of-care diagnostic devices to facilitate, for instance, bed-side diagnostics and personalized medicine. Another important field is systems biology, where many substances need to be quantitatively detected in parallel at very low concentrations: in these situations, the platform being developed fulfills the requirements ideally and will have a strong impact and provide new insights, e.g. into the metabolic processes of cells, organisms or organs.
There is nowadays a growing need for sensing devices offering rapid and portable analytical functionality in real-time as well as massively parallel capabilities with very high sensitivity at the molecular level. Such devices are essential to facilitate research and foster advances in fields such as drug discovery, proteomics, medical diagnostics, systems biology or environmental monitoring.
In this context, an ideal solution is an ion-sensitive field-effect transistor sensor platform based on silicon nanowires to be integrated in a CMOS architecture. Indeed, in addition to the expected high sensitivity and superior signal quality, such nanowire sensors could be mass manufactured at reasonable costs, and readily integrated into electronic diagnostic devices to facilitate bed-site diagnostics and personalized medicine. Moreover, their small size makes them ideal candidates for future implanted sensing devices. While promising biosensing experiments based on silicon nanowire field-effect transistors have been reported, real-life applications still require improved control, together with a detailed understanding of the basic sensing mechanisms. For instance, it is crucial to optimize the geometry of the wire, a still rather unexplored aspect up to now, as well as its surface functionalization or its selectivity to the targeted analytes.
This project seeks to develop a modular, scalable and integrateable sensor platform for the electronic detection of analytes in solution. The idea is to integrate silicon nanowire field-effect transistors as a sensor array and combine them with state-of-the-art microfabricated interface electronics as well as with microfluidic channels for liquid handling. Such sensors have the potential to be mass manufactured at reasonable costs, allowing their integration as the active sensor part in electronic point-of-care diagnostic devices to facilitate, for instance, bed-side diagnostics and personalized medicine. Another important field is systems biology, where many substances need to be quantitatively detected in parallel at very low concentrations: in these situations, the platform being developed fulfills the requirements ideally and will have a strong impact and provide new insights, e.g. into the metabolic processes of cells, organisms or organs.
This is a talk I gave at the Nano Cafe in February. It is a quick overview of the things I am doing in KochLab and some of the things we hope to achieve.
Assembling the Norway Spruce Genome: 20Gb and many challenges, Umeå Plant Sci...Copenhagenomics
Dr. Douglas G. Scofield is Principal Research Engineer at Umeå Plant Science Centre at Umeå University in Sweden. Slides for his presentation: Assembling the Norway Spruce genome.
Uncovering the impacts of circumcision on the penis microbiome, Translational...Copenhagenomics
Dr. Lance Price, Director of Center for Food Microbiology and Environmental Health
Translational Genomics Research Institute (TGen) presents his talk: Uncovering the impacts of circumcision on the penis microbiome
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
The Indian economy is classified into different sectors to simplify the analysis and understanding of economic activities. For Class 10, it's essential to grasp the sectors of the Indian economy, understand their characteristics, and recognize their importance. This guide will provide detailed notes on the Sectors of the Indian Economy Class 10, using specific long-tail keywords to enhance comprehension.
For more information, visit-www.vavaclasses.com
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
Ethnobotany and Ethnopharmacology:
Ethnobotany in herbal drug evaluation,
Impact of Ethnobotany in traditional medicine,
New development in herbals,
Bio-prospecting tools for drug discovery,
Role of Ethnopharmacology in drug evaluation,
Reverse Pharmacology.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
How to Create Map Views in the Odoo 17 ERPCeline George
The map views are useful for providing a geographical representation of data. They allow users to visualize and analyze the data in a more intuitive manner.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
2. BCM-HGSC Sequencer Fleet
Life Tech SOLiDTM 4
Life Tech 3730 system Life Tech Ion Torrent PGM
Roche 454 FLX system Pacific Biosciences
Illumina GAIIx & Hiseq2000 2
3. Big Science Projects
• 1,000 Genomes Project
– Discovery of rare (1%) SNVs & SVs in normal genomes
• The Cancer Genome Atlas
– Discovery of sequence variants in major cancers
• Personal Genome Project
– Discovery of sequence variants associated with medical
information
• Human Microbiome Project
– Study of communities of mixed microbes within human niches
• The Exome Project
– Discovery of sequence variants in protein coding regions
• Pharmacogenomics Research Network
– Discovery of sequence variants involving drug-gene interactions
3
4. NGS Applications
• Human biology
– Genotype – phenotype interactions
• Pharmacogenomics
– Drug – gene interactions
• Diagnostics
– Actionable variants
• Forensics
– Linking suspects to a crime scene
• Human Microbiome
– Study of microbe communities
• Many more than time to cover…
4
5. Capture Sequencing at BCM-HGSC
Library Automation
Decrease Reagent cost
Decrease Labor cost
Increase capture production
Multiplex Sequence Capture
5
7. Diagnostic Exome Sequencing
Joint effort between BCM’s HGSC and BCM’s
Medical Genetics Laboratories (MGL) to provide
exome sequencing with clinical interpretation 7
8. HIV forensics
State of Louisiana
v. Richard J.
Schmidt Metzker et al. (2002)
PNAS 99: 14292-14297
Patient → Trahan
State of Washington v.
Anthony Eugene
Whitfield
Whitfield → 5 partners
Scaduto et al. (2010)
PNAS 107: 21242-21247
State of Texas v.
Philippe Padieu
Padieu → 6 partners
8
9. Direction of transmission
(source → recipient)
Providing evidence for the direction of transmission would
further strengthen the a priori hypothesis.
Genetic bottleneck during transmission
•Paraphyly: Evidence for direction of transmission
Study design:
•identities of case subjects were blinded to investigators
•case sample handling were separated both temporally and
spatially to eliminate the possibility of cross contamination
•case allegations were multiple transmissions from a single
source
9
10. HIV genes: pol and env
RT (1-221 aa) gp120 (c2-v5)
Methods involved were:
•Fractionation of PBMCs
•Isolation of genomic DNA
•PCR and cloning
•Sanger sequencing
•Multiple sequence alignments
10
11. Texas case: pol tree
CC01 exhibited a
paraphyletic relationship
to all CC case sequences
•Bayesian posterior
probabilities (1.00)
•ML bootstrapping proportions
(0.98)
Red circle represents the
most recent common
ancestor of sequences
from CC01
Scaduto et al. (2010) PNAS 107: 21242-21247
11
12. Texas case: env tree
CC01 exhibited a
paraphyletic relationship to
all CC case sequences but
CC05
•Bayesian posterior probabilities
(1.00)
•ML bootstrapping proportions
(1.00)
Red circle represents
the most recent
common ancestor of
sequences from CC01
Scaduto et al. (2010) PNAS 107: 21242-21247
12
13. NGS in HIV forensics
Development of the ‘pathogen toolkit’
Long-range PCR Clone analysis: EcoRI
10kb
5kb
4kb
3kb
Large insert cloning
NIJ grant: 2011-DN-BX-K534
13
14. NGS in HIV forensics
Development of the ‘pathogen toolkit’
Case sample 01 Case sample 02 so forth
Molecular Fragment, add Molecular Fragment, add
clone 01 forward adaptor with MC01, clone 01 forward adaptor with MC01,
reverse adaptor with CS01 reverse adaptor with CS02
… …
… …
… …
Molecular Fragment, add Molecular Fragment, add
clone 20 forward adaptor with MC20, clone 20 forward adaptor with MC20,
reverse adaptor with CS01 reverse adaptor with CS02
Pool libraries,
then clonally amplify &
sequence by NGS technologies
NIJ grant: 2011-DN-BX-K534
14
18. Lightning Terminators™
H Fluor H Fluor
N N
Properties: O O
OMe OMe
• 3’-OH unblocked O 2N
NH 2
O2 N
O
t -Bu O t-Bu O
reversible terminators N
N
N
NH
N N NH 2
HO O O O HO O O O
• Fast incorporation
P P P O P P P O
O O O O O O O O O O O O
OH OH
kinetics LT-dA LT-dG
• Fast cleavage kinetics H
N
Fluor H
N
Fluor
O O
• High fidelity → OMe OMe
high accuracy O2 N NH 2 O 2N O
t-Bu O N t -Bu O NH
• Single-base HO
P
O
P
O
P
O
O
N O
HO
P P
O O
P
O
O
N O
termination O O O O O O
OH
O O O O O O
OH
LT-dC LT-dU
18
19. Fast Incorporation Kinetics
k pol KD k pol/K D Selection
Nucleotide -1
(s ) (μM) (μM-1 s-1) (analog/TTP)
TTP 170 ± 4 73 ± 3 2.3 1.0
HOMedUTP 250 ± 11 33 ± 7 7.6 3.3
dU.V 37 ± 6 15 ± 2 2.5 1.1
dU.VI 36 ± 7 12 ± 1 3.0 1.3
• Fast incorporation rates
• Lower KD gives kinetic advantage over natural dNTPs
• As efficient as natural dNTPs
Gardner et al. (2012) Nucleic Acids Res., published May 8, 2012
19
20. High Fidelity
Mutant
10
100004
Molecular tuning: polymerases "C"
Wild-type selectivity
"G"
•Key structural site drop fidelity "T"
identified 10
10003
)0
5
o
i C
I
t
a d
•Increasing size = R
y
t
i
v
i
t
e
h
c
t
a
c M
/
better specificity e
l
e
S
e
5 102
0
C 100
I
d
d
i e
t h
c
o
e t
l
c a
u m
s
N i
M
(
101
10
O NO2
CH 3
HN O CHCH3
3
H 3C CH 3
CH
3
O N
HO O O O
P P P O 100
1
O O O O O O
HOMedUTP HOMedUTP
HOMedUTP dU.I
Cpd dU.I dU.II
Cpd dU.II dU.III
Cpd dU.III dU.IV
Cpd dU.IV dU.V
Cpd dU.V
OH Vent(exo-) Therminator
Litosh et al. (2011) Nucleic Acids Res., 39:e39
20
21. High Fidelity
Nucleotide selectivity
Template k pol KD k pol/K D k pol/K D (Corr.) IC50 (MisM) /
Nucleotide
base -1
(s ) (μM) (μM s )
-1 -1 / k pol/K D IC50 (Corr.)
a (MisM)
TTP C 72 ± 1 150 ± 8 0.48 4.9 11
G 55 ± 2 340 ± 50 0.16 14 22
T 97 ± 4 290 ± 19 0.33 7.0 44
a -3
dU.V C 0.045 ± 0.035 12 ± 2 3.8 x 10 630 1300
-3
G 0.030 ± 0.002 25 ± 1 1.2 x 10 2000 740
-3
T 0.053 ± 0.011 45 ± 4 1.2 x 10 2000 850
b -3
dU.VI C 0.063 ± 0.020 13 ± 3 4.8 x 10 620 590
-3
G 0.048 ± 0.016 44 ± 6 1.1 x 10 2800 400
-3
T 0.035 ± 0.010 34 ± 10 1.0 x 10 2900 540
Gardner et al. (2012) Nucleic Acids Res., published May 8, 2012
21
22. Current progress
Status: UV
source
•E. coli genome
sequenced
•Pilot phase for mixed
culture studies
•Pathogen detection Microfluidic
flowcell
paper in preparation
Objective
Spectral
filters
Excitation
source
Digital
camera Mirror
Hertzog et al. (2011) BioOptics World DoD contract: W81XWH-12-C-0061
22
23. Acknowledgements
LaserGen, Inc. BCM-HGSC NHGRI grants
Megan Hersh Priyanka R21 HG002443
David Hertzog Kshatriya R41 HG003072
Weidong Wu Huyen Dinh R01 HG003573
Hong Li Donna R43 HG003443
Brian Stupi Muzny R21 HG004757
Jinchun Wang Eric
Sidney Morris NEB
Boerwinkle NIJ grant
Cyril Chen Andy
Richard A. 2011-DN-BX-K534
Peng Chen Gardner
Gibbs
Michael Paras Bill DoD contract
U of Texas
Mimi Healy Jack W81XWH-12-C-0061
David
Hillis
LSU
Jeremy
Brown
23