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News:
posted 01/26/2007: Faculty Research Presentation:
Lecture Title: Heritability and Multivariate Analyses
of Endophenotypic Measures for Schizophrenia:
The Consortium On The Genetics Of Schizophrenia (COGS)
Speaker: Tiffany Greenwood, Ph.D.
Time: 12:00 noon - 1:00 pm Friday, February 2, 2007
Location: Basic Science Building
Room: Room 2071
Abstract:
The exploration of the genetic architecture of
specific endophenotypes is a powerful strategy for
understanding the genetic basis of schizophrenia. A
major advantage of the use of endophenotypes is that
they are likely to be more correlated with the genetic
and neural substrate abnormalities than is the fuzzy,
qualitative DSM-IV diagnosis of schizophrenia itself.
The Consortium on the Genetics of Schizophrenia (COGS)
has undertaken a large 7-site study to characterize
the genetic basis of some key endophenotypic
measures. The COGS assesses the automatic processing
measures of Prepulse Inhibition (PPI) of the startle
response and P50 suppression, as well as the
effortful, controlled processing measures of the
Antisaccade Task (AS), the Degraded Stimulus
Continuous Performance Test (DS-CPT), the California
Verbal Learning Task, Second Edition (CVLT-II), the
Letter-Number Span (LNS) test, and six measures from
the University of Pennsylvania Computerized
Neuropsychological Battery. At the time of these data
analyses, 183 probands with schizophrenia and their
family members (N=638) have been assessed for these
endophenotypes. Variance component models were used
to assess heritability, as well as the environmental
and genetic correlations among the endophenotypes. All
of the endophenotypes, with the exception of P50
suppression, were found to be significantly heritable
(p<0.05), with heritabilities ranging from 24 to 55%.
Significant environmental and genetic correlations
were also observed between many of the endophenotypic
measures, providing some evidence for pleiotropy.
Additionally, probands with complete data for all
endophenotypic measures were selected for analysis
with a novel multivariate method for testing the
relationship between variation in a similarity matrix
and ancillary information collected on a sample of
individuals that obviates the need for cluster
analysis by testing more global hypotheses about the
patterns of similarity in the matrix. This method is
also the perfect companion for heat map and tree-based
representations of high-dimensional data organized by
some feature or grouping factor meant to reveal the
relationship between the variables used for their
construction. Our multivariate approach has also
revealed a number of interesting associations, as well
as possible subgroups of schizophrenia patients. This
is the first large-scale, multi-site, family-based
heritability study of a large collection of
endophenotypes for schizophrenia families and suggests
that endophenotypes will be important measures to
consider in characterizing the genetic basis of
schizophrenia.
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posted 08/09/06: Workshop
Workshop Title: Applying Ingenuity Pathways
Analysis
Host: Moores Cancer Center, UCSD and Ingenuity Systems,
Inc.
Date: Thursday, August 24th 2006
Time: 10:30am - 2:15pm (see schedule below)
Location: Moores Cancer Center
Room: Goldberg Auditorium (Room 2110)
Contact: Lucas
Hickey, Ingenuity Systems, 650.381.5056
Ingenuity Pathways Analysis
is an application used to identify relevant biological
pathways, functions, and interaction networks for
genes and proteins.
| 10:30 - 11:15am |
Introduction to Ingenuity &
Pathways Analysis, Use Cases.
Dr. Armin Spura, Ingenuity Systems
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| 11:15 - 11:45am |
Central Nervous System Use Case
Dr. Rich Roth, Neurocrine
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| 11:30 - 12:15pm |
Lunch will be provided
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| 12:30 - 01:15pm |
Drug Mechanism of Action Use Case
Dr. John Walker, GNF
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| 01:30 - 02:15pm |
Hands-on Demonstrations; Breakout Discussions
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| 02:30 - 02:15pm |
Closing
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posted 04/03/2006 Seminar:
Lecture Title: Genomic Approaches to Understanding the
Genetic Basis of Human Disease
Speaker: Eleazar Eskin
Time: Wednesday, April 5 10:00-11:00 am
Location: Moores Cancer Center
Room: Goldberg Auditorium
Abstract: Variation in human DNA sequences account
for a significant amount of the genetic risk factors
for common disease such as hypertension, diabetes,
Alzheimer's disease, and cancer. Identifying the
common variation that influences susceptibility
to disease will usher in a new era of personalized
medicine where treatment decisions are based not only
on clinical observations, but also take into account
an individual's genetic makeup. Recent technological
advances in high-throughput genotyping technology
allow us for the first time to collect human variation
information on a large enough scale to identify the
variation involved in disease. This talk focuses
on two challenges associated with the analysis of
high-throughput genotype data. Since the new cost
effective technologies obtain human variation information
from both pairs of human chromosomes simultaneously, the
first step in analysis of these datasets is computational
prediction of the human variation on each chromosome or
the haplotype phasing problem. We discuss the results
of our collaboration with Perlegen Sciences on the
phasing of whole genome human haplotypes. A second
challenge is the association of whole genome variation
data to phenotypic data or clinical traits. Using the
inbred mouse as a model organism, we demonstrate how
our methods are able to discover many regions in the
mouse genome associated with phenotypes and how many
of our predictions are consistent with genes known to
influence specific traits.
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posted 03/05/2006
The latest version of the FBPP data files is
currently v3.10. If you are using this data,
please email Charles for information on how
to download them.
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posted 02/15/2006
Lecture Title: The Next Generation High Density
Microarrays: Introduction to genome tiling arrays
and the human exon array.
Speaker: Keith Brown, Affymetrix
Date: Thursday, Feb 16th
Time: 12:00 pm - 1:00 pm
Location: UCSD, Moores Cancer Center
Room: Goldberg Auditorium
RSVP: to Nick Webster
(needed to determine food quantity)
Seminar will provide detailed information on the
latest arrays, assays, and analysis tools developed
by Affymetrix and our partners. Lunch will be provided.
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posted 01/25/2006
Lecture Title: DNA Repair and Cancer: Model for
estimating the role of genetic variation in risk of
common disease following exposure
Speaker: Harvey Mohrenweiser
Date: February 2, 2006
Time: 12 noon
Location: UCSD School of Medicine
Room: Leichtag Building, Room 107
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01/24/2006
Lecture Title: THE PLEASURES AND PERILS OF STUDYING
EMOTIONAL AROUSAL IN MID-AIR AT 165 MPH AND 11,500 FEET
Speaker: Lilianne R. Mujica-Paroli, Ph.D.
Date: Friday, January 27, 2006
Time: 2:00 noon - 1:00 pm
Location: UCSD School of Medicine
Room: David Segal Conference Room 2071 Basic Science
Building
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08/15/2005
Lecture Title: Molecular, Clinical, and Population
Profiling via Similarity Matrix Analysis
Speaker: Nicholas J. Schork
Date: Wednesday, August 24, 2005
Time: 3:00 - 4:00 p.m.
Location: The Rebecca and John Moores UCSD Cancer Center
Room: Fung Auditorium, Powell-Focht Building
Abstract:
Modern genomics-based research is incredibly data
intensive. Although the analysis of high-dimensional data
is problematic, such data may be dealt with through the
use appropriate statistical models. Analysis methods
that build off the notions of similarity, correlation
and agreement, and "random" matrices can be used to
draw meaningful inferences from large data sets. Recent
developments in linear and non-linear models that
assess similarity and distance matrices, rather than
individual data points, are extremely relevant in this
light. These methods have desirable properties, such
as degree-of-freedom reduction and a sound basis in
multivariate analysis and matrix theory. These methods
also have extremely wide applicability and can be used
to analyze DNA sequence data, gene expression data,
proteomic data, subclinical/physiological data,
clinical data, epidemiological data, population
genetic/evolutionary data, or combinations of these
data types. In addition, these methods can be used in
additional applications such as QSAR, protein structure,
and pathway analysis. There are additional items that one
should consider in this (and other) analysis methods,
such as the accommodation of measurement error and the
use of appropriate functionals. This talk will consider,
in a largely non-mathematical way, the foundation and
potential of these analysis methods but focus heavily
on their application in multiple, integrated human
genomic research areas.
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08/12/2005
As part of the workshop series on Methods in Genetics
and Neuroimaging Sponsored by the Stein Institute
for Research on Aging there will be a visit to the
Polymorphism Research Lab led by Brinda K. Rana, Ph.D.
When: Tuesday, August 16th, 2005 from 1pm to 2pm
Where: Bonner Hall 2429
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07/29/2005
- GeneChip Core Seminar
Title: "Using high definition genomics to scan the whole
genome: gene expression, break point analysis,
amplifications, deletions, transcription factor
localization"
Sponsor: GeneChip Core
Speaker: Dan Clutter, PhD., Vice President of Sales,
NimbleGen
Where: Leichtag Biomedical Research Building 205
When: 11 am, Monday 1st August 2005
Symposium
The 6th International Symposium on Familial
Amyloidotic Polyneuropathy and Other Transthyretin
Related Disorders, and The 5th International Workshop on
Liver Transplantation in Familial Amyloid Polyneuropathy
will be held August 24th - August 26th.
Nik is chairing The A Session for the Genetics Track.
Speaker schedule for this is as follows:
- Nicholas Schork, University of California, San Diego,
La Jolla CA, USA
- Fabrizio Salvi, Bellaria Hopital, Bologna, ITALY
Different prognoses in genetically defined AH-TTR
amyloidosis
- Clem Tagoe, Albert Einstein College of Medicine, Bronx
NY, USA
TTR V122I Evidence for the clinical significance of the
allele
- Gosta Holmgren, Umea University Hospital, Umea, SWEDEN
Impact of homozygosity for an amyloidogenic transthyretin
mutation on phenotype and long-term outcome
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07/28/2005
Upcoming Workshop:
Methods in Genetics and Neuroimaging
Sponsored by the Stein Institute for Research on Aging
- 11am-2pm: Workshop 5: Tuesday, August 9th, 2005,
Stein Building, Room 344A
- 11:00-12:15pm: Susan Tapert, PhD "Analysis of fMRI
Data at the Individual Level"
- 12:15pm-12:45pm: LUNCH
- 12:45pm-2:00pm: Nicholas Webster, PhD "Microarrays
and Gene Expression Analysis Techniques"
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07/28/2005
A tour has been arranged for the Skaggs
Building site on August 1, 2005 at 2pm. Details in the
lab email provided by Natasha (wear protective clothing as
it's a hard-hat environment.)
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07/28/2005
Human Genetics Seminar Series
Contemporary Issues in Human Genetics
Location: 107 Leichtag
Time: 11:30am 1:30pm
Next Seminar Date: September 15th
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07/28/2005
Upcoming Workshop:
Methods in Genetics and Neuroimaging
Sponsored by the Stein Institute for Research on Aging
- 11am-2pm: Workshop 5: Tuesday, August 9th, 2005,
Stein Building, Room 344A
- 11:00-12:15pm: Susan Tapert, PhD "Analysis of fMRI
Data at the Individual Level"
- 12:15pm-12:45pm: LUNCH
- 12:45pm-2:00pm: Nicholas Webster, PhD "Microarrays
and Gene Expression Analysis Techniques"
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07/28/2005
A tour has been arranged for the Skaggs
Building site on August 1, 2005 at 2pm. Details in the
lab email provided by Natasha (wear protective clothing as
it's a hard-hat environment.)
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07/20/2005
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The current FBPP data version is 3.8. If you are working
on this and would like a copy of the data, contact Charles
for details on its location and software requirements.
He also has the data in cvs form (thanks, Rany!) if you
prefer that.
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In addition, many minor changes to the web pages (New
pictures on the People page!
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Complearn is being
added to the lab core competencies. Complearn is a method
of calculating association distances using compressed data.
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06/14/2005
The following have been updated:
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06/07/2005
Doug Smith has updated his analysis of
the Sequenome SNPs, and much much more. Click on the
link to see the overview of the
PPG SNP Data,
Public Domain and Proprietary. Recent changes include
- Subgroup analyses of the Sequenom nnnn.Unrelateds SNP
data
- Analysis of TCGA resequencing data
- Presentation to Schork lab on 10 May, 2005, entitled:
"Primary Analysis of new SNP Genotype Data"
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05/26/2005
We have a new design for our website. The
pages are still static and the webmaster is still the one
that updates them, but he hopes to arrange it so that lab
members can themselves add news items to this page, modify
their own bio content, and update the programs page,
articles page, etc. |
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