Papers for Journal Clubs
Here is the list of papers for the Journal Clubs, most of them you will find as pdf files
(please refer to “pdf PAPERS for JOURNAL CLUBS”, some are references that you will
have to find and print.
May 16 (Monday)
Journal Club: Kathryn Becker and Alex Mathews (Vysis/Abbott)
1-Wa C et al. Clinical application of array-based Comparative Genomic
Hybridization to define the relationship between multiple synchronous
tumors.
Modern Pathology (2005) 1-7. (pdf# 1)
2-Kirchhoff M et al. Prospective study comparing HR-CGH and
subtelomeric FISH for investigation of individuals with mental
retardation and dysmorphic features and an update of a study using
only HR-CGH.
American Journal of Medical Genetics, 127A:111-117 (2004). (pdf# 2)
May 17 (Tuesday)
Journal Club: Dr. Jeremy Squire and Mona Prasad (Ontario Cancer
Institute)
1-Sebat J et al. Large-scale copy number Polymorphism in the Human
Genome.
Science vol 305, 23 July 2004, 525-528. www.sciencemag.org. (pdf# 3)
For further reading/discussion:
2-Leaf C. Why we’re losing the war on Cancer (and how to win it).
Fortune March 22, 2004, 77-94. (pdf# 4)
3-Tanaka H et al. Widespread and nonrandom distribution of DNA
palindromes in cancer cells provides a structural platform for
subsequent gene amplification.
Nature Genetics, 2005, 1-8. Technical reports.
www.nature.com/naturegenetics. (pdf# 5)
May 18 (Wednesday)
Exercise:
To: CIHR Workshop Attendees
From: P. A. Jansson
Re:
Preparation for Deconvolution Lecture
I am honored by the invitation to address your group. To best
take advantage of the material presented, it would be helpful to
work an exercise. I will connect the exercise to microscopy
during the talk.
You can work the exercise in columns on a sheet of paper, on a
spreadsheet like EXCEL, or with a simple computer program.
You are probably familiar with the concept of a weighted average.
We are going to compute a simple moving weighted average of a
list of sample values. Then, temporarily discarding the original
sample values, from the resulting list of weighted average
numbers, we will try to recover them.
Below we see columns containing indices, sample values, weights,
and a single weighted average of the first 9 values, recorded in
the fourth column and opposite the largest weight. The weighted
average is obtained by multiplying each of the nine sample values
opposite each of the weights by their respective weights, then
adding those products together. Because the first nine values
are zero, the sum is zero. For this particular set of weights,
the sum is the same as the average because the weights are
normalized, i.e., adding them together gives unity.
1
2
3
4
Sample
Indices
Sample
Values
Weights
Weighted
Average
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
0
0
0
0
0
0
0
0
0
0
2
0
3
0
0
x
x
x
x
x
x
x
x
x
0.04
0.08
0.12
0.16
0.20
0.16
0.12
0.08
0.04
=
=
=
=
=
=
=
=
=
0
0
0
0
0
0
0
0
0
|
|
| (slide down)
V
\
|
|(sum)
|
> =
|
|
|
/
0
16
17
18
19
20
21
22
23
24
25
26
0
0
0
0
0
0
0
0
0
0
0
Now, slide the nine weights down so that they are opposite sample
values 2 through 10, and repeat the process. You will note that
after the second sliding, the bottom weight has encountered the
sample having a value of 2, so it then contributes to the
weighted average.
When the bottom weight encounters sample 26, you are finished,
and should have 18 numbers in the weighted-average column.
At this point it will be instructive to plot the original sample
values and weighted averages on a “y” axis vs. the sample indices
on the “x” axis.
Now, here is the part where you have to think. Suppose the
original sample values are unknown or inaccessible to us. Let us
try to recover those values, based on our knowledge of the
weights and weighted averages alone, starting from the top of the
weighted-average column. We are permitted to assume that the
first eight values are zeroes. Because the weighted average of
the first nine values is also zero, the ninth value must be zero
too. Now it is up to you to consider the second weighted-average
to see if you can infer the next original sample value on the
list, having determined the previous one, and so forth. A little
algebra will permit you to develop a formula for each new unknown
sample value in terms of the previous values and the newly
introduced weighted-average number. By this means recover and
plot all the original sample values. Do not use "canned"
deconvolution program(s) to perform this exercise. Carefully
follow the directions given.
Were the sample values recovered correctly? (Hopefully “yes,” if
you carried enough precision in your calculations.)
Now, add a small error, 0.02, to the weighted-average number
opposite sample index 11, then repeat the recovery process,
plotting the result. What did you observe?
Examples like this are contained in the introductory chapter of
my text Deconvolution of Images and Spectra, Academic Press,
1997. This volume goes on to treat the mathematics and practical
applications of deconvolution. For those who are sufficiently
interested, this volume should be accessible to anyone with a
background in elementary calculus. It and/or its first edition,
Deconvolution, with Applications in Spectroscopy, Academic Press,
1984, can be found in nearly all major university libraries.
May 20 (Thursday)
Journal Club: Dr. Yuval Garini and Bart Vermolen (University of Delft,
The Netherlands)
1-Eils R and Athale C. Computational Imaging in Cell Biology.
The Journal of Cell Biology, vol 161, number 3, 2003, 447-481. (pdf# 6)
2-Gerlich D et al. Global chromosome positions are transmitted through
mitosis in mammalian cells.
Cell, vol 112, 751-764, March 21, 2003. (pdf# 7)
3-Tanabe H et al. Evolutionary conservation of chromosome territory
arrangements in cell niclei in higher primates.
PNAS, April 2, 2002, vol 99, number 7, 4424-4429. (pdf# 8)
4-Schrock E et al. Multicolor Spectral Karyotyping of Human
Chromosomes.
Science, vol 273, 26 July 1996, 494-497. (pdf# 9)
5-Huth U et al. Fourier transformed spectral bio-imaging for studying
intracellular fate of liposomes.
Cytometry Part A, 57A:10-21 (2004). (pdf# 10)
May 24 (Tuesday)
Journal Club: Dr. Regen Drouin (University of Sherbrooke, Quebec)
1-Roy L, Coullin P, Vitrat N, Hellio R, Debili N, Weinstein J, Bernheim
A, Vainchenker W. Asymmetrical segregation of chromosomes with a
normal metaphase/anaphase checkpoint in polyploid megakaryocytes.
Blood. 2001; 97:2238-47.
2-Yan J, Chen BZ, Bouchard EF, Drouin R. The labeling efficiency of
human telomeres is increased by double-strand PRINS.
Chromosoma 2004; 113: 204-9.
Further reading:
-Koch JE, Kolvraa S, Petersen KB, Gregersen N, Bolund L.
Oligonucleotide-priming methods for the chromosome-specific labelling
of alpha satellite DNA in situ. Chromosoma 1989; 98: 259-65.
-Kadandale JS, Wachtel SS, Tunca Y, Martens PR, Wilroy RS,
Tharapel AT. Deletion of RBM and DAZ in azoospermia: Evaluation by
PRINS. Am J Med Genet 2002; 107: 105-8.
-Tharapel AT, Kadandale JS, Martens PR, Wachtel SS, Wilroy RS.
Prader Willi/Angelman and DiGeorge/Velocardiofacial syndrome
deletions: Diagnosis by Primed In Situ Labeling (PRINS). Am J Med
Genet 2002; 107: 119-22.
-Tharapel SA, Kadandale JS. Primed in situ labeling (PRINS) for
evaluation of gene deletions in cancer. Am J Med Genet 2002; 107:123126.
-Coullin P, Roy L, Pellestor F, et al. PRINS, the other in situ labeling
method useful in cellular biology. Am J Med Genet 2002; 107: 127-35.
-Yan J, Bronsard M, Drouin R. Creating a new color by omission of 3
end blocking step for simultaneous detection of different chromosomes
in multi-PRINS technique. Chromosoma 2001; 109: 565-70.
-Yan J, Zhang XX, Fetni R, Drouin R. Trisomy 8 and monosomy 7
detected in bone marrow using primed in situ labeling, fluorescence in
situ hybridization, and conventional cytogenetic analyses. A study of 54
cases with hematological disorders. Cancer Genet Cytogenet 2001; 125:
30-40.
-Pellestor F, Quenesson I, Coignet L, et al. FISH and PRINS, a strategy
for rapid chromosome screening: application to the assessment of
aneuploidy in human sperm. Cytogenet Cell Genet 1996; 72: 34-6.
-Pellestor F, Malki S, Andreo B, Lefort G. Ultra-rapid multicolor
PRINS protocol for chromosome detection in human sperm.
Chromosome Res. 2002;10:359-67.
-Pellestor F, Anahory T, Andreo B, Regnier-Vigouroux G, Soulie JP,
Baudouin M, Demaille J. Fast multicolor primed in situ protocol for
chromosome identification in isolated cells may be used for human
oocytes and polar bodies. Fertil Steril. 2004; 81:408-15.
May 27 (Friday)
Journal Club: Dr. Ulrich Klingbeil (MetaSystems Group Inc., Boston.
USA).
1-MetaSystems XCyte Lab Manual. (pdf# 11)
2- Chudoba, A. et al. High resolution multicolor-banding: a new
technique for refined FISH analysis of human chromosomes.
Cytogenetics and Cell Genetics, 1999, 84, 156-160.