medical pedigrees: typography and interface › tug2009 › preprints › veytsman-pedigree.pdf ·...
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Medical Pedigrees: Typography andInterface
Boris Veytsman∗ Leila Akhmadeeva †
TUG 2009, Notre Dame, IN, USA
∗Computational Materials Science Center, MS 6A2, George Mason Univer-sity, Fairfax, VA 22030
†Bashkir State Medical University, 3 Lenina Str. Ufa, 450000, Russia
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1. Introduction
Ethnic Background Ethnic BackgroundO’Type ?
I1
b
2 3 4 5 6
?
d. 72 y7
d. 70 y8
9–14
5
IIProto
1 ∗
Sterrie
32 yE3−
E4+(45n/18n)2
?
3
D
?
4
D
5 ∗
Gary
36 yE3−
6
∗
Gene
36 yE3−
7
O’Type
Feene
35 y8
9
//Stacey
33y10
Sam
31 yE2+
11
b
Donald
29 yE2+
12
13 14
S n
III1 2
P
6 wk3
P female18wk
E1+(tri 21)4
16wk5
P 6female19 wk
7
10 y8
9 male20 wk
E1+ (tri 18)10
SB32 wk
11
12P
A Complex Pedigree1
1Robin L. Bennett et al., “Recommendations for Standardized Human Pedi-gree Nomenclature,” Am. J. Hum. Genet. 56/3 (1995).
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Our package for pedigree drawing was described in several papers2:
1. A TEX-PSTricks package to draw diagrams as complex as theycan get3.
2. A Perl program to automatically generate TEX input for 90%cases4.
2Boris Veytsman and Leila Akhmadeeva, “Drawing Medical Pedigree Treeswith TEX and PSTricks,” TUGboat 28/1 (2007); Boris Veytsman and LeilaAkhmadeeva, “Medical Pedigrees with TEX and PSTricks: New Advances andChallenges,” TUGboat 29/3 (2008)
3Boris Veytsman and Leila Akhmadeeva, Creating Medical Pedigrees withPSTricks and LATEX, 2007.
4Boris Veytsman and Leila Akhmadeeva, A Program For Automatic PedigreeConstruction With pst-pdgr. User Manual and Algorithm Description, 2007.
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Our package for pedigree drawing was described in several papers2:
1. A TEX-PSTricks package to draw diagrams as complex as theycan get3.
2. A Perl program to automatically generate TEX input for 90%cases4.
New challenges:How to make things beautiful &user-friendly?
2Boris Veytsman and Leila Akhmadeeva, “Drawing Medical Pedigree Treeswith TEX and PSTricks,” TUGboat 28/1 (2007); Boris Veytsman and LeilaAkhmadeeva, “Medical Pedigrees with TEX and PSTricks: New Advances andChallenges,” TUGboat 29/3 (2008)
3Boris Veytsman and Leila Akhmadeeva, Creating Medical Pedigrees withPSTricks and LATEX, 2007.
4Boris Veytsman and Leila Akhmadeeva, A Program For Automatic PedigreeConstruction With pst-pdgr. User Manual and Algorithm Description, 2007.
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2. History of Pedigrees
This is based on the great work by Resta5. A quotation from there:
A complete pedigree is often a work of great labour, andits finished form is frequently a work of art.
Karl Pearson, 1912
Pedigrees vs. genealogical trees: traits instead of individuals.
Pedigrees are relatively modern: since the middle of 19 century.
5Robert G. Resta, “The Crane’s Foot: The Rise of the Pedigree in TheHuman Genetics,” J. Genetic Couns. 2/4 (1993).
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2.1. Musical Notes for Symbols
Pliny Earle, 18456:
Incidentally, these are females of the author’s family!
Generations are marked on margins. No marking for individuals.
6Idem
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2.2. Tabular System
Galton, 18897:
7Idem
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2.3. Mars and Venus
Pearson, 19128:
This chart shows inheritance of “commercial and legal ability”.
The numbering is almost modern. Symbols are quite different.Marriage lines are under the symbols. Peculiar marking for twins.
8Idem
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2.4. German Style
Rüdin, 19109:
Proband in center, radial composition.9Idem
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2.5. Galton-Pearson Style
Mott, 191010:
Stylized Mars and Venus for males and females. Note marriagelines.
Was used in some journals up to 1970s!
10Idem
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2.6. Davenport-Goddard Style
Goddard, 191111:
This is almost modern! Note interesting proband notation.
11Idem
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3. Modern Pedigrees
A hand drawn pedigree12:
12Robin L. Bennett, The Practical Guide to the Genetic Family History (NewYork; Chichester; Weinheim; Brisbane; Singapore; Toronto: Wiley-Liss, Inc.,1999).
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A typical pedigree13:
13Üner Tan et al., “Unertan Syndrome: A Case Series Demonstrating HumanDevolution,” Int. J. Neurosci. 118/1 (2008), http://search.ebscohost.com/
login.aspx?direct=true&db=pbh&AN=27625823&site=ehost-live.
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Use of pedigree for conveying additional information14:
14Mitsuko Nakashima et al., “Genome-wide linkage analysis and muta-tion analysis of hereditary congenital blepharoptosis in a Japanese family.,”J. of Hum. Gen. 53/1 (2008), http://search.ebscohost.com/login.aspx?
direct=true&db=a9h&AN=27978113&site=ehost-live.
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A complex situation with self-intersections15:
15Stefan Krüger et al., “Homozygous PMS2 Germline Mutations in Two Fam-ilies With Early-Onset Haematological Malignancy, Brain Tumours, HNPCC-Associated Tumours, and Signs of Neurofibromatosis Type 1,” Eur.
J. Hum. Gen. 16/1 (2008), http://search.ebscohost.com/login.aspx?
direct=true&db=a9h&AN=27879615&site=ehost-live.
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4. Samples of Our Output
Joseph Smith
I:1
Jim Brown
I:3
Lisa Brown
I:4
Joan Smith
I:2
b
Ann Gold
II:1
Mary Smith
II:3
Bill Smith
II:2
Rebecca Smith
III:3
Alexander Smith
III:4
John Smith
III:2
Jenny Smith
III:1
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Adam
I:1
John
II:2
Sam
II:1
Jane
II:3
George
IV:1
Ann
IV:4
Jane
IV:3
John
IV:2
Jack
III:2
Pam
III:1
Mike
III:3
?
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Jane
I:1
Jane
III:1
Mary
III:3
Paul
III:2
John
II:4
Samantha
II:2
Nancy
II:1
Ann
II:3
Laura
IV:1
Jack
IV:2
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5. Interfaces and User-Friendliness
“Sure, Unix is a user-friendly operating system. It’sjust picky with whom it chooses to be friends.”
Anonymous
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5. Interfaces and User-Friendliness
“Sure, Unix is a user-friendly operating system. It’sjust picky with whom it chooses to be friends.”
Anonymous
Database Perl Program Optional Adjustment
Manual Creation TEX File
TEX Processing Result
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5.1. TEX Part
\rput(-6, 2){\pstPerson[male, condition=normal, belowtext={\small
I:1}, deceased, abovetext={\scriptsize Joseph Smith}]{GF1}}
\rput(0, 2){\pstPerson[male, condition=normal, belowtext={\small I:3},
abovetext={\scriptsize Jim Brown}]{GF2}}
\rput(4, 2){\pstPerson[female, condition=normal, belowtext={\small
I:4}, abovetext={\scriptsize Lisa Brown}]{GM2}}
\rput(2, 2){\pnode{GF2_m_GM2}}
\rput(-4, 2){\pnode{GF1_m_GM1}}
\rput(-2, 2){\pstPerson[female, asymptomatic, belowtext={\small I:2},
deceased, abovetext={\scriptsize Joan Smith}]{GM1}}
\rput(0, 0){\pnode{F1_m_M1}}
...
This is not user-friendly16—and is not intended to be!
16At least for some users
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5.2. Perl Part
This is supposed to be user-friendly—and it is17!
Id |Name |Sex |DoB | DoD |Mother|Father|Proband
P |John Smith |male |1970/02/05| |M1 |F1 | yes
M1 |Mary Smith |female|1940/02/05| |GM2 |GF2 |
F1 |Bill Smith |male |1938/04/03| |GM1 | GF1 |
GM1|Joan Smith |female|1902/07/01|1975/12/13| | |
...
17If you like spreadsheets. . .
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How do we change the parameters?
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How do we change the parameters?
# Do we want to print a legend?
#
$printlegend=1;
# Fields to include in the legend. Delete Name for privacy
# protection.
#
@fieldsforlegend = qw(Name DoB AgeAtDeath Comment);
#
# Fields to put at the node. Delete Name for privacy
# protection.
#
@fieldsforchart = qw(Name);
This is not user-friendly. . .
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Changes: paper size, fonts, scaling. . .
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Changes: paper size, fonts, scaling. . .
Ad hoc solution: specialliy designed Makefile. Definitely not foreverybody.
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6. Conclusions
We started a journey to check our typographyand our programs.
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6. Conclusions
We started a journey to check our typographyand our programs.
An unexpected result: our typography is good. . .
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6. Conclusions
We started a journey to check our typographyand our programs.
An unexpected result: our typography is good. . .
But our interfaces needs changes. . .
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References
Bennett, Robin L. The Practical Guide to the Genetic Family
History. New York; Chichester; Weinheim; Brisbane; Singapore;Toronto: Wiley-Liss, Inc., 1999.
Bennett, Robin L. et al. “Recommendations for Standardized Hu-man Pedigree Nomenclature.” Am. J. Hum. Genet. 56/3 (1995):745–752.
Krüger, Stefan et al. “Homozygous PMS2 Germline Mutationsin Two Families With Early-Onset Haematological Malignancy,Brain Tumours, HNPCC-Associated Tumours, and Signs ofNeurofibromatosis Type 1.” Eur. J. Hum. Gen. 16/1 (2008):62–72. http://search.ebscohost.com/login.aspx?direct=true&
db=a9h&AN=27879615&site=ehost-live.
Nakashima, Mitsuko et al. “Genome-wide linkage analysisand mutation analysis of hereditary congenital blepharopto-sis in a Japanese family..” J. of Hum. Gen. 53/1 (2008):34–41. http://search.ebscohost.com/login.aspx?direct=true&
db=a9h&AN=27978113&site=ehost-live.
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Resta, Robert G. “The Crane’s Foot: The Rise of the Pedigree inThe Human Genetics.” J. Genetic Couns. 2/4 (1993): 235–260.
Tan, Üner et al. “Unertan Syndrome: A Case Series Demon-strating Human Devolution.” Int. J. Neurosci. 118/1 (2008):1–25. http://search.ebscohost.com/login.aspx?direct=true&
db=pbh&AN=27625823&site=ehost-live.
Veytsman, Boris and Leila Akhmadeeva. Creating Medical Pedi-grees with PSTricks and LATEX. July 2007. http://ctan.tug.org/tex-archive/graphics/pstricks/contrib/pedigree/pst-pdgr.
. “Drawing Medical Pedigree Trees with TEX and PSTricks.”TUGboat 28/1 (2007): 100–109. http://www.tug.org/TUGboat/
Articles/tb28-1/tb88veytsman-pedigree.pdf.
. A Program For Automatic Pedigree ConstructionWith pst-pdgr. User Manual and Algorithm Description.July 2007. http://ctan.tug.org/tex-archive/graphics/pstricks/contrib/pedigree/pedigree-perl.
. “Medical Pedigrees with TEX and PSTricks: New Advancesand Challenges.” TUGboat 29/3 (2008): 484. http://www.tug.
org/TUGboat/Articles/tb29-3/tb93abstracts.pdf.