DNA Fingerprinting: State of the Science

453 Pages·1993·15.71 MB·English

by  A. J. Jeffreys, S. D. J. Pena (auth.), Prof. Dr. S. D. J. Pena, Prof. R. Chakraborty, Prof. Dr. J. T. Epplen, Prof. A. J. Jeffreys (eds.)

EXS 67
DNA Fingerprinting:
State of the Science
Edited by S. D. J. Pena
R. Chakraborty
J. T. Epplen
A. J . Jeffreys
Birkhiuser Verlag
Basel . Boston . Berlin
Editors
Prof. Dr. S. D. J. Pena Prof. R. Chakraborty
Nucleo de Genetica Medica Genetics Center
de Minas Gerais (GENE/MG) University of Texas
Av. Afonso Pena 3111/9 Health Science Center
30130-909 Belo Horizonte PO Box 20334
Brazil Houston, Texas 77225
USA
Prof. Dr. J. T. Epplen Prof. Alec J. Jeffreys
Molekulare Humangenetik, MA Department of Genetics
Ruhr-Universitat University of Leicester
Universitatsstr. 150 Leicester LEI 7RH
44780 Bochum England
Germany
Library of Congress CataIoging-in-Pnblication Data
DNA fingerprinting: state of the science/edited by S. D. J. Pena ... let al.].
p. cm.-(EXS; 67)
Includes bibliographical references and index.
ISBN 3-7643-2781-2 (hardcover).-ISBN 3-7643-2906-8 (softcover).-
ISBN 0-8176-2781-2 (hardcover).-ISBN 0-8176-2906-8 (softcover)
1. DNA fingerprints-Congresses. I. Pena, S. D. J. (Sergio D. J.) II. Series.
[DNLM: 1. DNA Fingerprinting-Congresses. WI E65 v.67 1993/ W 750 06291 1993]
RA1057.55.D637 1993
575.I-dc20
DNLM/DLC
for Library of Congress
Deutsche Bibliotbek Cataloging-in-Pnbtication Data
DNA fingerprinting: state of the science/ed. by S. D. J. Pena ... - Basel; Boston; Berlin;
Birkhauser, 1993
(EXS; 67)
ISBN 3-7643-2906-8 (Basel ...) brosch.
ISBN 3-7643-2781-2 (Basel ...) Gb.
ISBN 0-8176-2906-8 (Boston) brosch.
ISBN 0-8176-2781-2 (Boston) Gb.
NE: Pena, Sergio D. J. [Hrsg.]; GT
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ISBN 3-7643-2781-2 ISBN 3-7643-2906-8
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Contents
Preface. . . . . . . . . . .. . . . . . . . . . .. . . . . . . . . .. . .. . . . . .. . . . . . .. . Xl
Part I Basic Aspects of DNA Fingerprints: Genomic
Organization, Dynamics and Variability of Tandemly Repeated
DNA Sequences
A Overview
1 A. J. Jeffreys and S. D. J. Pena
Brief introduction to human DNA fingerprinting ........... .
B Tandemly Repeated DNA Sequences in Eukaryotic Genomes
D. Tautz
Notes on the definition and nomenclature of tandemly repetitive
DNA sequences. . . . . . . . . . . . . . ... . . . .. . . . . . . . . . . . . .. . . . .. 21
2 C. Epplen, G. Melmer, I. Siedlaczck, F.-W. Schwaiger,
W. Miiueler and J. T. Epplen
On the essence of "meaningless" simple repetitive DNA in
eukaryote genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
3 G. Vergnaud, D. Gauguier, J.-J. Schott, D. Lepetit, V. Lauthier,
D. Mariat and J. Buard
Detection, cloning, and distribution of mini satellites in some
mammalian genomes .................................... 47
4 I. Balazs, J. Neuweiler, L. Perlee and J. Venturini
Frequency of restriction site polymorphisms in the region
surrounding VNTR loci. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
5 B. Olaisen, M. Bekkemoen, P. Hoff-Olsen and P. Gill
Human VNTR mutation and sex . . . . . . . . . . . . . . . . . . . . . . . . . 63
6 P. Vagnarelli, E. Giulotto, P. Fattorini, E. Mucciolo, M. Bensi,
L. Tessera and L. De Carli
Variation of minisatellites in chemically induced mutagenesis
and in gene amplification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
7 K. J. Huebscher, G. Dolf and J. Frey
Iterons of stringently controlled plasmids and DNA finger-
printing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
VI
C New Methodological and Technical Approaches to the Study of
Genome Variation
1 J. Buitkamp, W. Schwaiger, C. Epplen, M. Gomolka, E. Weyers
and J. T. Epplen
Towards covering immunological genes with highly informative
markers: A trans-species approach . . . . . . . . . . . . . . . . . . . . . . . . 87
2 M. MCClelland, K. Chada, J. Welsh and D. Ralph
Arbitrary primed PCR fingerprinting of RNA applied to
mapping differentially expressed genes . . . . . . . . . . . . . . . . . . . .. 103
3 M. J. Pearce and N. D. Watson
Rapid analysis of PCR components and products by acidic
non-gel capillary electrophoresis .......................... 117
Part n Application of DNA Fingerprinting to the Study of
Human Populations
A New Developments in the Study of Human Genetic Variability
1 A. J. Jeffreys, D. G. Monckton, K. Tamaki, D. L. Neil,
J. A. L. Armour, A. MacLeod, A. Collick, M. Allen and
M. Jobling
Minisatellite variant repeat mapping: Application to DNA
typing and mutation analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . .. 125
2 K. Wrogemann, V. Biancalana, D. Devys, G. Imbert, Y. Trottier
and J.-L. Mandel
Microsatellites and disease: A new paradigm. . . . . . . . . . . . . .. 141
B Population Genetics of Tandem Repeat Polymorphisms
I R. Chakraborty and L. Jin
A unified approach to study hypervariable polymorphisms:
Statistical considerations of determining relatedness and popula-
tion distances. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
2 B. Budowle and K. L. Monson
The forensic significance of various reference population data-
bases for estimating the rarity of variable number of tandem
repeat (VNTR) loci profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
3 I. Balazs
Population genetics of 14 ethnic groups using phenotypic data
from VNTR loci.. . .. . . . . . . .. . . . . . . .. .. . . .. . . ... . . . . . . .. 193
4 C. Ginther, D. Corach, G. A. Penacino, J. A. Rey, F. R. Carnese,
M. H. Hutz, A. Anderson, J. Just, F. M. Salzano and
M.-C. King
Genetic variation among the Mapuche Indians from the Pata-
gonian region of Argentina: Mitochondrial DNA sequence
variation and allelt; frequencies of several nuclear genes. . . . .. 211
vii
5 L. Roewer, M. Nagy, P. Schmidt, J. T. Epplen and
G. Herzog-Schroder
Microsatellite and HLA class II oligonucleotide typing in a
population of Yanomami Indians . . . . . . . . . . . . . . . . . . . . . . . .. 221
6 C. Brandt-Casadevall, N. Dimo-Simonin, A. Sutter and
H.-R. Gujer
Iserables: A Bedouin village in Switzerland? . . . . . . . . . . . . . . .. 231
C Paternity Testing and Forensic Applications of Tandem Repeat
Polymorphisms
1 S. D. J. Pena, P. C. Santos, M. C. B. N. Campos and
A. M. Macedo
Paternity testing with the FlO multilocus DNA fingerprinting
probe.................................................. 237
2 M. Krawczak and B. Bockel
The formal analysis of multilocus DNA fingerprints. . . . . . . .. 249
3 l. Bohm, M. Krawczak, P. Niirnberg, J. Hampe, J. Hundrieser,
H. Poche, C. Peters, R. Slomski, J. Kwiatkowska, M. Nagy,
A. Popperl, J. T. Epplen, and J. Schmidtke
Oligonucleotide DNA fingerprinting: Results of a multi-center
study on reliability and validity. . . . . . . . . . . . . . . . . . . . . . . . . .. 257
4 F. R. Santos, J. T. Epplen and S. D. J. Pena
Testing deficiency paternity cases with a Y -linked tetra-
nucleotide repeat polymorphism .......................... 261
5 M. M. Holland, D. L. Fisher, D. A. Lee, C. K. Bryson and
V. W. Weedn
Short tandem repeat loci: Application to forensic and human
remains identification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 267
6 A.-C. Syviinen, A. Sajantila and M. Lukka
Forensic DNA typing by the solid-phase mini sequencing
method................................................ 275
7 G. E. Novick, T. Gonzalez, J. Garrison, C. C. Novick,
M. A. Batzer, P. L. Deininger and R. J. Herrera
The use of polymorphic Alu insertions in human DNA finger-
printing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 283
Part m Application of DNA Fingerprinting to the Study of
Microorganisms, Plants, and Animals
A Plants
1 H. Nybom
Applications of DNA fingerprinting in plant population
studies ............................................... " 293
Vlll
B Microorganisms, Parasites, and Invertebrates
1 W. Meyer, E. Lieckfeldt, K. Kuhls, E. Z. Freedman, T. Borner
and T. G. Mitchell
DNA- and PCR-fingerprinting in fungi. . . . .. . . . .... . . . . ... 311
2 A. M. Macedo, G. A. Vallejo, E. Chiari and S. D. J. Pena
DNA fingerprinting reveals relationships between strains of
Trypanosoma rangeli and Trypanosoma cruzi. . . . . . . . . . . . . . .. 321
3 A. J. G. Simpson, E. Dias Neto, M. Steindel,
O. L. S. D. Caballero, L. K. J. Passos and S. D. J. Pena
The use of RAPDs for the analysis of parasites. . . . . . . . . . . .. 331
4 E. Dias Neto, M. Steindel, L. K. F. Passos, C. Pereira de Souza,
D. Rollinson, N. Katz, A. J. Romanha, S. D. J. Pena and
A. J. G. Simpson
The use of RAPDs for the study of the genetic diversity of
Schistosoma mansoni and Trypanosoma cruzi. . . . . . . . . . . . . . .. 339
5 A. Blanchetot
Variability and intra nest genetic relationships in Hymenoptera:
DNA fingerprinting applied to the solitary bee Megachille
rotundata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 347
6 J. Corley, M. Rabinovich, M. Seigelchifer, J. Zorzopulos and
E. Corley
Sperm utilization in honeybees as detected by M13 DNA finger-
prints ............................................... '" 355
C Fishes and Birds
1 M. Schartl, C. Erbelding-Denk, S. Holter, l. ,Nanda, M. Schmid,
J. H. Schroder and J. T. Epplen
High mating success of low rank males in Limia perugiae
(Pisces: Poeciliidae) as determined by DNA fingerprinting. . .. 363
2 G. Dolj, J. Schliipfer, C. Hagger, G.Stranzinger and C. Gaillard
Quantitative traits in chicken associated with DNA fingerprint
bands................................................. 371
3 T. Lubjuhn, E. Curio, S. C. Muth, J. Briin and J. T. Epplen
Influence of extra-pair paternity on parental care in great tits
(Parus major). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 379
4 J. Mathe, c. Eisenmann and A. Seitz
Paternity testing of endangered species of birds by DNA finger-
printing with non-radioactive labelled oligonucleotide probes. 387
5 C. Y. Miyaki, O. Hanotte, A. Wajntal and T. Burke
Characterization and applications of multilocus DNA finger-
prints in Brazilian endangered macaws. . . . . . . . . . . . . . . . . . . .. 395
IX
D Mammals
1 G. Brockmann, J. Buitkamp, L. Bunger, J. T. Epplen and
M. Schwerin
DNA fingerprinting of trait-selected mouse lines and linkage
analysis in reference families. . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 403
2 D. Mariat and L. Robert
Dog genetic polymorphism revealed by synthetic tandem
repeats ........................... . . . . . . . . . . . . . . . . . . . .. 411
3 N. G. Holmes, S. J. Humphreys, M. M. Binns, R. Curtis,
A. Holliman and A. M. Scott
Characterization of canine micro satellites .................. 415
4 E. N. Signer and A. J. Jeffreys
Application of human minisatellite probes to the development
of informative DNA fingerprints and the isolation of locus-
specific markers in animals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 421
5 J. L. Ruth and S. R. Fain
The 'individualization' of large North American mammals. .. 429
6 S.-L. Varvio and J. Kaukinen
Bovine microsatellites: Racial differences and association with
SINE-elements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 437
7 P. Numberg, J. D. Berard, F. Bercovitch, J. T. Epplen,
J. Schmidtke and M. Krawczak
Oligonucleotide fingerprinting of free-ranging and captive
rhesus macaques from Cayo Santiago: Paternity assignment
and comparison of heterozygosity. . . . . . . . . . . . . . . . . . . . . . . .. 445
8 T. Schmidt, K. Boblenz and K. Weising
Use of highly repeated DNA polymorphisms for genome
diagnosis and evolutionary studies in the genus Beta. . . . . . . .. 453
Subject index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 461