allele determination

http://crop.scijournals.org/cgi/content/full/46/5/2084
Crop Science PLANT GENETIC RESOURCES
Accuracy and Reliability of High-Throughput Microsatellite Genotyping for Cacao Clone Identification


http://www-naweb.iaea.org/nafa/aph/stories/dna-manual.pdf
A practical approach to microsatellite genotyping with special reference to livestock population genetics

allele determination

http://www.plantmethods.com/content/1/1/3
High throughput, high resolution selection of polymorphic microsatellite loci for multiplex analysis


http://www.gse-journal.org/index.php?option=article&access=standard&Itemid=129&url=/articles/gse/pdf/2002/03/g340301.pdf

http://www.cdfd.org.in/jnagpdf/jfc.pdf
Capillary Electrophoresis Is Essential for Microsatellite Marker Based Detection and Quantification of Adulteration of Basmati Rice (Oryza sativa)

http://crop.scijournals.org/cgi/content/full/43/5/1828
A Low-Cost, High-Throughput Polyacrylamide Gel Electrophoresis System for Genotyping with Microsatellite DNA Markers

allele age dtermination

P. Fearnhead, R. M. Harding, J. A. Schneider, S. Myers, and P. Donnelly
Application of Coalescent Methods to Reveal Fine-Scale Rate Variation and Recombination Hotspots
Genetics, August 1, 2004; 167(4): 2067 - 2081.


J. M. Burrows, L. Bromham, M. Woolfit, G. Piganeau, J. Tellam, G. Connolly, N. Webb, L. Poulsen, L. Cooper, S. R. Burrows, et al.
Selection Pressure-Driven Evolution of the Epstein-Barr Virus-Encoded Oncogene LMP1 in Virus Isolates from Southeast Asia
J. Virol., July 1, 2004; 78(13): 7131 - 7137.


P. Lemey, O. G. Pybus, A. Rambaut, A. J. Drummond, D. L. Robertson, P. Roques, M. Worobey, and A.-M. Vandamme
The Molecular Population Genetics of HIV-1 Group O
Genetics, July 1, 2004; 167(3): 1059 - 1068.


J. D. Wall
Estimating Recombination Rates Using Three-Site Likelihoods
Genetics, July 1, 2004; 167(3): 1461 - 1473.


D. T. Haydon, A. D. S. Bastos, and P. Awadalla
Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments
J. Gen. Virol., May 1, 2004; 85(5): 1095 - 1100.


N. Li and M. Stephens
Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data
Genetics, December 1, 2003; 165(4): 2213 - 2233.


S. D. Polley, W. Chokejindachai, and D. J. Conway
Allele Frequency-Based Analyses Robustly Map Sequence Sites Under Balancing Selection in a Malaria Vaccine Candidate Antigen
Genetics, October 1, 2003; 165(2): 555 - 561.


M. Anisimova, R. Nielsen, and Z. Yang
Effect of Recombination on the Accuracy of the Likelihood Method for Detecting Positive Selection at Amino Acid Sites
Genetics, July 1, 2003; 164(3): 1229 - 1236.

Microsatellite analysis and other Tools

Genetics - J.-F. Lefebvre and D. Labuda
Fraction of Informative Recombinations: A Heuristic Approach to Analyze Recombination Rates
Genetics, April 1, 2008; 178(4): 2069 - 2079.


Proceedings B
A. J McCarthy, M.-A. Shaw, and S. J Goodman
Pathogen evolution and disease emergence in carnivores
Proc R Soc B, December 22, 2007; 274(1629): 3165 - 3174.


Genetics
S. De Mita, J. Ronfort, H. I. McKhann, C. Poncet, R. El Malki, and T. Bataillon
Investigation of the Demographic and Selective Forces Shaping the Nucleotide Diversity of Genes Involved in Nod Factor Signaling in Medicago truncatula
Genetics, December 1, 2007; 177(4): 2123 - 2133.
-
D. Garrigan, S. B. Kingan, M. M. Pilkington, J. A. Wilder, M. P. Cox, H. Soodyall, B. Strassmann, G. Destro-Bisol, P. de Knijff, A. Novelletto, et al.
Inferring Human Population Sizes, Divergence Times and Rates of Gene Flow From Mitochondrial, X and Y Chromosome Resequencing Data
Genetics, December 1, 2007; 177(4): 2195 - 2207.
-
J. Gay, S. Myers, and G. McVean
Estimating Meiotic Gene Conversion Rates From Population Genetic Data
Genetics, October 1, 2007; 177(2): 881 - 894.


D. T. Gerrard and A. Meyer
Positive Selection and Gene Conversion in SPP120, a Fertilization-Related Gene, during the East African Cichlid Fish Radiation
Mol. Biol. Evol., October 1, 2007; 24(10): 2286 - 2297.


S. R. Miller, R. W. Castenholz, and D. Pedersen
Phylogeography of the Thermophilic Cyanobacterium Mastigocladus laminosus
Appl. Envir. Microbiol., August 1, 2007; 73(15): 4751 - 4759.


A. Auton and G. McVean
Recombination rate estimation in the presence of hotspots
Genome Res., August 1, 2007; 17(8): 1219 - 1227.



A. RoyChoudhury and M. Stephens
Fast and Accurate Estimation of the Population-Scaled Mutation Rate, {theta}, From Microsatellite Genotype Data
Genetics, June 1, 2007; 176(2): 1363 - 1366.


X. Didelot and D. Falush
Inference of Bacterial Microevolution Using Multilocus Sequence Data
Genetics, March 1, 2007; 175(3): 1251 - 1266.


A. Ojeda, J. Rozas, J. M. Folch, and M. Perez-Enciso
Unexpected High Polymorphism at the FABP4 Gene Unveils a Complex History for Pig Populations
Genetics, December 1, 2006; 174(4): 2119 - 2127.


P. Fearnhead
SequenceLDhot: detecting recombination hotspots
Bioinformatics, December 15, 2006; 22(24): 3061 - 3066.


X. Liu, M. M. Gutacker, J. M. Musser, and Y.-X. Fu
Evidence for Recombination in Mycobacterium tuberculosis
J. Bacteriol., December 1, 2006; 188(23): 8169 - 8177.



D. S. Guttman, S. J. Gropp, R. L. Morgan, and P. W. Wang
Diversifying Selection Drives the Evolution of the Type III Secretion System Pilus of Pseudomonas syringae
Mol. Biol. Evol., December 1, 2006; 23(12): 2342 - 2354.


C. T. T. Edwards, E. C. Holmes, O. G. Pybus, D. J. Wilson, R. P. Viscidi, E. J. Abrams, R. E. Phillips, and A. J. Drummond
Evolution of the Human Immunodeficiency Virus Envelope Gene Is Dominated by Purifying Selection
Genetics, November 1, 2006; 174(3): 1441 - 1453.


S. L. Kosakovsky Pond, D. Posada, M. B. Gravenor, C. H. Woelk, and S. D. W. Frost
Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm
Mol. Biol. Evol., October 1, 2006; 23(10): 1891 - 1901.


B. C. Verrelli, S. A. Tishkoff, A. C. Stone, and J. W. Touchman
Contrasting Histories of G6PD Molecular Evolution and Malarial Resistance in Humans and Chimpanzees
Mol. Biol. Evol., August 1, 2006; 23(8): 1592 - 1601.



P. L. Morrell, D. M. Toleno, K. E. Lundy, and M. T. Clegg
Estimating the Contribution of Mutation, Recombination and Gene Conversion in the Generation of Haplotypic Diversity
Genetics, July 1, 2006; 173(3): 1705 - 1723.


T. C. Bruen, H. Philippe, and D. Bryant
A Simple and Robust Statistical Test for Detecting the Presence of Recombination
Genetics, April 1, 2006; 172(4): 2665 - 2681.



A. Carvajal-Rodriguez, K. A. Crandall, and D. Posada
Recombination Estimation Under Complex Evolutionary Models with the Coalescent Composite-Likelihood Method
Mol. Biol. Evol., April 1, 2006; 23(4): 817 - 827.


C. Charpentier, T. Nora, O. Tenaillon, F. Clavel, and A. J. Hance
Extensive Recombination among Human Immunodeficiency Virus Type 1 Quasispecies Makes an Important Contribution to Viral Diversity in Individual Patients
J. Virol., March 1, 2006; 80(5): 2472 - 2482.


D. J. Wilson and G. McVean
Estimating Diversifying Selection and Functional Constraint in the Presence of Recombination
Genetics, March 1, 2006; 172(3): 1411 - 1425.


D. H. Bos and B. Waldman
Evolution by Recombination and Transspecies Polymorphism in the MHC Class I Gene of Xenopus laevis
Mol. Biol. Evol., January 1, 2006; 23(1): 137 - 143.


N. G. C. Smith and P. Fearnhead
A Comparison of Three Estimators of the Population-Scaled Recombination Rate: Accuracy and Robustness
Genetics, December 1, 2005; 171(4): 2051 - 2062.


K. Roselius, W. Stephan, and T. Stadler
The Relationship of Nucleotide Polymorphism, Recombination Rate and Selection in Wild Tomato Species
Genetics, October 1, 2005; 171(2): 753 - 763.


G. A.T McVean and N. J Cardin
Approximating the coalescent with recombination
Phil Trans R Soc B, July 29, 2005; 360(1459): 1387 - 1393.


L. Zhu and C. D. Bustamante
A Composite-Likelihood Approach for Detecting Directional Selection From DNA Sequence Data
Genetics, July 1, 2005; 170(3): 1411 - 1421.


D. Shriner, A. G. Rodrigo, D. C. Nickle, and J. I. Mullins
Pervasive Genomic Recombination of HIV-1 in Vivo
Genetics, August 1, 2004; 167(4): 1573 - 1583.

Microsatellite Allele Sizing and Analysis

doi:10.1016/S0021-9673(97)00542-6
Journal of Chromatography A
Volume 781, Issues 1-2, 26 September 1997, Pages 295-305
9th International Symposium on High Performance Capillary Electrophoresis and Related Microsale Techniques

Copyright © 1997 Published by Elsevier Science B.V.
Nucleic acids and their constituents
Rapid sizing of polymorphic microsatellite markers by capillary array electrophoresis

http://www.cdfd.org.in/jnagpdf/jfc.pdf
Capillary Electrophoresis Is Essential for Microsatellite Marker Based Detection and Quantification of Adulteration of Basmati Rice (Oryza sativa)


http://www.scfbm.org/content/3/1/15
Permutation – based statistical tests for multiple hypotheses

http://www3.interscience.wiley.com/journal/94516676/abstract?CRETRY=1&SRETRY=0
Permutation tests for detecting and estimating mixtures in task performance within groups

http://www.biomedcentral.com/1471-2105/9/511
Comparison of methods for estimating the nucleotide substitution matrix


http://www.genetics.org/cgi/content/abstract/160/3/1231
A Coalescent-Based Method for Detecting and Estimating Recombination From Gene Sequences



Genetics
M. Carneiro, N. Ferrand, and M. W. Nachman
Recombination and Speciation: Loci Near Centromeres Are More Differentiated Than Loci Near Telomeres Between Subspecies of the European Rabbit (Oryctolagus cuniculus)
Genetics, February 1, 2009; 181(2): 593 - 606.
[Abstract] [Full Text] [PDF]


Philosophical Transactions B
Y. Wang and B. Rannala
Bayesian inference of fine-scale recombination rates using population genomic data
Phil Trans R Soc B, December 27, 2008; 363(1512): 3921 - 3930.
[Abstract] [Full Text] [PDF]



Molecular Biology and Evolution
B. C. Verrelli, C. M. Lewis Jr, A. C. Stone, and G. H. Perry
Different Selective Pressures Shape the Molecular Evolution of Color Vision in Chimpanzee and Human Populations
Mol. Biol. Evol., December 1, 2008; 25(12): 2735 - 2743.
[Abstract] [Full Text] [PDF]



Genome Research
A. F. McRae, E. M. Byrne, Z. Z. Zhao, G. W. Montgomery, and P. M. Visscher
Power and SNP tagging in whole mitochondrial genome association studies
Genome Res., June 1, 2008; 18(6): 911 - 917.
[Abstract] [Full Text] [PDF]


doi:
10.1101/gr.8.1.69
Genome Res. 1998. 8: 69-80
Copyright © 1998, by Cold Spring Harbor Laboratory Press
High-Precision Genotyping by Denaturing Capillary Electrophoresis
H.-Michael Wenz, James M. Robertson, Steve Menchen, Frank Oaks, David M. Demorest, Don Scheibler, Barnett B. Rosenblum, Carla Wike, Dennis A. Gilbert, and J. William Efcavitch



From the Cover: Single-nucleotide polymorphism discovery by targeted DNA photocleavage
J. R. Hart, M. D. Johnson, and J. K. Barton
Proc. Natl. Acad. Sci. USA September 28, 2004 101: 14040-14044



Single nucleotide polymorphism detection by combinatorial fluorescence energy transfer tags and biotinylated dideoxynucleotides
A. K. Tong andJ. Ju
Nucleic Acids Res March 1, 2002 30: e19


Analysis of short tandem repeat polymorphisms by electrospray ion trap mass spectrometry
S. Hahner, A. Schneider, A. Ingendoh, and J. Mosner
Nucleic Acids Res September 15, 2000 28: e82

Highthrough-out put microsatellite allele sizing with high resolution

http://crop.scijournals.org/cgi/reprint/43/5/1828
Published in Crop Sci. 43:1828-1832 (2003).
© 2003 Crop Science Society of America
677 S. Segoe Rd., Madison, WI 53711 USA

GENOMICS, MOLECULAR GENETICS & BIOTECHNOLOGY
A Low-Cost, High-Throughput Polyacrylamide Gel Electrophoresis System for Genotyping with Microsatellite DNA Markers

D. Wang, J. Shi, S. R. Carlson, P. B. Cregan, R. W. Ward, and B. W. Diers*
Microsatellite DNA markers are widely used in genetic research. Their use, however, can be costly and throughput is sometimes limited. The objective of this paper is to introduce a simple, low-cost, high-throughput system that detects amplification products from microsatellite markers by nondenaturing polyacrylamide gel electrophoresis. This system is capable of separating DNA fragments that differ by as little as two base pairs. The electrophoresis unit holds two vertical 100-sample gels allowing standards and samples from a 96-well plate to be analyzed on a single gel. DNA samples are stained during electrophoresis by ethidium bromide in the running buffer. In addition, one of the gel plates is UV-transparent so that gels can be photographed immediately after electrophoresis without disassembling the gel-plate sandwich. Electrophoresis runs are generally less than two hours. The cost per gel, excluding PCR cost, is currently estimated at about $2.60, or less than $0.03 per data point. This system has been used successfully with soybean [Glycine max (L.) Merr.] and wheat (Triticum aestivum L.) microsatellite markers and could be a valuable tool for researchers employing markers in other species.


Abbreviations: bp, base pair • ITMI, International Triticeae Initiative • PCR, polymerase chain reaction • QTL, quantitative trait loci • SSR, simple sequence repeat



http://www.plantmethods.com/content/1/1/3
High throughput, high resolution selection of polymorphic microsatellite loci for multiplex analysis
Nicholas C Cryer1 , David R Butler2 and Mike J Wilkinson1

1School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6AS, UK

2Cocoa Research Unit, The University of West Indies, St. Augustine, Trinidad and Tobago

author email corresponding author email

Plant Methods 2005, 1:3doi:10.1186/1746-4811-1-3

The electronic version of this article is the complete one and can be found online at: http://www.plantmethods.com/content/1/1/3

Received: 25 May 2005
Accepted: 18 August 2005
Published: 18 August 2005

© 2005 Cryer et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Keywords: Multiplex, Microsatellite, High Throughput, Fluorescent, Dinucleotide, High-Resolution, Allelic Ladder

Abstract
Background
Large-scale genetic profiling, mapping and genetic association studies require access to a series of well-characterised and polymorphic microsatellite markers with distinct and broad allele ranges. Selection of complementary microsatellite markers with non-overlapping allele ranges has historically proved to be a bottleneck in the development of multiplex microsatellite assays. The characterisation process for each microsatellite locus can be laborious and costly given the need for numerous, locus-specific fluorescent primers.

Results
Here, we describe a simple and inexpensive approach to select useful microsatellite markers. The system is based on the pooling of multiple unlabelled PCR amplicons and their subsequent ligation into a standard cloning vector. A second round of amplification utilising generic labelled primers targeting the vector and unlabelled locus-specific primers targeting the microsatellite flanking region yield allelic profiles that are representative of all individuals contained within the pool. Suitability of various DNA pool sizes was then tested for this purpose. DNA template pools containing between 8 and 96 individuals were assessed for the determination of allele ranges of individual microsatellite markers across a broad population. This helped resolve the balance between using pools that are large enough to allow the detection of many alleles against the risk of including too many individuals in a pool such that rare alleles are over-diluted and so do not appear in the pooled microsatellite profile. Pools of DNA from 12 individuals allowed the reliable detection of all alleles present in the pool.

Conclusion
The use of generic vector-specific fluorescent primers and unlabelled locus-specific primers provides a high resolution, rapid and inexpensive approach for the selection of highly polymorphic microsatellite loci that possess non-overlapping allele ranges for use in large-scale multiplex assays.


Frasier TR, Wilson PJ, White BN: Rapid screening of microsatellite markers for polymorphisms using SYBR® green 1 and a DNA sequencer.

BioTechniques 2004, 36:408-409. PubMed Abstract

Return to text


Narvel JM, Chu WC, Fehr WR, Cregan PB, Shoemaker RC: Development of multiplex sets of simple sequence repeat DNA markers covering the soybean genome.

Molecular Breeding 2000, 6:175-183. Publisher Full Text

Return to text


Tang S, Kishore VK, Knapp SJ: PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower.

Theor Appl Genet 2003, 107:6-19. PubMed Abstract | Publisher Full Text

Return to text


Tommasini L, Batley J, Arnold GM, Cooke RJ, Donini P, Law JR, Lowe C, Moule C, Trick M, Edwards KJ: The development of multiplex simple sequence repeat (SSR) markers to complement distinctness, uniformity and stability testing of rape (Brassica napus L.) varieties. Theor Apl Genet 2003, 106:1091-1101. PubMed Abstract | Publisher Full Text

Morin PA, Smith DG: Non-radioactive detection of hypervariable simple sequence repeats in short polyacrylamide gels. BioTechniques 1995, 19:223-228. PubMed Abstract

Scrimshaw BJ: Non-radioactive detection of hypervariable simple sequence repeats in short polyacrylamide gels. BioTechniques 1992, 13:188. PubMed Abstract

Agarose-based system for separation of short tandem repeat loci.

BioTechniques 1997, 22:976-980. PubMed Abstract


Houriham RN, O'Sullivan GC, Morgan JG: High-resolution detection of loss of heterozygosity of dinucleotide microsatellite markers.





http://www.biotechniques.com/biotechniques/BiotechniquesJournal/2007/April/Microsatellite-marker-identification-using-genome-screening-and-restriction-ligation/biotechniques-41700.html?autnID=588199

Microsatellite marker identification using genome screening and restriction-ligation

Helena Korpelainen, Kirsi Kostamo, Viivi VirtanenUniversity of Helsinki, Helsinki, FinlandBioTechniques, Vol. 42, No. 4, April 2007, pp. 479–486 Full Text (PDF) Supplementary MaterialKorpSUPP424 (.pdf)


http://www.biotechniques.com/biotechniques/multimedia/archive/00010/97225pf01_10994a.pdf
Agarose-Based System for Separation of Short Tandem Repeat Loci


http://www.academicjournals.org/AJB/PDF/pdf2009/3Jun/Wang%20et%20al.pdf
A new electrophoresis technique to separate microsatellite alleles - QiAxcell System

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp418v1?etoc

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp418v1?etoc

Identification of distant family relationships

Øivind Skare 1,2, Nuala Sheehan 3 and Thore Egeland 4,5,*
1Norwegian Institute of Public Health, 0403 Oslo, Norway and 2 Department of Public Health and Primary Health Care, University of Bergen, 5018 Bergen, Norway and 3Department of Health Sciences and Department of Genetics, University of Leicester, UK and 4 Institute of Forensic Medicine, University of Oslo, 0027 Oslo, Norway and 5 Oslo University College


*To whom correspondence should be addressed. Thore Egeland, E-mail: Thore.Egeland@medisin.uio.no



Abstract



Motivation: Family relationships can be estimated from DNA marker data. Applications arise in a large number of areas including evolution and conservation research, genealogical research in human, plant and animal populations, forensic problems and genetic mapping via linkage and association analyses. Traditionally, likelihood-based approaches to relationship estimation have used unlinked genetic markers. Due to the fact that some relationships cannot be distinguished from data at unlinked markers, and given the limited number of such markers available, there are considerable constraints on the type of identification problem that can be satisfactorily addressed with such approaches. The aim of this paper is to explore the potential of linked autosomal SNP markers in this context. Throughout, we will view the problem of relationship estimation as one of pedigree identification rather than identity-by-descent, and thus focus on applications where determination of the exact relationship is important.

Results: We show that the increase in information obtained by exploiting large sets of linked markers substantially increases the number of problems that can be solved. Results are presented based on simulations as well as on real data.

Availability: The R library FEST is freely available from http://folk.uio.no/thoree/FEST.

Contact: Thore.Egeland@medisin.uio.no