SNP discovery references

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20 Φεβ 2013 (πριν από 4 χρόνια και 1 μήνα)

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1


SNP Discovery

References

Application and Discovery
Reviews

Helyar S.J., Hemmer
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Hansen J., Bekkevold D.

et al.

(2011) Application of SNPs for population genetics of
nonmodel organisms: new opportunities and challenges.
Molecular Ecology Resources

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123
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Morin P.A., Luikart G., Wayne R.K. (2004) SNPs in ecology, evolution and conservation.
Trends in Ecology
& Evolution

19
, 208
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216.

Morin P.A., Martien K.K., Archer F.I.

et al.

(2010) Applied conservation genetics and the need for quality
control an
d reporting of genetic data used in fisheries and wildlife management.
Journal of Heredity

101
,
1
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10.

Ogden R.O.B. (2011) Unlocking the potential of genomic technologies for wildlife forensics.
Molecular
Ecology Resources

11
, 109
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116.

Seeb J.E., Carvalho G
., Hauser L., Naish K., Roberts S., Seeb L.W. (2011a) Single
-
nucleotide polymorphism
(SNP) discovery and applications of SNP genotyping in nonmodel organisms.
Molecular Ecology
Resources

11
, 1
-
8.

Shendure J., Ji H.L. (2008) Next
-
generation DNA sequencing.
Nature Biotechnology

26
, 1135
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1145.

Slate J., Gratten J., Beraldi D., Stapley J., Hale M., Pemberton J.M. (2009) Gene mapping in the wild with
SNPs: guidelines and future directions.
Genetica

136
, 97
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107.


EST mining and
Sanger sequencing of targeted genes

Aitken N., Smith S., Schwarz C., Morin P.A. (2004) Single nucleotide polymorphism (SNP) discovery in
mammals: a targeted
-
gene approach.
Molecular Ecology

13
, 1423
-
1431.

Campbell N.R., Narum S.R. (2011) Development of 54 novel single
-
nucleotide polymorphis
m (SNP)
assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the
Columbia River.
Molecular Ecology Resources

11
, 20
-
30.

Elfstrom C.M., Gaffney P.M., Smith C.T., Seeb J.E. (2005a) Characterization of 12 single n
ucleotide
polymorphisms in weathervane scallop.
Molecular Ecology Notes

5
, 406
-
409.

Elfstrom C.M., Smith C.T., Seeb J.E. (2006) Thirty
-
two single nucleotide polymorphism markers for high
-
throughput genotyping of sockeye salmon.
Molecular Ecology Notes

6
, 1
255
-
1259.

Elfstrom C.M., Smith C.T., Seeb L.W. (2007) Thirty
-
eight single nucleotide polymorphism markers for
high
-
throughput genotyping of chum salmon.
Molecular Ecology Notes

7
, 1211
-
1215.

Hansen M.H.H., Young S., Jorgensen H.B.H., Pascal C., Henryon M.,

Seeb J. (2011) Assembling a dual
purpose TaqMan
-
based panel of single
-
nucleotide polymorphism markers in rainbow trout and
2


steelhead (Oncorhynchus mykiss) for association mapping and population genetics analysis.
Molecular
Ecology Resources

11
, 67
-
70.

He
C., Chen L., Simmons M., Li P., Kim S., Liu Z.J. (2003) Putative Snp Discovery in Interspecific Hybrids of
Catfish by Comparative Est Analysis.
Animal Genetics

34
, 445
-
448.

Labate J.A., Baldo A.M. (2005) Tomato Snp Discovery by Est Mining and Resequencing.

Molecular
Breeding

16
, 343
-
349.

Morin P.A., Aitken N.C., Rubio
-
Cisneros N., Dizon A.E., Mesnick S. (2007) Characterization of 18 SNP
markers for sperm whale (Physeter macrocephalus).
Molecular Ecology Notes

7
, 626
-
630.

Ollitrault P., Terol J., Garcia
-
Lor
A.

et al.

(2012) SNP mining in C. clementina BAC end sequences;
transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic
mapping.
Bmc Genomics

13
.

Smith C.T., Baker J., Park L.

et al.

(2005a) Characterization of 13 single nucleotide polymorphism markers
for chum salmon.
Molecular Ecology Notes

5
, 259
-
262.

Smith C.T., Elfstrom C.M., Seeb L.W., Seeb J.E. (2005b) Use of sequence data from rainbow trout and
Atlantic salmon for SNP detectio
n in Pacific salmon.
Molecular Ecology

14
, 4193
-
4203.

Smith C.T., Grant W.S., Seeb L.W. (2005c) A rapid, high
-
throughput technique for detecting Tanner crabs
Chionoecetes bairdi
illegally taken in Alaska's snow crab fishery.
Transactions of the American Fi
sheries
Society

134
, 620
-
623.

Smith C.T., Park L., Vandoornik D., Seeb L.W., Seeb J.E. (2006) Characterization of 19 single nucleotide
polymorphism markers for coho salmon.
Molecular Ecology Notes

6
, 715
-
720.

Sprowles A.E., Stephens M.R., Clipperton N.W.,
May B.P. (2006) Fishing for SNPs: A targeted locus
approach for single nucleotide polymorphism discovery in rainbow trout.
Transactions of the American
Fisheries Society

135
, 1698
-
1721.


Transcriptome seq
uencing

Barbazuk W.B., Emrich S.J., Chen H.D., Li L., Schnable P.S. (2007) SNP discovery via 454 transcriptome
sequencing.
Plant Journal

51
, 910
-
918.

Everett M.V., Grau E.D., Seeb J.E. (2011) Short reads and nonmodel species: exploring the complexities
of next
-
gen
eration sequence assembly and SNP discovery in the absence of a reference genome.
Molecular Ecology Resources

11
, 93
-
108.

Geraldes A., Pang J., Thiessen N.

et al.

(2011) SNP discovery in black cottonwood (Populus trichocarpa)
by population transcriptome re
sequencing.
Molecular Ecology Resources

11
, 81
-
92.


Milano I., Babbucci M., Panitz F.

et al.

(2011) Novel Tools for Conservation Genomics: Comparing Two
High
-
Throughput Approaches for SNP Discovery in the Transcriptome of the European Hake.
Plos One

6
.

3


Roberts S.B., Hauser L., Seeb L.W., Seeb J.E. (2012) Development of Genomic Resources for Pacific
Herring through Targeted Transcriptome Pyrosequencing.
PLoS ONE

7
, e30908.

Seeb J.E., Pascal C.E., Grau E.D.

et al.

(2011b) Transcriptome sequencing and high
-
resolution melt
analysis advance single nucleotide polymorphism discovery in duplicated salmonids.
Molecular Ecology
Resources

11
, 335
-
348.


Next generation sequencing of reduced representation libraries

Baird N.A., Etter P.D., Atwood T.S.

et al.

(2008) R
apid SNP Discovery and Genetic Mapping Using
Sequenced RAD Markers.
PLoS ONE

3
.

Chutimanitsakun Y., Nipper R.W., Cuesta
-
Marcos A.

et al.

(2011) Construction and application for QTL
analysis of a Restriction Site Associated DNA (RAD) linkage map in barley.
Bmc Genomics

12
.

Cosart T., Beja
-
Pereira A., Chen S.Y., Ng S.B., Shendure J., Luikart G. (2011) Exome
-
wide DNA capture and
next generation sequencing in domestic and wild species.
Bmc Genomics

12
.

Crouch J., Oudemans P., Polashock J. (2010) Sequenced restr
iction
-
associated DNA (RAD) markers for
SNP discovery in the genus Colletotrichum.
Phytopathology

100
, S27
-
S27.

Fridjonsson O., Olafsson K., Tompsett S.

et al.

(2011) Detection and mapping of mtDNA SNPs in Atlantic
salmon using high throughput DNA sequenci
ng.
Bmc Genomics

12
.

Sanchez C.C., Smith T.P.L., Wiedmann R.T.

et al.

(2009) Single nucleotide polymorphism discovery in
rainbow trout by deep sequencing of a reduced representation library.
Bmc Genomics

10
.

Wiedmann R.T., Smith T.P.L., Nonneman D.J. (2008) SNP discovery in swine by reduced representation
and high throughput pyrosequencing.
Bmc Genetics

9
.

Van Tassell C.P., Smith T.P.L., Matukumalli L.K.

et al.

(2008) SNP discovery and allele frequency
estimat
ion by deep sequencing of reduced representation libraries.
Nature Methods

5
, 247
-
252.


High
-
resolution melt analysis

Bignell P.A., Keeling D.M., Giangrande P. (2008) Detection of F8 Mutations by High Resolution Melting
(HRM) Analysis.
Blood

112
, 446
-
446.

Cho M.H., Ciulla D., Klanderman B.J., Raby B.A., Silverman E.K. (2008) High
-
Resolution Melting Curve
Analysis of Genomic and Whole
-
Genome Amplified DNA.
Clinical Chemistry

54
, 2055
-
2058.

McGlauflin M.T., Smith M.J., Wang J.T.

et al.

(2010) High
-
resolution
melting analysis for the discovery of
novel single
-
nucleotide polymorphisms in rainbow and cutthroat trout for species identification.
Transactions of the American Fisheries Society

139
, 676
-
684.

4


Wu S.B., Wirthensohn M., Hunt P., Gibson J., Sedgley M. (200
8) High resolution melting analysis of
almond SNPs derived from ESTs.
Theoretical and Applied Genetics

118
, 1
-
14.

Yuan J.Z., Haroon M., Lightfoot D., Pelletier Y., Liu Q., Li X.Q. (2009) A High
-
Resolution Melting Approach
for Analyzing Allelic Expression D
ynamics.
Current Issues in Molecular Biology

11
, I1
-
i9.

Smith B.L., Lu C.P., Bremer J.R.A. (2010) High
-
resolution melting analysis (HRMA): a highly sensitive
inexpensive genotyping alternative for population studies.
Molecular Ecology Resources

10
,
193
-
196.

Tajiri
-
Utagawa E., Hara M., Takahashi K., Watanabe M., Wakita T. (2009) Development of a Rapid High
-
Throughput Method for High
-
Resolution Melting Analysis for Routine Detection and Genotyping of
Noroviruses.
Journal of Clinical Microbiology

47
, 43
5
-
440.


Other

Hyten D.L., Smith J.R., Frederick R.D., Tucker M.L., Song Q.J., Cregan P.B. (2009) Bulked Segregant
Analysis Using the GoldenGate Assay to Locate the Rpp3 Locus that Confers Resistance to Soybean Rust
in Soybean.
Crop Science

49
, 265
-
271.

Gilchrist E.J., Haughn G.W., Ying C.C.

et al.

(2006) Use of Ecotilling as an Efficient Snp Discovery Tool to
Survey Genetic Variation in Wild Populations of Populus Trichocarpa.
Molecular Ecology

15
, 1367
-
1378.

Olsen M.T., Volny V.H., BÉRubÉ M.

et al.

(201
1) A simple route to single
-
nucleotide polymorphisms in a
nonmodel species: identification and characterization of SNPs in the Artic ringed seal (Pusa hispida
hispida).
Molecular Ecology Resources

11
, 9
-
19.


Roden S.E., Dutton P.H., Morin P.A. (2009) AFLP
Fragment Isolation Technique as a Method to Produce
Random Sequences for Single Nucleotide Polymorphism Discovery in the Green Turtle, Chelonia mydas.
Journal of Heredity

100
, 390
-
393.

Seddon J.M., Parker H.G., Ostrander E.A., Ellegren H. (2005) SNPs in ec
ological and conservation Studies:
a test in the Scandinavian wolf population.
Molecular Ecology

14
, 503
-
511.


Ascertainment bias and SNP discovery

Akey J.M., Zhang K., Xiong M.M., Jin L. (2003) The effect of single nucleotide polymorphism
identification strategies on estimates of linkage disequilibrium.
Molecular Biology and Evolution

20
, 232
-
242.

Albrechtsen A., Nielsen F.C., Nielsen R. (2010) Ascer
tainment Biases in SNP Chips Affect Measures of
Population Divergence.
Molecular Biology and Evolution

27
, 2534
-
2547.

Clark A.G., Hubisz M.J., Bustamante C.D., Williamson S.H., Nielsen R. (2005) Ascertainment bias in
studies of human genome
-
wide polymorphi
sm.
Genome Research

15
, 1496
-
1502.

5


Didion J.P., Yang H.N., Sheppard K.

et al.

(2012) Discovery of novel variants in genotyping arrays
improves genotype retention and reduces ascertainment bias.
Bmc Genomics

13
.

Nielsen R. (2004) Population genetic analysis

of ascertained SNP data.
Human Genomics

1
, 218
-
224.

Ramirez
-
Soriano A., Nielsen R. (2009) Correcting Estimators of theta and Tajima's D for Ascertainment
Biases Caused by the Single
-
Nucleotide Polymorphism Discovery Process.
Genetics

181
, 701
-
710.

Rosenbl
um E.B., Novembre J. (2007) Ascertainment bias in spatially structured populations: A case study
in the eastern fence lizard.
Journal of Heredity

98
, 331
-
336.

Wang Y., Nielsen R. (2012) Estimating population divergence time and phylogeny from single
-
nucleo
tide
polymorphisms data with outgroup ascertainment bias.
Molecular Ecology

21
, 974
-
986.