The efficacy of short tandem repeat polymorphisms versus single-nucleotide polymorphisms for resolving population structure.

paper Primary Public

Authors: Kauwe, John S K; Bertelsen, Sarah; Bierut, Laura Jean; Dunn, Gerald; Hinrichs, Anthony L; Jin, Carol H; Suarez, Brian K
Year: 2005
Journal: BMC genetics
PMID: 16451699
DOI: 10.1186/1471-2156-6-S1-S84
PMCID: PMC1866696

#	Section	Preview
0	Background	Accurately resolving population structure in a sample is important for both linkage and association…
1	Background	Short tandem repeat polymorphisms (STRPs) are highly variable markers that have proven to be very…
2	Background	In this study we investigate the power of SNPs in detecting population substructure using results…
3	Methods — Sample	This study includes 286 unrelated individuals from the Collaborative Study on the Genetics of…
4	Methods — Analyses	SNPs from each dataset were ranked according to MAF. To construct the Illumina and Affymetrix "low…
5	Methods — Analyses	Each of these groups was then analyzed with the computer program STRUCTURE to identify possible…
6	Methods — Analyses	To compare the assignment probabilities of each individual between the SNPs and STRPs we took the…
7	Methods — Analyses	We also compared the frequency of SNPs in the self-reported European and African American groups.…
8	Results	The results of the STRP and 1,000 SNP runs in STRUCTURE were in concordance with self-reported race…
9	Results	In the case of the Affymetrix low frequency SNPs, the results do converge on that of the STRPs, but…
10	Results	The distribution of information content in the SNPs is shown in Figure 2. We performed regression of…
11	Discussion	The results in Figure 1 support the findings of a previous study that suggests that approximately…
12	Discussion	increase in useful information. It is also interesting to note that the similarity between the STRP…
13	Discussion	By our measure of information content, low-frequency SNPs have the greatest potential to be…
14	Discussion	In these analyses we have identified a set of highly informative SNPs. Previous studies have shown…
15	Conclusion	These data suggest that SNPs are a cost effective and informative replacement for STRPs when used to…
16	Abbreviations	COGA: Collaborative Study on the Genetics of Alcoholism
17	Abbreviations	MAF: Minor allele frequencies
18	Abbreviations	MCMC: Markov chain Monte Carlo
19	Abbreviations	SNP: Single-nucleotide polymorphisms

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In this knowledge base

Title	Year	PMID
Microsatellites versus single-nucleotide polymorphisms in linkage analysis for quantitative and qualitative measures.	2005	16451580
Multipoint identity-by-descent computations for single-point polymorphism and microsatellite maps.	2005	16451644

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Microsatellites versus single-nucleotide polymorphisms in linkage analysis for quantitative and qualitative measures.	Dunn G et al.	—	2005	→
Multipoint identity-by-descent computations for single-point polymorphism and microsatellite maps.	Hinrichs AL et al.	—	2005	→