The advantages of SNP arrays over CGH arrays.

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The advantages of SNP arrays over CGH arrays.

Mol Cytogenet. 2014;7(Suppl 1 Proceedings of the International Conference on Human):I31

Authors: Keren B

PMID: 24949096 [PubMed]

Genetic differentiation of brackish water populations of cod Gadus morhua in the southern Baltic, inferred from genotyping using SNP-arrays.

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Genetic differentiation of brackish water populations of cod Gadus morhua in the southern Baltic, inferred from genotyping using SNP-arrays.

Mar Genomics. 2014 Jun 5;

Authors: Poćwierz-Kotus A, Kijewska A, Petereit C, Bernaś R, Więcaszek B, Arnyasi M, Lien S, Kent MP, Wenne R

Abstract
The Baltic is a semi-enclosed sea characterised by decreasing salinity in the eastern and northern direction with only the deeper parts of the southern Baltic suitable as spawning grounds for marine species like cod. Baltic cod exhibits various adaptations to brackish water conditions, yet the inflow of salty North Sea water near the bottom remains an influence on the spawning success of the Baltic cod. The eastern Baltic population has been very weakly studied in comparison with the western population. The aim of this study is to demonstrate for the first time genetic differentiation by the use of a large number of SNPs between eastern and western Baltic populations existing in differentiated salinity conditions. Two cod samples were collected from the Bay of Gdańsk, Poland and one from the Kiel Bight, Germany. Samples were genotyped using a cod derived SNP-array (Illumina) with 10 913 SNPs. A selection of diagnostic SNPs was performed. A set of 7944 validated SNPs were analysed to assess the differentiation of three samples of cod. Results indicated a clear distinctness of the Kiel Bight from the populations of the eastern Baltic. FST comparison between both eastern samples was non-significant. Clustering analysis, principal coordinates analysis and assignment test clearly indicated that the eastern samples should be considered as one subpopulation, well differentiated from the western subpopulation. With the SNP approach, no differentiation between groups containing 'healthy' and 'non-healthy' cod individuals was observed.

PMID: 24910372 [PubMed - as supplied by publisher]

Alternate (non-array) SNP detection methods.

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Alternate (non-array) SNP detection methods.

MLO Med Lab Obs. 2014 May;46(5):42-3

Authors: Brunstein J

PMID: 24902384 [PubMed - in process]

Performance comparison of SNP detection tools with illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data.

Performance comparison of SNP detection tools with illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data.

Nucleic Acids Res. 2014 May 15;

Authors: Yi M, Zhao Y, Jia L, He M, Kebebew E, Stephens RM

Abstract
To apply exome-seq-derived variants in the clinical setting, there is an urgent need to identify the best variant caller(s) from a large collection of available options. We have used an Illumina exome-seq dataset as a benchmark, with two validation scenarios-family pedigree information and SNP array data for the same samples, permitting global high-throughput cross-validation, to evaluate the quality of SNP calls derived from several popular variant discovery tools from both the open-source and commercial communities using a set of designated quality metrics. To the best of our knowledge, this is the first large-scale performance comparison of exome-seq variant discovery tools using high-throughput validation with both Mendelian inheritance checking and SNP array data, which allows us to gain insights into the accuracy of SNP calling through such high-throughput validation in an unprecedented way, whereas the previously reported comparison studies have only assessed concordance of these tools without directly assessing the quality of the derived SNPs. More importantly, the main purpose of our study was to establish a reusable procedure that applies high-throughput validation to compare the quality of SNP discovery tools with a focus on exome-seq, which can be used to compare any forthcoming tool(s) of interest.

PMID: 24831545 [PubMed - as supplied by publisher]

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