Silhouette scores for assessment of SNP genotype clusters

Lovmar, Lovisa; Ahlford, Annika; Jönsson, Mats; Syvänen, Ann Christine

doi:10.1186/1471-2164-6-35

Cited by 130 publications

(103 citation statements)

References 11 publications

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“…We run spectral clustering for various choices of the number K of clusters. The clustering that achieves the highest silhouette score [56] is then inspected further.…”

Section: Methodsmentioning

confidence: 99%

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data

2016

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Chromosome conformation capture (3C) techniques have revealed many fascinating insights into the spatial organization of genomes. 3C methods typically provide information about chromosomal contacts in a large population of cells, which makes it difficult to draw conclusions about the three-dimensional organization of genomes in individual cells. Recently it became possible to study single cells with Hi-C, a genome-wide 3C variant, demonstrating a high cell-to-cell variability of genome organization. In principle, restraint-based modeling should allow us to infer the 3D structure of chromosomes from single-cell contact data, but suffers from the sparsity and low resolution of chromosomal contacts. To address these challenges, we adapt the Bayesian Inferential Structure Determination (ISD) framework, originally developed for NMR structure determination of proteins, to infer statistical ensembles of chromosome structures from single-cell data. Using ISD, we are able to compute structural error bars and estimate model parameters, thereby eliminating potential bias imposed by ad hoc parameter choices. We apply and compare different models for representing the chromatin fiber and for incorporating singe-cell contact information. Finally, we extend our approach to the analysis of diploid chromosome data.

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“…We run spectral clustering for various choices of the number K of clusters. The clustering that achieves the highest silhouette score [56] is then inspected further.…”

Section: Methodsmentioning

confidence: 99%

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data

2016

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“…The following settings were assigned in the Cluster 3.0 graphical user interface: (1) Organize genes (2) k = 3 (3) Iterations = 100 (4) k-Means (5) Similarity metric = Euclidean distance. Resulting genotype assignments were then used to generate Silhouette scores for assessment of cluster quality [29]. SNP assays resulting in Silhouette scores less than 0.70 were considered failed assays when assessing conversion rate.…”

Section: Methodsmentioning

confidence: 99%

Improvements to Bead-Based Oligonucleotide Ligation SNP Genotyping Assays

et al. 2008

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We describe a bead-based, multiplexed, oligonucleotide ligation assay (OLA) performed on the Luminex flow cytometer. Differences between this method and those previously reported include the use of far fewer beads and the use of a universal oligonucleotide for signal detection. These innovations serve to significantly reduce the cost of the assay, while maintaining robustness and accuracy. Comparisons are made between the Luminex OLA and both pyrosequencing and direct sequencing. Experiments to assess conversion rates, call rates, and concordance across technical replicates are also presented.

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“…Two tests were carried out for this possible artefact of SNP-SCALE. First, the silhouette score, which provides a numerical estimate of cluster quality, was calculated using ClusterA (Lovmar et al 2005) for the peak-intensity cluster plot for every locus. These scores were compared between allo-and autotype SNPs, using t-tests, after normalizing using the mean and SD of each species to remove any bias in distribution between the species.…”

Section: Validating Multiplex Snp-scalementioning

confidence: 99%

Multiplex SNP‐SCALE: a cost‐effective medium‐throughput single nucleotide polymorphism genotyping method

Kenta¹,

Gratten²,

Haigh³

et al. 2008

Molecular Ecology Resources

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We describe a convenient, cost-effective and flexible medium-throughput single nucleotide polymorphism (SNP) genotyping method, Multiplex SNP-SCALE, which enables the simultaneous amplification by polymerase chain reaction (PCR) of up to 25 (or potentially more) loci followed by electrophoresis in an automated DNA sequencer. We extended the original SNP-SCALE method to include (i) use of a commercial multiplex PCR kit, (ii) a four-dye system, (iii) much-reduced (2-µL) reaction volumes, (iv) drying down of template DNA before PCR, (v) use of pig-tailed primers, (vi) a PCR product weighting system, (vii) a standard optimized touchdown PCR thermocycling programme, and (viii) software (SNP-SCALE Primer Designer) that automatically designs suitable SNP-SCALE primers for a batch of loci. This new protocol was validated for different types of SNPs. The method is cost- and time-effective for medium-scale evolutionary and ecological projects involving 10s to 100s of loci.

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Silhouette scores for assessment of SNP genotype clusters

Cited by 130 publications

References 11 publications

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data

Improvements to Bead-Based Oligonucleotide Ligation SNP Genotyping Assays

Multiplex SNP‐SCALE: a cost‐effective medium‐throughput single nucleotide polymorphism genotyping method

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