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Hierarchical Classes Analysis (HICLAS): A novel data reduction method to examine associations between biallelic SNPs and perceptual organization phenotypes in schizophrenia.

Joseph J, Gara MA, Silverstein SM - Schizophr Res Cogn (2015)

Bottom Line: HICLAS reduced the total number of candidate SNPs for subsequent phenotype association analyses from 6 to 3.MANCOVAs indicated that rs10503929 and rs1978340 were associated with the Kanizsa shape perception filling in metric but not the global shape detection metric. rs10503929 was also associated with altered contour integration performance.While the contribution of candidate SNPs to perceptual impairments requires further clarification, this study reports the first application of HICLAS as a hypothesis-independent mathematical method for SNP data reduction.

View Article: PubMed Central - PubMed

Affiliation: Rutgers University Graduate School of Biomedical Sciences, 675 Hoes Lane, Piscataway, NJ 08854, USA ; Rutgers University Behavioral Health Care, 151 Centennial Ave, Piscataway, NJ 08854, USA.

ABSTRACT

The power of SNP association studies to detect valid relationships with clinical phenotypes in schizophrenia is largely limited by the number of SNPs selected and non-specificity of phenotypes. To address this, we first assessed performance on two visual perceptual organization tasks designed to avoid many generalized deficit confounds, Kanizsa shape perception and contour integration, in a schizophrenia patient sample. Then, to reduce the total number of candidate SNPs analyzed in association with perceptual organization phenotypes, we employed a two-stage strategy: first a priori SNPs from three candidate genes were selected (GAD1, NRG1 and DTNBP1); then a Hierarchical Classes Analysis (HICLAS) was performed to reduce the total number of SNPs, based on statistically related SNP clusters. HICLAS reduced the total number of candidate SNPs for subsequent phenotype association analyses from 6 to 3. MANCOVAs indicated that rs10503929 and rs1978340 were associated with the Kanizsa shape perception filling in metric but not the global shape detection metric. rs10503929 was also associated with altered contour integration performance. SNPs not selected by the HICLAS model were unrelated to perceptual phenotype indices. While the contribution of candidate SNPs to perceptual impairments requires further clarification, this study reports the first application of HICLAS as a hypothesis-independent mathematical method for SNP data reduction. HICLAS may be useful for future larger scale genotype-phenotype association studies.

No MeSH data available.


Related in: MedlinePlus

JOVI task stimuli. The top left panel of the figure is an example of a lower jitter degree condition presented to participants (7–8°). The top right panel of the figure shows the highest jitter degree presented (15–16°). The bottom left and right panels represent the catch trial stimuli included in each trial block to account for momentary attentional lapses.
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Figure 1: JOVI task stimuli. The top left panel of the figure is an example of a lower jitter degree condition presented to participants (7–8°). The top right panel of the figure shows the highest jitter degree presented (15–16°). The bottom left and right panels represent the catch trial stimuli included in each trial block to account for momentary attentional lapses.

Mentions: The JOVI is a symmetric 1 alternative forced choice task in which participants responded whether the narrow end of the oblong contour was pointing left or right for each trial (Fig. 1). Each stimulus was presented for 2 s followed by a 1 s inter stimulus interval during which responses were no longer recorded. 48 stimulus trials per jitter condition were presented in blocks of 12 trials. Two types of catch stimuli (i.e., no errors expected) using 0° jitter were administered during each block to assess momentary attention lapses. One had curved lines drawn through the contours to highlight contour salience, and the other contained contour elements without background elements to eliminate distractor noise effects. The task stimuli were created using E-prime (Psychology Software Tools, Pittsburgh, PA).


Hierarchical Classes Analysis (HICLAS): A novel data reduction method to examine associations between biallelic SNPs and perceptual organization phenotypes in schizophrenia.

Joseph J, Gara MA, Silverstein SM - Schizophr Res Cogn (2015)

JOVI task stimuli. The top left panel of the figure is an example of a lower jitter degree condition presented to participants (7–8°). The top right panel of the figure shows the highest jitter degree presented (15–16°). The bottom left and right panels represent the catch trial stimuli included in each trial block to account for momentary attentional lapses.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4559868&req=5

Figure 1: JOVI task stimuli. The top left panel of the figure is an example of a lower jitter degree condition presented to participants (7–8°). The top right panel of the figure shows the highest jitter degree presented (15–16°). The bottom left and right panels represent the catch trial stimuli included in each trial block to account for momentary attentional lapses.
Mentions: The JOVI is a symmetric 1 alternative forced choice task in which participants responded whether the narrow end of the oblong contour was pointing left or right for each trial (Fig. 1). Each stimulus was presented for 2 s followed by a 1 s inter stimulus interval during which responses were no longer recorded. 48 stimulus trials per jitter condition were presented in blocks of 12 trials. Two types of catch stimuli (i.e., no errors expected) using 0° jitter were administered during each block to assess momentary attention lapses. One had curved lines drawn through the contours to highlight contour salience, and the other contained contour elements without background elements to eliminate distractor noise effects. The task stimuli were created using E-prime (Psychology Software Tools, Pittsburgh, PA).

Bottom Line: HICLAS reduced the total number of candidate SNPs for subsequent phenotype association analyses from 6 to 3.MANCOVAs indicated that rs10503929 and rs1978340 were associated with the Kanizsa shape perception filling in metric but not the global shape detection metric. rs10503929 was also associated with altered contour integration performance.While the contribution of candidate SNPs to perceptual impairments requires further clarification, this study reports the first application of HICLAS as a hypothesis-independent mathematical method for SNP data reduction.

View Article: PubMed Central - PubMed

Affiliation: Rutgers University Graduate School of Biomedical Sciences, 675 Hoes Lane, Piscataway, NJ 08854, USA ; Rutgers University Behavioral Health Care, 151 Centennial Ave, Piscataway, NJ 08854, USA.

ABSTRACT

The power of SNP association studies to detect valid relationships with clinical phenotypes in schizophrenia is largely limited by the number of SNPs selected and non-specificity of phenotypes. To address this, we first assessed performance on two visual perceptual organization tasks designed to avoid many generalized deficit confounds, Kanizsa shape perception and contour integration, in a schizophrenia patient sample. Then, to reduce the total number of candidate SNPs analyzed in association with perceptual organization phenotypes, we employed a two-stage strategy: first a priori SNPs from three candidate genes were selected (GAD1, NRG1 and DTNBP1); then a Hierarchical Classes Analysis (HICLAS) was performed to reduce the total number of SNPs, based on statistically related SNP clusters. HICLAS reduced the total number of candidate SNPs for subsequent phenotype association analyses from 6 to 3. MANCOVAs indicated that rs10503929 and rs1978340 were associated with the Kanizsa shape perception filling in metric but not the global shape detection metric. rs10503929 was also associated with altered contour integration performance. SNPs not selected by the HICLAS model were unrelated to perceptual phenotype indices. While the contribution of candidate SNPs to perceptual impairments requires further clarification, this study reports the first application of HICLAS as a hypothesis-independent mathematical method for SNP data reduction. HICLAS may be useful for future larger scale genotype-phenotype association studies.

No MeSH data available.


Related in: MedlinePlus