Limits...
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

Kanizsa shape perception stimuli and trial sequence. (A) Participants discriminated illusory or fragmented squares, which were accompanied by distractor lines for some half of the trials. (B) The task was to say left/right for the fragmented condition or fat/thin for the illusory condition.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4559868&req=5

Figure 2: Kanizsa shape perception stimuli and trial sequence. (A) Participants discriminated illusory or fragmented squares, which were accompanied by distractor lines for some half of the trials. (B) The task was to say left/right for the fragmented condition or fat/thin for the illusory condition.

Mentions: Stimuli consisted of four white sectored circles (diameter = 3.0°; wedge = 45°) centered at the vertices of an invisible square (side = 9.0°), which itself was centered on the screen (Fig. 2). The unrotated pac-men in the illusory condition formed a square, one third of which was physically specified (support ratio = .33) (Kellman and Shipley, 1991). Certain trials contained distractor lines (dimensions = 4.0 × 0.1°), which were centered between the sectored circles and had a length equal to 2/3 of the illusory edge. A fixation point appeared at the screen center at the beginning of each trial.


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)

Kanizsa shape perception stimuli and trial sequence. (A) Participants discriminated illusory or fragmented squares, which were accompanied by distractor lines for some half of the trials. (B) The task was to say left/right for the fragmented condition or fat/thin for the illusory condition.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Kanizsa shape perception stimuli and trial sequence. (A) Participants discriminated illusory or fragmented squares, which were accompanied by distractor lines for some half of the trials. (B) The task was to say left/right for the fragmented condition or fat/thin for the illusory condition.
Mentions: Stimuli consisted of four white sectored circles (diameter = 3.0°; wedge = 45°) centered at the vertices of an invisible square (side = 9.0°), which itself was centered on the screen (Fig. 2). The unrotated pac-men in the illusory condition formed a square, one third of which was physically specified (support ratio = .33) (Kellman and Shipley, 1991). Certain trials contained distractor lines (dimensions = 4.0 × 0.1°), which were centered between the sectored circles and had a length equal to 2/3 of the illusory edge. A fixation point appeared at the screen center at the beginning of each trial.

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