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Table 2 Summary of NN Studies Reviewed

From: Neural networks for genetic epidemiology: past, present, and future

Publication Input Output Hidden Layer
  Type Coding Type Coding Number Layers Number Nodes
Bhat et al. 1999 Binary 0 = absence of allele Binary 1/0/0 = unaffected 1 15
   1 = presence of allele   0/1/0 = mildly affected   
     0/0/1 = severely affected   
Bush et al 2005 Discrete -1, -1 = 1/1 genotype Binary 0 = unaffected GP evolved
   0, + 2 = 1/2 genotype   1 = affected   
   +1, -1 = 2/2 genotype     
Costello et al. 2003 Dicrete Varied Binary 0 = unaffected Multiple variations
     1 = affected   
Curtis et al. 2001 Discrete 0 = AA genotype Binary 0 = unaffected 2 3
   1 = AB genotype   1 = affected   
   2 = BB genotype     
Curtis 2007 Discrete 0 = AA genotype Binary 0 = unaffected 2 3
   1 = AB genotype   1 = affected   
   2 = BB genotype     
Giachino et al 2007 Discrete and Continuous Categorical values of genotypes and clinical features Binary 0 = unaffected 1 unknown
     1 = affected   
Li et al. 1999 Discrete IBD sharing Binary 0/1 = concordant or not Multiple variations
   +1= shared allele   0/1 = affected or unaffected   
   -1 = unshared allele     
   0 = uninformative     
Lin et al 2006 Discrete Categories of genotype combinations Binary 0 = non-response Multiple variations
     1 = response   
Lucek and Ott 1997 Binary 0 = absence of allele Binary 4 nodes for each trait (20 total nodes) 1 70
   1 = presence of allele   0 = quantitative trait off   
     1 = quantitative trait on   
Lucek et al. 1998 Discrete IBD sharing Binary +1,+1 = target output 1 √220
   +1= shared allele   0, +1 = noise   
   -1 = unshared allele     
   0 = uninformative     
Marinov and Weeks 2001 Discrete IBD sharing Binary +1,+1 = target output 1 √220
   +1= shared allele   0, +1 = noise   
   -1 = unshared allele     
   0 = uninformative     
Matchenko-Shimko and Dube 2006 Discrete Three combinations of possible allele combinations, transformed to a 0–1 range Binary 0 = control Multiple variations
     1 = case   
Motsinger et al (2006a) Discrete -1, -1 = 1/1 genotype Binary 0 = unaffected GP Evolved
   0, + 2 = 1/2 genotype   1 = affected   
   +1, -1 = 2/2 genotype     
Motsinger et al (2006b) Discrete -1, -1 = 1/1 genotype Binary 0 = unaffected GE Evolved
   0, + 2 = 1/2 genotype   1 = affected   
   +1, -1 = 2/2 genotype     
North et al 2003 Discrete 0 = AA genotype Binary 0 = unaffected Multiple Variations
   1 = AB genotype   1 = affected   
   2 = BB genotype     
Ott 2001 Discrete -1, -1 = 1/1 genotype Binary 0 = unaffected NA
   0, +2 = 1/2 genotype   1 = affected   
   +1, -1 = 2/2 genotype     
Pankratz et al. 2001 Discrete IBD sharing Binary 1/1 = affected/affected 1 4
   +1 = shared allele   0/1 = affected/unaffected   
   -1 = unshared allele     
   0 = uninformative     
Penco et al 2005 Discrete Categories of allele combinations at each genotype Binary 0 = unaffected Multiple variations, including and evolutionary process
     1 = affected   
Pociot et al. 2004 Discrete Number of categories per sliding window Binary 0 = unaffected Multiple variations
     1 = affected   
Ritchie et al. 2003 Discrete -1, -1 = 1/1 genotype Binary 0 = unaffected GP evolved
   0, + 2 = 1/2 genotype   1 = affected   
   +1, -1 = 2/2 genotype     
Saccone et al. 1999 Discrete IBD sharing Binary 1/1 = affected/affected 18 variations
   +1= shared allele   0/1 = affected/unaffected   
   -1 = unshared allele     
   0 = uninformative     
Serretti and Smeraldi 2004 Discrete SERPR*l/l = 1 Binary 0 = nonresponse 1 7
   SERPR*l/s = 2   1 = response   
   SERPR*s/s = 2     
   TPH*C/C = 1     
   TPH*C/A = 2     
   TPH*A/A = 2     
Shoemaker et al. 2001 Varied Varied Binary 0 = unaffected 1 unknown
     1 = affected   
Tomita et al 2004 Discrete Homozygous for major allele = (0.1, 0.1) Binary 0.9 = case Multiple variations
   Heterozygous = (0.1, 0.9)   0.1 = control   
   Homozygous for minor allele = (0.9, 0.9)     
Zandi et al. 2001 Contin. Pedigree-specific NPL scores Binary 1,1 = case pedigree 15 variations
     1,0 = control pedigree